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Sample records for miniature inverted-repeat transposable

  1. Detection and characterization of miniature inverted-repeat transposable elements in “Candidatus Liberibacter asiaticus”

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Miniature inverted-repeat transposable elements (MITEs) are non-autonomous transposons (devoid a transposase gene, tps) involving insertion/deletion of genomic DNA in bacterial genomes influencing gene functions. No transposon has yet been reported in “Candidatus Liberibacter asiaticus”, an alpha-pr...

  2. Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria

    SciTech Connect

    Zhou Fengfeng; Tran Thao; Xu Ying

    2008-01-25

    Miniature inverted-repeat transposable elements (MITEs) were first identified in plants and exerted extensive proliferations throughout eukaryotic and archaeal genomes. But very few MITEs have been characterized in bacteria. We identified a novel MITE, called Nezha, in cyanobacteria Anabaena variabilis ATCC 29413 and Nostoc sp. PCC 7120. Nezha, like most previously known MITEs in other organisms, is small in size, non-coding, carrying TIR and DR signals, and of potential to form a stable RNA secondary structure, and it tends to insert into A+T-rich regions. Recent transpositions of Nezha were observed in A. variabilis ATCC 29413 and Nostoc sp. PCC 7120, respectively. Nezha might have proliferated recently with aid from the transposase encoded by ISNpu3-like elements. A possible horizontal transfer event of Nezha from cyanobacteria to Polaromonas JS666 is also observed.

  3. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Small RNAs regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). Although miniature inverted-repeat transposable elements (MITEs) are closely associated with euchromatic genes, the br...

  4. detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes.

    PubMed

    Ye, Congting; Ji, Guoli; Liang, Chun

    2016-01-01

    Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes, including plants and animals. Classified as a type of non-autonomous DNA transposable elements, they play important roles in genome organization and evolution. Comprehensive and accurate genome-wide detection of MITEs in various eukaryotic genomes can improve our understanding of their origins, transposition processes, regulatory mechanisms, and biological relevance with regard to gene structures, expression, and regulation. In this paper, we present a new MATLAB-based program called detectMITE that employs a novel numeric calculation algorithm to replace conventional string matching algorithms in MITE detection, adopts the Lempel-Ziv complexity algorithm to filter out MITE candidates with low complexity, and utilizes the powerful clustering program CD-HIT to cluster similar MITEs into MITE families. Using the rice genome as test data, we found that detectMITE can more accurately, comprehensively, and efficiently detect MITEs on a genome-wide scale than other popular MITE detection tools. Through comparison with the potential MITEs annotated in Repbase, the widely used eukaryotic repeat database, detectMITE has been shown to find known and novel MITEs with a complete structure and full-length copies in the genome. detectMITE is an open source tool (https://sourceforge.net/projects/detectmite). PMID:26795595

  5. detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes

    PubMed Central

    Ye, Congting; Ji, Guoli; Liang, Chun

    2016-01-01

    Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes, including plants and animals. Classified as a type of non-autonomous DNA transposable elements, they play important roles in genome organization and evolution. Comprehensive and accurate genome-wide detection of MITEs in various eukaryotic genomes can improve our understanding of their origins, transposition processes, regulatory mechanisms, and biological relevance with regard to gene structures, expression, and regulation. In this paper, we present a new MATLAB-based program called detectMITE that employs a novel numeric calculation algorithm to replace conventional string matching algorithms in MITE detection, adopts the Lempel-Ziv complexity algorithm to filter out MITE candidates with low complexity, and utilizes the powerful clustering program CD-HIT to cluster similar MITEs into MITE families. Using the rice genome as test data, we found that detectMITE can more accurately, comprehensively, and efficiently detect MITEs on a genome-wide scale than other popular MITE detection tools. Through comparison with the potential MITEs annotated in Repbase, the widely used eukaryotic repeat database, detectMITE has been shown to find known and novel MITEs with a complete structure and full-length copies in the genome. detectMITE is an open source tool (https://sourceforge.net/projects/detectmite). PMID:26795595

  6. Characterization of active miniature inverted-repeat transposable elements in the peanut genome.

    PubMed

    Shirasawa, Kenta; Hirakawa, Hideki; Tabata, Satoshi; Hasegawa, Makoto; Kiyoshima, Hiroyuki; Suzuki, Sigeru; Sasamoto, Sigemi; Watanabe, Akiko; Fujishiro, Tsunakazu; Isobe, Sachiko

    2012-05-01

    Miniature inverted-repeat transposable elements (MITEs), some of which are known as active nonautonomous DNA transposons, are found in the genomes of plants and animals. In peanut (Arachis hypogaea), Ah-MITE1 has been identified in a gene for fatty-acid desaturase, and possessed excision activity. However, the AhMITE1 distribution and frequency of excision have not been determined for the peanut genome. In order to characterize AhMITE1s, their genomic diversity and transposition ability was investigated. Southern blot analysis indicated high AhMITE1 copy number in the genomes of A. hypogaea, A. magna and A. monticola, but not in A. duranensis. A total of 504 AhMITE1s were identified from the MITE-enriched genomic libraries of A. hypogaea. The representative AhMITE1s exhibited a mean length of 205.5 bp and a GC content of 30.1%, with AT-rich, 9 bp target site duplications and 25 bp terminal inverted repeats. PCR analyses were performed using primer pairs designed against both flanking sequences of each AhMITE1. These analyses detected polymorphisms at 169 out of 411 insertional loci in the four peanut lines. In subsequent analyses of 60 gamma-irradiated mutant lines, four Ah-MITE1 excisions showed footprint mutations at the 109 loci tested. This study characterizes AhMITE1s in peanut and discusses their use as DNA markers and mutagens for the genetics, genomics and breeding of peanut and its relatives. PMID:22294450

  7. Detection and Characterization of Miniature Inverted-Repeat Transposable Elements in “Candidatus Liberibacter asiaticus”

    PubMed Central

    Wang, Xuefeng; Tan, Jin; Bai, Ziqin; Su, Huanan; Deng, Xiaoling; Li, Zhongan

    2013-01-01

    Miniature inverted-repeat transposable elements (MITEs) are nonautonomous transposons (devoid of the transposase gene tps) that affect gene functions through insertion/deletion events. No transposon has yet been reported to occur in “Candidatus Liberibacter asiaticus,” an alphaproteobacterium associated with citrus Huanglongbing (HLB, yellow shoot disease). In this study, two MITEs, MCLas-A and MCLas-B, in “Ca. Liberibacter asiaticus” were detected, and the genome was characterized using 326 isolates collected in China and Florida. MCLas-A had three variants, ranging from 237 to 325 bp, and was inserted into a TTTAGG site of a prophage region. MCLas-A had a pair of 54-bp terminal inverted repeats (TIRs), which contained three tandem repeats of TGGTAACCAC. Both “filled” (with MITE) and “empty” (without MITE) states were detected, suggesting the MITE mobility. The empty sites of all bacterial isolates had TIR tandem repeat remnants (TRR). Frequencies of TRR types varied according to geographical origins. MCLas-B had four variants, ranging from 238 to 250 bp, and was inserted into a TA site of another “Ca. Liberibacter” prophage. The MITE, MCLas-B, had a pair of 23-bp TIRs containing no tandem repeats. No evidence of MCLas-B mobility was found. An identical open reading frame was found upstream of MCLas-A (229 bp) and MCLas-B (232 bp) and was predicted to be a putative tps, suggesting an in cis tps-MITE configuration. MCLas-A and MCLas-B were predominantly copresent in Florida isolates, whereas MCLas-A alone or MCLas-B alone was found in Chinese isolates. PMID:23813735

  8. Abundant Degenerate Miniature Inverted-Repeat Transposable Elements in Genomes of Epichloid Fungal Endophytes of Grasses

    PubMed Central

    Fleetwood, Damien J.; Khan, Anar K.; Johnson, Richard D.; Young, Carolyn A.; Mittal, Shipra; Wrenn, Ruth E.; Hesse, Uljana; Foster, Simon J.; Schardl, Christopher L.; Scott, Barry

    2011-01-01

    Miniature inverted-repeat transposable elements (MITEs) are abundant repeat elements in plant and animal genomes; however, there are few analyses of these elements in fungal genomes. Analysis of the draft genome sequence of the fungal endophyte Epichloë festucae revealed 13 MITE families that make up almost 1% of the E. festucae genome, and relics of putative autonomous parent elements were identified for three families. Sequence and DNA hybridization analyses suggest that at least some of the MITEs identified in the study were active early in the evolution of Epichloë but are not found in closely related genera. Analysis of MITE integration sites showed that these elements have a moderate integration site preference for 5′ genic regions of the E. festucae genome and are particularly enriched near genes for secondary metabolism. Copies of the EFT-3m/Toru element appear to have mediated recombination events that may have abolished synthesis of two fungal alkaloids in different epichloae. This work provides insight into the potential impact of MITEs on epichloae evolution and provides a foundation for analysis in other fungal genomes. PMID:21948396

  9. Mobilization and evolutionary history of miniature inverted-repeat transposable elements (MITEs) in Beta vulgaris L.

    PubMed

    Menzel, Gerhard; Dechyeva, Daryna; Keller, Heiko; Lange, Cornelia; Himmelbauer, Heinz; Schmidt, Thomas

    2006-01-01

    We have identified three families of miniature inverted-repeat transposable elements (VulMITEs) in the genome of sugar beet (Beta vulgaris L.), evidently derived from a member of the Vulmar family of mariner transposons. While VulMITEs I are typical stowaway-like MITEs, VulMITEs II and VulMITEs III are rearranged stowaway elements of increased size. The integration of divergent moderately and highly repetitive sequences into VulMITEs II and, in particular in VulMITEs III, respectively, shows that amplification of repetitive DNA by MITEs contribute to the increase of genome size with possible implications for plant genome evolution. Fluorescent in-situ hybridization (FISH), for the first time visualizing stowaway MITE distribution on plant chromosomes, revealed a dispersed localization of VulMITEs along all B. vulgaris chromosomes. Analysis of the flanking sequences identified a dispersed repeat as target site for the integration of the stowaway element VulMITE I. Recent transposition of VulMITE I, which most likely occurred during the domestication of cultivated beets, was concluded from insertional polymorphisms between different B. vulgaris cultivars and species. PMID:17171577

  10. P-MITE: a database for plant miniature inverted-repeat transposable elements.

    PubMed

    Chen, Jiongjiong; Hu, Qun; Zhang, Yu; Lu, Chen; Kuang, Hanhui

    2014-01-01

    Miniature inverted-repeat transposable elements (MITEs) are prevalent in eukaryotic species including plants. MITE families vary dramatically and usually cannot be identified based on homology. In this study, we de novo identified MITEs from 41 plant species, using computer programs MITE Digger, MITE-Hunter and/or Repetitive Sequence with Precise Boundaries (RSPB). MITEs were found in all, but one (Cyanidioschyzon merolae), species. Combined with the MITEs identified previously from the rice genome, >2.3 million sequences from 3527 MITE families were obtained from 41 plant species. In general, higher plants contain more MITEs than lower plants, with a few exceptions such as papaya, with only 538 elements. The largest number of MITEs is found in apple, with 237 302 MITE sequences. The number of MITE sequences in a genome is significantly correlated with genome size. A series of databases (plant MITE databases, P-MITE), available online at http://pmite.hzau.edu.cn/django/mite/, was constructed to host all MITE sequences from the 41 plant genomes. The databases are available for sequence similarity searches (BLASTN), and MITE sequences can be downloaded by family or by genome. The databases can be used to study the origin and amplification of MITEs, MITE-derived small RNAs and roles of MITEs on gene and genome evolution. PMID:24174541

  11. Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica.

    PubMed

    Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J S

    2015-12-01

    Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers. PMID:26129767

  12. terMITEs: miniature inverted-repeat transposable elements (MITEs) in the termite genome (Blattodea: Termitoidae).

    PubMed

    Luchetti, Andrea

    2015-08-01

    Transposable elements (TEs) are discrete DNA sequences which are able to replicate and jump into different genomic locations. Miniature inverted-repeats TEs (MITEs) are non-autonomous DNA elements whose origin is still poorly understood. Recently, some MITEs were found to contain core repeats that can be arranged in tandem arrays; in some instances, these arrays have even given rise to satellite DNAs in the (peri)centromeric region of the host chromosomes. I report the discovery and analysis of three new MITEs found in the genome of several termite species (hence the name terMITEs) in two different families. For two of the MITEs (terMITE1-Tc1/mariner superfamily; terMITE2-piggyBac superfamily), evidence of past mobility was retrieved. Moreover, these two MITEs contained core repeats, 16 bp and 114 bp long respectively, exhibiting copy number variation. In terMITE2, the tandem duplication appeared associated with element degeneration, in line with a recently proposed evolutionary model on MITEs and the origin of tandem arrays. Concerning their genomic distribution, terMITE1 and terMITE3 appeared more frequently inserted close to coding regions while terMITE2 was mostly associated with TEs. Although MITEs are commonly distributed in coding regions, terMITE2 distribution is in line with that of other insects' piggyBac-related elements and of other small TEs found in termite genomes. This has been explained through insertional preference rather than through selective processes. Data presented here add to the knowledge on the poorly exploited polyneopteran genomes and will provide an interesting framework in which to study TEs' evolution and host's life history traits. PMID:25711308

  13. MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi.

    PubMed

    Chen, Yong; Zhou, Fengfeng; Li, Guojun; Xu, Ying

    2009-05-01

    Transposable elements (TE) are functionally important genetic elements that can move within a genome. Miniature inverted-repeat transposable elements (MITEs) constitute a class of transposable elements that are usually small in size and have high numbers of conserved copies. Identifying all the MITEs in a genome could provide new insights about gene evolution and genome dynamics of the organism. We present a web-based MITE Uncovering SysTem (MUST) for prediction and analyses of MITEs at a genome level. MUST reliably found both the previously known and novel MITEs in the two bacterial genomes, Anabaena variabilis ATCC 29413 and Haloquadratum walsbyi DSM 16790. MUST is available at http://csbl1.bmb.uga.edu/ffzhou/MUST/ (the standalone version is available upon request). Supplementary data associated with this article are available in the online version or at: http://csbl1.bmb.uga.edu/ffzhou/MUST/supp/. PMID:19393167

  14. Isolation and characterization of a novel family (Mild-4) of miniature subterminal inverted repeat transposable element from the Colorado potato beetle, Leptinotarsa decemlineata

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determining the genomic structure of DAT-2 and -3 led to the isolation of four novel families of miniature subterminal inverted repeat transposable elements (MSITE): Mild-1, -2, -3 and -4. Mild-1a is inserted within the first intron of diapause protein-1. Mild-1a is 284 bp in length, has a 14 bp tar...

  15. The Complex Genetic Context of blaPER-1 Flanked by Miniature Inverted-Repeat Transposable Elements in Acinetobacter johnsonii

    PubMed Central

    Zong, Zhiyong

    2014-01-01

    On a large plasmid of Acinetobacter johnsonii strain XBB1 from hospital sewage, blaPER-1 and ISCR1 were found in a complex Tn402-like integron carrying an arr3-aacA4 cassette array. The integron was truncated by the same 439-bp miniature inverted-repeat transposable element (MITE) at both ends. blaPER-1 and its complex surroundings might have been mobilized by the MITEst into an orf of unknown function, evidenced by the presence of the characteristic 5-bp direct target repeats. The same 439-bp MITEs have also been found flanking class 1 integrons carrying metallo-β-lactamases genes blaIMP-1, blaIMP-5 and blaVIM-2 before but without ISCR1. Although the cassette arrays are different, integrons have always been truncated by the 439-bp MITEs at the exact same locations. The results suggested that MITEs might be able to mobilize class 1 integrons via transposition or homologous recombination and therefore represent a possible common mechanism for mobilizing antimicrobial resistance determinants. PMID:24587208

  16. The Origin and Evolution of Six Miniature Inverted-Repeat Transposable Elements in Bombyx mori and Rhodnius prolixus

    PubMed Central

    Zhang, Hua-Hao; Xu, Hong-En; Shen, Yi-Hong; Han, Min-Jin; Zhang, Ze

    2013-01-01

    Miniature inverted-repeat transposable elements (MITEs) are a specific group of nonautonomous DNA transposons, and they are distributed in a wide range of hosts. However, the origin and evolutionary history of MITEs in eukaryotic genomes remain unclear. In this study, six MITEs were identified in the silkworm (Bombyx mori). Five elements are grouped into four known superfamilies of DNA transposons, and one represents a novel class of MITEs. Unexpectedly, six similar MITEs are also present in the triatomine bug (Rhodnius prolixus) that diverged from the common ancestor with the silkworm about 370 Ma. However, they show different lengths in two species, suggesting that they are different derivatives of progenitor transposons. Three direct progenitor transposons (Sola1, hobo/Ac/Tam [hAT], and Ginger2) are also identified in some other organisms, and several lines of evidence suggested that these autonomous elements might have been independently and horizontally transferred into their hosts. Furthermore, it is speculated that the twisted-wing parasites may be the candidate vectors for these horizontal transfers. The data presented in this study provide some new insights into the origin and evolutionary history of MITEs in the silkworm and triatomine bug. PMID:24115603

  17. Efficient transposition of the youngest miniature inverted repeat transposable element family of yellow fever mosquito in yeast.

    PubMed

    Fattash, Isam; Lee, Chia-Ni; Mo, Kaiguo; Yang, Guojun

    2015-05-01

    Miniature inverted repeat transposable elements (MITEs) are often the most numerous DNA transposons in plant and animal genomes. The dramatic amplification of MITE families during evolution is puzzling, because the transposase sources for the vast majority of MITE families are unknown. The yellow fever mosquito genome contains > 220-Mb MITE sequences; however, transposition activity has not been demonstrated for any of the MITE families. The Gnome elements are the youngest MITE family in this genome, with at least 116 identical copies. To test whether the putative autonomous element Ozma is capable of mobilizing Gnome and its two sibling MITEs, analyses were performed in a yeast transposition assay system. Whereas the wild-type transposase resulted in very low transposition activity, mutations in the region containing a putative nuclear export signal motif resulted in a dramatic (at least 4160-fold) increase in transposition frequency. We have also demonstrated that each residue of the novel DD37E motif is required for the activity of the Ozma transposase. Footprint sequences left at the donor sites suggest that the transposase may cleave between the second and the third nucleotides from the 5' ends of the elements. The excised elements reinsert specifically at dinucleotide 'TA', ~ 55% of them in yeast genes. The elements described in this article could potentially be useful as genetic tools for genetic manipulation of mosquitoes. PMID:25754725

  18. Genome-Wide Comparative Analysis of 20 Miniature Inverted-Repeat Transposable Element Families in Brassica rapa and B. oleracea

    PubMed Central

    Sampath, Perumal; Murukarthick, Jayakodi; Izzah, Nur Kholilatul; Lee, Jonghoon; Choi, Hong-Il; Shirasawa, Kenta; Choi, Beom-Soon; Liu, Shengyi; Nou, Ill-Sup; Yang, Tae-Jin

    2014-01-01

    Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion. PMID:24747717

  19. Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.

    PubMed

    Sampath, Perumal; Murukarthick, Jayakodi; Izzah, Nur Kholilatul; Lee, Jonghoon; Choi, Hong-Il; Shirasawa, Kenta; Choi, Beom-Soon; Liu, Shengyi; Nou, Ill-Sup; Yang, Tae-Jin

    2014-01-01

    Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion. PMID:24747717

  20. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

    PubMed Central

    Kuang, Hanhui; Padmanabhan, Chellappan; Li, Feng; Kamei, Ayako; Bhaskar, Pudota B.; Ouyang, Shu; Jiang, Jiming; Buell, C. Robin; Baker, Barbara

    2009-01-01

    Small RNAs regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). Although miniature inverted-repeat transposable elements (MITEs) are closely associated with euchromatic genes, the broader functional impact of these short TE insertions in genes is largely unknown. We identified 22 families of MITEs in the Solanaceae (MiS1–MiS22) and found abundant MiS insertions in Solanaceae genomic DNA and expressed sequence tags (EST). Several Solanaceae MITEs generate genome changes that potentially affect gene function and regulation, most notably, a MiS insertion that provides a functionally indispensable alternative exon in the tobacco mosaic virus N resistance gene. We show that MITEs generate small RNAs that are primarily 24 nt in length, as detected by Northern blot hybridization and by sequencing small RNAs of Solanum demissum, Nicotiana glutinosa, and Nicotiana benthamiana. Additionally, we show that stable RNAi lines silencing DICER-LIKE3 (DCL3) in tobacco and RNA-dependent RNA polymerase 2 (RDR2) in potato cause a reduction in 24-nt MITE siRNAs, suggesting that, as in Arabidopsis, TE-derived siRNA biogenesis is DCL3 and RDR2 dependent. We provide evidence that DICER-LIKE4 (DCL4) may also play a role in MITE siRNA generation in the Solanaceae. PMID:19037014

  1. Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize

    PubMed Central

    Zhang, Qiang; Arbuckle, John; Wessler, Susan R.

    2000-01-01

    A 314-bp DNA element called Heartbreaker-hm1 (Hbr-hm1) was previously identified in the 3′ untranslated region of a mutant allele of the maize disease resistance gene HM1. This element has structural features of miniature inverted-repeat transposable elements (MITEs) and is a member of a large family of approximately 4,000 copies in the maize genome. Unlike previously described MITEs, most members of the Hbr family display over 90% sequence identity. This, coupled with the insertion of an Hbr element into an allele of the HM1 gene, suggested that this family might have spread recently throughout the genome. Consistent with this view is the finding that Hbr insertion sites are remarkably polymorphic. Ten of ten loci containing Hbr elements were found to be polymorphic for the presence or absence of Hbr among a collection of maize inbred lines and teosinte strains. Despite the fact that over 80% of the maize genome contain moderate to highly repetitive DNA, we find that randomly chosen Hbr elements are predominantly in single or low copy regions. Furthermore, when used to query both the public and private databases of plant genes, over 50% of the sequences flanking these Hbr elements resulted in significant “hits.” Taken together, these data indicate that the presence or absence of Hbr elements is a significant contributory factor to the high level of polymorphism associated with maize genic regions. PMID:10655501

  2. The characteristics and functions of a miniature inverted-repeat transposable element TaMITE81 in the 5' UTR of TaCHS7BL from Triticum aestivum.

    PubMed

    Xi, Xinyuan; Li, Na; Li, Shiming; Chen, Wenjie; Zhang, Bo; Liu, Baolong; Zhang, Huaigang

    2016-10-01

    Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in eukaryotic and prokaryotic genomes. In this article, a MITE, TaMITE81, was isolated from the 5' untranslated region (UTR) of TaCHS7BL, chalcone synthase (CHS) catalyzing the first committed step of anthocyanin biosynthesis, in the wheat cultivar 'Opata' with white grain. TaMITE81 was only 81 nucleotides, including a terminal inverted repeat with 39 nucleotides and was flanked by two nucleotides, "TA", target site duplications that were typical features of stowaway-like MITEs. Compared with the wheat cultivar 'Gy115' with purple grain, which is without the insertion, the expression of TaCHS7BL was lower in several organs of 'Opata'. The insertion of TaMITE81 into the 5' UTR of the GUS gene also reduced the transient expression of GUS on the coleoptiles of 'Opata', which means the insertion of TaMITE81 was the reason for the low expression of TaCHS7BL in 'Opata'. But the genotype of TaCHS7BL was not linked to phenotype of grain color in the RILs derived from a cross 'Gy115' and 'Opata'. The TaMITE81 density of the hexaploid variety of T. aestivum was more than 10 times that of diploid relatives, which implies that polyploidization caused the amplification of TaMITE81 homologous sequences. Further research should be conducted on decoding the relationship between TaCHS7BL and other traits relative to anthocyanin biosynthesis in wheat, and discovering the mechanism of TaMITE81 transposon action. PMID:27481288

  3. DcSto, stowaway-like miniature inverted-repeat transposable elements (MITEs), are abundant and polymorphic in the carrot genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transposable elements constitute a large fraction of plant genomes and strongly influence gene and genome evolution. Stowaway elements, a group of MITEs present in high copy number, are preferentially located in the vicinity of coding regions. Stowaway elements are characterized by short length, sim...

  4. Mobility and Generation of Mosaic Non-Autonomous Transposons by Tn3-Derived Inverted-Repeat Miniature Elements (TIMEs)

    PubMed Central

    Szuplewska, Magdalena; Ludwiczak, Marta; Lyzwa, Katarzyna; Czarnecki, Jakub; Bartosik, Dariusz

    2014-01-01

    Functional transposable elements (TEs) of several Pseudomonas spp. strains isolated from black shale ore of Lubin mine and from post-flotation tailings of Zelazny Most in Poland, were identified using a positive selection trap plasmid strategy. This approach led to the capture and characterization of (i) 13 insertion sequences from 5 IS families (IS3, IS5, ISL3, IS30 and IS1380), (ii) isoforms of two Tn3-family transposons – Tn5563a and Tn4662a (the latter contains a toxin-antitoxin system), as well as (iii) non-autonomous TEs of diverse structure, ranging in size from 262 to 3892 bp. The non-autonomous elements transposed into AT-rich DNA regions and generated 5- or 6-bp sequence duplications at the target site of transposition. Although these TEs lack a transposase gene, they contain homologous 38-bp-long terminal inverted repeat sequences (IRs), highly conserved in Tn5563a and many other Tn3-family transposons. The simplest elements of this type, designated TIMEs (Tn3 family-derived Inverted-repeat Miniature Elements) (262 bp), were identified within two natural plasmids (pZM1P1 and pLM8P2) of Pseudomonas spp. It was demonstrated that TIMEs are able to mobilize segments of plasmid DNA for transposition, which results in the generation of more complex non-autonomous elements, resembling IS-driven composite transposons in structure. Such transposon-like elements may contain different functional genetic modules in their core regions, including plasmid replication systems. Another non-autonomous element “captured” with a trap plasmid was a TIME derivative containing a predicted resolvase gene and a res site typical for many Tn3-family transposons. The identification of a portable site-specific recombination system is another intriguing example confirming the important role of non-autonomous TEs of the TIME family in shuffling genetic information in bacterial genomes. Transposition of such mosaic elements may have a significant impact on diversity and evolution

  5. Insights on genome size evolution from a miniature inverted repeat transposon driving a satellite DNA.

    PubMed

    Scalvenzi, Thibault; Pollet, Nicolas

    2014-12-01

    The genome size in eukaryotes does not correlate well with the number of genes they contain. We can observe this so-called C-value paradox in amphibian species. By analyzing an amphibian genome we asked how repetitive DNA can impact genome size and architecture. We describe here our discovery of a Tc1/mariner miniature inverted-repeat transposon family present in Xenopus frogs. These transposons named miDNA4 are unique since they contain a satellite DNA motif. We found that miDNA4 measured 331 bp, contained 25 bp long inverted terminal repeat sequences and a sequence motif of 119 bp present as a unique copy or as an array of 2-47 copies. We characterized the structure, dynamics, impact and evolution of the miDNA4 family and its satellite DNA in Xenopus frog genomes. This led us to propose a model for the evolution of these two repeated sequences and how they can synergize to increase genome size. PMID:25193611

  6. Insertion of miniature subterminal inverted repeat-like elements in diapause-regulated genes in the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determining the genomic structure of diapause-associated transcripts (DAT) -2 and -3 led to the isolation of four novel miniature subterminal inverted repeat-like elements (MSITE): Mild-1, -2, -3 and -4. Mild-1a is inserted within the first intron of diapause protein-1. Mild-1a is 284 bp in length, ...

  7. Miniature inverted-repeat transposable element identification and genetic marker development in Agrostis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Creeping bentgrass (Agrostis stolonifera L.) is an important species to the turfgrass industry because of its adaptation for use in high quality turf stands such as golf course putting greens, tees, and fairways. A. stolonifera is a highly outcrossing allotetraploid making genetic marker developmen...

  8. Identification and purification of a Drosophila protein that binds to the terminal 31-base-pair inverted repeats of the P transposable element

    SciTech Connect

    Rio, D.C.; Rubin, G.M.

    1988-12-01

    We have used DNase I footprinting and partially fractionated nuclear extracts from Drosophila Kc tissue culture cells to identify DNA-binding proteins that interact with the terminal repeats of P transposable elements. We have identified a binding activity that interacts specifically with a region of the 31-base-pair terminal inverted repeats that is directly adjacent to the duplication of target site DNA. Binding occurs to both the 5' and 3' inverted terminal repeats irrespective of the sequence of the duplicated target DNA. UV photochemical crosslinking studies suggest that the binding activity resides in a polypeptide of 65-70 kDa. Biochemical fractionation and oligonucleotide affinity chromatography have been used to purify the binding activity to near homogeneity and identify a polypeptide of 66 kDa in the highly purified preparations. The site to which binding occurs is included in a region absolutely required for P element transposition, suggesting that this binding protein may be a cellular factor involved in P element transposition.

  9. The Hermes transposable element from the house fly, Musca domestica, is a short inverted repeat-type element of the hobo, Ac, and Tam3 (hAT) element family.

    PubMed

    Warren, W D; Atkinson, P W; O'Brochta, D A

    1994-10-01

    The genome of the house fly, Musca domestica, contains an active transposable element system, called Hermes. Using PCR and inverse PCR we amplified and sequenced overlapping segments of several Hermes elements and from these data we have constructed a 2749 bp consensus Hermes DNA sequence. Hermes termini are composed of 17 bp imperfect inverted repeats that are almost identical to the inverted terminal repeats of the hobo element of Drosophila melanogaster. Full length Hermes elements contain a single long ORF capable of encoding a protein of 612 amino acids which is 55% identical to the amino acid sequence of the hobo transposase. Comparison of the ends of the Hermes and hobo elements to those of the Ac element of Zea mays, and the Tam3 element of Antirrhinum majus, as well as several other plant and insect elements, revealed a conserved terminal sequence motif. Thus Hermes is clearly a member of the hobo, Ac and Tam3 (hAT) transposable element family, other members of which include the Tag1 element from Arabidopsis thaliana and the Bg element from Zea mays. The evolution of this class of transposable elements and the potential utility of Hermes as a genetic tool in M. domestica and related species are discussed. PMID:7813905

  10. Miniature Transposable Sequences Are Frequently Mobilized in the Bacterial Plant Pathogen Pseudomonas syringae pv. phaseolicola

    PubMed Central

    Bardaji, Leire; Añorga, Maite; Jackson, Robert W.; Martínez-Bilbao, Alejandro; Yanguas-Casás, Natalia; Murillo, Jesús

    2011-01-01

    Mobile genetic elements are widespread in Pseudomonas syringae, and often associate with virulence genes. Genome reannotation of the model bean pathogen P. syringae pv. phaseolicola 1448A identified seventeen types of insertion sequences and two miniature inverted-repeat transposable elements (MITEs) with a biased distribution, representing 2.8% of the chromosome, 25.8% of the 132-kb virulence plasmid and 2.7% of the 52-kb plasmid. Employing an entrapment vector containing sacB, we estimated that transposition frequency oscillated between 2.6×10−5 and 1.1×10−6, depending on the clone, although it was stable for each clone after consecutive transfers in culture media. Transposition frequency was similar for bacteria grown in rich or minimal media, and from cells recovered from compatible and incompatible plant hosts, indicating that growth conditions do not influence transposition in strain 1448A. Most of the entrapped insertions contained a full-length IS801 element, with the remaining insertions corresponding to sequences smaller than any transposable element identified in strain 1448A, and collectively identified as miniature sequences. From these, fragments of 229, 360 and 679-nt of the right end of IS801 ended in a consensus tetranucleotide and likely resulted from one-ended transposition of IS801. An average 0.7% of the insertions analyzed consisted of IS801 carrying a fragment of variable size from gene PSPPH_0008/PSPPH_0017, showing that IS801 can mobilize DNA in vivo. Retrospective analysis of complete plasmids and genomes of P. syringae suggests, however, that most fragments of IS801 are likely the result of reorganizations rather than one-ended transpositions, and that this element might preferentially contribute to genome flexibility by generating homologous regions of recombination. A further miniature sequence previously found to affect host range specificity and virulence, designated MITEPsy1 (100-nt), represented an average 2.4% of the total

  11. BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species

    PubMed Central

    2014-01-01

    Background MITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops. Findings We have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences. Conclusions BrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a

  12. Inverted repeats in the promoter as an autoregulatory sequence for TcrX in Mycobacterium tuberculosis

    SciTech Connect

    Bhattacharya, Monolekha; Das, Amit Kumar

    2011-11-11

    Highlights: Black-Right-Pointing-Pointer The regulatory sequences recognized by TcrX have been identified. Black-Right-Pointing-Pointer The regulatory region comprises of inverted repeats segregated by 30 bp region. Black-Right-Pointing-Pointer The mode of binding of TcrX with regulatory sequence is unique. Black-Right-Pointing-Pointer In silico TcrX-DNA docked model binds one of the inverted repeats. Black-Right-Pointing-Pointer Both phosphorylated and unphosphorylated TcrX binds regulatory sequence in vitro. -- Abstract: TcrY, a histidine kinase, and TcrX, a response regulator, constitute a two-component system in Mycobacterium tuberculosis. tcrX, which is expressed during iron scarcity, is instrumental in the survival of iron-dependent M. tuberculosis. However, the regulator of tcrX/Y has not been fully characterized. Crosslinking studies of TcrX reveal that it can form oligomers in vitro. Electrophoretic mobility shift assays (EMSAs) show that TcrX recognizes two regions in the promoter that are comprised of inverted repeats separated by {approx}30 bp. The dimeric in silico model of TcrX predicts binding to one of these inverted repeat regions. Site-directed mutagenesis and radioactive phosphorylation indicate that D54 of TcrX is phosphorylated by H256 of TcrY. However, phosphorylated and unphosphorylated TcrX bind the regulatory sequence with equal efficiency, which was shown with an EMSA using the D54A TcrX mutant.

  13. Miniature Inverted–Repeat Transposable Elements (MITEs) Have Been Accumulated through Amplification Bursts and Play Important Roles in Gene Expression and Species Diversity in Oryza sativa

    PubMed Central

    Lu, Chen; Chen, Jiongjiong; Zhang, Yu; Hu, Qun; Su, Wenqing; Kuang, Hanhui

    2012-01-01

    Miniature inverted–repeat transposable elements (MITEs) are predicted to play important roles on genome evolution. We developed a BLASTN-based approach for de novo identification of MITEs and systematically analyzed MITEs in rice genome. The genome of rice cultivar Nipponbare (Oryza sativa ssp. japonica) harbors 178,533 MITE-related sequences classified into 338 families. Pairwise nucleotide diversity and phylogenetic tree analysis indicated that individual MITE families were resulted from one or multiple rounds of amplification bursts. The timing of amplification burst varied considerably between different MITE families or subfamilies. MITEs are associated with 23,623 (58.2%) genes in rice genome. At least 7,887 MITEs are transcribed and more than 3,463 were transcribed with rice genes. The MITE sequences transcribed with rice coding genes form 1,130 pairs of potential natural sense/antisense transcripts. MITEs generate 23.5% (183,837 of 781,885) of all small RNAs identified from rice. Some MITE families generated small RNAs mainly from the terminals, while other families generated small RNAs predominantly from the central region. More than half (51.8%) of the MITE-derived small RNAs were generated exclusively by MITEs located away from genes. Genome-wide analysis showed that genes associated with MITEs have significantly lower expression than genes away from MITEs. Approximately 14.8% of loci with full-length MITEs have presence/absence polymorphism between rice cultivars 93-11 (O. sativa ssp. indica) and Nipponbare. Considering that different sets of genes may be regulated by MITE-derived small RNAs in different genotypes, MITEs provide considerable diversity for O. sativa. PMID:22096216

  14. Mutagenic Inverted Repeats Assisted Genome Engineering (MIRAGE) in Saccharomyces cerevisiae: deletion of gal7.

    PubMed

    Nair, Nikhil U; Zhao, Huimin

    2012-01-01

    MIRAGE is a unique in vivo genome editing technique that exploits the inherent instability of inverted repeats (palindromes) in the Saccharomyces cerevisiae chromosome. As a technique able to quickly create deletions as well as precise point mutations, it is valuable in applications that require creation of designer strains of this yeast. In particular, it has various potential applications in metabolic engineering, systems biology, synthetic biology, and molecular genetics. PMID:22144353

  15. Formation of large palindromic DNA by homologous recombination of short inverted repeat sequences in Saccharomyces cerevisiae.

    PubMed Central

    Butler, David K; Gillespie, David; Steele, Brandi

    2002-01-01

    Large DNA palindromes form sporadically in many eukaryotic and prokaryotic genomes and are often associated with amplified genes. The presence of a short inverted repeat sequence near a DNA double-strand break has been implicated in the formation of large palindromes in a variety of organisms. Previously we have established that in Saccharomyces cerevisiae a linear DNA palindrome is efficiently formed from a single-copy circular plasmid when a DNA double-strand break is introduced next to a short inverted repeat sequence. In this study we address whether the linear palindromes form by an intermolecular reaction (that is, a reaction between two identical fragments in a head-to-head arrangement) or by an unusual intramolecular reaction, as it apparently does in other examples of palindrome formation. Our evidence supports a model in which palindromes are primarily formed by an intermolecular reaction involving homologous recombination of short inverted repeat sequences. We have also extended our investigation into the requirement for DNA double-strand break repair genes in palindrome formation. We have found that a deletion of the RAD52 gene significantly reduces palindrome formation by intermolecular recombination and that deletions of two other genes in the RAD52-epistasis group (RAD51 and MRE11) have little or no effect on palindrome formation. In addition, palindrome formation is dramatically reduced by a deletion of the nucleotide excision repair gene RAD1. PMID:12136011

  16. detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.

    PubMed

    Ye, Congting; Ji, Guoli; Li, Lei; Liang, Chun

    2014-01-01

    Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir. PMID:25409465

  17. detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation

    PubMed Central

    Ye, Congting; Ji, Guoli; Li, Lei; Liang, Chun

    2014-01-01

    Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures – hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir. PMID:25409465

  18. Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification

    PubMed Central

    Brewer, Bonita J.; Payen, Celia; Di Rienzi, Sara C.; Higgins, Megan M.; Ong, Giang; Dunham, Maitreya J.; Raghuraman, M. K.

    2015-01-01

    DNA replication errors are a major driver of evolution—from single nucleotide polymorphisms to large-scale copy number variations (CNVs). Here we test a specific replication-based model to explain the generation of interstitial, inverted triplications. While no genetic information is lost, the novel inversion junctions and increased copy number of the included sequences create the potential for adaptive phenotypes. The model—Origin-Dependent Inverted-Repeat Amplification (ODIRA)—proposes that a replication error at pre-existing short, interrupted, inverted repeats in genomic sequences generates an extrachromosomal, inverted dimeric, autonomously replicating intermediate; subsequent genomic integration of the dimer yields this class of CNV without loss of distal chromosomal sequences. We used a combination of in vitro and in vivo approaches to test the feasibility of the proposed replication error and its downstream consequences on chromosome structure in the yeast Saccharomyces cerevisiae. We show that the proposed replication error—the ligation of leading and lagging nascent strands to create “closed” forks—can occur in vitro at short, interrupted inverted repeats. The removal of molecules with two closed forks results in a hairpin-capped linear duplex that we show replicates in vivo to create an inverted, dimeric plasmid that subsequently integrates into the genome by homologous recombination, creating an inverted triplication. While other models have been proposed to explain inverted triplications and their derivatives, our model can also explain the generation of human, de novo, inverted amplicons that have a 2:1 mixture of sequences from both homologues of a single parent—a feature readily explained by a plasmid intermediate that arises from one homologue and integrates into the other homologue prior to meiosis. Our tests of key features of ODIRA lend support to this mechanism and suggest further avenues of enquiry to unravel the origins of

  19. Efficiency of gene silencing in Arabidopsis: direct inverted repeats vs. transitive RNAi vectors.

    SciTech Connect

    Filichkin, Sergei A; DiFazio, Steven P; Brunner, Amy M; Davis, John M; Yang, Zamin Koo; Kalluri, Udaya C; Arias, Renee S; Etherington, Elizabeth; Tuskan, Gerald A; Strauss, S

    2007-01-01

    We investigated the efficiency of RNA interference (RNAi) in Arabidopsis using transitive and homologous inverted repeat (hIR) vectors. hIR constructs carry self-complementary intron-spliced fragments of the target gene whereas transitive vectors have the target sequence fragment adjacent to an intron-spliced, inverted repeat of heterologous origin. Both transitive and hIR constructs facilitated specific and heritable silencing in the three genes studied (AP1, ETTIN and TTG1). Both types of vectors produced a phenotypic series that phenocopied reduction of function mutants for the respective target gene. The hIR yielded up to fourfold higher proportions of events with strongly manifested reduction of function phenotypes compared to transitive RNAi. We further investigated the efficiency and potential off-target effects of AP1 silencing by both types of vectors using genome-scale microarrays and quantitative RT-PCR. The depletion of AP1 transcripts coincided with reduction of function phenotypic changes among both hIR and transitive lines and also showed similar expression patterns among differentially regulated genes. We did not detect significant silencing directed against homologous potential off-target genes when constructs were designed with minimal sequence similarity. Both hIR and transitive methods are useful tools in plant biotechnology and genomics. The choice of vector will depend on specific objectives such as cloning throughput, number of events and degree of suppression required.

  20. A transposable element in a NAC gene is associated with drought tolerance in maize seedlings.

    PubMed

    Mao, Hude; Wang, Hongwei; Liu, Shengxue; Li, Zhigang; Yang, Xiaohong; Yan, Jianbing; Li, Jiansheng; Tran, Lam-Son Phan; Qin, Feng

    2015-01-01

    Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. The 82-bp MITE represses ZmNAC111 expression via RNA-directed DNA methylation and H3K9 dimethylation when heterologously expressed in Arabidopsis. Increasing ZmNAC111 expression in transgenic maize enhances drought tolerance at the seedling stage, improves water-use efficiency and induces upregulation of drought-responsive genes under water stress. The MITE insertion in the ZmNAC111 promoter appears to have occurred after maize domestication and spread among temperate germplasm. The identification of this MITE insertion provides insight into the genetic basis for natural variation in maize drought tolerance. PMID:26387805

  1. A transposable element in a NAC gene is associated with drought tolerance in maize seedlings

    PubMed Central

    Mao, Hude; Wang, Hongwei; Liu, Shengxue; Li, Zhigang; Yang, Xiaohong; Yan, Jianbing; Li, Jiansheng; Tran, Lam-Son Phan; Qin, Feng

    2015-01-01

    Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. The 82-bp MITE represses ZmNAC111 expression via RNA-directed DNA methylation and H3K9 dimethylation when heterologously expressed in Arabidopsis. Increasing ZmNAC111 expression in transgenic maize enhances drought tolerance at the seedling stage, improves water-use efficiency and induces upregulation of drought-responsive genes under water stress. The MITE insertion in the ZmNAC111 promoter appears to have occurred after maize domestication and spread among temperate germplasm. The identification of this MITE insertion provides insight into the genetic basis for natural variation in maize drought tolerance. PMID:26387805

  2. Maize genetic diversity and association mapping using transposable element insertion polymorphisms.

    PubMed

    Zerjal, Tatiana; Rousselet, Agnès; Mhiri, Corinne; Combes, Valérie; Madur, Delphine; Grandbastien, Marie-Angèle; Charcosset, Alain; Tenaillon, Maud I

    2012-05-01

    Transposable elements are the major component of the maize genome and presumably highly polymorphic yet they have not been used in population genetics and association analyses. Using the Transposon Display method, we isolated and converted into PCR-based markers 33 Miniature Inverted Repeat Transposable Elements (MITE) polymorphic insertions. These polymorphisms were genotyped on a population-based sample of 26 American landraces for a total of 322 plants. Genetic diversity was high and partitioned within and among landraces. The genetic groups identified using Bayesian clustering were in agreement with published data based on SNPs and SSRs, indicating that MITE polymorphisms reflect maize genetic history. To explore the contribution of MITEs to phenotypic variation, we undertook an association mapping approach in a panel of 367 maize lines phenotyped for 26 traits. We found a highly significant association between the marker ZmV1-9, on chromosome 1, and male flowering time. The variance explained by this association is consistent with a flowering delay of +123 degree-days. This MITE insertion is located at only 289 nucleotides from the 3' end of a Cytochrome P450-like gene, a region that was never identified in previous association mapping or QTL surveys. Interestingly, we found (i) a non-synonymous mutation located in the exon 2 of the gene in strong linkage disequilibrium with the MITE polymorphism, and (ii) a perfect sequence homology between the MITE sequence and a maize siRNA that could therefore potentially interfere with the expression of the Cytochrome P450-like gene. Those two observations among others offer exciting perspectives to validate functionally the role of this region on phenotypic variation. PMID:22350086

  3. Structure and organization of Marchantia polymorpha chloroplast genome. IV. Inverted repeat and small single copy regions.

    PubMed

    Kohchi, T; Shirai, H; Fukuzawa, H; Sano, T; Komano, T; Umesono, K; Inokuchi, H; Ozeki, H; Ohyama, K

    1988-09-20

    We characterized the genes in the regions of large inverted repeats (IRA and IRB, 10,058 base-pairs each) and a small single copy (SSC 19,813 bp) of chloroplast DNA from Marchantia polymorpha. The inverted repeat (IR) regions contain genes for four ribosomal RNAs (16 S, 23 S, 4.5 S and 5 S rRNAs) and five transfer RNAs (valine tRNA(GAC), isoleucine tRNA(GAU), alanine tRNA(UGC), arginine tRNA(ACG) and asparagine tRNA(GUU)). The gene organization of the IR regions in the liverwort chloroplast genome is conserved, although the IR regions are smaller (10,058 base-pairs) than any reported in higher plant chloroplasts. The small single-copy region (19,813 base-pairs) encoded genes for 17 open reading frames, a leucine tRNA(UAG) and a proline tRNA(GGG)-like sequence. We identified 12 open reading frames by homology of their coding sequences to a 4Fe-4S-type ferredoxin protein, a bacterial nitrogenase reductase component (Fe-protein), five human mitochondrial components of NADH dehydrogenase (ND1, ND4, ND4L, ND5 and ND6), two Escherichia coli ribosomal proteins (S15 and L21), two putative proteins encoded in the kinetoplast maxicircle DNA of Leishmania tarentolae (LtORF 3 and LtORF 4), and a bacterial permease inner membrane component (encoded by malF in E. coli or hisQ in Salmonella typhimurium). PMID:3199437

  4. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.

    PubMed

    Linheiro, Raquel S; Bergman, Casey M

    2012-01-01

    Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes. PMID:22347367

  5. Sequence of retrovirus provirus resembles that of bacterial transposable elements

    NASA Astrophysics Data System (ADS)

    Shimotohno, Kunitada; Mizutani, Satoshi; Temin, Howard M.

    1980-06-01

    The nucleotide sequences of the terminal regions of an infectious integrated retrovirus cloned in the modified λ phage cloning vector Charon 4A have been elucidated. There is a 569-base pair direct repeat at both ends of the viral DNA. The cell-virus junctions at each end consist of a 5-base pair direct repeat of cell DNA next to a 3-base pair inverted repeat of viral DNA. This structure resembles that of a transposable element and is consistent with the protovirus hypothesis that retroviruses evolved from the cell genome.

  6. Centromeres of the Yeast Komagataella phaffii (Pichia pastoris) Have a Simple Inverted-Repeat Structure.

    PubMed

    Coughlan, Aisling Y; Hanson, Sara J; Byrne, Kevin P; Wolfe, Kenneth H

    2016-01-01

    Centromere organization has evolved dramatically in one clade of fungi, the Saccharomycotina. These yeasts have lost the ability to make normal eukaryotic heterochromatin with histone H3K9 methylation, which is a major component of pericentromeric regions in other eukaryotes. Following this loss, several different types of centromere emerged, including two types of sequence-defined ("point") centromeres, and the epigenetically defined "small regional" centromeres of Candida albicans Here we report that centromeres of the methylotrophic yeast Komagataella phaffii (formerly called Pichia pastoris) are structurally defined. Each of its four centromeres consists of a 2-kb inverted repeat (IR) flanking a 1-kb central core (mid) region. The four centromeres are unrelated in sequence. CenH3 (Cse4) binds strongly to the cores, with a decreasing gradient along the IRs. This mode of organization resembles Schizosaccharomyces pombe centromeres but is much more compact and lacks the extensive flanking heterochromatic otr repeats. Different isolates of K. phaffii show polymorphism for the orientation of the mid regions, due to recombination in the IRs. CEN4 is located within a 138-kb region that changes orientation during mating-type switching, but switching does not induce recombination of centromeric IRs. Our results demonstrate that evolutionary transitions in centromere organization have occurred in multiple yeast clades. PMID:27497317

  7. Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content.

    PubMed

    Li, Fay-Wei; Kuo, Li-Yaung; Pryer, Kathleen M; Rothfels, Carl J

    2016-01-01

    Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution in the IR compared to the SC region. In addition, the organization and structure of plastomes is fluid, and rearrangements through time have repeatedly shuffled genes into and out of the IR, providing recurrent natural experiments on how chloroplast genome structure can impact rates and patterns of molecular evolution. Here we examine four loci (psbA, ycf2, rps7, and rps12 exon 2-3) that were translocated from the SC into the IR during fern evolution. We use a model-based method, within a phylogenetic context, to test for substitution rate shifts. All four loci show a significant, 2- to 3-fold deceleration in their substitution rate following translocation into the IR, a phenomenon not observed in any other, nontranslocated plastid genes. Also, we show that after translocation, the GC content of the third codon position and of the noncoding regions is significantly increased, implying that gene conversion within the IR is GC-biased. Taken together, our results suggest that the IR region not only reduces substitution rates, but also impacts nucleotide composition. This finding highlights a potential vulnerability of correlating substitution rate heterogeneity with organismal life history traits without knowledge of the underlying genome structure. PMID:27401175

  8. Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content

    PubMed Central

    Li, Fay-Wei; Kuo, Li-Yaung; Pryer, Kathleen M.; Rothfels, Carl J.

    2016-01-01

    Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution in the IR compared to the SC region. In addition, the organization and structure of plastomes is fluid, and rearrangements through time have repeatedly shuffled genes into and out of the IR, providing recurrent natural experiments on how chloroplast genome structure can impact rates and patterns of molecular evolution. Here we examine four loci (psbA, ycf2, rps7, and rps12 exon 2–3) that were translocated from the SC into the IR during fern evolution. We use a model-based method, within a phylogenetic context, to test for substitution rate shifts. All four loci show a significant, 2- to 3-fold deceleration in their substitution rate following translocation into the IR, a phenomenon not observed in any other, nontranslocated plastid genes. Also, we show that after translocation, the GC content of the third codon position and of the noncoding regions is significantly increased, implying that gene conversion within the IR is GC-biased. Taken together, our results suggest that the IR region not only reduces substitution rates, but also impacts nucleotide composition. This finding highlights a potential vulnerability of correlating substitution rate heterogeneity with organismal life history traits without knowledge of the underlying genome structure. PMID:27401175

  9. Replication stalling at unstable inverted repeats: Interplay between DNA hairpins and fork stabilizing proteins

    PubMed Central

    Voineagu, Irina; Narayanan, Vidhya; Lobachev, Kirill S.; Mirkin, Sergei M.

    2008-01-01

    DNA inverted repeats (IRs) are hotspots of genomic instability in both prokaryotes and eukaryotes. This feature is commonly attributed to their ability to fold into hairpin- or cruciform-like DNA structures interfering with DNA replication and other genetic processes. However, direct evidence that IRs are replication stall sites in vivo is currently lacking. Here, we show by 2D electrophoretic analysis of replication intermediates that replication forks stall at IRs in bacteria, yeast, and mammalian cells. We found that DNA hairpins, rather than DNA cruciforms, are responsible for the replication stalling by comparing the effects of specifically designed imperfect IRs with varying lengths of their central spacer. Finally, we report that yeast fork-stabilizing proteins, Tof1 and Mrc1, are required to counteract repeat-mediated replication stalling. We show that the function of the Tof1 protein at DNA structure-mediated stall sites is different from its previously described effect on protein-mediated replication fork barriers. PMID:18632578

  10. Inverted repeats and genome architecture conversions of terrestrial isopods mitochondrial DNA.

    PubMed

    Doublet, Vincent; Helleu, Quentin; Raimond, Roland; Souty-Grosset, Catherine; Marcadé, Isabelle

    2013-09-01

    Mitochondrial DNA (mtDNA) is usually depicted as a circular molecule, however, there is increasing evidence that linearization of mtDNA evolved independently many times in organisms such as fungi, unicellular eukaryotes, and animals. Recent observations in various models with linear mtDNA revealed the presence of conserved inverted repeats (IR) at both ends that, when they become single-stranded, may be able to fold on themselves to create telomeric-hairpins involved in genome architecture conversions. The atypical mtDNA of terrestrial isopods (Crustacea: Oniscidea) composed of linear monomers and circular dimers is an interesting model to study genome architecture conversions. Here, we present the mtDNA control region sequences of two species of the genus Armadillidium: A. vulgare and A. pelagicum. All features of arthropods mtDNA control regions are present (origin of replication, poly-T stretch, GA and TA-rich blocks and one variable domain), plus a conserved IR. This IR can potentially fold into a hairpin structure and is present in two different orientations among the A. vulgare populations: either in one sense or in its reverse complement. This polymorphism, also observed in a single individual (heteroplasmy), might be a signature of genome architecture conversions from linear to circular monomeric mtDNA via successive opening and closing of the molecules. PMID:24068302

  11. Centromeres of the Yeast Komagataella phaffii (Pichia pastoris) Have a Simple Inverted-Repeat Structure

    PubMed Central

    Coughlan, Aisling Y.; Hanson, Sara J.; Byrne, Kevin P.; Wolfe, Kenneth H.

    2016-01-01

    Centromere organization has evolved dramatically in one clade of fungi, the Saccharomycotina. These yeasts have lost the ability to make normal eukaryotic heterochromatin with histone H3K9 methylation, which is a major component of pericentromeric regions in other eukaryotes. Following this loss, several different types of centromere emerged, including two types of sequence-defined (“point”) centromeres, and the epigenetically defined “small regional” centromeres of Candida albicans. Here we report that centromeres of the methylotrophic yeast Komagataella phaffii (formerly called Pichia pastoris) are structurally defined. Each of its four centromeres consists of a 2-kb inverted repeat (IR) flanking a 1-kb central core (mid) region. The four centromeres are unrelated in sequence. CenH3 (Cse4) binds strongly to the cores, with a decreasing gradient along the IRs. This mode of organization resembles Schizosaccharomyces pombe centromeres but is much more compact and lacks the extensive flanking heterochromatic otr repeats. Different isolates of K. phaffii show polymorphism for the orientation of the mid regions, due to recombination in the IRs. CEN4 is located within a 138-kb region that changes orientation during mating-type switching, but switching does not induce recombination of centromeric IRs. Our results demonstrate that evolutionary transitions in centromere organization have occurred in multiple yeast clades. PMID:27497317

  12. The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

    PubMed Central

    Benson, Gary; Gelfand, Yevgeniy; Benham, Craig J.

    2010-01-01

    Although a variety of possible functions have been proposed for inverted repeat sequences (IRs), it is not known which of them might occur in vivo. We investigate this question by assessing the distributions and properties of IRs in the Saccharomyces cerevisiae (SC) genome. Using the IRFinder algorithm we detect 100,514 IRs having copy length greater than 6 bp and spacer length less than 77 bp. To assess statistical significance we also determine the IR distributions in two types of randomization of the S. cerevisiae genome. We find that the S. cerevisiae genome is significantly enriched in IRs relative to random. The S. cerevisiae IRs are significantly longer and contain fewer imperfections than those from the randomized genomes, suggesting that processes to lengthen and/or correct errors in IRs may be operative in vivo. The S. cerevisiae IRs are highly clustered in intergenic regions, while their occurrence in coding sequences is consistent with random. Clustering is stronger in the 3′ flanks of genes than in their 5′ flanks. However, the S. cerevisiae genome is not enriched in those IRs that would extrude cruciforms, suggesting that this is not a common event. Various explanations for these results are considered. Electronic supplementary material The online version of this article (doi:10.1007/s00294-010-0302-6) contains supplementary material, which is available to authorized users. PMID:20446088

  13. The complete chloroplast genome of Ginkgo biloba reveals the mechanism of inverted repeat contraction.

    PubMed

    Lin, Ching-Ping; Wu, Chung-Shien; Huang, Ya-Yi; Chaw, Shu-Miaw

    2012-01-01

    We determined the complete chloroplast genome (cpDNA) of Ginkgo biloba (common name: ginkgo), the only relict of ginkgophytes from the Triassic Period. The cpDNA molecule of ginkgo is quadripartite and circular, with a length of 156,945 bp, which is 6,458 bp shorter than that of Cycas taitungensis. In ginkgo cpDNA, rpl23 becomes pseudo, only one copy of ycf2 is retained, and there are at least five editing sites. We propose that the retained ycf2 is a duplicate of the ancestral ycf2, and the ancestral one has been lost from the inverted repeat A (IR(A)). This loss event should have occurred and led to the contraction of IRs after ginkgos diverged from other gymnosperms. A novel cluster of three transfer RNA (tRNA) genes, trnY-AUA, trnC-ACA, and trnSeC-UCA, was predicted to be located between trnC-GCA and rpoB of the large single-copy region. Our phylogenetic analysis strongly suggests that the three predicted tRNA genes are duplicates of trnC-GCA. Interestingly, in ginkgo cpDNA, the loss of one ycf2 copy does not significantly elevate the synonymous rate (Ks) of the retained copy, which disagrees with the view of Perry and Wolfe (2002) that one of the two-copy genes is subjected to elevated Ks when its counterpart has been lost. We hypothesize that the loss of one ycf2 is likely recent, and therefore, the acquired Ks of the retained copy is low. Our data reveal that ginkgo possesses several unique features that contribute to our understanding of the cpDNA evolution in seed plants. PMID:22403032

  14. Cell culture-induced gradual and frequent epigenetic reprogramming of invertedly repeated tobacco transgene epialleles.

    PubMed

    Krizova, Katerina; Fojtova, Miloslava; Depicker, Ann; Kovarik, Ales

    2009-03-01

    Using a two-component transgene system involving two epiallelic variants of the invertedly repeated transgenes in locus 1 (Lo1) and a homologous single-copy transgene locus 2 (Lo2), we have studied the stability of the methylation patterns and trans-silencing interactions in cell culture and regenerated tobacco (Nicotiana tabacum) plants. The posttranscriptionally silenced (PTGS) epiallele of the Lo1 trans-silences and trans-methylates the target Lo2 in a hybrid (Lo1/Lo2 line), while its transcriptionally silenced variant (Lo1E) does not. This pattern was stable over several generations in plants. However, in early Lo1E/Lo2 callus, decreased transgene expression and partial loss of Lo1E promoter methylation compared with leaf tissue in the parental plant were observed. Analysis of small RNA species and coding region methylation suggested that the transgenes were silenced by a PTGS mechanism. The Lo1/Lo2 line remained silenced, but the nonmethylated Lo1 promoter acquired partial methylation in later callus stages. These data indicate that a cell culture process has brought both epialleles to a similar epigenetic ground. Bisulfite sequencing of the 35S promoter within the Lo1 silencer revealed molecules with no, intermediate, and high levels of methylation, demonstrating, to our knowledge for the first time, cell-to-cell methylation diversity of callus. Regenerated plants showed high interindividual but low intraindividual epigenetic variability, indicating that the callus-induced epiallelic variants were transmitted to plants and became fixed. We propose that epigenetic changes associated with dedifferentiation might influence regulatory pathways mediated by trans-PTGS processes. PMID:19129419

  15. Conserved Gene Order and Expanded Inverted Repeats Characterize Plastid Genomes of Thalassiosirales

    PubMed Central

    Ashworth, Matt P.; Baeshen, Nabih A.; Baeshen, Mohammad N.; Bahieldin, Ahmed; Theriot, Edward C.; Jansen, Robert K.

    2014-01-01

    Diatoms are mostly photosynthetic eukaryotes within the heterokont lineage. Variable plastid genome sizes and extensive genome rearrangements have been observed across the diatom phylogeny, but little is known about plastid genome evolution within order- or family-level clades. The Thalassiosirales is one of the more comprehensively studied orders in terms of both genetics and morphology. Seven complete diatom plastid genomes are reported here including four Thalassiosirales: Thalassiosira weissflogii, Roundia cardiophora, Cyclotella sp. WC03_2, Cyclotella sp. L04_2, and three additional non-Thalassiosirales species Chaetoceros simplex, Cerataulina daemon, and Rhizosolenia imbricata. The sizes of the seven genomes vary from 116,459 to 129,498 bp, and their genomes are compact and lack introns. The larger size of the plastid genomes of Thalassiosirales compared to other diatoms is due primarily to expansion of the inverted repeat. Gene content within Thalassiosirales is more conserved compared to other diatom lineages. Gene order within Thalassiosirales is highly conserved except for the extensive genome rearrangement in Thalassiosira oceanica. Cyclotella nana, Thalassiosira weissflogii and Roundia cardiophora share an identical gene order, which is inferred to be the ancestral order for the Thalassiosirales, differing from that of the other two Cyclotella species by a single inversion. The genes ilvB and ilvH are missing in all six diatom plastid genomes except for Cerataulina daemon, suggesting an independent gain of these genes in this species. The acpP1 gene is missing in all Thalassiosirales, suggesting that its loss may be a synapomorphy for the order and this gene may have been functionally transferred to the nucleus. Three genes involved in photosynthesis, psaE, psaI, psaM, are missing in Rhizosolenia imbricata, which represents the first documented instance of the loss of photosynthetic genes in diatom plastid genomes. PMID:25233465

  16. Structural similarities between viroids and transposable genetic elements.

    PubMed Central

    Kiefer, M C; Owens, R A; Diener, T O

    1983-01-01

    The primary structures of the tomato planta macho and tomato apical stunt viroids have been determined, and probable secondary structures are proposed. Both viroids can assume the rodlike conformation with extensive base-pairing characteristic of all known viroids. Sequence homologies between the two viroids (75%) and with members of the potato spindle tuber viroid group (73-83%) indicate that they both belong to this group. Comparative sequence analysis of all members of the group reveals striking similarities with the ends of transposable genetic elements. These similarities, the presence of inverted repeats often ending with the dinucleotides U-G and C-A, and flanking imperfect direct repeats suggest that viroids may have originated from transposable elements or retroviral proviruses by deletion of interior portions of the viral (or element) DNA. PMID:6312450

  17. Transposable element interactions in insects: crossmobilization of hobo and Hermes.

    PubMed

    Sundararajan, P; Atkinson, P W; O'Brochta, D A

    1999-08-01

    There are four non-drosophilid insect gene vector systems available that have been constructed from the short inverted repeat-type transposable elements Minos, piggyBac, mariner and Hermes. These elements (with the possible exception of piggyBac) are members of transposable element families that appear to be widespread in nature. Because these transposable element families are large it is possible that an insect species targeted for transformation will contain related transposable elements. The data presented here begin to address directly the question of interaction between diverged but related members of transposable element families. We tested the ability of the hAT elements hobo and Hermes to interact and cause crossmobilization. Using plasmid-based and chromosome-based element mobility assays we found that the terminal sequences of hobo and Hermes were almost equally good substrates for hobo transposase. However, this ability to crossmobilize was not reciprocal. Hermes transposase was only rarely able to cause the excision of hobo elements from plasmids and was never observed from germline chromosomes. These results have important implications for transgenic insect studies in the future. PMID:10469253

  18. Inverted repeats: computer analysis of microorganism genome and imaging of cruciform structure in DNA by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Limansky, Alex; Limanskaya, Olga Y.

    2003-04-01

    Inverted repeats may regulate genetic procceses by formation of hairpin secondary structures that block DNA polymerases. Two different DNA conformations may cor-respond to inverted repeats: either a linear double stranded helix or a cruciform struc-ture consisting of two symmetrical hairpins. Theoretical and experimental studies have shown that cruciform structures can exist in negatively supercoiled DNA, cont-rary to relaxed molecules. Cruciform formation depends on many factors, firstly, on temperature and supercoils density. Recently application of the scanning probe mic-roscopy has allowed for significant progress in cruciform structure studies. The goal of present work is computer analysis of inverted repeats in viruses, bac-teria and plasmid DNA (human immunodeficiency virus (HIV), bovine immunode-ficiency virus (BIV), bovine leukemia virus (BLV), mycobacterium tuberculosis (MTB), plasmid pUC8) and direct visualization of the cruciform structure in super-coiled DNA by atomic force microscopy (AFM). The cruciform dimensions were determined. Analysis and modeling of the most thermodynamically stable cruciform formations in viral and bacterial DNA were carried out. The complete genome sequence of HIV, BIV, BLV is ~9000 base pairs (bp), my-cobacterium tuberculosis - over 4000000 bp, pUC8 DNA - 2665 bp. Computer ana-lysis showed that two different isolates of MTB with complete genome contain 45 and 50 inverted repeats; HIV, BIV, BLV and plasmid pUC8 contain only one palin-drome which can form cruciform structure in buffer solution. Cruciform in plasmid pUC8 supercoiled DNA, was directly visualized by atomic force microscopy. Cruciform is seen as clear-cut extrusions on the DNA filaments with the lengths of the arms fully consistent with the size of the hairpins expected from a 26 bp inverted repeat in pUC8 plasmid DNA. Application of the aminomodi-fied mica allowed to obtain stable DNA images. DNA molecules on aminomica are not stretched and their contours are

  19. Birth of three stowaway-like MITE families via microhomology-mediated miniaturization of a Tc1/Mariner element in the yellow fever mosquito.

    PubMed

    Yang, Guojun; Fattash, Isam; Lee, Chia-Ni; Liu, Kun; Cavinder, Brad

    2013-01-01

    Eukaryotic genomes contain numerous DNA transposons that move by a cut-and-paste mechanism. The majority of these elements are self-insufficient and dependent on their autonomous relatives to transpose. Miniature inverted repeat transposable elements (MITEs) are often the most numerous nonautonomous DNA elements in a higher eukaryotic genome. Little is known about the origin of these MITE families as few of them are accompanied by their direct ancestral elements in a genome. Analyses of MITEs in the yellow fever mosquito identified its youngest MITE family, designated as Gnome, that contains at least 116 identical copies. Genome-wide search for direct ancestral autonomous elements of Gnome revealed an elusive single copy Tc1/Mariner-like element, named as Ozma, that encodes a transposase with a DD37E triad motif. Strikingly, Ozma also gave rise to two additional MITE families, designated as Elf and Goblin. These three MITE families were derived at different times during evolution and bear internal sequences originated from different regions of Ozma. Upon close inspection of the sequence junctions, the internal deletions during the formation of these three MITE families always occurred between two microhomologous sites (6-8 bp). These results suggest that multiple MITE families may originate from a single ancestral autonomous element, and formation of MITEs can be mediated by sequence microhomology. Ozma and its related MITEs are exceptional candidates for the long sought-after endogenous active transposon tool in genetic control of mosquitoes. PMID:24068652

  20. Birth of Three Stowaway-like MITE Families via Microhomology-Mediated Miniaturization of a Tc1/Mariner Element in the Yellow Fever Mosquito

    PubMed Central

    Yang, Guojun; Fattash, Isam; Lee, Chia-Ni; Liu, Kun; Cavinder, Brad

    2013-01-01

    Eukaryotic genomes contain numerous DNA transposons that move by a cut-and-paste mechanism. The majority of these elements are self-insufficient and dependent on their autonomous relatives to transpose. Miniature inverted repeat transposable elements (MITEs) are often the most numerous nonautonomous DNA elements in a higher eukaryotic genome. Little is known about the origin of these MITE families as few of them are accompanied by their direct ancestral elements in a genome. Analyses of MITEs in the yellow fever mosquito identified its youngest MITE family, designated as Gnome, that contains at least 116 identical copies. Genome-wide search for direct ancestral autonomous elements of Gnome revealed an elusive single copy Tc1/Mariner-like element, named as Ozma, that encodes a transposase with a DD37E triad motif. Strikingly, Ozma also gave rise to two additional MITE families, designated as Elf and Goblin. These three MITE families were derived at different times during evolution and bear internal sequences originated from different regions of Ozma. Upon close inspection of the sequence junctions, the internal deletions during the formation of these three MITE families always occurred between two microhomologous sites (6–8 bp). These results suggest that multiple MITE families may originate from a single ancestral autonomous element, and formation of MITEs can be mediated by sequence microhomology. Ozma and its related MITEs are exceptional candidates for the long sought-after endogenous active transposon tool in genetic control of mosquitoes. PMID:24068652

  1. Turn-on of Inactive Genes by Promoter Recruitment in ESCHERICHIA COLI: Inverted Repeats Resulting in Artificial Divergent Operons

    PubMed Central

    Charlier, Daniel; Severne, Yvonne; Zafarullah, Muhamad; Glansdorff, Nicolas

    1983-01-01

    We have characterized two rearrangements consisting of inverted repeats of the argE gene. The promoters (p) of argE and of argCBH face each other over an internal operator. The rearrangements were obained as reactivations of argE in a strain harboring an argEp deletion on a λdarg prophage. In both cases the repeat included argE and argCBHp on either side of a unique sequence; the result is a divergent operon in which each copy of argCBHp reads into the adjacent argE repeat. In one case, the pair of repeats adjoins the silent parental gene, forming a triplication (← → ←). The other rearrangement consists of a single argE palindrome, but the whole prophage is rearranged into an inverted repeat, analogous to certain λdv's. Both structures could be explained by breakage of a replication fork passing argE and by inaccurate rejoining of strands. The λdv-like rearrangement would result from breakage at both replication forks of a phage or prophage replicating during transient release of immunity. The triplication would imply breaking of a chromosomal replication fork, formation of a cyclic intermediate by recombination between the daughter duplex molecules and reinsertion into the parental argE gene. Formation of a triplication by replication errors involving appropriate strand switchings and branch migrations can not be excluded however. PMID:6227522

  2. Correlations between long inverted repeat (LIR) features, deletion size and distance from breakpoint in human gross gene deletions

    PubMed Central

    Aygun, Nevim

    2015-01-01

    Long inverted repeats (LIRs) have been shown to induce genomic deletions in yeast. In this study, LIRs were investigated within ±10 kb spanning each breakpoint from 109 human gross deletions, using Inverted Repeat Finder (IRF) software. LIR number was significantly higher at the breakpoint regions, than in control segments (P < 0.001). In addition, it was found that strong correlation between 5′ and 3′ LIR numbers, suggesting contribution to DNA sequence evolution (r = 0.85, P < 0.001). 138 LIR features at ±3 kb breakpoints in 89 (81%) of 109 gross deletions were evaluated. Significant correlations were found between distance from breakpoint and loop length (r = −0.18, P < 0.05) and stem length (r = −0.18, P < 0.05), suggesting DNA strands are potentially broken in locations closer to bigger LIRs. In addition, bigger loops cause larger deletions (r = 0.19, P < 0.05). Moreover, loop length (r = 0.29, P < 0.02) and identity between stem copies (r = 0.30, P < 0.05) of 3′ LIRs were more important in larger deletions. Consequently, DNA breaks may form via LIR-induced cruciform structure during replication. DNA ends may be later repaired by non-homologous end-joining (NHEJ), with following deletion. PMID:25657065

  3. A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences

    PubMed Central

    Sreeskandarajan, Sutharzan; Flowers, Michelle M.; Karro, John E.; Liang, Chun

    2014-01-01

    Summary: Palindromic sequences, or inverted repeats (IRs), in DNA sequences involve important biological processes such as DNA–protein binding, DNA replication and DNA transposition. Development of bioinformatics tools that are capable of accurately detecting perfect IRs can enable genome-wide studies of IR patterns in both prokaryotes and eukaryotes. Different from conventional string-comparison approaches, we propose a novel algorithm that uses a cumulative score system based on a prime number representation of nucleotide bases. We then implemented this algorithm as a MATLAB-based program for perfect IR detection. In comparison with other existing tools, our program demonstrates a high accuracy in detecting nested and overlapping IRs. Availability and implementation: The source code is freely available on (http://bioinfolab.miamioh.edu/bioinfolab/palindrome.php) Contact: liangc@miamioh.edu or karroje@miamioh.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24215021

  4. Validation and genotyping of multiple human polymorphic inversions mediated by inverted repeats reveals a high degree of recurrence.

    PubMed

    Aguado, Cristina; Gayà-Vidal, Magdalena; Villatoro, Sergi; Oliva, Meritxell; Izquierdo, David; Giner-Delgado, Carla; Montalvo, Víctor; García-González, Judit; Martínez-Fundichely, Alexander; Capilla, Laia; Ruiz-Herrera, Aurora; Estivill, Xavier; Puig, Marta; Cáceres, Mario

    2014-03-01

    In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR) protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6-24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼ 12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies. PMID:24651690

  5. Validation and Genotyping of Multiple Human Polymorphic Inversions Mediated by Inverted Repeats Reveals a High Degree of Recurrence

    PubMed Central

    Aguado, Cristina; Gayà-Vidal, Magdalena; Villatoro, Sergi; Oliva, Meritxell; Izquierdo, David; Giner-Delgado, Carla; Montalvo, Víctor; García-González, Judit; Martínez-Fundichely, Alexander; Capilla, Laia; Ruiz-Herrera, Aurora; Estivill, Xavier; Puig, Marta; Cáceres, Mario

    2014-01-01

    In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR) protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6–24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies. PMID:24651690

  6. Characterization of Transposable Elements in Laccaria bicolor

    SciTech Connect

    Labbe, Jessy L; Murat, Claude; Morin, Emmanuelle; Tuskan, Gerald A; Le Tacon, F; Martin, Francis

    2012-01-01

    Background: The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome. Methodology/Principal Findings: TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copies elements distributed within 172 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs are ancient except some terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TEs expansion in L. bicolor; the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 500,000 years ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea. Conclusions: This analysis represents an initial characterization of TEs in the L. bicolor genome, contributes to genome assembly and to a greater understanding of the role TEs played in genome organization and evolution, and provides a valuable resource for the ongoing Laccaria Pan-Genome project supported by the U.S.-DOE Joint Genome Institute.

  7. Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice.

    PubMed

    Wei, Liya; Gu, Lianfeng; Song, Xianwei; Cui, Xiekui; Lu, Zhike; Zhou, Ming; Wang, Lulu; Hu, Fengyi; Zhai, Jixian; Meyers, Blake C; Cao, Xiaofeng

    2014-03-11

    Transposable elements (TEs) and repetitive sequences make up over 35% of the rice (Oryza sativa) genome. The host regulates the activity of different TEs by different epigenetic mechanisms, including DNA methylation, histone H3K9 methylation, and histone H3K4 demethylation. TEs can also affect the expression of host genes. For example, miniature inverted repeat TEs (MITEs), dispersed high copy-number DNA TEs, can influence the expression of nearby genes. In plants, 24-nt small interfering RNAs (siRNAs) are mainly derived from repeats and TEs. However, the extent to which TEs, particularly MITEs associated with 24-nt siRNAs, affect gene expression remains elusive. Here, we show that the rice Dicer-like 3 homolog OsDCL3a is primarily responsible for 24-nt siRNA processing. Impairing OsDCL3a expression by RNA interference caused phenotypes affecting important agricultural traits; these phenotypes include dwarfism, larger flag leaf angle, and fewer secondary branches. We used small RNA deep sequencing to identify 535,054 24-nt siRNA clusters. Of these clusters, ∼82% were OsDCL3a-dependent and showed significant enrichment of MITEs. Reduction of OsDCL3a function reduced the 24-nt siRNAs predominantly from MITEs and elevated expression of nearby genes. OsDCL3a directly targets genes involved in gibberellin and brassinosteroid homeostasis; OsDCL3a deficiency may affect these genes, thus causing the phenotypes of dwarfism and enlarged flag leaf angle. Our work identifies OsDCL3a-dependent 24-nt siRNAs derived from MITEs as broadly functioning regulators for fine-tuning gene expression, which may reflect a conserved epigenetic mechanism in higher plants with genomes rich in dispersed repeats or TEs. PMID:24554078

  8. Jordan, an active Volvox transposable element similar to higher plant transposons.

    PubMed Central

    Miller, S M; Schmitt, R; Kirk, D L

    1993-01-01

    We have isolated a 1595-bp transposable element from the multicellular green alga Volvox carteri following its insertion into the nitrate reductase (nitA) locus. This element, which we have named Jordan, has short (12-bp) terminal inverted repeats and creates a 3-bp target site duplication, like some higher plant transposons of the classic type. Contained within the first 200 bp of one end of the element are 55-bp inverted repeats, one of which begins with the terminal inverted repeat. Revertants of the transposon insertion into the nitA locus were obtained at a rate of approximately 10(-4) per Volvox embryo per generation. In each revertant examined, all transposon sequences were completely excised, but footprints containing both sets of duplicated bases, in addition to three to nine extra bases, were left behind. Jordan contains no significant open reading frames and so appears to be nonautonomous. DNA gel blot analysis indicates that Jordan is a member of a large family of homologous elements in the Volvox genome. We have isolated and characterized several of these homologs and found that they contain terminal very similar to those of Jordan. Efforts to utilize Jordan and its homologs as tools to tag and clone developmentally interesting genes of Volvox are discussed. PMID:8400878

  9. Terminal Bacteroid Differentiation Is Associated With Variable Morphological Changes in Legume Species Belonging to the Inverted Repeat-Lacking Clade.

    PubMed

    Montiel, Jesús; Szűcs, Attila; Boboescu, Iulian Z; Gherman, Vasile D; Kondorosi, Éva; Kereszt, Attila

    2016-03-01

    Medicago and closely related legume species from the inverted repeat-lacking clade (IRLC) impose terminal differentiation onto their bacterial endosymbionts, manifested in genome endoreduplication, cell enlargement, and loss of cell-division capacity. Nodule-specific cysteine-rich (NCR) secreted host peptides are plant effectors of this process. As bacteroids in other IRLC legumes, such as Cicer arietinum and Glycyrrhiza lepidota, were reported not to display features of terminal differentiation, we investigated the fate of bacteroids in species from these genera as well as in four other species representing distinct genera of the phylogenetic tree for this clade. Bacteroids in all tested legumes proved to be larger in size and DNA content than cultured cells; however, the degree of cell elongation was rather variable in the different species. In addition, the reproductive ability of the bacteroids isolated from these legumes was remarkably reduced. In all IRLC species with available sequence data, the existence of NCR genes was found. These results indicate that IRLC legumes provoke terminal differentiation of their endosymbionts with different morphotypes, probably with the help of NCR peptides. PMID:26713350

  10. Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates.

    PubMed

    Zhu, Andan; Guo, Wenhu; Gupta, Sakshi; Fan, Weishu; Mower, Jeffrey P

    2016-03-01

    Rates of nucleotide substitution were previously shown to be several times slower in the plastid inverted repeat (IR) compared with single-copy (SC) regions, suggesting that the IR provides enhanced copy-correction activity. To examine the generality of this synonymous rate dependence on the IR, we compared plastomes from 69 pairs of closely related species representing 52 families of angiosperms, gymnosperms, and ferns. We explored the breadth of IR boundary shifts in land plants and demonstrate that synonymous substitution rates are, on average, 3.7 times slower in IR genes than in SC genes. In addition, genes moved from the SC into the IR exhibit lower synonymous rates consistent with other IR genes, while genes moved from the IR into the SC exhibit higher rates consistent with other SC genes. Surprisingly, however, several plastid genes from Pelargonium, Plantago, and Silene have highly accelerated synonymous rates despite their IR localization. Together, these results provide strong evidence that the duplicative nature of the IR reduces the substitution rate within this region. The anomalously fast-evolving genes in Pelargonium, Plantago, and Silene indicate localized hypermutation, potentially induced by a higher level of error-prone double-strand break repair in these regions, which generates substitutional rate variation. PMID:26574731

  11. Construction of effective inverted repeat silencing constructs using sodium bisulfite treatment coupled with strand-specific PCR.

    PubMed

    Taylor, Sarah H; Harmse, Johan; Arbuthnot, Patrick; Van Den Berg, Fiona; Weinberg, Marco S; Rey, Marie E C

    2012-04-01

    RNA silencing has been exploited to produce transgenic plants with resistance to viral pathogens via posttranscriptional gene silencing (PTGS). In some cases, this technology is difficult to apply due to the instability of inverted repeat (IR) constructs during cloning and plant transformation. Although such constructs have been shown to be stabilized with introns and efficiently induce RNA silencing, we found that the Pdk intron did not stabilize South African cassava mosaic virus (SACMV) silencing constructs. Therefore, we developed a method for producing long SACMV IR constructs through bisulfite-induced base pair mismatches on the sense arm prior to IR assembly. Expression of SACMV BC1 mismatched IR constructs in the model test plant Nicotiana benthamiana resulted in a reduction in viral BC1 transcript levels, hence viral replication, upon SACMV infection. Mismatched SACMV AC1 IR constructs induced PTGS more efficiently in a N. benthamiana callus system than nonmismatched IR constructs. Our novel method for IR construct generation should be applicable to many sequences where the generation of these constructs has proven difficult in the past. PMID:22482441

  12. Deletion of a 77-Base-Pair Inverted Repeat Element Alters the Synthesis of Surface Polysaccharides in Porphyromonas gingivalis

    PubMed Central

    Bainbridge, Brian W.; Hirano, Takanori; Grieshaber, Nicole

    2015-01-01

    ABSTRACT Bacterial cell surface glycans, such as capsular polysaccharides and lipopolysaccharides (LPS), influence host recognition and are considered key virulence determinants. The periodontal pathogen Porphyromonas gingivalis is known to display at least three different types of surface glycans: O-LPS, A-LPS, and K-antigen capsule. We have shown that PG0121 (in strain W83) encodes a DNABII histone-like protein and that this gene is transcriptionally linked to the K-antigen capsule synthesis genes, generating a large ∼19.4-kb transcript (PG0104-PG0121). Furthermore, production of capsule is deficient in a PG0121 mutant strain. In this study, we report on the identification of an antisense RNA (asRNA) molecule located within a 77-bp inverted repeat (77bpIR) element located near the 5′ end of the locus. We show that overexpression of this asRNA decreases the amount of capsule produced, indicating that this asRNA can impact capsule synthesis in trans. We also demonstrate that deletion of the 77bpIR element and thereby synthesis of the large 19.4-kb transcript also diminishes, but does not eliminate, capsule synthesis. Surprisingly, LPS structures were also altered by deletion of the 77bpIR element, and reactivity to monoclonal antibodies specific to both O-LPS and A-LPS was eliminated. Additionally, reduced reactivity to these antibodies was also observed in a PG0106 mutant, indicating that this putative glycosyltransferase, which is required for capsule synthesis, is also involved in LPS synthesis in strain W83. We discuss our finding in the context of how DNABII proteins, an antisense RNA molecule, and the 77bpIR element may modulate expression of surface polysaccharides in P. gingivalis. IMPORTANCE The periodontal pathogen Porphyromonas gingivalis displays at least three different types of cell surface glycans: O-LPS, A-LPS, and K-antigen capsule. We have shown using Northern analysis that the K-antigen capsule locus encodes a large transcript (∼19.4 kb

  13. Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae

    PubMed Central

    Li, Jia; Gao, Lei; Chen, Shanshan; Tao, Ke; Su, Yingjuan; Wang, Ting

    2016-01-01

    Sciadopitys verticillata is an evergreen conifer and an economically valuable tree used in construction, which is the only member of the family Sciadopityaceae. Acquisition of the S. verticillata chloroplast (cp) genome will be useful for understanding the evolutionary mechanism of conifers and phylogenetic relationships among gymnosperm. In this study, we have first reported the complete chloroplast genome of S. verticillata. The total genome is 138,284 bp in length, consisting of 118 unique genes. The S. verticillata cp genome has lost one copy of the canonical inverted repeats and shown distinctive genomic structure comparing with other cupressophytes. Fifty-three simple sequence repeat loci and 18 forward tandem repeats were identified in the S. verticillata cp genome. According to the rearrangement of cupressophyte cp genome, we proposed one mechanism for the formation of inverted repeat: tandem repeat occured first, then rearrangement divided the tandem repeat into inverted repeats located at different regions. Phylogenetic estimates inferred from 59-gene sequences and cpDNA organizations have both shown that S. verticillata was sister to the clade consisting of Cupressaceae, Taxaceae, and Cephalotaxaceae. Moreover, accD gene was found to be lost in the S. verticillata cp genome, and a nucleus copy was identified from two transcriptome data. PMID:26865528

  14. Transposable Phage Mu.

    PubMed

    Harshey, Rasika M

    2014-10-01

    Transposable phage Mu has played a major role in elucidating the mechanism of movement of mobile DNA elements. The high efficiency of Mu transposition has facilitated a detailed biochemical dissection of the reaction mechanism, as well as of protein and DNA elements that regulate transpososome assembly and function. The deduced phosphotransfer mechanism involves in-line orientation of metal ion-activated hydroxyl groups for nucleophilic attack on reactive diester bonds, a mechanism that appears to be used by all transposable elements examined to date. A crystal structure of the Mu transpososome is available. Mu differs from all other transposable elements in encoding unique adaptations that promote its viral lifestyle. These adaptations include multiple DNA (enhancer, SGS) and protein (MuB, HU, IHF) elements that enable efficient Mu end synapsis, efficient target capture, low target specificity, immunity to transposition near or into itself, and efficient mechanisms for recruiting host repair and replication machineries to resolve transposition intermediates. MuB has multiple functions, including target capture and immunity. The SGS element promotes gyrase-mediated Mu end synapsis, and the enhancer, aided by HU and IHF, participates in directing a unique topological architecture of the Mu synapse. The function of these DNA and protein elements is important during both lysogenic and lytic phases. Enhancer properties have been exploited in the design of mini-Mu vectors for genetic engineering. Mu ends assembled into active transpososomes have been delivered directly into bacterial, yeast, and human genomes, where they integrate efficiently, and may prove useful for gene therapy. PMID:26104374

  15. The Hermes element from Musca domestica can transpose in four families of cyclorrhaphan flies.

    PubMed

    Sarkar, A; Coates, C J; Whyard, S; Willhoeft, U; Atkinson, P W; O'Brochta, D A

    1997-01-01

    Transgenic insect technology will provide opportunities to explore the basic biology of a broad range of insect species in ways that will prove insightful and important. It is also a technology that will provide opportunities to manipulate the genotypes of insects of practical significance to the health and welfare of humans. The Hermes transposable element from the housefly, Musca domestica, is a short inverted repeat-type element related to hobo from Drosophila melanogaster, Ac from Zea mays, and Tam3 from Antirrhinum majus. It has potential to become a versatile and efficient broad host-range insect transformation vector. The ability of Hermes to transpose when introduced into five species of diptera from four divergent families was tested using an in vivo, interplasmid transpositional recombination assay. Hermes was capable of transposing in all species tested, demonstrating that Hermes has a broad host-range. In addition, the rates of transposition were sufficiently high in all species tested to suggest that Hermes will be an efficient gene transfer vector in a wide range of insect species. The Hermes element also revealed a pattern of integration into the target substrate that permitted factors determining integration site selection to be identified. Primary nucleotide sequence of the integration site played a role as did proximity to preferred integration sites and the nucleosomal organization of the target. PMID:9226434

  16. Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor

    SciTech Connect

    Labbe, Jessy L; Murat, Claude; Morin, Emmanuelle; Tuskan, Gerald A; Le Tacon, F; Martin, Francis

    2012-01-01

    Background: The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TEspecific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome. Methodology/Principal Findings: TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea. Conclusions: This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.

  17. An Annotated Catalog of Inverted Repeats of Caenorhabditis elegans Chromosomes III and X, with Observations Concerning Odd/Even Biases and Conserved Motifs

    PubMed Central

    LeBlanc, Mark D.; Aspeslagh, Glen; Buggia, Nathan P.; Dyer, Betsey D.

    2000-01-01

    We have taken a computational approach to the problem of discovering and deciphering the grammar and syntax of gene regulation in eukaryotes. A logical first step is to produce an annotated catalog of all regulatory sites in a given genome. Likely candidates for such sites are direct and indirect repeats, including three subcategories of indirect repeats: inverted (palindromic), everted, and mirror-image repeats. To that end we have produced a searchable database of inverted repeats of chromosomes III and X of Caenorhabditis elegans, the first completely sequenced multicellular eukaryote. Initial results from the use of this catalog are observations concerning odd/even biases in perfect IRs. The potential usefulness of the catalog as a discovery tool for promoters was shown for some of the genes involved with G-protein functions and for heat shock protein 104 (hsp104). PMID:10984456

  18. Eukaryotic transposable elements as mutagenic agents

    SciTech Connect

    Lambert, M.E. . Banbury Center); McDonald, J.F. ); Weinstein, I.B. )

    1988-01-01

    This book contains the proceedings on eukaryotic transposable elements as mutagenic agents. Topics covered include: overview of prokaryotic transposable elements, mutational effects of transposable element insertions, inducers/regulators of transposable element expression and transposition, genomic stress and environmental effects, and inducers/regulators of retroviral element expression.

  19. Similarity of the Cin1 repetitive family of Zea mays to eukaryotic transposable elements.

    PubMed

    Shepherd, N S; Schwarz-Sommer, Z; Blumberg vel Spalve, J; Gupta, M; Wienand, U; Saedler, H

    It has been suggested that the middle repetitive class of sequences that make up a large proportion of the eukaryotic genome have been amplified and dispersed by DNA transposition. Transposition is a phenomenon first postulated by Barbara McClintock on the basis of her genetic analysis of mutants in Zea mays. Since then, DNA transposition has been studied genetically in various plant systems and is well documented on the molecular level in both prokaryotes and eukaryotes. This has included the isolation of DNA inserts at various loci in several plants; however, the prevalence of transposition in plants is not established. We report here DNA nucleotide sequence data which show that some members of the Cin1 middle repetitive family of maize have features characteristic of known transposable elements. One cloned Cin1 repeat has a 6-base pair (bp) perfect inverted repeat sequence at its ends. The terminal five base pairs (5' TGTTG . . . CAACA 3') are identical to the termini of Drosophila copia transposable elements. Two other Cin1 alleles are flanked by 5-bp direct repeats. A comparison is made with the long terminal repeat (LTR) of the copia-Ty1-retrovirus families of moveable genetic elements. PMID:6318125

  20. Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis

    PubMed Central

    Matvienko, Marta; Piskurewicz, Urszula; Xu, Huaqin; Martineau, Belinda; Wong, Joan; Govindarajulu, Manjula; Kozik, Alexander; Michelmore, Richard W.

    2014-01-01

    The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE SYNTHASE (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes. PMID:25344399

  1. Sinorhizobium fredii HH103 bacteroids are not terminally differentiated and show altered O-antigen in nodules of the Inverted Repeat-Lacking Clade legume Glycyrrhiza uralensis.

    PubMed

    Crespo-Rivas, Juan C; Guefrachi, Ibtissem; Mok, Kenny C; Villaécija-Aguilar, José A; Acosta-Jurado, Sebastián; Pierre, Olivier; Ruiz-Sainz, José E; Taga, Michiko E; Mergaert, Peter; Vinardell, José M

    2016-09-01

    In rhizobial species that nodulate inverted repeat-lacking clade (IRLC) legumes, such as the interaction between Sinorhizobium meliloti and Medicago, bacteroid differentiation is driven by an endoreduplication event that is induced by host nodule-specific cysteine rich (NCR) antimicrobial peptides and requires the participation of the bacterial protein BacA. We have studied bacteroid differentiation of Sinorhizobium fredii HH103 in three host plants: Glycine max, Cajanus cajan and the IRLC legume Glycyrrhiza uralensis. Flow cytometry, microscopy analyses and viability studies of bacteroids as well as confocal microscopy studies carried out in nodules showed that S. fredii HH103 bacteroids, regardless of the host plant, had deoxyribonucleic acid (DNA) contents, cellular sizes and survival rates similar to those of free-living bacteria. Contrary to S. meliloti, S. fredii HH103 showed little or no sensitivity to Medicago NCR247 and NCR335 peptides. Inactivation of S. fredii HH103 bacA neither affected symbiosis with Glycyrrhiza nor increased bacterial sensitivity to Medicago NCRs. Finally, HH103 bacteroids isolated from Glycyrrhiza, but not those isolated from Cajanus or Glycine, showed an altered lipopolysaccharide. Our studies indicate that, in contrast to the S. meliloti-Medicago model symbiosis, bacteroids in the S. fredii HH103-Glycyrrhiza symbiosis do not undergo NCR-induced and bacA-dependent terminal differentiation. PMID:26521863

  2. Modulation of ccrAB Expression and SCCmec Excision by an Inverted Repeat Element and SarS in Methicillin-Resistant Staphylococcus aureus

    PubMed Central

    Zhang, Shijie; Ma, Ronghua; Liu, Xiaoyu; Zhang, Xu

    2015-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a notorious human pathogen that can cause a broad spectrum of infections. MRSA strains are resistant to almost the entire family of β-lactam antibiotics due to the acquisition of staphylococcal cassette chromosome mec (SCCmec). The chromosome cassette recombinases A and B, encoded by ccrAB genes located on SCCmec, play a key role in the excision of SCCmec. Studies have shown that ccrAB genes are expressed in only a minority of cells, suggesting the involvement of a subtle regulatory mechanism in ccrAB expression which has not been uncovered. Here, we found that an inverted repeat (IR) element, existing extensively and conservatively within the ccrAB promoter of different SCCmec types, played a repressive role in ccrAB expression and SCCmec excision in MRSA strain N315. Replacement of the IR sequence led to a significant increase in ccrAB expression and curing of SCCmec from strain N315 cells. In addition, we identified the transcriptional regulator SarS using DNA-affinity chromatography and further demonstrated that SarS can bind to the IR sequence and upregulate ccrAB expression and SCCmec excision. These findings reveal a molecular mechanism regulating ccrAB expression and SCCmec excision and may provide mechanic insights into the lateral transfer of SCCmec and spread of antibiotic resistance in S. aureus. PMID:26248371

  3. Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis.

    PubMed

    Wroblewski, Tadeusz; Matvienko, Marta; Piskurewicz, Urszula; Xu, Huaqin; Martineau, Belinda; Wong, Joan; Govindarajulu, Manjula; Kozik, Alexander; Michelmore, Richard W

    2014-12-01

    The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE Synthase (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes. PMID:25344399

  4. Transposable elements for insect transformation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The germ-line of more than 35 species from five orders of insects have been genetically transformed, using vectors derived from Class II transposable elements. Initially the P and hobo vector systems developed for D. melanogaster were not applicable to other species, but four transposons found in ot...

  5. A Helitron-like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A+T content (62.3%),...

  6. Transposed compression piston and cylinder

    SciTech Connect

    Ross, M.A.

    1992-04-14

    This patent describes an improved V-type two piston Stirling engine wherein the improvement is a transposed compression piston slidably engaged in a mating cylinder. It comprises: a cylindrical body which is pivotally connected to a connecting rod at a pivot axis which is relatively nearer the outer end of the cylindrical body and has a seal relatively nearer the inner end of the cylindrical body.

  7. Positive partial transpose from spectra

    SciTech Connect

    Hildebrand, Roland

    2007-11-15

    In this paper we solve the following problem. Let H{sub nm} be a Hilbert space of dimension nm, and let A be a positive semidefinite self-adjoint linear operator on H{sub nm}. Under which conditions on the spectrum has A a positive partial transpose (is PPT) with respect to any partition H{sub n} x H{sub m} of the space H{sub nm} as a tensor product of an n-dimensional and an m-dimensional Hilbert space? We show that the necessary and sufficient conditions can be expressed as a set of linear matrix inequalities (LMIs) on the eigenvalues of A.

  8. Sparse Biclustering of Transposable Data

    PubMed Central

    Tan, Kean Ming

    2013-01-01

    We consider the task of simultaneously clustering the rows and columns of a large transposable data matrix. We assume that the matrix elements are normally distributed with a bicluster-specific mean term and a common variance, and perform biclustering by maximizing the corresponding log likelihood. We apply an ℓ1 penalty to the means of the biclusters in order to obtain sparse and interpretable biclusters. Our proposal amounts to a sparse, symmetrized version of k-means clustering. We show that k-means clustering of the rows and of the columns of a data matrix can be seen as special cases of our proposal, and that a relaxation of our proposal yields the singular value decomposition. In addition, we propose a framework for bi-clustering based on the matrix-variate normal distribution. The performances of our proposals are demonstrated in a simulation study and on a gene expression data set. This article has supplementary material online. PMID:25364221

  9. Sparse Biclustering of Transposable Data.

    PubMed

    Tan, Kean Ming; Witten, Daniela M

    2014-01-01

    We consider the task of simultaneously clustering the rows and columns of a large transposable data matrix. We assume that the matrix elements are normally distributed with a bicluster-specific mean term and a common variance, and perform biclustering by maximizing the corresponding log likelihood. We apply an ℓ1 penalty to the means of the biclusters in order to obtain sparse and interpretable biclusters. Our proposal amounts to a sparse, symmetrized version of k-means clustering. We show that k-means clustering of the rows and of the columns of a data matrix can be seen as special cases of our proposal, and that a relaxation of our proposal yields the singular value decomposition. In addition, we propose a framework for bi-clustering based on the matrix-variate normal distribution. The performances of our proposals are demonstrated in a simulation study and on a gene expression data set. This article has supplementary material online. PMID:25364221

  10. Quantum states with strong positive partial transpose

    SciTech Connect

    Chruscinski, Dariusz; Jurkowski, Jacek; Kossakowski, Andrzej

    2008-02-15

    We construct a large class of bipartite M x N quantum states which defines a proper subset of states with positive partial transposes (PPTs). Any state from this class has PPT but the positivity of its partial transposition is recognized with respect to canonical factorization of the original density operator. We propose to call elements from this class states with strong positive partial transposes (SPPTs). We conjecture that all SPPT states are separable.

  11. Chromosome rearrangements and transposable elements.

    PubMed

    Lonnig, Wolf-Ekkehard; Saedler, Heinz

    2002-01-01

    There has been limited corroboration to date for McClintock's vision of gene regulation by transposable elements (TEs), although her proposition on the origin of species by TE-induced complex chromosome reorganizations in combination with gene mutations, i.e., the involvement of both factors in relatively sudden formations of species in many plant and animal genera, has been more promising. Moreover, resolution is in sight for several seemingly contradictory phenomena such as the endless reshuffling of chromosome structures and gene sequences versus synteny and the constancy of living fossils (or stasis in general). Recent wide-ranging investigations have confirmed and enlarged the number of earlier cases of TE target site selection (hot spots for TE integration), implying preestablished rather than accidental chromosome rearrangements for nonhomologous recombination of host DNA. The possibility of a partly predetermined generation of biodiversity and new species is discussed. The views of several leading transposon experts on the rather abrupt origin of new species have not been synthesized into the macroevolutionary theory of the punctuated equilibrium school of paleontology inferred from thoroughly consistent features of the fossil record. PMID:12429698

  12. Cloning of the Mutator Transposable Element Mua2, a Putative Regulator of Somatic Mutability of the A1-Mum2 Allele in Maize

    PubMed Central

    Qin, M.; Robertson, D. S.; Ellingboe, A. H.

    1991-01-01

    The identification of the autonomous or transposase-encoding element of the Mutator (Mu) transposable element system of maize is necessary to the characterization of the system. We reported previously that a transcript homologous to the internal region of the MuA element is associated with activity of the Mutator system. We describe here the cloning of another Mu element, designated MuA2, that cosegregates with Mutator activity as assayed by somatic instability of the a1-Mum2 allele. The MuA2 element has features typical of the transposable elements of the Mutator family, including the 210-bp terminal inverted repeats. Several lines of evidence suggest that MuA2 is an autonomous or transposase-encoding element of the Mu family: (1) MuA2 cosegregates with a genetically defined element that regulates somatic mutability of the a1-Mum2 allele; (2) MuA2 is hypomethylated while most other MuA2-hybridizing sequences in the genome are extensively methylated; (3) the increase of the copy number of MuA2 is concomitant with the increase of regulator elements; (4) MuA2-like elements are found in Mutator lines but not in non-Mutator inbreds. We propose that autonomous or transposase-encoding elements of the Mu family may be structurally conserved and MuA2-like. PMID:1661256

  13. Miniature Earthmover

    NASA Technical Reports Server (NTRS)

    1996-01-01

    International Machinery Corporation (IMC) developed a miniature earthmover, the 1/8 scale Caterpillar D11N Track-type Tractor, with trademark product approval and manufacturing/marketing license from Caterpillar, Inc. Through Marshall Space Flight Center assistance, the company has acquired infrared remote control technology, originally developed for space exploration. The technology is necessary for exports because of varying restrictions on radio frequency in foreign countries. The Cat D11N weighs only 340 pounds and has the world's first miniature industrial internal combustion engine. The earthmover's uses include mining, construction and demolition work, and hazardous environment work. IMC also has designs of various products for military use and other Caterpillar replicas.

  14. The En/Spm transposable element of Zea mays contains splice sites at the termini generating a novel intron from a dSpm element in the A2 gene.

    PubMed Central

    Menssen, A; Höhmann, S; Martin, W; Schnable, P S; Peterson, P A; Saedler, H; Gierl, A

    1990-01-01

    The A2 locus of Zea mays, identified as one of the genes affecting anthocyanin biosynthesis, was cloned using the transposable elements rcy and dSpm as gene tags. The A2 gene encodes a putative protein of 395 amino acids and is devoid of introns. Two a2-m1 alleles, containing dSpm insertions of different sizes, were characterized. The dSpm element from the original state allele has perfect termini and undergoes frequent transposition. The element from the class II state allele is no longer competent to transpose. It has retained the 13 bp terminal inverted repeat but has lost all subterminal sites at the 5' end, which are recognized by tnpA protein, the most abundant product of the En/Spm transposable element system. The relatively high A2 gene expression of one a2-m1 allele is due to removal of almost all dSpm sequences by splicing. The slightly altered A2 enzyme is still functional as shown by complementation of an a2 mutant with the corresponding cDNA. The 5' and 3' splice sites are constituted by the termini of the dSpm element; it therefore represents a novel intron of the A2 gene. Images Fig. 3. Fig. 4. Fig. 6. Fig. 8. PMID:2170105

  15. CACTA-superfamily transposable element is inserted in MYB transcription factor gene of soybean line producing variegated seeds.

    PubMed

    Yan, Fan; Di, Shaokang; Takahashi, Ryoji

    2015-08-01

    The R gene of soybean, presumably encoding a MYB transcription factor, controls seed coat color. The gene consists of multiple alleles, R (black), r-m (black spots and (or) concentric streaks on brown seed), and r (brown seed). This study was conducted to determine the structure of the MYB transcription factor gene in a near-isogenic line (NIL) having r-m allele. PCR amplification of a fragment of the candidate gene Glyma.09G235100 generated a fragment of about 1 kb in the soybean cultivar Clark, whereas a fragment of about 14 kb in addition to fragments of 1 and 1.4 kb were produced in L72-2040, a Clark 63 NIL with the r-m allele. Clark 63 is a NIL of Clark with the rxp and Rps1 alleles. A DNA fragment of 13 060 bp was inserted in the intron of Glyma.09G235100 in L72-2040. The fragment had the CACTA motif at both ends, imperfect terminal inverted repeats (TIR), inverse repetition of short sequence motifs close to the 5' and 3' ends, and a duplication of three nucleotides at the site of integration, indicating that it belongs to a CACTA-superfamily transposable element. We designated the element as Tgm11. Overall nucleotide sequence, motifs of TIR, and subterminal repeats were similar to those of Tgm1 and Tgs1, suggesting that these elements comprise a family. PMID:26360633

  16. Molecular characterization of a nonautonomous transposable element (dTph1) of petunia.

    PubMed Central

    Gerats, A G; Huits, H; Vrijlandt, E; Maraña, C; Souer, E; Beld, M

    1990-01-01

    An insertion sequence of 283 base pairs has been isolated from the DFR-C gene (dihydroflavonol-4-reductase) of petunia. This insert was found only in a line unstable for the An1 locus (anthocyanin 1, located on chromosome VI) and not in fully pigmented progenitor and revertant lines or in stable white derivative lines. This implies that the An1 locus encodes the DFR-C gene. The unstable An1 system in the line W138 is known to be a two-element system, the autonomous element being located on chromosome I. In the presence of the autonomous element, W138 flowers exhibit a characteristic pattern of red revertant spots and sectors on a white background. In the absence of the autonomous element, the W138 allele gives rise to a stable recessive (white) phenotype. Sequence analysis of progenitor, unstable, and revertant alleles revealed dTph1 to contain perfect terminal inverted repeats of 12 base pairs. In DFR-C, it is flanked by an 8-base pair target site duplication. Sequences homologous to dTph1 are present in at least 50 copies in the line W138. Sequence analysis of An1 revertant alleles indicated that excision, including removal of the target site duplication, is required for reversion to the wild-type phenotype. Derivative stable recessive alleles showed excision of dTph1 and a rearrangement of the target site duplication. dTph1 is the smallest transposable element described to date that is still capable of transposition. The use of dTph1 in tagging experiments and subsequent gene isolation is discussed. PMID:1967052

  17. The Arabidopsis transposable element Tag1 is widely distributed among Arabidopsis ecotypes.

    PubMed

    Frank, M J; Preuss, D; Mack, A; Kuhlmann, T C; Crawford, N M

    1998-02-01

    Tag1 is an autonomous transposable element (3.3 kb in length) first identified as an insertion in the CHL1 (NRT1) gene of Arabidopsis thaliana. Tag1 has been found in the Landsberg erecta ecotype of A. thaliana but not in Columbia or WS. In this paper, 41 additional ecotypes were examined for the presence of Tag1. Using an internal Tag1 fragment as probe, we found that DNA form 19 of the 41 ecotypes strongly hybridized to Tag1. Almost all of the Tag1-containing ecotypes had only one or two copies of Tag1 per haploid genome, as determined by Southern blot analysis. The only exception, Bf-1 from Bretagny-sur-Orge, France, had four copies. Two ecotypes, Di-G and S96, gave identical Southern blot patterns to that of Landsberg erecta and were subsequently shown to contain Tag1 at the same two positions found in Landsberg erecta (loci designated as Tag1-2 and Tag1-3). Two other ecotypes, Ag-0 and Lo-1, had a Tag1 element located at Tag1-2 but not at Tag1-3. The distance between these two loci was determined to be 0.37 cM. Analysis of DNA from two related species, A. griffithiana and A. pumila, showed that both species contain sequences that hybridize to Tag1 and that could be amplified with an oligonucleotide specific to the terminal inverted repeats of Tag1. These results show that Tag1 and related elements are present, and may be useful for insertional mutagenesis, in many A. thaliana ecotypes and several Arabidopsis species. PMID:9529529

  18. Transposable elements as catalysts for chromosome rearrangements.

    PubMed

    Zhang, Jianbo; Yu, Chuanhe; Krishnaswamy, Lakshminarasimhan; Peterson, Thomas

    2011-01-01

    Barbara McClintock first showed that transposable elements in maize can induce major chromosomal rearrangements, including duplications, deletions, inversions, and translocations. More recently, researchers have made significant progress in elucidating the mechanisms by which transposons can induce genome rearrangements. For the Ac/Ds transposable element system, rearrangements are generated when the termini of different elements are used as substrates for transposition. The resulting alternative transposition reaction directly generates a variety of rearrangements. The size and type of rearrangements produced depend on the location and orientation of transposon insertion. A single locus containing a pair of alternative transposition-competent elements can produce a virtually unlimited number of genome rearrangements. With a basic understanding of the mechanisms involved, researchers are beginning to utilize both naturally occurring and in vitro-generated configurations of transposable elements in order to manipulate chromosome structure. PMID:21181539

  19. Revised Nomenclature for Transposable Genetic Elements

    PubMed Central

    Roberts, Adam P.; Chandler, Michael; Courvalin, Patrice; Guédon, Gérard; Mullany, Peter; Pembroke, Tony; Rood, Julian I.; Smith, C. Jeffery; Summers, Anne O.; Tsuda, Masataka; Berg, Douglas E.

    2013-01-01

    Transposable DNA elements occur naturally in the genomes of nearly all species of prokaryotes. A proposal for a uniform transposable element nomenclature was published prominently in the 1970s but is not, at present, available online even in abstract form, and many of the newly discovered elements have been named without reference to it. We propose here an updated version of the original nomenclature system for all of the various types of prokaryotic, autonomous, transposable elements excluding insertion sequences, for which a nomenclature system already exists. The use of this inclusive and sequential Tn numbering system for transposable elements described here recognizes the ease of interspecies spread of individual elements, and allows for the naming of mosaic elements containing segments from two or more previously described types of transposons or plasmids. It will guard against a future necessity to rename elements following changes in bacterial nomenclature which occurs constantly with our increased understanding of bacterial phylogenies and taxonomic groupings. It also takes into account the increasing importance of metagenomic sequencing projects and the continued identification of new mobile elements from unknown hosts. PMID:18778731

  20. Jumping Genes: The Transposable DNAs of Bacteria.

    ERIC Educational Resources Information Center

    Berg, Claire M.; Berg, Douglas E.

    1984-01-01

    Transposons are transposable elements that carry genes for antibiotic resistance. Provides background information on the structure and organization of these "jumping genes" in bacteria. Also describes the use of transposons in tagging genes and lists pertinent references and resource materials. (DH)

  1. Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries

    PubMed Central

    Moore, Michael J.; Neubig, Kurt M.; Williams, Norris H.; Whitten, W. Mark; Kim, Joo-Hwan

    2015-01-01

    Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability. PMID:26558895

  2. Transition from a heterozygous to a homozygous state of a pair of loci in the inverted repeat sequences of the L component of the herpes simplex virus type 1 genome.

    PubMed Central

    Umene, K

    1987-01-01

    The behavior of herpes simplex virus type 1 heterozygous isolates, in which the two inverted repeats of the L component (RL) were differentiated by a polymorphism marker (the presence [type B] or absence [type A] of a SalI site), was investigated. The progeny viruses derived from the heterozygote (A/B) consisted of heterozygotes (A/B), type A homozygotes (A/A), and type B homozygotes (B/B). The heterology between RL, albeit tolerated, was unstable, as is the case with heterology between the repeats of the S component. The two repeats TRL (terminal) and IRL (internal) were equipotent in generating homozygotes from a heterozygote. Data obtained from an analysis of 426 progeny viruses derived from heterozygous clones supported the hypothesis that the two loci in RL of a herpes simplex virus type 1 genome are determined as a random combination of the corresponding two loci in RL of the parent virus and that the ratio of heterozygotes/type A homozygotes/type B homozygotes in the progeny viruses from a heterozygote is expected to be 2:1:1. An ephemeral dominance of one type of homozygote over the other was observed in subclones from several heterozygous clones. Images PMID:3029414

  3. Transposable elements as a molecular evolutionary force

    NASA Technical Reports Server (NTRS)

    Fedoroff, N. V.

    1999-01-01

    This essay addresses the paradoxes of the complex and highly redundant genomes. The central theses developed are that: (1) the distinctive feature of complex genomes is the existence of epigenetic mechanisms that permit extremely high levels of both tandem and dispersed redundancy; (2) the special contribution of transposable elements is to modularize the genome; and (3) the labilizing forces of recombination and transposition are just barely contained, giving a dynamic genetic system of ever increasing complexity that verges on the chaotic.

  4. Circulant states with positive partial transpose

    SciTech Connect

    Chruscinski, Dariusz; Kossakowski, Andrzej

    2007-09-15

    We construct a large class of quantum dxd states which are positive under partial transposition (so called PPT states). The construction is based on certain direct sum decomposition of the total Hilbert space displaying characteristic circular structure - that is why we call them circulant states. It turns out that partial transposition maps any such decomposition into another one and hence both original density matrix and its partially transposed partner share similar cyclic properties. This class contains many well-known examples of PPT states from the literature and gives rise to a huge family of completely new states.

  5. Transposed-Letter and Laterality Effects in Lexical Decision

    ERIC Educational Resources Information Center

    Perea, Manuel; Fraga, Isabel

    2006-01-01

    Two divided visual field lexical decision experiments were conducted to examine the role of the cerebral hemispheres in transposed-letter similarity effects. In Experiment 1, we created two types of nonwords: nonadjacent transposed-letter nonwords ("TRADEGIA"; the base word was "TRAGEDIA," the Spanish for "TRAGEDY") and two-letter different…

  6. Transposed-Letter Priming of Prelexical Orthographic Representations

    ERIC Educational Resources Information Center

    Kinoshita, Sachiko; Norris, Dennis

    2009-01-01

    A prime generated by transposing two internal letters (e.g., jugde) produces strong priming of the original word (judge). In lexical decision, this transposed-letter (TL) priming effect is generally weak or absent for nonword targets; thus, it is unclear whether the origin of this effect is lexical or prelexical. The authors describe the Bayesian…

  7. Experiment in Learning to Discriminate Frequency Transposed Speech.

    ERIC Educational Resources Information Center

    Ahlstrom, K.G.; And Others

    In order to improve speech perception by transposing the speech signals to lower frequencies, to determine which aspects of the information in the acoustic speech signals were influenced by transposition, and to compare two different methods of training speech perception, 44 subjects were trained to discriminate between transposed words or…

  8. Multiple Miniature Avionic Displays

    NASA Technical Reports Server (NTRS)

    Rye, Jeffrey M. (Inventor); Dorneich, Michael C. (Inventor); Gannon, Aaron J. (Inventor)

    2008-01-01

    A display screen for displaying multiple sets of information is provided. In one embodiment, an aviation display screen includes a main window and a plurality of miniature windows. The main window is adapted to illustrate one set of information. Each miniature window is adapted to display a set of avionic information. The avionic display is further adapted to toggle a select set of avionic information in one of the miniature windows into the main window.

  9. Miniature propulsion systems

    NASA Astrophysics Data System (ADS)

    Campbell, John G.

    1992-07-01

    Miniature solenoid valves, check valves and a hydrazine gas generator typify the miniaturization used in the liquid propulsion system for the Army Light Weight Exo-Atmospheric Projectile (LEAP). The pressure control subsystem uses a solenoid valve weighing 24 grams to control flow of helium to pressurize the propellant tanks. The attitude control subsystem uses a gas generator weighing 71 grams to produce decomposed hydrazine as the gaseous propellant for miniature 1 lbf ACS thrusters weighing 5.4 grams. The successful use of these miniature components in development tests and a hover test of the LEAP is described.

  10. Transposable elements in fish functional genomics: technical challenges and perspectives

    PubMed Central

    Parinov, Serguei; Emelyanov, Alexander

    2007-01-01

    The recent introduction of several transposable elements in zebrafish opens new frontiers for genetic manipulation in this important vertebrate model. This review discusses transposable elements as mutagenesis tools for fish functional genomics. We review various mutagenesis strategies that were previously applied in other genetic models, such as Drosophila, Arabidopsis, and mouse, that may be beneficial if applied in fish. We also discuss the forthcoming challenges of high-throughput functional genomics in fish. PMID:18047698

  11. Transposable elements and G-quadruplexes.

    PubMed

    Kejnovsky, Eduard; Tokan, Viktor; Lexa, Matej

    2015-09-01

    A significant part of eukaryotic genomes is formed by transposable elements (TEs) containing not only genes but also regulatory sequences. Some of the regulatory sequences located within TEs can form secondary structures like hairpins or three-stranded (triplex DNA) and four-stranded (quadruplex DNA) conformations. This review focuses on recent evidence showing that G-quadruplex-forming sequences in particular are often present in specific parts of TEs in plants and humans. We discuss the potential role of these structures in the TE life cycle as well as the impact of G-quadruplexes on replication, transcription, translation, chromatin status, and recombination. The aim of this review is to emphasize that TEs may serve as vehicles for the genomic spread of G-quadruplexes. These non-canonical DNA structures and their conformational switches may constitute another regulatory system that, together with small and long non-coding RNA molecules and proteins, contribute to the complex cellular network resulting in the large diversity of eukaryotes. PMID:26403244

  12. Transposable element origins of epigenetic gene regulation.

    PubMed

    Lisch, Damon; Bennetzen, Jeffrey L

    2011-04-01

    Transposable elements (TEs) are massively abundant and unstable in all plant genomes, but are mostly silent because of epigenetic suppression. Because all known epigenetic pathways act on all TEs, it is likely that the specialized epigenetic regulation of regular host genes (RHGs) was co-opted from this ubiquitous need for the silencing of TEs and viruses. With their internally repetitive and rearranging structures, and the acquisition of fragments of RHGs, the expression of TEs commonly makes antisense RNAs for both TE genes and RHGs. These antisense RNAs, particularly from heterochromatic reservoirs of 'zombie' TEs that are rearranged to form variously internally repetitive structures, may be advantageous because their induction will help rapidly suppress active TEs of the same family. RHG fragments within rapidly rearranging TEs may also provide the raw material for the ongoing generation of miRNA genes. TE gene expression is regulated by both environmental and developmental signals, and insertions can place nearby RHGs under the regulation (both standard and epigenetic) of the TE. The ubiquity of TEs, their frequent preferential association with RHGs, and their ability to be programmed by epigenetic signals all indicate that RGHs have nearly unlimited access to novel regulatory cassettes to assist plant adaptation. PMID:21444239

  13. Transposable elements: powerful facilitators of evolution.

    PubMed

    Oliver, Keith R; Greene, Wayne K

    2009-07-01

    Transposable elements (TEs) are powerful facilitators of genome evolution, and hence of phenotypic diversity as they can cause genetic changes of great magnitude and variety. TEs are ubiquitous and extremely ancient, and although harmful to some individuals, they can be very beneficial to lineages. TEs can build, sculpt, and reformat genomes by both active and passive means. Lineages with active TEs or with abundant homogeneous inactive populations of TEs that can act passively by causing ectopic recombination are potentially fecund, adaptable, and taxonate readily. Conversely, taxa deficient in TEs or possessing heterogeneous populations of inactive TEs may be well adapted in their niche, but tend to prolonged stasis and may risk extinction by lacking the capacity to adapt to change, or diversify. Because of recurring intermittent waves of TE infestation, available data indicate a compatibility with punctuated equilibrium, in keeping with widely accepted interpretations of evidence from the fossil record. We propose a general and holistic synthesis on how the presence of TEs within genomes makes them flexible and dynamic, so that genomes themselves are powerful facilitators of their own evolution. PMID:19415638

  14. Transposable elements in response to environmental stressors&

    PubMed Central

    Miousse, Isabelle R.; Chalbot, Marie-Cecile G.; Lumen, Annie; Ferguson, Alesia; Kavouras, Ilias G.; Koturbash, Igor

    2015-01-01

    Transposable elements (TEs) comprise a group of repetitive sequences that bring positive, negative, as well as neutral effects to the host organism. Earlier considered as “junk DNA,” TEs are now well-accepted driving forces of evolution and critical regulators the of expression of genetic information. Their activity is regulated by epigenetic mechanisms, including methylation of DNA and histone modifications. The loss of epigenetic control over TEs, exhibited as loss of DNA methylation and decondensation of the chromatin structure, may result in TEs reactivation, initiation of their insertional mutagenesis (retrotransposition) and has been reported in numerous human diseases, including cancer. Accumulating evidence suggests that these alterations are not the simple consequences of the disease, but often may drive the pathogenesis, as they can be detected early during disease development. Knowledge derived from the in vitro, in vivo, and epidemiological studies, clearly demonstrates that exposure to ubiquitous environmental stressors, many of which are carcinogens or suspected carcinogens, are capable of causing alterations in methylation and expression of TEs and initiate retrotransposition events. Evidence summarized in this review suggests that TEs are the sensitive endpoints for detection of effects caused by such environmental stressors, as ionizing radiation (terrestrial, space, and UV-radiation), air pollution (including particulate matter [PM]-derived and gaseous), persistent organic pollutants, and metals. Furthermore, the significance of these effects is characterized by their early appearance, persistence and presence in both, target organs and peripheral blood. Altogether, these findings suggest that TEs may potentially be introduced into safety and risk assessment and serve as biomarkers of exposure to environmental stressors. Furthermore, TEs also show significant potential to become invaluable surrogate biomarkers in clinic and possible targets

  15. Response of transposable elements to environmental stressors.

    PubMed

    Miousse, Isabelle R; Chalbot, Marie-Cecile G; Lumen, Annie; Ferguson, Alesia; Kavouras, Ilias G; Koturbash, Igor

    2015-01-01

    Transposable elements (TEs) comprise a group of repetitive sequences that bring positive, negative, as well as neutral effects to the host organism. Earlier considered as "junk DNA," TEs are now well-accepted driving forces of evolution and critical regulators of the expression of genetic information. Their activity is regulated by epigenetic mechanisms, including methylation of DNA and histone modifications. The loss of epigenetic control over TEs, exhibited as loss of DNA methylation and decondensation of the chromatin structure, may result in TEs reactivation, initiation of their insertional mutagenesis (retrotransposition) and has been reported in numerous human diseases, including cancer. Accumulating evidence suggests that these alterations are not the simple consequences of the disease, but often may drive the pathogenesis, as they can be detected early during disease development. Knowledge derived from the in vitro, in vivo, and epidemiological studies, clearly demonstrates that exposure to ubiquitous environmental stressors, many of which are carcinogens or suspected carcinogens, are capable of causing alterations in methylation and expression of TEs and initiate retrotransposition events. Evidence summarized in this review suggests that TEs are the sensitive endpoints for detection of effects caused by such environmental stressors, as ionizing radiation (terrestrial, space, and UV-radiation), air pollution (including particulate matter [PM]-derived and gaseous), persistent organic pollutants, and metals. Furthermore, the significance of these effects is characterized by their early appearance, persistence and presence in both, target organs and peripheral blood. Altogether, these findings suggest that TEs may potentially be introduced into safety and risk assessment and serve as biomarkers of exposure to environmental stressors. Furthermore, TEs also show significant potential to become invaluable surrogate biomarkers in clinic and possible targets for

  16. Reflections on Miniature Golf.

    ERIC Educational Resources Information Center

    Powell, Nancy Norem; And Others

    1994-01-01

    Describes a transformational geometry project in which groups of students explore symmetry, reflections, translations, rotations, and dilations to design and create one hole of miniature golf large enough to play on. Includes unit plan for transformational geometry. (MKR)

  17. Miniature TV Camera

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Originally devised to observe Saturn stage separation during Apollo flights, Marshall Space Flight Center's Miniature Television Camera, measuring only 4 x 3 x 1 1/2 inches, quickly made its way to the commercial telecommunications market.

  18. Miniature oxygen resuscitator

    NASA Technical Reports Server (NTRS)

    Johnson, G.; Teegen, J. T.; Waddell, H.

    1969-01-01

    Miniature, portable resuscitation system is used during evacuation of patients to medical facilities. A carrying case contains a modified resuscitator head, cylinder of oxygen, two-stage oxygen regulator, low pressure tube, and a mask for mouth and nose.

  19. Parallel matrix transpose algorithms on distributed memory concurrent computers

    SciTech Connect

    Choi, J.; Walker, D.W.; Dongarra, J.J. |

    1993-10-01

    This paper describes parallel matrix transpose algorithms on distributed memory concurrent processors. It is assumed that the matrix is distributed over a P x Q processor template with a block scattered data distribution. P, Q, and the block size can be arbitrary, so the algorithms have wide applicability. The communication schemes of the algorithms are determined by the greatest common divisor (GCD) of P and Q. If P and Q are relatively prime, the matrix transpose algorithm involves complete exchange communication. If P and Q are not relatively prime, processors are divided into GCD groups and the communication operations are overlapped for different groups of processors. Processors transpose GCD wrapped diagonal blocks simultaneously, and the matrix can be transposed with LCM/GCD steps, where LCM is the least common multiple of P and Q. The algorithms make use of non-blocking, point-to-point communication between processors. The use of nonblocking communication allows a processor to overlap the messages that it sends to different processors, thereby avoiding unnecessary synchronization. Combined with the matrix multiplication routine, C = A{center_dot}B, the algorithms are used to compute parallel multiplications of transposed matrices, C = A{sup T}{center_dot}B{sup T}, in the PUMMA package. Details of the parallel implementation of the algorithms are given, and results are presented for runs on the Intel Touchstone Delta computer.

  20. Characterization of three active transposable elements recently inserted in three independent DFR-A alleles and one high-copy DNA transposon isolated from the Pink allele of the ANS gene in onion (Allium cepa L.).

    PubMed

    Kim, Sunggil; Park, Jee Young; Yang, Tae-Jin

    2015-06-01

    Intact retrotransposon and DNA transposons inserted in a single gene were characterized in onions (Allium cepa) and their transcription and copy numbers were estimated in this study. While analyzing diverse onion germplasm, large insertions in the DFR-A gene encoding dihydroflavonol 4-reductase (DFR) involved in the anthocyanin biosynthesis pathway were found in two accessions. A 5,070-bp long terminal repeat (LTR) retrotransposon inserted in the active DFR-A (R4) allele was identified from one of the large insertions and designated AcCOPIA1. An intact ORF encoded typical domains of copia-like LTR retrotransposons. However, AcCOPIA1 contained atypical 'TG' and 'TA' dinucleotides at the ends of the LTRs. A 4,615-bp DNA transposon was identified in the other large insertion. This DNA transposon, designated AcCACTA1, contained an ORF coding for a transposase showing homology with the CACTA superfamily transposable elements (TEs). Another 5,073-bp DNA transposon was identified from the DFR-A (TRN) allele. This DNA transposon, designated AchAT1, belonged to the hAT superfamily with short 4-bp terminal inverted repeats (TIRs). Finally, a 6,258-bp non-autonomous DNA transposon, designated AcPINK, was identified in the ANS-p allele encoding anthocyanidin synthase, the next downstream enzyme to DFR in the anthocyanin biosynthesis pathway. AcPINK also possessed very short 3-bp TIRs. Active transcription of AcCOPIA1, AcCACTA1, and AchAT1 was observed through RNA-Seq analysis and RT-PCR. The copy numbers of AcPINK estimated by mapping the genomic DNA reads produced by NextSeq 500 were predominantly high compared with the other TEs. A series of evidence indicated that these TEs might have transposed in these onion genes very recently, providing a stepping stone for elucidation of enormously large-sized onion genome structure. PMID:25515665

  1. Transposable Elements and Genetic Instabilities in Crop Plants

    DOE R&D Accomplishments Database

    Burr, B.; Burr, F.

    1981-04-10

    Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

  2. Transposable elements and genetic instabilities in crop plants

    SciTech Connect

    Burr, B.; Burr, F.

    1981-04-10

    Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

  3. [The influence of transposable elements on genome size].

    PubMed

    Biémont, Christian; Vieira, Cristina

    2004-01-01

    Genome size displays an important variability between species without any direct link to complexity. This paradox, so-called "C value paradox", now becomes understood as resulting from a differential abundance of numerous repeated sequences, among which transposable elements. Genomes indeed contain a important proportion of such sequences (95 % of DNA in man, about 45 % of which are transposable elements, up to 99 % of DNA in some plants). While most investigations until now are focalized on genes or coding sequences, which thus represent a small part of the genome, more attention now is dedicated on so-called non-coding sequences. Transposable elements, which are capable of moving around in genomes, inducing mutations, chromosomal rearrangements, gene expression regulations, thus appear as major actors in diversity and evolution. We present here a brief review of the most prominent acquisition in this expanding domain. PMID:15969348

  4. Miniaturized handheld hyperspectral imager

    NASA Astrophysics Data System (ADS)

    Wu, Huawen; Haibach, Frederick G.; Bergles, Eric; Qian, Jack; Zhang, Charlie; Yang, William

    2014-05-01

    A miniaturized hyperspectral imager is enabled with image sensor integrated with dispersing elements in a very compact form factor, removing the need for expensive, moving, bulky and complex optics that have been used in conventional hyperspectral imagers for decades. The result is a handheld spectral imager that can be installed on miniature UAV drones or conveyor belts in production lines. Eventually, small handhelds can be adapted for use in outpatient medical clinics for point-of-care diagnostics and other in-field applications.

  5. Transposable genetic elements in Spirulina and potential applications for genetic engineering

    NASA Astrophysics Data System (ADS)

    Hiroyuki, Kojima; Qin, Song; Thankappan, Ajith Kumar; Yoshikazu, Kawata; Shin-Ichi, Yano

    1998-03-01

    Transposable elements in cyanobacteria are briefly reviewed. Evidence is presented to show that transposable elements in Spirulina platensis is actually reflected on the phenotype change, i e., helical to straight filaments. Transposition intermediates of DNA were isolated from the extrachromosome and the transposition was related to helical variations in Spirulina. Uses of transposable elements for microalgal recombination are discussed based on the transposition mechanism.

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

    PubMed

    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. PMID:23908136

  7. Miniature Centrifugal Compressor

    NASA Technical Reports Server (NTRS)

    Sixsmith, Herbert

    1989-01-01

    Miniature turbocompressor designed for reliability and long life. Cryogenic system includes compressor, turboexpander, and heat exchanger provides 5 W of refrigeration at 70 K from 150 W input power. Design speed of machine 510,000 rpm. Compressor has gas-lubricated journal bearings and magnetic thrust bearing. When compressor runs no bearing contact and no wear.

  8. Throw a Miniature Vase

    ERIC Educational Resources Information Center

    Sapiro, Maurice

    1977-01-01

    A direct correlation exists between the acquisition of skills on the potter's wheel and the vertical dimension of the finished pot. Ability equals height. Overlooked somewhere in the search for acquiring technical facility and a means of demonstrating it, is the fascinating world of miniature pottery. Describes the mechanics peculiar to small…

  9. ModuleOrganizer: detecting modules in families of transposable elements

    PubMed Central

    2010-01-01

    Background Most known eukaryotic genomes contain mobile copied elements called transposable elements. In some species, these elements account for the majority of the genome sequence. They have been subject to many mutations and other genomic events (copies, deletions, captures) during transposition. The identification of these transformations remains a difficult issue. The study of families of transposable elements is generally founded on a multiple alignment of their sequences, a critical step that is adapted to transposons containing mostly localized nucleotide mutations. Many transposons that have lost their protein-coding capacity have undergone more complex rearrangements, needing the development of more complex methods in order to characterize the architecture of sequence variations. Results In this study, we introduce the concept of a transposable element module, a flexible motif present in at least two sequences of a family of transposable elements and built on a succession of maximal repeats. The paper proposes an assembly method working on a set of exact maximal repeats of a set of sequences to create such modules. It results in a graphical view of sequences segmented into modules, a representation that allows a flexible analysis of the transformations that have occurred between them. We have chosen as a demonstration data set in depth analysis of the transposable element Foldback in Drosophila melanogaster. Comparison with multiple alignment methods shows that our method is more sensitive for highly variable sequences. The study of this family and the two other families AtREP21 and SIDER2 reveals new copies of very different sizes and various combinations of modules which show the potential of our method. Conclusions ModuleOrganizer is available on the Genouest bioinformatics center at http://moduleorganizer.genouest.org PMID:20860790

  10. Transposable Element Targeting by piRNAs in Laurasiatherians with Distinct Transposable Element Histories.

    PubMed

    Vandewege, Michael W; Platt, Roy N; Ray, David A; Hoffmann, Federico G

    2016-01-01

    PIWI proteins and PIWI-interacting RNAs (piRNAs) are part of a cellular pathway that has evolved to protect genomes against the proliferation of transposable elements (TEs). PIWIs and piRNAs assemble into complexes that are involved in epigenetic and post-transcriptional repression of TEs. Most of our understanding of the mechanisms of piRNA-mediated TE silencing comes from fruit fly and mouse models. However, even in these well-studied animals it is unclear how piRNA responses relate to variable TE expression and whether the strength of the piRNA response affects TE content over time. Here, we assessed the evolutionary interactions between TE and piRNAs in a statistical framework using three nonmodel laurasiatherian mammals as a study system: dog, horse, and a vesper bat. These three species diverged ∼80 million years ago and have distinct genomic TE contents. By comparing species with distinct TE landscapes, we aimed to identify clear relationships among TE content, expression, and piRNAs. We found that the TE subfamilies that are the most transcribed appear to elicit the strongest "ping-pong" response. This was most evident among long interspersed elements, but the relationships between expression and ping-pong pilRNA (piRNA-like) expression were more complex among SINEs. SINE transcripts were equally abundant in the dog and horse yet new SINE insertions were relatively rare in the horse genome, where we identified a stronger piRNA response. Our analyses suggest that the piRNA response can have a strong impact on the TE composition of a genome. However, our results also suggest that the presence of a robust piRNA response is apparently not sufficient to stop TE mobilization and accumulation. PMID:27060702

  11. Transposable Element Targeting by piRNAs in Laurasiatherians with Distinct Transposable Element Histories

    PubMed Central

    Vandewege, Michael W.; Platt, Roy N.; Ray, David A.; Hoffmann, Federico G.

    2016-01-01

    PIWI proteins and PIWI-interacting RNAs (piRNAs) are part of a cellular pathway that has evolved to protect genomes against the proliferation of transposable elements (TEs). PIWIs and piRNAs assemble into complexes that are involved in epigenetic and post-transcriptional repression of TEs. Most of our understanding of the mechanisms of piRNA-mediated TE silencing comes from fruit fly and mouse models. However, even in these well-studied animals it is unclear how piRNA responses relate to variable TE expression and whether the strength of the piRNA response affects TE content over time. Here, we assessed the evolutionary interactions between TE and piRNAs in a statistical framework using three nonmodel laurasiatherian mammals as a study system: dog, horse, and a vesper bat. These three species diverged ∼80 million years ago and have distinct genomic TE contents. By comparing species with distinct TE landscapes, we aimed to identify clear relationships among TE content, expression, and piRNAs. We found that the TE subfamilies that are the most transcribed appear to elicit the strongest “ping-pong” response. This was most evident among long interspersed elements, but the relationships between expression and ping-pong pilRNA (piRNA-like) expression were more complex among SINEs. SINE transcripts were equally abundant in the dog and horse yet new SINE insertions were relatively rare in the horse genome, where we identified a stronger piRNA response. Our analyses suggest that the piRNA response can have a strong impact on the TE composition of a genome. However, our results also suggest that the presence of a robust piRNA response is apparently not sufficient to stop TE mobilization and accumulation. PMID:27060702

  12. Miniaturized Environmental Monitoring Instrumentation

    SciTech Connect

    C. B. Freidhoff

    1997-09-01

    The objective of the Mass Spectrograph on a Chip (MSOC) program is the development of a miniature, multi-species gas sensor fabricated using silicon micromachining technology which will be orders of magnitude smaller and lower power consumption than a conventional mass spectrometer. The sensing and discrimination of this gas sensor are based on an ionic mass spectrograph, using magnetic and/or electrostatic fields. The fields cause a spatial separation of the ions according to their respective mass-to-charge ratio. The fabrication of this device involves the combination of microelectronics with micromechanically built sensors and, ultimately, vacuum pumps. The prototype of a chemical sensor would revolutionize the method of performing environmental monitoring for both commercial and government applications. The portable unit decided upon was the miniaturized gas chromatograph with a mass spectrometer detector, referred to as a GC/MS in the analytical marketplace.

  13. Miniaturization in Biocatalysis

    PubMed Central

    Fernandes, Pedro

    2010-01-01

    The use of biocatalysts for the production of both consumer goods and building blocks for chemical synthesis is consistently gaining relevance. A significant contribution for recent advances towards further implementation of enzymes and whole cells is related to the developments in miniature reactor technology and insights into flow behavior. Due to the high level of parallelization and reduced requirements of chemicals, intensive screening of biocatalysts and process variables has become more feasible and reproducibility of the bioconversion processes has been substantially improved. The present work aims to provide an overview of the applications of miniaturized reactors in bioconversion processes, considering multi-well plates and microfluidic devices, update information on the engineering characterization of the hardware used, and present perspective developments in this area of research. PMID:20479988

  14. Miniature ceramic fuel cell

    DOEpatents

    Lessing, Paul A.; Zuppero, Anthony C.

    1997-06-24

    A miniature power source assembly capable of providing portable electricity is provided. A preferred embodiment of the power source assembly employing a fuel tank, fuel pump and control, air pump, heat management system, power chamber, power conditioning and power storage. The power chamber utilizes a ceramic fuel cell to produce the electricity. Incoming hydro carbon fuel is automatically reformed within the power chamber. Electrochemical combustion of hydrogen then produces electricity.

  15. Miniature implantable ultrasonic echosonometer

    NASA Technical Reports Server (NTRS)

    Kojima, G. K. (Inventor)

    1978-01-01

    A miniature echosonometer adapted for implantation in the interior of an animal for imaging the internal structure of a organ, tissue or vessel is presented. The echosonometer includes a receiver/transmitter circuit which is coupled to an ultrasonic transducer. Power is coupled to the echosonometer by electromagnetic induction through the animal's skin. Imaging signals from the echosonometer are electromagnetically transmitted through the animal's skin to an external readout apparatus.

  16. A miniaturized applanation tonometer.

    PubMed

    Ma, J G; Xu, D Z

    1999-08-01

    A miniaturized hand-held applanation tonometer is introduced, in which a special cone prism is employed to be an applanation probe to flatten the eye vertically. The self-weight of the probe is just the applanation force, and the applanation area of the ocular cornea is monitored by the optoelectronic signal. The preliminary test demonstrates its good clinical acceptance and its accuracy meeting clinical needs. PMID:10431459

  17. Miniature multichannel biotelemeter system

    NASA Technical Reports Server (NTRS)

    Carraway, J. B.; Sumida, J. T. (Inventor)

    1974-01-01

    A miniature multichannel biotelemeter system is described. The system includes a transmitter where signals from different sources are sampled to produce a wavetrain of pulses. The transmitter also separates signals by sync pulses. The pulses amplitude modulate a radio frequency carrier which is received at a receiver unit. There the sync pulses are detected by a demultiplexer which routes the pulses from each different source to a separate output channel where the pulses are used to reconstruct the signals from the particular source.

  18. Miniaturizing RFID for magnamosis.

    PubMed

    Jiang, Hao; Chen, Shijie; Kish, Shad; Loh, Lokkee; Zhang, Junmin; Zhang, Xiaorong; Kwiat, Dillon; Harrison, Michael; Roy, Shuvo

    2014-01-01

    Anastomosis is a common surgical procedure using staples or sutures in an open or laparoscopic surgery. A more effective and much less invasive alternative is to apply the mechanical pressure on the tissue over a few days [1]. Since the pressure is produced by the attractive force between two permanent magnets, the procedure is called magnamosis[1]. To ensure the two magnets are perfectly aligned during the surgery, a miniaturized batteryless Radio Frequency IDentification (RFID) tag is developed to wirelessly telemeter the status of a pressure sensitive mechanical switch. Using the multi-layer circular spiral coil design, the diameter of the RFID tag is shrunk to 10, 15, 19 and 27 mm to support the magnamosis for children as well as adults. With the impedance matching network, the operating distance of these four RFID tags are longer than 10 cm in a 20 × 22 cm(2) area, even when the tag's normal direction is 45° off the antenna's normal direction. Measurement results also indicate that there is no noticeable degradation on the operating distance when the tag is immersed in saline or placed next to the rare-earth magnet. The miniaturized RFID tag presented in this paper is able to support the magnamosis and other medical applications that require the miniaturized RFID tag. PMID:25570040

  19. Insertional mutagenesis by transposable elements in the mammalian genome.

    PubMed

    Amariglio, N; Rechavi, G

    1993-01-01

    Several mammalian repetitive transposable genetic elements were characterized in recent years, and their role in mutagenesis is delineated in this review. Two main groups have been described: elements with symmetrical termini such as the murine IAP sequences and the human THE 1 elements and elements characterized by a poly-A rich tail at the 3' end such as the SINE and LINE sequences. The characteristic property of such mobile elements to spread and integrate in the host genome leads to insertional mutagenesis. Both germline and somatic mutations have been documented resulting from the insertion of the various types of mammalian repetitive transposable genetic elements. As foreseen by Barbara McClintock, such genetic events can cause either the activation or the inactivation of specific genes, resulting in their identification via an altered phenotype. Several disease states, such as hemophilia and cancer, are the result of this apparent aspect of genome instability. PMID:8385004

  20. Parallel matrix transpose algorithms on distributed memory concurrent computers

    SciTech Connect

    Choi, Jaeyoung; Dongarra, J. |; Walker, D.W.

    1994-12-31

    This paper describes parallel matrix transpose algorithms on distributed memory concurrent processors. We assume that the matrix is distributed over a P {times} Q processor template with a block scattered data distribution. P, Q, and the block size can be arbitrary, so the algorithms have wide applicability. The algorithms make use of non-blocking, point-to-point communication between processors. The use of nonblocking communication allows a processor to overlap the messages that it sends to different processors, thereby avoiding unnecessary synchronization. Combined with the matrix multiplication routine, C = A {center_dot} B, the algorithms are used to compute parallel multiplications of transposed matrices, C = A{sup T} {center_dot} B{sup T}, in the PUMMA package. Details of the parallel implementation of the algorithms are given, and results are presented for runs on the Intel Touchstone Delta computer.

  1. BLAT-based comparative analysis for transposable elements: BLATCAT.

    PubMed

    Lee, Sangbum; Oh, Sumin; Kang, Keunsoo; Han, Kyudong

    2014-01-01

    The availability of several whole genome sequences makes comparative analyses possible. In primate genomes, the priority of transposable elements (TEs) is significantly increased because they account for ~45% of the primate genomes, they can regulate the gene expression level, and they are associated with genomic fluidity in their host genomes. Here, we developed the BLAST-like alignment tool (BLAT) based comparative analysis for transposable elements (BLATCAT) program. The BLATCAT program can compare specific regions of six representative primate genome sequences (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) on the basis of BLAT and simultaneously carry out RepeatMasker and/or Censor functions, which are widely used Windows-based web-server functions to detect TEs. All results can be stored as a HTML file for manual inspection of a specific locus. BLATCAT will be very convenient and efficient for comparative analyses of TEs in various primate genomes. PMID:24959585

  2. DNA sequence of the maize transposable element Dissociation.

    PubMed

    Döring, H P; Tillmann, E; Starlinger, P

    The DNA sequence of the terminal 4.2 kilobases (kb) of the 30-kb insertion in the endosperm sucrose synthase gene of maize mutant sh-m5933 shows that it comprises two identical 2,040-base pair (bp) segments, one inserted in the reverse direction into the other. We suggest that the 2,040-bp sequence is an example of the transposable element Dissociation described by Barbara McClintock. PMID:6318121

  3. Mars Miniature Science Instruments

    NASA Technical Reports Server (NTRS)

    Kim, Soon Sam; Hayati, Samad; Lavery, David; McBrid, Karen

    2006-01-01

    For robotic Mars missions, all the science information is gathered through on-board miniature instruments that have been developed through many years of R&D. Compared to laboratory counterparts, the rover instruments require miniaturization, such as low mass (1-2 kg), low power (> 10 W) and compact (1-2 liter), yet with comparable sensitivity. Since early 1990's, NASA recognized the need for the miniature instruments and launched several instrument R&D programs, e.g., PIDDP (Planetary Instrument Definition and Development). However, until 1998, most of the instrument R&D programs supported only up to a breadboard level (TRL 3, 4) and there is a need to carry such instruments to flight qualifiable status (TU 5, 6) to respond to flight AOs (Announcement of Opportunity). Most of flight AOs have only limited time and financial resources, and can not afford such instrument development processes. To bridge the gap between instrument R&D programs and the flight instrument needs, NASA's Mars Technology Program (MTP) created advanced instrumentation program, Mars Instrument Development Project (MIDP). MIDP candidate instruments are selected through NASA Research Announcement (NRA) process [l]. For example, MIDP 161998-2000) selected and developed 10 instruments, MIDP II (2003-2005) 16 instruments, and MIDP III (2004-2006) II instruments.Working with PIs, JPL has been managing the MIDP tasks since September 1998. All the instruments being developed under MIDP have been selected through a highly competitive NRA process, and employ state-of-the-art technology. So far, four MIDP funded instruments have been selected by two Mars missions (these instruments have further been discussed in this paper).

  4. Miniature Laser Magnetometer

    NASA Technical Reports Server (NTRS)

    Slocum, Robert; Brown, Andy

    2011-01-01

    A conceptual design has been developed for a miniature laser magnetometer (MLM) that will measure the scalar magnitude and vector components of near-Earth magnetic fields. The MLM incorporates a number of technical innovations to achieve high-accuracy and high-resolution performance while significantly reducing the size of the laser-pumped helium magnetometer for use on small satellites and unmanned aerial vehicles (UAVs). and electronics sections that has the capability of measuring both the scalar magnetic field magnitude and the vector magnetic field components. Further more, the high-accuracy scalar measurements are used to calibrate and correct the vector component measurements in order to achieve superior vector accuracy and stability. The correction algorithm applied to the vector components for calibration and the same cell for vector and scalar measurements are major innovations. The separate sensor and electronics section of the MLM instrument allow the sensor to be installed on a boom or otherwise located away from electronics and other noisy magnetic components. The MLM s miniaturization will be accomplished through the use of advanced miniaturized components and packaging methods for the MLM sensor and electronics. The MLM conceptual design includes three key innovations. The first is a new non-magnetic laser package that will allow the placement of the laser pump source near the helium cell sensing elements. The second innovation is the design of compact, nested, triaxial Braunbek coils used in the vector measurements that reduce the coil size by a factor of two compared to existing Helmholtz coils with similar field-generation performance. The third innovation is a compact sensor design that reduces the sensor volume by a factor of eight compared to MLM s predecessor.

  5. Miniature biaxial strain transducer

    NASA Technical Reports Server (NTRS)

    Hoffman, I. S. (Inventor)

    1976-01-01

    A reusable miniature strain transducer for use in the measurement of static or quasi-static, high level, biaxial strain on the surface of test specimens or structures was studied. Two cantilever arms, constructed by machining the material to appropriate flexibility, are self-aligning and constitute the transducing elements of the device. Used in conjunction with strain gages, the device enables testing beyond normal gage limits for high strains and number of load cycles. The device does not require conversion computations since the electrical output of the strain gages is directly proportional to the strain measured.

  6. Miniaturized radiation chirper

    DOEpatents

    Umbarger, C. John; Wolf, Michael A.

    1980-01-01

    The disclosure relates to a miniaturized radiation chirper for use with a small battery supplying on the order of 5 volts. A poor quality CdTe crystal which is not necessarily suitable for high resolution gamma ray spectroscopy is incorporated with appropriate electronics so that the chirper emits an audible noise at a rate that is proportional to radiation exposure level. The chirper is intended to serve as a personnel radiation warning device that utilizes new and novel electronics with a novel detector, a CdTe crystal. The resultant device is much smaller and has much longer battery life than existing chirpers.

  7. Miniature electrical connector

    DOEpatents

    Casper, Robert F.

    1976-01-01

    A miniature coaxial cable electrical connector includes an annular compressible gasket in a receptacle member, the gasket having a generally triangular cross section resiliently engaging and encircling a conically tapered outer surface of a plug member to create an elongated current leakage path at their interface; means for preventing rotation of the plug relative to the receptacle; a metal sleeve forming a portion of the receptacle and encircling the plug member when interconnected; and a split ring in the plug having outwardly and rearwardly projecting fingers spaced from and encircling a portion of a coaxial cable and engageable with the metal sleeve to interlock the receptacle and plug.

  8. Perspectives on Simulation and Miniaturization.

    ERIC Educational Resources Information Center

    McCluskey, Michael R.

    Training applications of simulation and miniaturization are examined, as are areas where research is needed to develop cost-effectiveness simulation methodologies for training. In order for simulation and miniaturization techniques to reach maximum levels of effectiveness, systems analysis is needed to define physical and psychological dimensions,…

  9. Transposable Elements and Genome Size Variations in Plants

    PubMed Central

    Lee, Sung-Il

    2014-01-01

    Although the number of protein-coding genes is not highly variable between plant taxa, the DNA content in their genomes is highly variable, by as much as 2,056-fold from a 1C amount of 0.0648 pg to 132.5 pg. The mean 1C-value in plants is 2.4 pg, and genome size expansion/contraction is lineage-specific in plant taxonomy. Transposable element fractions in plant genomes are also variable, as low as ~3% in small genomes and as high as ~85% in large genomes, indicating that genome size is a linear function of transposable element content. Of the 2 classes of transposable elements, the dynamics of class 1 long terminal repeat (LTR) retrotransposons is a major contributor to the 1C value differences among plants. The activity of LTR retrotransposons is under the control of epigenetic suppressing mechanisms. Also, genome-purging mechanisms have been adopted to counter-balance the genome size amplification. With a wealth of information on whole-genome sequences in plant genomes, it was revealed that several genome-purging mechanisms have been employed, depending on plant taxa. Two genera, Lilium and Fritillaria, are known to have large genomes in angiosperms. There were twice times of concerted genome size evolutions in the family Liliaceae during the divergence of the current genera in Liliaceae. In addition to the LTR retrotransposons, non-LTR retrotransposons and satellite DNAs contributed to the huge genomes in the two genera by possible failure of genome counter-balancing mechanisms. PMID:25317107

  10. P transposable elements in Drosophila and other eukaryotic organisms

    PubMed Central

    Majumdar, Sharmistha; Rio, Donald C.

    2015-01-01

    P transposable elements were discovered in Drosophila as the causative agents of a syndrome of genetic traits called hybrid dysgenesis. Hybrid dysgenesis exhibits a unique pattern of maternal inheritance linked to the germline-specific small RNA piwi-interacting (piRNA) pathway. The use of P transposable elements as vectors for gene transfer and as genetic tools revolutionized the field of Drosophila molecular genetics. P element transposons have served as a useful model to investigate mechanisms of cut-and-paste transposition in eukaryotes. Biochemical studies have revealed new and unexpected insights into how eukaryotic DNA-based transposons are mobilized. For example, the P element transposase makes unusual 17nt-3’ extended double-strand DNA breaks at the transposon termini and uses guanosine triphosphate (GTP) as a cofactor to promote synapsis of the two transposon ends early in the transposition pathway. The N-terminal DNA binding domain of the P element transposase, called a THAP domain, contains a C2CH zinc-coordinating motif and is the founding member of a large family of animal-specific site-specific DNA binding proteins. Over the past decade genome sequencing efforts have revealed the presence of P element-like transposable elements or P element transposase-like genes (called THAP9) in many eukaryotic genomes, including vertebrates, such as primates including humans, zebrafish and Xenopus, as well as the human parasite Trichomonas vaginalis, the sea squirt Ciona, sea urchin and hydra. Surprisingly, the human and zebrafish P element transposase-related THAP9 genes promote transposition of the Drosophila P element transposon DNA in human and Drosophila cells, indicating that the THAP9 genes encode active P element “transposase” proteins. PMID:25893144

  11. P Transposable Elements in Drosophila and other Eukaryotic Organisms.

    PubMed

    Majumdar, Sharmistha; Rio, Donald C

    2015-04-01

    P transposable elements were discovered in Drosophila as the causative agents of a syndrome of genetic traits called hybrid dysgenesis. Hybrid dysgenesis exhibits a unique pattern of maternal inheritance linked to the germline-specific small RNA piwi-interacting (piRNA) pathway. The use of P transposable elements as vectors for gene transfer and as genetic tools revolutionized the field of Drosophila molecular genetics. P element transposons have served as a useful model to investigate mechanisms of cut-and-paste transposition in eukaryotes. Biochemical studies have revealed new and unexpected insights into how eukaryotic DNA-based transposons are mobilized. For example, the P element transposase makes unusual 17nt-3' extended double-strand DNA breaks at the transposon termini and uses guanosine triphosphate (GTP) as a cofactor to promote synapsis of the two transposon ends early in the transposition pathway. The N-terminal DNA binding domain of the P element transposase, called a THAP domain, contains a C2CH zinc-coordinating motif and is the founding member of a large family of animal-specific site-specific DNA binding proteins. Over the past decade genome sequencing efforts have revealed the presence of P element-like transposable elements or P element transposase-like genes (called THAP9) in many eukaryotic genomes, including vertebrates, such as primates including humans, zebrafish and Xenopus, as well as the human parasite Trichomonas vaginalis, the sea squirt Ciona, sea urchin and hydra. Surprisingly, the human and zebrafish P element transposase-related THAP9 genes promote transposition of the Drosophila P element transposon DNA in human and Drosophila cells, indicating that the THAP9 genes encode active P element "transposase" proteins. PMID:26104714

  12. Transposable elements domesticated and neofunctionalized by eukaryotic genomes.

    PubMed

    Alzohairy, Ahmed M; Gyulai, Gábor; Jansen, Robert K; Bahieldin, Ahmed

    2013-01-01

    Whole genome sequencing has provided a massive amount of information about the origin, diversity and genomic impact of repetitive DNA sequences (repDNA). Among the many classes of repDNA, prokaryotic transposable elements (TEs) replicate, move, amplify and accumulate in invaded genomes and thus represent the major force in restructuring host genes and genomes during evolution. Similar to retroviruses, autonomous TEs became part of the host genomes, and after their molecular domestication, they became functional genes (genomic fossils) in eukaryotic genomes. In this review, examples of the domestication events are discussed, some of which are known to be induced by biotic and abiotic stressors. PMID:22960324

  13. Miniature Heat Pipes

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Small Business Innovation Research contracts from Goddard Space Flight Center to Thermacore Inc. have fostered the company work on devices tagged "heat pipes" for space application. To control the extreme temperature ranges in space, heat pipes are important to spacecraft. The problem was to maintain an 8-watt central processing unit (CPU) at less than 90 C in a notebook computer using no power, with very little space available and without using forced convection. Thermacore's answer was in the design of a powder metal wick that transfers CPU heat from a tightly confined spot to an area near available air flow. The heat pipe technology permits a notebook computer to be operated in any position without loss of performance. Miniature heat pipe technology has successfully been applied, such as in Pentium Processor notebook computers. The company expects its heat pipes to accommodate desktop computers as well. Cellular phones, camcorders, and other hand-held electronics are forsible applications for heat pipes.

  14. Miniature drag force anemometer

    NASA Technical Reports Server (NTRS)

    Krause, L. N.; Fralick, G. C.

    1977-01-01

    A miniature drag force anemometer is described which is capable of measuring dynamic velocity head and flow direction. The anemometer consists of a silicon cantilevered beam 2.5 mm long, 1.5 mm wide, and 0.25 mm thick with an integrated diffused strain gage bridge, located at the base of the beam, as the force measuring element. The dynamics of the beam are like that of a second order system with a natural frequency of about 42 kHz and a damping coefficient of 0.007. The anemometer can be used in both forward and reversed flow. Measured flow characteristics up to Mach 0.6 are presented along with application examples including turbulence measurements.

  15. Miniature, ruggedized data collector

    NASA Astrophysics Data System (ADS)

    Jackson, Scott; Calcutt, Wade; Knobler, Ron; Jones, Barry; Klug, Robert

    2009-05-01

    McQ has developed a miniaturized, programmable, ruggedized data collector intended for use in weapon testing or data collection exercises that impose severe stresses on devices under test. The recorder is designed to survive these stresses which include acceleration and shock levels up to 100,000 G. The collector acquires and stores up to four channels of signal data to nonvolatile memory for later retrieval by a user. It is small (< 7 in3), light weight (< 1 lb), and can operate from various battery chemistries. A built-in menuing system, accessible via a USB interface, allows the user to configure parameters of the recorder operation, such as channel gain, filtering, and signal offsets, and also to retrieve recorded data for analysis. An overview of the collector, its features, performance, and potential uses, is presented.

  16. Miniature spectrally selective dosimeter

    NASA Technical Reports Server (NTRS)

    Adams, R. R.; Macconochie, I. O.; Poole, B. D., Jr. (Inventor)

    1980-01-01

    A miniature spectrally selective dosimeter capable of measuring selected bandwidths of radiation exposure on small mobile areas is described. This is achieved by the combination of photovoltaic detectors, electrochemical integrators (E-cells) and filters in a small compact case which can be easily attached in close proximity to and substantially parallel to the surface being measured. In one embodiment two photovoltaic detectors, two E-cells, and three filters are packaged in a small case with attaching means consisting of a safety pin. In another embodiment, two detectors, one E-cell, three filters are packaged in a small case with attaching means consisting of a clip to clip over a side piece of an eye glass frame.

  17. Miniature Latching Valve

    NASA Technical Reports Server (NTRS)

    Johnson, A. David; Benson, Glendon M.

    2008-01-01

    A miniature latching valve has been invented to satisfy a need for an electrically controllable on/off pneumatic valve that is lightweight and compact and remains in the most recently commanded open or closed state when power is not supplied. The valve includes a poppet that is moved into or out of contact with a seat to effect closure or opening, respectively, of the flow path. Motion of the poppet is initiated by electrical heating of one of two opposing pairs of nickel/titanium shape-memory alloy (SMA) wires above their transition temperature: heated wires contract to their remembered length, applying tension to pull the poppet toward or away from the seat. A latch consisting mainly of a bistable Belleville washer (a conical spring) made of a hardened stainless steel operates between two stable positions corresponding to the fully closed or fully open state, holding the poppet in one of these positions when power is not applied to either pair of SMA wires. To obtain maximum actuation force and displacement, the SMA wires must be kept in tension. The mounting fixtures at the ends of the wires must support large tensile stresses without creating stress concentrations that would limit the fatigue lives of the wires. An earlier design provided for each wire to be crimped in a conical opening with a conical steel ferrule that was swaged into the opening to produce a large, uniformly distributed holding force. In a subsequent design, the conical ferrule was replaced with a larger crimped cylindrical ferrule depicted in the figure. A major problem in designing the valve was to protect the SMA wires from a bake-out temperature of 300 C. The problem was solved by incorporating the SMA wires into an actuator module that is inserted into a barrel of the valve body and is held in place by miniature clip rings.

  18. C-GATE - catalogue of genes affected by transposable elements

    PubMed Central

    2012-01-01

    Background Functional regulatory sequences are present in many transposable element (TE) copies, resulting in TEs being frequently exapted by host genes. Today, many examples of TEs impacting host gene expression can be found in the literature and we believe a new catalogue of such exaptations would be useful for the field. Findings We have established the catalogue of genes affected by transposable elements (C-GATE), which can be found at https://sites.google.com/site/tecatalog/. To date, it holds 221 cases of biologically verified TE exaptations and more than 10,000 in silico TE-gene partnerships. C-GATE is interactive and allows users to include missed or new TE exaptation data. C-GATE provides a graphic representation of the entire library, which may be used for future statistical analysis of TE impact on host gene expression. Conclusions We hope C-GATE will be valuable for the TE community but also for others who have realized the role that TEs may have in their research. PMID:22621612

  19. DPTEdb, an integrative database of transposable elements in dioecious plants

    PubMed Central

    Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

    2016-01-01

    Dioecious plants usually harbor ‘young’ sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants. Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php PMID:27173524

  20. Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera

    PubMed Central

    2013-01-01

    Background Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. Results We determined that TEs comprise ~25% of the genome. The predominant class of TEs (~12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. Conclusions Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group. PMID:24088337

  1. DPTEdb, an integrative database of transposable elements in dioecious plants.

    PubMed

    Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

    2016-01-01

    Dioecious plants usually harbor 'young' sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants.Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php. PMID:27173524

  2. TRANSPOSED LETTER EFFECTS IN PREFIXED WORDS: IMPLICATIONS FOR MORPHOLOGICAL DECOMPOSITION.

    PubMed

    Masserang, Kathleen M; Pollatsek, Alexander

    2012-01-01

    A crucial issue in word encoding is whether morphemes are involved in early stages. One paradigm that tests for this employs the transposed letter (TL) effect - the difference in the times to process a word (misfile) when it is preceded by a TL prime (mifsile) and when it is preceded by a substitute letter (SL) prime (mintile) - and examines whether the TL effect is smaller when the two adjacent letters cross a morpheme boundary. The evidence from prior studies is not consistent. Experiments 1 and 2 employed a parafoveal preview paradigm in which the transposed letters either crossed the prefix-stem boundary or did not, and found a clear TL effect regardless of whether the two letters crossed the morpheme boundary. Experiment 3 replicated this finding employing a masked priming lexical-decision paradigm. It thus appears that morphemes are not involved in early processes in English that are sensitive to letter order. There is some evidence for morphemic modulation of the TL effect in other languages; thus, the properties of the language may modulate when morphemes influence early letter position encoding. PMID:23082239

  3. Evolutionary interaction between W/Y chromosome and transposable elements.

    PubMed

    Śliwińska, Ewa B; Martyka, Rafał; Tryjanowski, Piotr

    2016-06-01

    The W/Y chromosome is unique among chromosomes as it does not recombine in its mature form. The main side effect of cessation of recombination is evolutionary instability and degeneration of the W/Y chromosome, or frequent W/Y chromosome turnovers. Another important feature of W/Y chromosome degeneration is transposable element (TEs) accumulation. Transposon accumulation has been confirmed for all W/Y chromosomes that have been sequenced so far. Models of W/Y chromosome instability include the assemblage of deleterious mutations in protein coding genes, but do not include the influence of transposable elements that are accumulated gradually in the non-recombining genome. The multiple roles of genomic TEs, and the interactions between retrotransposons and genome defense proteins are currently being studied intensively. Small RNAs originating from retrotransposon transcripts appear to be, in some cases, the only mediators of W/Y chromosome function. Based on the review of the most recent publications, we present knowledge on W/Y evolution in relation to retrotransposable element accumulation. PMID:27000053

  4. Producing miniature threads. Final report

    SciTech Connect

    Gillespie, L.K.; Robb, J.M.

    1981-11-01

    Miniature precision actuators, timers, and switches typically utilize miniature threads to provide convenient assembly, disassembly and adjustment. Thread rolling provides high-quality external threads with greater strength and lower cost than other thread-producing techniques. Tap breakage is a significant problem when 0.5 and 0.6 Unified National Miniature (UNM) threads must be produced in hard materials such as SAE K95100 high-permeability magnetic steel. Aluminum parts can be tapped with no difficulty in these sizes. Stainless steel 0.5 UNM screws break at loads of 21 lb (53 N). Thread failure occurs at thread heights of 62% full thread or lower.

  5. Transposable elements as artisans of the heterochromatic genome in Drosophila melanogaster.

    PubMed

    Dimitri, P; Corradini, N; Rossi, F; Mei, E; Zhimulev, I F; Vernì, F

    2005-01-01

    Over 50 years ago Barbara McClintock discovered that maize contains mobile genetic elements, but her findings were at first considered nothing more than anomalies. Today it is widely recognized that transposable elements have colonized all eukaryotic genomes and represent a major force driving evolution of organisms. Our contribution to this special issue deals with the theme of transposable element-host genome interactions. We bring together published and unpublished work to provide a picture of the contribution of transposable elements to the evolution of the heterochromatic genome in Drosophila melanogaster. In particular, we discuss data on 1) colonization of constitutive heterochromatin by transposable elements, 2) instability of constitutive heterochromatin induced by the I factor, and 3) evolution of constitutive heterochromatin and heterochromatic genes driven by transposable elements. Drawing attention to these topics may have direct implications on important aspects of genome organization and gene expression. PMID:16093669

  6. Miniature electron microscopes for lithography

    NASA Astrophysics Data System (ADS)

    Feinerman, Alan D.; Crewe, David A.; Perng, Dung-Ching; Spindt, Capp A.; Schwoebel, Paul R.; Crewe, Albert V.

    1994-05-01

    Two inexpensive and extremely accurate methods for fabricating miniature 10 - 50 kV and 0.5 - 10 kV electron beam columns have been developed: `slicing,' and `stacking.' Two or three miniature columns could be used to perform a 20 nm or better alignment of an x-ray mask to a substrate. An array of miniature columns could be used for rapid wafer inspection and high throughput electron beam lithography. The column fabrication methods combine the precision of semiconductor processing and fiber optic technologies to create macroscopic structures consisting of charged particle sources, deflecting and focusing electrodes, and detectors. The overall performance of the miniature column also depends on the emission characteristics of the micromachined electron source which is currently being investigated.

  7. Summary of Miniature NMR Development

    SciTech Connect

    Friedman, Gennady; Feinerman, Alan

    2000-12-31

    The effort in this project has been in 3 distinct directions: (1) First, they focused on development of miniature microfabricated micro-coil NMR detectors with maximum Signal-to-Noise (SNR) ratio. (2) Secondly, they focused on design of miniature micro-coil NMR detectors that have minimal effect on the NMR spectrum distortions. (3) Lastly they focused on the development of a permanent magnet capable of generating fields on the order of 1 Tesla with better than 10 ppm uniformity.

  8. Miniature Chemical Sensor

    SciTech Connect

    Andrew C. R. Pipino

    2004-12-13

    A new chemical detection technology has been realized that addresses DOE environmental management needs. The new technology is based on a variant of the sensitive optical absorption technique, cavity ring-down spectroscopy (CRDS). Termed evanescent-wave cavity ring-down spectroscopy (EW-CRDS), the technology employs a miniature solid-state optical resonator having an extremely high Q-factor as the sensing element, where the high-Q is achieved by using ultra-low-attenuation optical materials, ultra-smooth surfaces, and ultra-high reflectivity coatings, as well as low-diffraction-loss designs. At least one total-internal reflection (TIR) mirror is integral to the resonator permitting the concomitant evanescent wave to probe the ambient environment. Several prototypes have been designed, fabricated, characterized, and applied to chemical detection. Moreover, extensions of the sensing concept have been explored to enhance selectivity, sensitivity, and range of application. Operating primarily in the visible and near IR regions, the technology inherently enables remote detection by optical fiber. Producing 11 archival publications, 5 patents, 19 invited talks, 4 conference proceedings, a CRADA, and a patent-license agreement, the project has realized a new chemical detection technology providing >100 times more sensitivity than comparable technologies, while also providing practical advantages.

  9. The Whole new world of miniature technology

    SciTech Connect

    Gillespie, L.K.

    1980-07-01

    In the past ten years, miniaturization of both electrical and mechanical parts has significantly increased. Documentation of the design and production capabilities of miniaturization in the electronics industry is well-defined. Literature on the subject of miniaturization of metal piece parts, however, is hard to find. Some of the current capabilities in the manufacture of miniature metal piece parts or miniature features in larger piece parts are discussed.

  10. Transposable Elements: From DNA Parasites to Architects of Metazoan Evolution

    PubMed Central

    Piskurek, Oliver; Jackson, Daniel J.

    2012-01-01

    One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to advances in high throughput sequencing technologies it is now clear that TEs comprise the largest molecular class within most metazoan genomes. TEs, once categorised as "junk DNA", are now known to influence genomic structure and function by increasing the coding and non-coding genetic repertoire of the host. In this way TEs are key elements that stimulate the evolution of metazoan genomes. This review highlights several lines of TE research including the horizontal transfer of TEs through host-parasite interactions, the vertical maintenance of TEs over long periods of evolutionary time, and the direct role that TEs have played in generating morphological novelty. PMID:24704977

  11. Study of Transposable Elements and Their Genomic Impact.

    PubMed

    Muñoz-Lopez, Martin; Vilar-Astasio, Raquel; Tristan-Ramos, Pablo; Lopez-Ruiz, Cesar; Garcia-Pérez, Jose L

    2016-01-01

    Transposable elements (TEs) have been considered traditionally as junk DNA, i.e., DNA sequences that despite representing a high proportion of genomes had no evident cellular functions. However, over the last decades, it has become undeniable that not only TE-derived DNA sequences have (and had) a fundamental role during genome evolution, but also TEs have important implications in the origin and evolution of many genomic disorders. This concise review provides a brief overview of the different types of TEs that can be found in genomes, as well as a list of techniques and methods used to study their impact and mobilization. Some of these techniques will be covered in detail in this Method Book. PMID:26895043

  12. Transposable elements in sexual and ancient asexual taxa

    PubMed Central

    Arkhipova, Irina; Meselson, Matthew

    2000-01-01

    Sexual reproduction allows deleterious transposable elements to proliferate in populations, whereas the loss of sex, by preventing their spread, has been predicted eventually to result in a population free of such elements [Hickey, D. A. (1982) Genetics 101, 519–531]. We tested this expectation by screening representatives of a majority of animal phyla for LINE-like and gypsy-like reverse transcriptases and mariner/Tc1-like transposases. All species tested positive for reverse transcriptases except rotifers of the class Bdelloidea, the largest eukaryotic taxon in which males, hermaphrodites, and meiosis are unknown and for which ancient asexuality is supported by molecular genetic evidence. Mariner-like transposases are distributed sporadically among species and are present in bdelloid rotifers. The remarkable lack of LINE-like and gypsy-like retrotransposons in bdelloids and their ubiquitous presence in other taxa support the view that eukaryotic retrotransposons are sexually transmitted nuclear parasites and that bdelloid rotifers evolved asexually. PMID:11121049

  13. Transposable Elements in TDP-43-Mediated Neurodegenerative Disorders

    PubMed Central

    Hammell, Molly; Dubnau, Josh

    2012-01-01

    Elevated expression of specific transposable elements (TEs) has been observed in several neurodegenerative disorders. TEs also can be active during normal neurogenesis. By mining a series of deep sequencing datasets of protein-RNA interactions and of gene expression profiles, we uncovered extensive binding of TE transcripts to TDP-43, an RNA-binding protein central to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Second, we find that association between TDP-43 and many of its TE targets is reduced in FTLD patients. Third, we discovered that a large fraction of the TEs to which TDP-43 binds become de-repressed in mouse TDP-43 disease models. We propose the hypothesis that TE mis-regulation contributes to TDP-43 related neurodegenerative diseases. PMID:22957047

  14. Adaptation to Global Change: A Transposable Element-Epigenetics Perspective.

    PubMed

    Rey, Olivier; Danchin, Etienne; Mirouze, Marie; Loot, Céline; Blanchet, Simon

    2016-07-01

    Understanding how organisms cope with global change is a major scientific challenge. The molecular pathways underlying rapid adaptive phenotypic responses to global change remain poorly understood. Here, we highlight the relevance of two environment-sensitive molecular elements: transposable elements (TEs) and epigenetic components (ECs). We first outline the sensitivity of these elements to global change stressors and review how they interact with each other. We then propose an integrative molecular engine coupling TEs and ECs and allowing organisms to fine-tune phenotypes in a real-time fashion, adjust the production of phenotypic and genetic variation, and produce heritable phenotypes with different levels of transmission fidelity. We finally discuss the implications of this molecular engine in the context of global change. PMID:27080578

  15. Chromatin structure and transposable elements in organismal aging

    PubMed Central

    Wood, Jason G.; Helfand, Stephen L.

    2013-01-01

    Epigenetic regulatory mechanisms are increasingly appreciated as central to a diverse array of biological processes, including aging. An association between heterochromatic silencing and longevity has long been recognized in yeast, and in more recent years evidence has accumulated of age-related chromatin changes in Caenorhabditis elegans, Drosophila, and mouse model systems, as well as in the tissue culture-based replicative senescence model of cell aging. In addition, a number of studies have linked expression of transposable elements (TEs), as well as changes in the RNAi pathways that cells use to combat TEs, to the aging process. This review summarizes the recent evidence linking chromatin structure and function to aging, with a particular focus on the relationship of heterochromatin structure to organismal aging. PMID:24363663

  16. Insights into the Transposable Mobilome of Paracoccus spp. (Alphaproteobacteria)

    PubMed Central

    Dziewit, Lukasz; Baj, Jadwiga; Szuplewska, Magdalena; Maj, Anna; Tabin, Mateusz; Czyzkowska, Anna; Skrzypczyk, Grazyna; Adamczuk, Marcin; Sitarek, Tomasz; Stawinski, Piotr; Tudek, Agnieszka; Wanasz, Katarzyna; Wardal, Ewa; Piechucka, Ewa; Bartosik, Dariusz

    2012-01-01

    Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial

  17. Miniature Intelligent Sensor Module

    NASA Technical Reports Server (NTRS)

    Beech, Russell S.

    2007-01-01

    An electronic unit denoted the Miniature Intelligent Sensor Module performs sensor-signal-conditioning functions and local processing of sensor data. The unit includes four channels of analog input/output circuitry, a processor, volatile and nonvolatile memory, and two Ethernet communication ports, all housed in a weathertight enclosure. The unit accepts AC or DC power. The analog inputs provide programmable gain, offset, and filtering as well as shunt calibration and auto-zeroing. Analog outputs include sine, square, and triangular waves having programmable frequencies and amplitudes, as well as programmable amplitude DC. One innovative aspect of the design of this unit is the integration of a relatively powerful processor and large amount of memory along with the sensor-signalconditioning circuitry so that sophisticated computer programs can be used to acquire and analyze sensor data and estimate and track the health of the overall sensor-data-acquisition system of which the unit is a part. The unit includes calibration, zeroing, and signalfeedback circuitry to facilitate health monitoring. The processor is also integrated with programmable logic circuitry in such a manner as to simplify and enhance acquisition of data and generation of analog outputs. A notable unique feature of the unit is a cold-junction compensation circuit in the back shell of a sensor connector. This circuit makes it possible to use Ktype thermocouples without compromising a housing seal. Replicas of this unit may prove useful in industrial and manufacturing settings - especially in such large outdoor facilities as refineries. Two features can be expected to simplify installation: the weathertight housings should make it possible to mount the units near sensors, and the Ethernet communication capability of the units should facilitate establishment of communication connections for the units.

  18. Massive contribution of transposable elements to mammalian regulatory sequences.

    PubMed

    Rayan, Nirmala Arul; Del Rosario, Ricardo C H; Prabhakar, Shyam

    2016-09-01

    Barbara McClintock discovered the existence of transposable elements (TEs) in the late 1940s and initially proposed that they contributed to the gene regulatory program of higher organisms. This controversial idea gained acceptance only much later in the 1990s, when the first examples of TE-derived promoter sequences were uncovered. It is now known that half of the human genome is recognizably derived from TEs. It is thus important to understand the scope and nature of their contribution to gene regulation. Here, we provide a timeline of major discoveries in this area and discuss how transposons have revolutionized our understanding of mammalian genomes, with a special emphasis on the massive contribution of TEs to primate evolution. Our analysis of primate-specific functional elements supports a simple model for the rate at which new functional elements arise in unique and TE-derived DNA. Finally, we discuss some of the challenges and unresolved questions in the field, which need to be addressed in order to fully characterize the impact of TEs on gene regulation, evolution and disease processes. PMID:27174439

  19. Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi.

    PubMed

    Hess, Jaqueline; Skrede, Inger; Wolfe, Benjamin E; LaButti, Kurt; Ohm, Robin A; Grigoriev, Igor V; Pringle, Anne

    2014-07-01

    Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanita fungi. Using methods developed to interrogate both assembled and unassembled sequences, we characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species' natural histories may have in shaping genome architecture. PMID:24923322

  20. Real-time transposable element activity in individual live cells

    PubMed Central

    Lee, Gloria; Martini, K. Michael

    2016-01-01

    The excision and reintegration of transposable elements (TEs) restructure their host genomes, generating cellular diversity involved in evolution, development, and the etiology of human diseases. Our current knowledge of TE behavior primarily results from bulk techniques that generate time and cell ensemble averages, but cannot capture cell-to-cell variation or local environmental and temporal variability. We have developed an experimental system based on the bacterial TE IS608 that uses fluorescent reporters to directly observe single TE excision events in individual cells in real time. We find that TE activity depends upon the TE’s orientation in the genome and the amount of transposase protein in the cell. We also find that TE activity is highly variable throughout the lifetime of the cell. Upon entering stationary phase, TE activity increases in cells hereditarily predisposed to TE activity. These direct observations demonstrate that real-time live-cell imaging of evolution at the molecular and individual event level is a powerful tool for the exploration of genome plasticity in stressed cells. PMID:27298350

  1. Tempo and Mode of Transposable Element Activity in Drosophila

    PubMed Central

    Kofler, Robert; Nolte, Viola; Schlötterer, Christian

    2015-01-01

    The evolutionary dynamics of transposable element (TE) insertions have been of continued interest since TE activity has important implications for genome evolution and adaptation. Here, we infer the transposition dynamics of TEs by comparing their abundance in natural D. melanogaster and D. simulans populations. Sequencing pools of more than 550 South African flies to at least 320-fold coverage, we determined the genome wide TE insertion frequencies in both species. We suggest that the predominance of low frequency insertions in the two species (>80% of the insertions have a frequency <0.2) is probably due to a high activity of more than 58 families in both species. We provide evidence for 50% of the TE families having temporally heterogenous transposition rates with different TE families being affected in the two species. While in D. melanogaster retrotransposons were more active, DNA transposons showed higher activity levels in D. simulans. Moreover, we suggest that LTR insertions are mostly of recent origin in both species, while DNA and non-LTR insertions are older and more frequently vertically transmitted since the split of D. melanogaster and D. simulans. We propose that the high TE activity is of recent origin in both species and a consequence of the demographic history, with habitat expansion triggering a period of rapid evolution. PMID:26186437

  2. Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

    PubMed Central

    Hess, Jaqueline; Skrede, Inger; Wolfe, Benjamin E.; LaButti, Kurt; Ohm, Robin A.; Grigoriev, Igor V.; Pringle, Anne

    2014-01-01

    Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanita fungi. Using methods developed to interrogate both assembled and unassembled sequences, we characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species’ natural histories may have in shaping genome architecture. PMID:24923322

  3. Considering Transposable Element Diversification in De Novo Annotation Approaches

    PubMed Central

    Flutre, Timothée; Duprat, Elodie; Feuillet, Catherine; Quesneville, Hadi

    2011-01-01

    Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species. PMID:21304975

  4. No Accumulation of Transposable Elements in Asexual Arthropods.

    PubMed

    Bast, Jens; Schaefer, Ina; Schwander, Tanja; Maraun, Mark; Scheu, Stefan; Kraaijeveld, Ken

    2016-03-01

    Transposable elements (TEs) and other repetitive DNA can accumulate in the absence of recombination, a process contributing to the degeneration of Y-chromosomes and other nonrecombining genome portions. A similar accumulation of repetitive DNA is expected for asexually reproducing species, given their entire genome is effectively nonrecombining. We tested this expectation by comparing the whole-genome TE loads of five asexual arthropod lineages and their sexual relatives, including asexual and sexual lineages of crustaceans (Daphnia water fleas), insects (Leptopilina wasps), and mites (Oribatida). Surprisingly, there was no evidence for increased TE load in genomes of asexual as compared to sexual lineages, neither for all classes of repetitive elements combined nor for specific TE families. Our study therefore suggests that nonrecombining genomes do not accumulate TEs like nonrecombining genomic regions of sexual lineages. Even if a slight but undetected increase of TEs were caused by asexual reproduction, it appears to be negligible compared to variance between species caused by processes unrelated to reproductive mode. It remains to be determined if molecular mechanisms underlying genome regulation in asexuals hamper TE activity. Alternatively, the differences in TE dynamics between nonrecombining genomes in asexual lineages versus nonrecombining genome portions in sexual species might stem from selection for benign TEs in asexual lineages because of the lack of genetic conflict between TEs and their hosts and/or because asexual lineages may only arise from sexual ancestors with particularly low TE loads. PMID:26560353

  5. MnTEdb, a collective resource for mulberry transposable elements.

    PubMed

    Ma, Bi; Li, Tian; Xiang, Zhonghuai; He, Ningjia

    2015-01-01

    Mulberry has been used as an economically important food crop for the domesticated silkworm for thousands of years, resulting in one of the oldest and well-known plant-herbivore interactions. The genome of Morus notabilis has now been sequenced and there is an opportunity to mine the transposable element (TE) data. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the mulberry genome, a specific, comprehensive and user-friendly web-based database, MnTEdb, was constructed. It was built based on a detailed and accurate identification of all TEs in mulberry. A total of 5925 TEs belonging to 13 superfamilies and 1062 families were deposited in this database. MnTEdb enables users to search, browse and download the mulberry TE sequences. Meanwhile, data mining tools, including BLAST, GetORF, HMMER, Sequence Extractor and JBrowse were also integrated into MnTEdb. MnTEdb will assist researchers to efficiently take advantage of our newly annotated TEs, which facilitate their studies in the origin, amplification and evolution of TEs, as well as the comparative analysis among the different species. Database URL: http://morus.swu.edu.cn/mntedb/ PMID:25725060

  6. Tc1-like transposable elements in plant genomes

    PubMed Central

    2014-01-01

    Background The Tc1/mariner superfamily of transposable elements (TEs) is widespread in animal genomes. Mariner-like elements, which bear a DDD triad catalytic motif, have been identified in a wide range of flowering plant species. However, as the founding member of the superfamily, Tc1-like elements that bear a DD34E triad catalytic motif are only known to unikonts (animals, fungi, and Entamoeba). Results Here we report the identification of Tc1-like elements (TLEs) in plant genomes. These elements bear the four terminal nucleotides and the characteristic DD34E triad motif of Tc1 element. The two TLE families (PpTc1, PpTc2) identified in the moss (Physcomitrella patens) genome contain highly similar copies. Multiple copies of PpTc1 are actively transcribed and the transcripts encode intact full length transposase coding sequences. TLEs are also found in angiosperm genome sequence databases of rice (Oryza sativa), dwarf birch (Betula nana), cabbage (Brassica rapa), hemp (Cannabis sativa), barley (Hordium valgare), lettuce (Lactuta sativa), poplar (Populus trichocarpa), pear (Pyrus x bretschneideri), and wheat (Triticum urartu). Conclusions This study extends the occurrence of TLEs to the plant phylum. The elements in the moss genome have amplified recently and may still be capable of transposition. The TLEs are also present in angiosperm genomes, but apparently much less abundant than in moss. PMID:24926322

  7. Differential detection of transposable elements between Saccharum species

    PubMed Central

    de Souza, Marislane Carvalho Paz; Silva, Jéssica Naiana; Almeida, Cícero

    2013-01-01

    Cultivars of sugarcane (Saccharum) are hybrids between species S. officinarum (x = 10, 2n = 8x = 80) and S. spontaneum (x = 8, 2n = 5 – 16x = 40 – 128). These accessions have 100 to 130 chromosomes, 80–85% of which are derived from S. officinarum, 10–15% from S. spontaneum, and 5–10% are possible recombinants between the two genomes. The aim of this study was to analyze the repetition of DNA sequences in S. officinarum and S. spontaneum. For this purpose, genomic DNA from S. officinarum was digested with restriction enzymes and the fragments cloned. Sixty-eight fragments, approximately 500 bp, were cloned, sequenced and had their identity analyzed in NCBI, and in the rice, maize, and sorghum genome databases using BLAST. Twelve clones containing partial transposable elements, one single-copy control, one DNA repetitive clone control and two genome controls were analyzed by DNA hybridization on membrane, using genomic probes from S. officinarum and S. spontaneum. The hybridization experiment revealed that six TEs had a similar repetitive DNA pattern in the genomes of S. officinarum and S. spontaneum, while six TEs were more abundant in the genome of S. officinarum. We concluded that the species S. officinarum and S. spontaneum have differential accumulation LTR retrotransposon families, suggesting distinct insertion or modification patterns. PMID:24130449

  8. Widespread and frequent horizontal transfers of transposable elements in plants.

    PubMed

    El Baidouri, Moaine; Carpentier, Marie-Christine; Cooke, Richard; Gao, Dongying; Lasserre, Eric; Llauro, Christel; Mirouze, Marie; Picault, Nathalie; Jackson, Scott A; Panaud, Olivier

    2014-05-01

    Vertical, transgenerational transmission of genetic material occurs through reproduction of living organisms. In addition to vertical inheritance, horizontal gene transfer between reproductively isolated species has recently been shown to be an important, if not dominant, mechanism in the evolution of prokaryotic genomes. In contrast, only a few horizontal transfer (HT) events have been characterized so far in eukaryotes and mainly concern transposable elements (TEs). Whether these are frequent and have a significant impact on genome evolution remains largely unknown. We performed a computational search for highly conserved LTR retrotransposons among 40 sequenced eukaryotic genomes representing the major plant families. We found that 26 genomes (65%) harbor at least one case of horizontal TE transfer (HTT). These transfers concern species as distantly related as palm and grapevine, tomato and bean, or poplar and peach. In total, we identified 32 cases of HTTs, which could translate into more than 2 million among the 13,551 monocot and dicot genera. Moreover, we show that these TEs have remained functional after their transfer, occasionally causing a transpositional burst. This suggests that plants can frequently exchange genetic material through horizontal transfers and that this mechanism may be important in TE-driven genome evolution. PMID:24518071

  9. No Accumulation of Transposable Elements in Asexual Arthropods

    PubMed Central

    Bast, Jens; Schaefer, Ina; Schwander, Tanja; Maraun, Mark; Scheu, Stefan; Kraaijeveld, Ken

    2016-01-01

    Transposable elements (TEs) and other repetitive DNA can accumulate in the absence of recombination, a process contributing to the degeneration of Y-chromosomes and other nonrecombining genome portions. A similar accumulation of repetitive DNA is expected for asexually reproducing species, given their entire genome is effectively nonrecombining. We tested this expectation by comparing the whole-genome TE loads of five asexual arthropod lineages and their sexual relatives, including asexual and sexual lineages of crustaceans (Daphnia water fleas), insects (Leptopilina wasps), and mites (Oribatida). Surprisingly, there was no evidence for increased TE load in genomes of asexual as compared to sexual lineages, neither for all classes of repetitive elements combined nor for specific TE families. Our study therefore suggests that nonrecombining genomes do not accumulate TEs like nonrecombining genomic regions of sexual lineages. Even if a slight but undetected increase of TEs were caused by asexual reproduction, it appears to be negligible compared to variance between species caused by processes unrelated to reproductive mode. It remains to be determined if molecular mechanisms underlying genome regulation in asexuals hamper TE activity. Alternatively, the differences in TE dynamics between nonrecombining genomes in asexual lineages versus nonrecombining genome portions in sexual species might stem from selection for benign TEs in asexual lineages because of the lack of genetic conflict between TEs and their hosts and/or because asexual lineages may only arise from sexual ancestors with particularly low TE loads. PMID:26560353

  10. A Hyperactive Transposase of the Maize Transposable Element Activator (Ac)

    PubMed Central

    Lazarow, Katina; Du, My-Linh; Weimer, Ruth; Kunze, Reinhard

    2012-01-01

    Activator/Dissociation (Ac/Ds) transposable elements from maize are widely used as insertional mutagenesis and gene isolation tools in plants and more recently also in medaka and zebrafish. They are particularly valuable for plant species that are transformation-recalcitrant and have long generation cycles or large genomes with low gene densities. Ac/Ds transposition frequencies vary widely, however, and in some species they are too low for large-scale mutagenesis. We discovered a hyperactive Ac transposase derivative, AcTPase4x, that catalyzes in the yeast Saccharomyces cerevisiae 100-fold more frequent Ds excisions than the wild-type transposase, whereas the reintegration frequency of excised Ds elements is unchanged (57%). Comparable to the wild-type transposase in plants, AcTPase4x catalyzes Ds insertion preferentially into coding regions and to genetically linked sites, but the mutant protein apparently has lost the weak bias of the wild-type protein for insertion sites with elevated guanine–cytosine content and nonrandom protein-DNA twist. AcTPase4x exhibits hyperactivity also in Arabidopsis thaliana where it effects a more than sixfold increase in Ds excision relative to wild-type AcTPase and thus may be useful to facilitate Ac/Ds-based insertion mutagenesis approaches. PMID:22562933

  11. Real-time transposable element activity in individual live cells.

    PubMed

    Kim, Neil H; Lee, Gloria; Sherer, Nicholas A; Martini, K Michael; Goldenfeld, Nigel; Kuhlman, Thomas E

    2016-06-28

    The excision and reintegration of transposable elements (TEs) restructure their host genomes, generating cellular diversity involved in evolution, development, and the etiology of human diseases. Our current knowledge of TE behavior primarily results from bulk techniques that generate time and cell ensemble averages, but cannot capture cell-to-cell variation or local environmental and temporal variability. We have developed an experimental system based on the bacterial TE IS608 that uses fluorescent reporters to directly observe single TE excision events in individual cells in real time. We find that TE activity depends upon the TE's orientation in the genome and the amount of transposase protein in the cell. We also find that TE activity is highly variable throughout the lifetime of the cell. Upon entering stationary phase, TE activity increases in cells hereditarily predisposed to TE activity. These direct observations demonstrate that real-time live-cell imaging of evolution at the molecular and individual event level is a powerful tool for the exploration of genome plasticity in stressed cells. PMID:27298350

  12. Transposable element insertions have strongly affected human evolution

    PubMed Central

    Britten, Roy J.

    2010-01-01

    Comparison of a full collection of the transposable element (TE) sequences of vertebrates with genome sequences shows that the human genome makes 655 perfect full-length matches. The cause is that the human genome contains many active TEs that have caused TE inserts in relatively recent times. These TE inserts in the human genome are several types of young Alus (AluYa5, AluYb8, AluYc1, etc.). Work in many laboratories has shown that such inserts have many effects including changes in gene expression, increases in recombination, and unequal crossover. The time of these very effective changes in the human lineage genome extends back about 4 million years according to these data and very likely much earlier. Rapid human lineage-specific evolution, including brain size is known to have also occurred in the last few million years. Alu insertions likely underlie rapid human lineage evolution. They are known to have many effects. Examples are listed in which TE sequences have influenced human-specific genes. The proposed model is that the many TE insertions created many potentially effective changes and those selected were responsible for a part of the striking human lineage evolution. The combination of the results of these events that were selected during human lineage evolution was apparently effective in producing a successful and rapidly evolving species. PMID:21041622

  13. Binaural hearing in children using Gaussian enveloped and transposed tones.

    PubMed

    Ehlers, Erica; Kan, Alan; Winn, Matthew B; Stoelb, Corey; Litovsky, Ruth Y

    2016-04-01

    Children who use bilateral cochlear implants (BiCIs) show significantly poorer sound localization skills than their normal hearing (NH) peers. This difference has been attributed, in part, to the fact that cochlear implants (CIs) do not faithfully transmit interaural time differences (ITDs) and interaural level differences (ILDs), which are known to be important cues for sound localization. Interestingly, little is known about binaural sensitivity in NH children, in particular, with stimuli that constrain acoustic cues in a manner representative of CI processing. In order to better understand and evaluate binaural hearing in children with BiCIs, the authors first undertook a study on binaural sensitivity in NH children ages 8-10, and in adults. Experiments evaluated sound discrimination and lateralization using ITD and ILD cues, for stimuli with robust envelope cues, but poor representation of temporal fine structure. Stimuli were spondaic words, Gaussian-enveloped tone pulse trains (100 pulse-per-second), and transposed tones. Results showed that discrimination thresholds in children were adult-like (15-389 μs for ITDs and 0.5-6.0 dB for ILDs). However, lateralization based on the same binaural cues showed higher variability than seen in adults. Results are discussed in the context of factors that may be responsible for poor representation of binaural cues in bilaterally implanted children. PMID:27106319

  14. Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements

    PubMed Central

    Brunet, Tyler D.P.; Doolittle, W. Ford

    2015-01-01

    One of several issues at play in the renewed debate over “junk DNA” is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to “speed evolution” or as an “evolutionary repository” could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs). In many species, not least our own, TEs comprise a large fraction of all nuclear DNA, and whether they individually or collectively contribute to fitness—or are instead junk— is a subject of ongoing contestation. Even if TEs generally owe their origin to selfish selection at the lowest level (that of genomes), their prevalence in extant organisms and the prevalence of extant organisms bearing them must also respond to selection within species (on organismal fitness) and between species (on rates of speciation and extinction). At an even higher level, the persistence of clades may be affected (positively or negatively) by TE carriage. If indeed TEs speed evolution, it is at these higher levels of selection that such a function might best be attributed to them as a class. PMID:26253318

  15. MnTEdb, a collective resource for mulberry transposable elements

    PubMed Central

    Ma, Bi; Li, Tian; Xiang, Zhonghuai; He, Ningjia

    2015-01-01

    Mulberry has been used as an economically important food crop for the domesticated silkworm for thousands of years, resulting in one of the oldest and well-known plant-herbivore interactions. The genome of Morus notabilis has now been sequenced and there is an opportunity to mine the transposable element (TE) data. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the mulberry genome, a specific, comprehensive and user-friendly web-based database, MnTEdb, was constructed. It was built based on a detailed and accurate identification of all TEs in mulberry. A total of 5925 TEs belonging to 13 superfamilies and 1062 families were deposited in this database. MnTEdb enables users to search, browse and download the mulberry TE sequences. Meanwhile, data mining tools, including BLAST, GetORF, HMMER, Sequence Extractor and JBrowse were also integrated into MnTEdb. MnTEdb will assist researchers to efficiently take advantage of our newly annotated TEs, which facilitate their studies in the origin, amplification and evolution of TEs, as well as the comparative analysis among the different species. Database URL: http://morus.swu.edu.cn/mntedb/ PMID:25725060

  16. AT-rich sequences from the arbuscular mycorrhizal fungus Gigaspora rosea exhibit ARS function in the yeast Saccharomyces cerevisiae.

    PubMed

    Bergero, Roberta

    2006-05-01

    Autonomous replicating sequences are DNA elements that trigger DNA replication and are widely used in the development of episomal transformation vectors for fungi. In this paper, a genomic library from the mycorrhizal fungus Gigaspora rosea was constructed in the integrative plasmid YIp5 and screened in the budding yeast Saccharomyces cerevisiae for sequences that act as ARS and trigger plasmid replication. Two genetic elements (GrARS2, GrARS6) promoted high-rates of yeast transformation. Sequence analysis of these elements shows them to be AT-rich (72-80%) and to contain multiple near-matches to the yeast autonomous consensus sequences ACS and EACS. GrARS2 contained a putative miniature inverted-repeat transposable element (MITE) delimited by 28-bp terminal inverted repeats (TIRs). Disruption of this element and removal of one TIR increased plasmid stability several fold. The potential for palindromes to affect DNA replication is discussed. PMID:16504551

  17. Chompy: an infestation of MITE-like repetitive elements in the crocodilian genome.

    PubMed

    Ray, David A; Hedges, Dale J; Herke, Scott W; Fowlkes, Justin D; Barnes, Erin W; LaVie, Daniel K; Goodwin, Lindsey M; Densmore, Llewellyn D; Batzer, Mark A

    2005-12-01

    Interspersed repeats are a major component of most eukaryotic genomes and have an impact on genome size and stability, but the repetitive element landscape of crocodilian genomes has not yet been fully investigated. In this report, we provide the first detailed characterization of an interspersed repeat element in any crocodilian genome. Chompy is a putative miniature inverted-repeat transposable element (MITE) family initially recovered from the genome of Alligator mississippiensis (American alligator) but also present in the genomes of Crocodylus moreletii (Morelet's crocodile) and Gavialis gangeticus (Indian gharial). The element has all of the hallmarks of MITEs including terminal inverted repeats, possible target site duplications, and a tendency to form secondary structures. We estimate the copy number in the alligator genome to be approximately 46,000 copies. As a result of their size and unique properties, Chompy elements may provide a useful source of genomic variation for crocodilian comparative genomics. PMID:16183215

  18. Visual thread quality for precision miniature mechanisms

    SciTech Connect

    Gillespie, L.K.

    1981-04-01

    Threaded features have eight visual appearance factors which can affect their function in precision miniature mechanisms. The Bendix practice in deburring, finishing, and accepting these conditions on miniature threads is described as is their impact in assemblies of precision miniature electromechanical assemblies.

  19. Horizontal Transfer and Evolution of Prokaryote Transposable Elements in Eukaryotes

    PubMed Central

    Gilbert, Clément; Cordaux, Richard

    2013-01-01

    Horizontal transfer (HT) of transposable elements (TEs) plays a key role in prokaryotic evolution, and mounting evidence suggests that it has also had an important impact on eukaryotic evolution. Although many prokaryote-to-prokaryote and eukaryote-to-eukaryote HTs of TEs have been characterized, only few cases have been reported between prokaryotes and eukaryotes. Here, we carried out a comprehensive search for all major groups of prokaryotic insertion sequences (ISs) in 430 eukaryote genomes. We uncovered a total of 80 sequences, all deriving from the IS607 family, integrated in the genomes of 14 eukaryote species belonging to four distinct phyla (Amoebozoa, Ascomycetes, Basidiomycetes, and Stramenopiles). Given that eukaryote IS607-like sequences are most closely related to cyanobacterial IS607 and that their phylogeny is incongruent with that of their hosts, we conclude that the presence of IS607-like sequences in eukaryotic genomes is the result of several HT events. Selection analyses further suggest that our ability to detect these prokaryote TEs today in eukaryotes is because HT of these sequences occurred recently and/or some IS607 elements were domesticated after HT, giving rise to new eukaryote genes. Supporting the recent age of some of these HTs, we uncovered intact full-length, potentially active IS607 copies in the amoeba Acanthamoeba castellani. Overall, our study shows that prokaryote-to-eukaryote HT of TEs occurred at relatively low frequency during recent eukaryote evolution and it sets IS607 as the most widespread TE (being present in prokaryotes, eukaryotes, and viruses). PMID:23563966

  20. Transposable Elements: Powerful Contributors to Angiosperm Evolution and Diversity

    PubMed Central

    Oliver, Keith R.; McComb, Jen A.; Greene, Wayne K.

    2013-01-01

    Transposable elements (TEs) are a dominant feature of most flowering plant genomes. Together with other accepted facilitators of evolution, accumulating data indicate that TEs can explain much about their rapid evolution and diversification. Genome size in angiosperms is highly correlated with TE content and the overwhelming bulk (>80%) of large genomes can be composed of TEs. Among retro-TEs, long terminal repeats (LTRs) are abundant, whereas DNA-TEs, which are often less abundant than retro-TEs, are more active. Much adaptive or evolutionary potential in angiosperms is due to the activity of TEs (active TE-Thrust), resulting in an extraordinary array of genetic changes, including gene modifications, duplications, altered expression patterns, and exaptation to create novel genes, with occasional gene disruption. TEs implicated in the earliest origins of the angiosperms include the exapted Mustang, Sleeper, and Fhy3/Far1 gene families. Passive TE-Thrust can create a high degree of adaptive or evolutionary potential by engendering ectopic recombination events resulting in deletions, duplications, and karyotypic changes. TE activity can also alter epigenetic patterning, including that governing endosperm development, thus promoting reproductive isolation. Continuing evolution of long-lived resprouter angiosperms, together with genetic variation in their multiple meristems, indicates that TEs can facilitate somatic evolution in addition to germ line evolution. Critical to their success, angiosperms have a high frequency of polyploidy and hybridization, with resultant increased TE activity and introgression, and beneficial gene duplication. Together with traditional explanations, the enhanced genomic plasticity facilitated by TE-Thrust, suggests a more complete and satisfactory explanation for Darwin’s “abominable mystery”: the spectacular success of the angiosperms. PMID:24065734

  1. Epigenetic regulation of transposable element derived human gene promoters.

    PubMed

    Huda, Ahsan; Bowen, Nathan J; Conley, Andrew B; Jordan, I King

    2011-04-01

    It was previously thought that epigenetic histone modifications of mammalian transposable elements (TEs) serve primarily to defend the genome against deleterious effects associated with their activity. However, we recently showed that, genome-wide, human TEs can also be epigenetically modified in a manner consistent with their ability to regulate host genes. Here, we explore the ability of TE sequences to epigenetically regulate individual human genes by focusing on the histone modifications of promoter sequences derived from TEs. We found 1520 human genes that initiate transcription from within TE-derived promoter sequences. We evaluated the distributions of eight histone modifications across these TE-promoters, within and between the GM12878 and K562 cell lines, and related their modification status with the cell-type specific expression patterns of the genes that they regulate. TE-derived promoters are significantly enriched for active histone modifications, and depleted for repressive modifications, relative to the genomic background. Active histone modifications of TE-promoters peak at transcription start sites and are positively correlated with increasing expression within cell lines. Furthermore, differential modification of TE-derived promoters between cell lines is significantly correlated with differential gene expression. LTR-retrotransposon derived promoters in particular play a prominent role in mediating cell-type specific gene regulation, and a number of these LTR-promoter genes are implicated in lineage-specific cellular functions. The regulation of human genes mediated by histone modifications targeted to TE-derived promoters is consistent with the ability of TEs to contribute to the epigenomic landscape in a way that provides functional utility to the host genome. PMID:21215797

  2. Prediction of transposable element derived enhancers using chromatin modification profiles.

    PubMed

    Huda, Ahsan; Tyagi, Eishita; Mariño-Ramírez, Leonardo; Bowen, Nathan J; Jjingo, Daudi; Jordan, I King

    2011-01-01

    Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for several different histone modifications. We modelled these enhancer chromatin profiles in the human genome and used them to guide the search for novel enhancers derived from transposable element (TE) sequences. To do this, a computational approach was taken to analyze the genome-wide histone modification landscape characterized by the ENCODE project in two human hematopoietic cell types, GM12878 and K562. We predicted the locations of 2,107 and 1,448 TE-derived enhancers in the GM12878 and K562 cell lines respectively. A vast majority of these putative enhancers are unique to each cell line; only 3.5% of the TE-derived enhancers are shared between the two. We evaluated the functional effect of TE-derived enhancers by associating them with the cell-type specific expression of nearby genes, and found that the number of TE-derived enhancers is strongly positively correlated with the expression of nearby genes in each cell line. Furthermore, genes that are differentially expressed between the two cell lines also possess a divergent number of TE-derived enhancers in their vicinity. As such, genes that are up-regulated in the GM12878 cell line and down-regulated in K562 have significantly more TE-derived enhancers in their vicinity in the GM12878 cell line and vice versa. These data indicate that human TE-derived sequences are likely to be involved in regulating cell-type specific gene expression on a broad scale and suggest that the enhancer activity of TE-derived sequences is mediated by epigenetic regulatory mechanisms. PMID:22087331

  3. Distributions of transposable elements reveal hazardous zones in mammalian introns.

    PubMed

    Zhang, Ying; Romanish, Mark T; Mager, Dixie L

    2011-05-01

    Comprising nearly half of the human and mouse genomes, transposable elements (TEs) are found within most genes. Although the vast majority of TEs in introns are fixed in the species and presumably exert no significant effects on the enclosing gene, some markedly perturb transcription and result in disease or a mutated phenotype. Factors determining the likelihood that an intronic TE will affect transcription are not clear. In this study, we examined intronic TE distributions in both human and mouse and found several factors that likely contribute to whether a particular TE can influence gene transcription. Specifically, we observed that TEs near exons are greatly underrepresented compared to random distributions, but the size of these "underrepresentation zones" differs between TE classes. Compared to elsewhere in introns, TEs within these zones are shorter on average and show stronger orientation biases. Moreover, TEs in extremely close proximity (<20 bp) to exons show a strong bias to be near splice-donor sites. Interestingly, disease-causing intronic TE insertions show the opposite distributional trends, and by examining expressed sequence tag (EST) databases, we found that the proportion of TEs contributing to chimeric TE-gene transcripts is significantly higher within their underrepresentation zones. In addition, an analysis of predicted splice sites within human long terminal repeat (LTR) elements showed a significantly lower total number and weaker strength for intronic LTRs near exons. Based on these factors, we selectively examined a list of polymorphic mouse LTR elements in introns and showed clear evidence of transcriptional disruption by LTR element insertions in the Trpc6 and Kcnh6 genes. Taken together, these studies lend insight into the potential selective forces that have shaped intronic TE distributions and enable identification of TEs most likely to exert transcriptional effects on genes. PMID:21573203

  4. Molecular Epidemiology and Genetic Characteristics of Various blaPER Genes in Shanghai, China.

    PubMed

    Xie, Lianyan; Wu, Jun; Zhang, Fangfang; Han, Lizhong; Guo, Xiaokui; Ni, Yuxing; Sun, Jingyong

    2016-06-01

    We describe the genetic characteristics and possible transmission mechanism of blaPER in 25 clinical Gram-negative bacilli in Shanghai. blaPER, including blaPER-1, blaPER-3, and blaPER-4, was located chromosomally or in different plasmids. Tn1213 harboring blaPER-1 was first identified in two Proteus mirabilis isolates in China. The other blaPER variants were preceded by an ISCR1 element inside the complex class 1 integron associated with IS26, Tn21, Tn1696, and a miniature inverted-repeat transposable element. PMID:27067315

  5. Miniature x-ray source

    DOEpatents

    Trebes, James E.; Stone, Gary F.; Bell, Perry M.; Robinson, Ronald B.; Chornenky, Victor I.

    2002-01-01

    A miniature x-ray source capable of producing broad spectrum x-ray emission over a wide range of x-ray energies. The miniature x-ray source comprises a compact vacuum tube assembly containing a cathode, an anode, a high voltage feedthru for delivering high voltage to the anode, a getter for maintaining high vacuum, a connection for an initial vacuum pump down and crimp-off, and a high voltage connection for attaching a compact high voltage cable to the high voltage feedthru. At least a portion of the vacuum tube wall is highly x-ray transparent and made, for example, from boron nitride. The compact size and potential for remote operation allows the x-ray source, for example, to be placed adjacent to a material sample undergoing analysis or in proximity to the region to be treated for medical applications.

  6. Miniature x-ray source

    DOEpatents

    Trebes, James E.; Bell, Perry M.; Robinson, Ronald B.

    2000-01-01

    A miniature x-ray source utilizing a hot filament cathode. The source has a millimeter scale size and is capable of producing broad spectrum x-ray emission over a wide range of x-ray energies. The miniature source consists of a compact vacuum tube assembly containing the hot filament cathode, an anode, a high voltage feedthru for delivering high voltage to the cathode, a getter for maintaining high vacuum, a connector for initial vacuum pump down and crimp-off, and a high voltage connection for attaching a compact high voltage cable to the high voltage feedthru. At least a portion of the vacuum tube wall is fabricated from highly x-ray transparent materials, such as sapphire, diamond, or boron nitride.

  7. Handheld interface for miniature sensors

    NASA Astrophysics Data System (ADS)

    Kedia, Sunny; Samson, Scott A.; Farmer, Andrew; Smith, Matthew C.; Fries, David; Bhansali, Shekhar

    2005-02-01

    Miniaturization of laboratory sensors has been enabled by continued evolution of technology. Field portable systems are often desired, because they reduce sample handling, provide rapid feedback capability, and enhance convenience. Fieldable sensor systems should include a method for initiating the analysis, storing and displaying the results, while consuming minimal power and being compact and portable. Low cost will allow widespread usage of these systems. In this paper, we discuss a reconfigurable Personal Data Assistant (PDA) based control and data collection system for use with miniature sensors. The system is based on the Handspring visor PDA and a custom designed motherboard, which connects directly to the PDA microprocessor. The PDA provides a convenient and low cost graphical user interface, moderate processing capability, and integrated battery power. The low power motherboard provides the voltage levels, data collection, and input/output (I/O) capabilities required by many MEMS and miniature sensors. These capabilities are relayed to connectors, where an application specific daughterboard is attached. In this paper, two applications are demonstrated. First, a handheld nucleic acid sequence-based amplification (NASBA) detection sensor consisting of a heated and optical fluorescence detection system is discussed. Second, an electrostatically actuated MEMS micro mirror controller is realized.

  8. Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum violaceum

    PubMed Central

    Hood, Michael E.; Katawczik, Melanie; Giraud, Tatiana

    2005-01-01

    Repeat-induced point mutation (RIP) is a genome defense in fungi that hypermutates repetitive DNA and is suggested to limit the accumulation of transposable elements. The genome of Microbotryum violaceum has a high density of transposable elements compared to other fungi, but there is also evidence of RIP activity. This is the first report of RIP in a basidiomycete and was obtained by sequencing multiple copies of the integrase gene of a copia-type transposable element and the helicase gene of a Helitron-type element. In M. violaceum, the targets for RIP mutations are the cytosine residues of TCG trinucleotide combinations. Although RIP is a linkage-dependent process that tends to increase the variation among repetitive sequences, a chromosome-specific substructuring was observed in the transposable element population. The observed chromosome-specific patterns are not consistent with RIP, but rather suggest an effect of gene conversion, which is also a linkage-dependent process but results in a homogenization of repeated sequences. Particular sequences were found more widely distributed within the genome than expected by chance and may reflect the recently active variants. Therefore, sequence variation of transposable elements in M. violaceum appears to be driven by selection for transposition ability in combination with the context-specific forces of the RIP and gene conversion.

  9. Eye Movements When Reading Transposed Text: The Importance of Word-Beginning Letters

    PubMed Central

    White, Sarah J.; Johnson, Rebecca L.; Liversedge, Simon P.; Rayner, Keith

    2009-01-01

    Participants’ eye movements were recorded as they read sentences with words containing transposed adjacent letters. Transpositions were either external (e.g., problme, rpoblem) or internal (e.g., porblem, probelm) and at either the beginning (e.g., rpoblem, porblem) or end (e.g., problme, probelm) of words. The results showed disruption for words with transposed letters compared to the normal baseline condition, and the greatest disruption was observed for word-initial transpositions. In Experiment 1, transpositions within low frequency words led to longer reading times than when letters were transposed within high frequency words. Experiment 2 demonstrated that the position of word-initial letters is most critical even when parafoveal preview of words to the right of fixation is unavailable. The findings have important implications for the roles of different letter positions in word recognition and the effects of parafoveal preview on word recognition processes. PMID:18823209

  10. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution.

    PubMed

    Schaack, Sarah; Gilbert, Clément; Feschotte, Cédric

    2010-09-01

    Horizontal transfer is the passage of genetic material between genomes by means other than parent-to-offspring inheritance. Although the transfer of genes is thought to be crucial in prokaryotic evolution, few instances of horizontal gene transfer have been reported in multicellular eukaryotes; instead, most cases involve transposable elements. With over 200 cases now documented, it is possible to assess the importance of horizontal transfer for the evolution of transposable elements and their host genomes. We review criteria for detecting horizontal transfers and examine recent examples of the phenomenon, shedding light on its mechanistic underpinnings, including the role of host-parasite interactions. We argue that the introduction of transposable elements by horizontal transfer in eukaryotic genomes has been a major force propelling genomic variation and biological innovation. PMID:20591532

  11. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution

    PubMed Central

    Schaack, Sarah; Gilbert, Clément; Feschotte, Cédric

    2010-01-01

    Horizontal transfer is the passage of genetic material between genomes by means other than parent-to-offspring inheritance. Although the transfer of genes is thought to be crucial in prokaryotic evolution, few instances of horizontal gene transfer have been reported in multicellular eukaryotes; instead, most cases involve transposable elements. With over 200 cases now documented, it is possible to assess the importance of horizontal transfer for the evolution of transposable elements and their host genomes. We review criteria for detecting horizontal transfers and examine recent examples of the phenomenon, shedding light on its mechanistic underpinnings, including the role of host-parasite interactions. We argue that the introduction of transposable elements by horizontal transfer in eukaryotic genomes has been a major force propelling genomic variation and biological innovation. PMID:20591532

  12. Miniaturization of flight deflection measurement system

    NASA Technical Reports Server (NTRS)

    Fodale, Robert (Inventor); Hampton, Herbert R. (Inventor)

    1990-01-01

    A flight deflection measurement system is disclosed including a hybrid microchip of a receiver/decoder. The hybrid microchip decoder is mounted piggy back on the miniaturized receiver and forms an integral unit therewith. The flight deflection measurement system employing the miniaturized receiver/decoder can be used in a wind tunnel. In particular, the miniaturized receiver/decoder can be employed in a spin measurement system due to its small size and can retain already established control surface actuation functions.

  13. What do we still need to know about transposable element Ac?

    PubMed

    Starlinger, P

    1993-12-15

    Transposable elements, originally discovered by Barbara McClintock, have been shown to occur in many if not all organisms. Their roles as selfish DNA (probable), as a major agent in evolution (unlikely) and as agents for the response to genomic stress (unclear) are discussed. Among the problems presently addressed are the mechanism of transposition and the regulation of transposition rate. The latter seems to differ in the Ac element of Zea mays compared to other transposable elements. The tendency of Ac transposase to form large aggregates is described, and the possible involvement of these aggregates in the control of the transposition rate is discussed. PMID:8276265

  14. Miniature Autonomous Robotic Vehicle (MARV)

    SciTech Connect

    Feddema, J.T.; Kwok, K.S.; Driessen, B.J.; Spletzer, B.L.; Weber, T.M.

    1996-12-31

    Sandia National Laboratories (SNL) has recently developed a 16 cm{sup 3} (1 in{sup 3}) autonomous robotic vehicle which is capable of tracking a single conducting wire carrying a 96 kHz signal. This vehicle was developed to assess the limiting factors in using commercial technology to build miniature autonomous vehicles. Particular attention was paid to the design of the control system to search out the wire, track it, and recover if the wire was lost. This paper describes the test vehicle and the control analysis. Presented in the paper are the vehicle model, control laws, a stability analysis, simulation studies and experimental results.

  15. Miniature drag-force anemometer

    NASA Technical Reports Server (NTRS)

    Krause, L. N.; Fralick, G. C.

    1981-01-01

    A miniature drag force anemometer is described which is capable of measuring unsteady as well as steady state velocity head and flow direction. It consists of a cantilevered beam with strain gages located at the base of the beam as the force measuring element. The dynamics of the beam are like those of lightly damped second order system with a natural frequency as high as 40 kilohertz depending on beam geometry and material. The anemometer is used in both forward and reversed flow. Anemometer characteristics and several designs are presented along with discussions of several applications.

  16. Personal miniature electrophysiological tape recorder

    NASA Astrophysics Data System (ADS)

    Green, H.

    1981-11-01

    The use of a personal miniature electrophysiological tape recorder to measure the physiological reactions of space flight personnel to space flight stress and weightlessness is described. The Oxford Instruments Medilog recorder, a battery-powered, four-channel cassette tape recorder with 24 hour endurance is carried on the person and will record EKG, EOG, EEG, and timing and event markers. The data will give information about heart rate and morphology changes, and document adaptation to zero gravity on the part of subjects who, unlike highly trained astronauts, are more representative of the normal population than were the subjects of previous space flight studies.

  17. Miniature drag-force anemometer

    NASA Technical Reports Server (NTRS)

    Krause, L. N.; Fralick, G. C.

    1981-01-01

    A miniature drag-force anemometer is described which is capable of measuring unsteady as well as steady-state velocity head and flow direction. It consists of a cantilevered beam with strain gages located at the base of the beam as the force measuring element. The dynamics of the beam are like those of a lightly damped second-order system with a natural frequency as high as 40 kilohertz depending on beam geometry and material. The anemometer can be used in both forward and reversed flow. Anemometer characteristics and several designs are presented along with discussions of several applications.

  18. Personal miniature electrophysiological tape recorder

    NASA Technical Reports Server (NTRS)

    Green, H.

    1981-01-01

    The use of a personal miniature electrophysiological tape recorder to measure the physiological reactions of space flight personnel to space flight stress and weightlessness is described. The Oxford Instruments Medilog recorder, a battery-powered, four-channel cassette tape recorder with 24 hour endurance is carried on the person and will record EKG, EOG, EEG, and timing and event markers. The data will give information about heart rate and morphology changes, and document adaptation to zero gravity on the part of subjects who, unlike highly trained astronauts, are more representative of the normal population than were the subjects of previous space flight studies.

  19. A miniature optical breathing sensor

    PubMed Central

    Mathew, Jinesh; Semenova, Yuliya; Farrell, Gerald

    2012-01-01

    We demonstrate a novel miniature optical breathing sensor based on an Agarose infiltrated photonic crystal fiber interferometer. The sensor detects the variation in relative humidity that occurs between inhaled and exhaled breath. The sensor interrogation system can determine the breathing pattern in real time and can also predict the breathing rate and the breathing status during respiration. The sensor is suitable for monitoring patients during a magnetic resonance imaging scan where use of sedatives and anesthetics necessitates breathing monitoring; electronic sensors are not suitable in such an environment and a visual observation of the patient's respiratory efforts is often difficult. PMID:23243581

  20. A miniature remote deadweight calibrator

    NASA Astrophysics Data System (ADS)

    Supplee, Frank H., Jr.; Tcheng, Ping

    A miniature, computer-controlled, deadweight calibrator was developed to remotely calibrate a force transducer mounted in a cryogenic chamber. This simple mechanism allows automatic loading and unloading of deadweights placed onto a skin friction balance during calibrations. Equipment for the calibrator includes a specially designed set of five interlocking 200-milligram weights, a motorized lifting platform, and a controller box taking commands from a microcomputer on an IEEE interface. The computer is also used to record and reduce the calibration data and control other calibration parameters. The full-scale load for this device is 1,000 milligrams; however, the concept can be extended to accommodate other calibration ranges.

  1. Orthographic Reading Deficits in Dyslexic Japanese Children: Examining the Transposed-Letter Effect in the Color-Word Stroop Paradigm.

    PubMed

    Ogawa, Shino; Shibasaki, Masahiro; Isomura, Tomoko; Masataka, Nobuo

    2016-01-01

    In orthographic reading, the transposed-letter effect (TLE) is the perception of a transposed-letter position word such as "cholocate" as the correct word "chocolate." Although previous studies on dyslexic children using alphabetic languages have reported such orthographic reading deficits, the extent of orthographic reading impairment in dyslexic Japanese children has remained unknown. This study examined the TLE in dyslexic Japanese children using the color-word Stroop paradigm comprising congruent and incongruent Japanese hiragana words with correct and transposed-letter positions. We found that typically developed children exhibited Stroop effects in Japanese hiragana words with both correct and transposed-letter positions, thus indicating the presence of TLE. In contrast, dyslexic children indicated Stroop effects in correct letter positions in Japanese words but not in transposed, which indicated an absence of the TLE. These results suggest that dyslexic Japanese children, similar to dyslexic children using alphabetic languages, may also have a problem with orthographic reading. PMID:27303331

  2. 33 CFR 13.01-40 - Miniature medals and bars.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... GENERAL DECORATIONS, MEDALS, RIBBONS AND SIMILAR DEVICES Gold and Silver Lifesaving Medals, Bars, and Miniatures § 13.01-40 Miniature medals and bars. (a) Miniature Gold and Silver Lifesaving Medals and bars...

  3. 33 CFR 13.01-40 - Miniature medals and bars.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... GENERAL DECORATIONS, MEDALS, RIBBONS AND SIMILAR DEVICES Gold and Silver Lifesaving Medals, Bars, and Miniatures § 13.01-40 Miniature medals and bars. (a) Miniature Gold and Silver Lifesaving Medals and bars...

  4. 33 CFR 13.01-40 - Miniature medals and bars.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... GENERAL DECORATIONS, MEDALS, RIBBONS AND SIMILAR DEVICES Gold and Silver Lifesaving Medals, Bars, and Miniatures § 13.01-40 Miniature medals and bars. (a) Miniature Gold and Silver Lifesaving Medals and bars...

  5. 33 CFR 13.01-40 - Miniature medals and bars.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... GENERAL DECORATIONS, MEDALS, RIBBONS AND SIMILAR DEVICES Gold and Silver Lifesaving Medals, Bars, and Miniatures § 13.01-40 Miniature medals and bars. (a) Miniature Gold and Silver Lifesaving Medals and bars...

  6. 33 CFR 13.01-40 - Miniature medals and bars.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... GENERAL DECORATIONS, MEDALS, RIBBONS AND SIMILAR DEVICES Gold and Silver Lifesaving Medals, Bars, and Miniatures § 13.01-40 Miniature medals and bars. (a) Miniature Gold and Silver Lifesaving Medals and bars...

  7. Miniature Telerobots in Space Applications

    NASA Technical Reports Server (NTRS)

    Venema, S. C.; Hannaford, B.

    1995-01-01

    Ground controlled telerobots can be used to reduce astronaut workload while retaining much of the human capabilities of planning, execution, and error recovery for specific tasks. Miniature robots can be used for delicate and time consuming tasks such as biological experiment servicing without incurring the significant mass and power penalties associated with larger robot systems. However, questions remain regarding the technical and economic effectiveness of such mini-telerobotic systems. This paper address some of these open issues and the details of two projects which will provide some of the needed answers. The Microtrex project is a joint University of Washington/NASA project which plans on flying a miniature robot as a Space Shuttle experiment to evaluate the effects of microgravity on ground-controlled manipulation while subject to variable time-delay communications. A related project involving the University of Washington and Boeing Defense and Space will evaluate the effectiveness f using a minirobot to service biological experiments in a space station experiment 'glove-box' rack mock-up, again while subject to realistic communications constraints.

  8. Miniature multimode monolithic flextensional transducers.

    PubMed

    Hladky-Hennion, Anne-Christine; Uzgur, A Erman; Markley, Douglas C; Safari, Ahmad; Cochran, Joe K; Newnham, Robert E

    2007-10-01

    Traditional flextensional transducers classified in seven groups based on their designs have been used extensively in 1-100 kHz range for mine hunting, fish finding, oil explorations, and biomedical applications. In this study, a new family of small, low cost underwater, and biomedical transducers has been developed. After the fabrication of transducers, finite-elements analysis (FEA) was used extensively in order to optimize these miniature versions of high-power, low-frequency flextensional transducer designs to achieve broad bandwidth for both transmitting and receiving, engineered vibration modes, and optimized acoustic directivity patterns. Transducer topologies with various shapes, cross sections, and symmetries can be fabricated through high-volume, low-cost ceramic and metal extrusion processes. Miniaturized transducers posses resonance frequencies in the range of above 1 MHz to below 10 kHz. Symmetry and design of the transducer, polling patterns, driving and receiving electrode geometries, and driving conditions have a strong effect on the vibration modes, resonance frequencies, and radiation patterns. This paper is devoted to small, multimode flextensional transducers with active shells, which combine the advantages of small size and low-cost manufacturing with control of the shape of the acoustic radiation/receive pattern. The performance of the transducers is emphasized. PMID:18019236

  9. Lightweight, Miniature Inertial Measurement System

    NASA Technical Reports Server (NTRS)

    Tang, Liang; Crassidis, Agamemnon

    2012-01-01

    A miniature, lighter-weight, and highly accurate inertial navigation system (INS) is coupled with GPS receivers to provide stable and highly accurate positioning, attitude, and inertial measurements while being subjected to highly dynamic maneuvers. In contrast to conventional methods that use extensive, groundbased, real-time tracking and control units that are expensive, large, and require excessive amounts of power to operate, this method focuses on the development of an estimator that makes use of a low-cost, miniature accelerometer array fused with traditional measurement systems and GPS. Through the use of a position tracking estimation algorithm, onboard accelerometers are numerically integrated and transformed using attitude information to obtain an estimate of position in the inertial frame. Position and velocity estimates are subject to drift due to accelerometer sensor bias and high vibration over time, and so require the integration with GPS information using a Kalman filter to provide highly accurate and reliable inertial tracking estimations. The method implemented here uses the local gravitational field vector. Upon determining the location of the local gravitational field vector relative to two consecutive sensors, the orientation of the device may then be estimated, and the attitude determined. Improved attitude estimates further enhance the inertial position estimates. The device can be powered either by batteries, or by the power source onboard its target platforms. A DB9 port provides the I/O to external systems, and the device is designed to be mounted in a waterproof case for all-weather conditions.

  10. Miniaturized neural interfaces and implants

    NASA Astrophysics Data System (ADS)

    Stieglitz, Thomas; Boretius, Tim; Ordonez, Juan; Hassler, Christina; Henle, Christian; Meier, Wolfgang; Plachta, Dennis T. T.; Schuettler, Martin

    2012-03-01

    Neural prostheses are technical systems that interface nerves to treat the symptoms of neurological diseases and to restore sensory of motor functions of the body. Success stories have been written with the cochlear implant to restore hearing, with spinal cord stimulators to treat chronic pain as well as urge incontinence, and with deep brain stimulators in patients suffering from Parkinson's disease. Highly complex neural implants for novel medical applications can be miniaturized either by means of precision mechanics technologies using known and established materials for electrodes, cables, and hermetic packages or by applying microsystems technologies. Examples for both approaches will be introduced and discussed. Electrode arrays for recording of electrocorticograms during presurgical epilepsy diagnosis have been manufactured using approved materials and a marking laser to achieve an integration density that is adequate in the context of brain machine interfaces, e.g. on the motor cortex. Microtechnologies have to be used for further miniaturization to develop polymer-based flexible and light weighted electrode arrays to interface the peripheral and central nervous system. Polyimide as substrate and insulation material will be discussed as well as several application examples for nerve interfaces like cuffs, filament like electrodes and large arrays for subdural implantation.

  11. Environmental study of miniature slip rings

    NASA Technical Reports Server (NTRS)

    Radnik, J. L.

    1967-01-01

    Investigation studied the long term operation of miniature slip ring assembles in high vacuum of space and included the influence of ring, brush, and insulator materials on electrical noise and mechanical wear. Results show that soft metal vapor plating and niobium diselenide miniature slip rings are beneficial.

  12. Miniature reaction chamber and devices incorporating same

    DOEpatents

    Mathies, Richard A.; Woolley, Adam T.

    2000-10-17

    The present invention generally relates to miniaturized devices for carrying out and controlling chemical reactions and analyses. In particular, the present invention provides devices which have miniature temperature controlled reaction chambers for carrying out a variety of synthetic and diagnostic applications, such as PCR amplification, nucleic acid hybridization, chemical labeling, nucleic acid fragmentation and the like.

  13. Anthrax vaccine associated deaths in miniature horses.

    PubMed

    Wobeser, Bruce K

    2015-04-01

    During a widespread anthrax outbreak in Canada, miniature horses were vaccinated using a live spore anthrax vaccine. Several of these horses died from an apparent immune-mediated vasculitis temporally associated with this vaccination. During the course of the outbreak, other miniature horses from different regions with a similar vaccination history, clinical signs, and necropsy findings were found. PMID:25829553

  14. RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transposable elements (TE) exist in the genomes of nearly all eukaryotes. TE mobilization through “cut-and-paste” or “copy-and-paste” mechanisms causes their insertions into other repetitive sequences, gene loci, and other DNA. An insertion of a TE produces a junction consisting of the TE-end sequen...

  15. Construction of three-qubit genuine entanglement with bipartite positive partial transposes

    NASA Astrophysics Data System (ADS)

    Ha, Kil-Chan; Kye, Seung-Hyeok

    2016-03-01

    We construct triqubit genuinely entangled states which have positive partial transposes (PPTs) with respect to the bipartition of systems. These examples disprove a conjecture [Novo, Moroder, and Gühne, Phys. Rev A 88, 012305 (2013), 10.1103/PhysRevA.88.012305] which claims that PPT mixtures are necessary and sufficient for the biseparability of three qubits.

  16. Transposed Letter Priming with Horizontal and Vertical Text in Japanese and English Readers

    ERIC Educational Resources Information Center

    Witzel, Naoko; Qiao, Xiaomei; Forster, Kenneth

    2011-01-01

    It is well established that in masked priming, a target word (e.g., "JUDGE") is primed more effectively by a transposed letter (TL) prime (e.g., "jugde") than by an orthographic control prime (e.g., "junpe"). This is inconsistent with the slot coding schemes used in many models of visual word recognition. Several alternative coding schemes have…

  17. Identification and characterization of the first active endogenous transposable element in soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In soybean [Glycine max (L.) Merr.], W4 is one of the loci that control anthocyanin biosynthesis in flowers and hypocotyls. A putative transposable element was suggested to reside within or adjacent to this locus in the mutable T322 line resulting in the w4-m allele. We have shown that the W4 locu...

  18. Preview Effects of Plausibility and Character Order in Reading Chinese Transposed Words: Evidence from Eye Movements

    ERIC Educational Resources Information Center

    Yang, Jinmian

    2013-01-01

    The current paper examined the role of plausibility information in the parafovea for Chinese readers by using two-character transposed words (in which the order of the component characters is reversed but are still words). In two eye-tracking experiments, readers received a preview of a target word that was (1) identical to the target word, (2) a…

  19. TEnest: Automated Chronological Annotation and Visualization of Nested Plant Transposable Elements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Organisms with a high density of transposable elements (TEs) exhibit nesting, with subsequent repeats found inside previously inserted elements. Nesting splits the sequence structure of TEs and makes annotation of repetitive areas challenging. We present TEnest, a repeat identification and display...

  20. Parafoveal Processing of Transposed-Letter Words and Nonwords: Evidence against Parafoveal Lexical Activation

    ERIC Educational Resources Information Center

    Johnson, Rebecca L.; Dunne, Maxine D.

    2012-01-01

    The current experiments explored the parafoveal processing of transposed-letter (TL) neighbors by using an eye-movement-contingent boundary change paradigm. In Experiment 1 readers received a parafoveal preview of a target word (e.g., "calm") that was either (1) identical to the target word ("calm"), (2) a TL-neighbor ("clam"), or (3) a…

  1. The coelacanth: Can a “living fossil” have active transposable elements in its genome?

    PubMed Central

    Naville, Magali; Chalopin, Domitille; Casane, Didier; Laurenti, Patrick; Volff, Jean-Nicolas

    2015-01-01

    The coelacanth has long been regarded as a “living fossil,” with extant specimens looking very similar to fossils dating back to the Cretaceous period. The hypothesis of a slowly or even not evolving genome has been proposed to account for this apparent morphological stasis. While this assumption seems to be sustained by different evolutionary analyses on protein-coding genes, recent studies on transposable elements have provided more conflicting results. Indeed, the coelacanth genome contains many transposable elements and has been shaped by several major bursts of transposition during evolution. In addition, comparison of orthologous genomic regions from the genomes of the 2 extant coelacanth species L. chalumnae and L. menadoensis revealed multiple species-specific insertions, indicating transposable element recent activity and contribution to post-speciation genome divergence. These observations, which do not support the genome stasis hypothesis, challenge either the impact of transposable elements on organismal evolution or the status of the coelacanth as a “living fossil.” Closer inspection of fossil and molecular data indicate that, even if coelacanths might evolve more slowly than some other lineages due to demographic and/or ecological factors, this variation is still in the range of a “non-fossil” vertebrate species. PMID:26442185

  2. TEnest 2.0: Computational annotation and visualization of nested transposable elements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grass genomes are highly repetitive, for example, Oryza sativa (rice) contains 35% repeat sequences, Zea mays (maize) comprise 75%, and Triticum aestivum (wheat) includes approximately 80%. Most of these repeats occur as abundant transposable elements (TE), which present unique challenges to sequen...

  3. Distributional Analysis of the Transposed-Letter Neighborhood Effect on Naming Latency

    ERIC Educational Resources Information Center

    Johnson, Rebecca L.; Staub, Adrian; Fleri, Amanda M.

    2012-01-01

    Printed words that have a transposed-letter (TL) neighbor (e.g., angel has the TL neighbor angle) have been shown to be more difficult to process, in a range of paradigms, than words that do not have a TL neighbor. However, eye movement evidence suggests that this processing difficulty may occur on only a subset of trials. To investigate this…

  4. The hobo transposable element has transposase-dependent and -independent excision activity in drosophilid species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mobility of the hobo transposable element was determined for several strains of Drosophila melanogaster and several Drosophila species. Mobility was assessed by use of an in vivo transient assay in the soma of developing embryos, which monitored hobo excision from injected indicator plasmids. Excisi...

  5. Rapid inactivation of the maize transposable element En/Spm in Medicago truncatula.

    PubMed

    d'Erfurth, I; Cosson, V; Eschstruth, A; Rippa, S; Messinese, E; Durand, P; Trinh, H; Kondorosi, A; Ratet, P

    2003-09-01

    Transposable elements have been widely used as mutagens in many organisms. Among them, the maize transposable element En/Spm has been shown to transpose efficiently in several plant species including the model plant Arabidopsis, where it has been used for large-scale mutagenesis. To determine whether we could use this transposon as a mutagen in the model legume plant Medicago truncatula, we tested the activity of the autonomous element, as well as two defective elements, in this plant, and in Arabidopsis as a positive control. In agreement with previous reports, we observed efficient excision of the autonomous En/Spm element in A. thaliana. This element was also active in M. truncatula, but the transposition activity was low and was apparently restricted to the tissue culture step necessary for the production of transgenic plants. The activity of one of the defective transposable elements, dSpm, was very low in A. thaliana and even lower in M. truncatula. The use of different sources of transposases suggested that this defect in transposition was associated with the dSpm element itself. Transposition of the other defective element, I6078, was also detected in M. truncatula, but, as observed with the autonomous element, transposition events were very rare and occurred during tissue culture. These results suggest that the En/Spm element is rapidly inactivated in the regenerated plants and their progeny, and therefore is not suitable for routine insertion mutagenesis in M. truncatula. PMID:12905070

  6. The Quiet Clam Is Quite Calm: Transposed-Letter Neighborhood Effects on Eye Movements during Reading

    ERIC Educational Resources Information Center

    Johnson, Rebecca L.

    2009-01-01

    In responses time tasks, inhibitory neighborhood effects have been found for word pairs that differ in a transposition of two adjacent letters (e.g., "clam/calm"). Here, the author describes two eye-tracking experiments conducted to explore transposed-letter (TL) neighborhood effects within the context of normal silent reading. In Experiment 1,…

  7. Excision of the piggyBac transposable element in maize cells is a precise event

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The piggyBac transposable element (TE) from the moth Trichoplusia ni encodes a ‘cut and paste’ DNA transposase that has been used to transform a number of insects, as well as planaria, mammalian cells, and mice. The wild type and a mutated piggyBac TE excised from a DNA vector in transient assays u...

  8. Advances in Miniaturized Instruments for Genomics

    PubMed Central

    2014-01-01

    In recent years, a lot of demonstrations of the miniaturized instruments were reported for genomic applications. They provided the advantages of miniaturization, automation, sensitivity, and specificity for the development of point-of-care diagnostics. The aim of this paper is to report on recent developments on miniaturized instruments for genomic applications. Based on the mature development of microfabrication, microfluidic systems have been demonstrated for various genomic detections. Since one of the objectives of miniaturized instruments is for the development of point-of-care device, impedimetric detection is found to be a promising technique for this purpose. An in-depth discussion of the impedimetric circuits and systems will be included to provide total consideration of the miniaturized instruments and their potential application towards real-time portable imaging in the “-omics” era. The current excellent demonstrations suggest a solid foundation for the development of practical and widespread point-of-care genomic diagnostic devices. PMID:25114919

  9. Activation and inactivation of Pseudomonas stutzeri methylbenzene catabolism pathways mediated by a transposable element

    SciTech Connect

    Bolognese, F.; Di Lecce, C.; Galli, E.; Barbieri, P.

    1999-05-01

    The arrangement of the genes involved in o-xylene, m-xylene, and p-xylene catabolism was investigated in three Pseudomonas stutzeri strains: the wild-type strain OX1, which is able to grow on o-xylene but not on the meta and para isomers; the mutant M1, which grows on m-xylene and p-xylene but is unable to utilize the ortho isomer; and the revertant R1, which can utilize all the three isomers of xylene. A 3-kb insertion sequence (IS) termed ISPs1, which inactivates the m-xylene and p-xylene catabolic pathway in P. stutzeri OX1 and the o-xylene catabolic genes in P. stutzeri M1, was detected. No IS was detected in the corresponding catabolic regions of the P. stutzeri R1 genome. ISPs1 is present in several copies in the genomes of the three strains. It is flanked by 24-bp imperfect inverted repeats, causes the direct duplication of 8 bp in the target DNA, and seems to be related to the ISL3 family.

  10. Miniaturized flow injection analysis system

    DOEpatents

    Folta, J.A.

    1997-07-01

    A chemical analysis technique known as flow injection analysis is described, wherein small quantities of chemical reagents and sample are intermixed and reacted within a capillary flow system and the reaction products are detected optically, electrochemically, or by other means. A highly miniaturized version of a flow injection analysis system has been fabricated utilizing microfabrication techniques common to the microelectronics industry. The microflow system uses flow capillaries formed by etching microchannels in a silicon or glass wafer followed by bonding to another wafer, commercially available microvalves bonded directly to the microflow channels, and an optical absorption detector cell formed near the capillary outlet, with light being both delivered and collected with fiber optics. The microflow system is designed mainly for analysis of liquids and currently measures 38{times}25{times}3 mm, but can be designed for gas analysis and be substantially smaller in construction. 9 figs.

  11. Miniature hybrid optical imaging lens

    DOEpatents

    Sitter, D.N. Jr.; Simpson, M.L.

    1997-10-21

    A miniature lens system that corrects for imaging and chromatic aberrations is disclosed, the lens system being fabricated from primarily commercially-available components. A first element at the input to a lens housing is an aperture stop. A second optical element is a refractive element with a diffractive element closely coupled to, or formed a part of, the rear surface of the refractive element. Spaced closely to the diffractive element is a baffle to limit the area of the image, and this is closely followed by a second refractive lens element to provide the final correction. The image, corrected for aberrations exits the last lens element to impinge upon a detector plane were is positioned any desired detector array. The diffractive element is fabricated according to an equation that includes, as variables, the design wavelength, the index of refraction and the radius from an optical axis of the lens system components. 2 figs.

  12. Miniature hybrid optical imaging lens

    DOEpatents

    Sitter, Jr., David N.; Simpson, Marc L.

    1997-01-01

    A miniature lens system that corrects for imaging and chromatic aberrations, the lens system being fabricated from primarily commercially-available components. A first element at the input to a lens housing is an aperture stop. A second optical element is a refractive element with a diffractive element closely coupled to, or formed a part of, the rear surface of the refractive element. Spaced closely to the diffractive element is a baffle to limit the area of the image, and this is closely followed by a second refractive lens element to provide the final correction. The image, corrected for aberrations exits the last lens element to impinge upon a detector plane were is positioned any desired detector array. The diffractive element is fabricated according to an equation that includes, as variables, the design wavelength, the index of refraction and the radius from an optical axis of the lens system components.

  13. Miniature drag-force anemometer

    NASA Technical Reports Server (NTRS)

    Krause, L. N.; Fralick, G. C.

    1977-01-01

    A miniature drag-force anemometer is described which is capable of measuring dynamic velocity head and flow direction. The anemometer consists of a silicon cantilever beam 2.5 mm long, 1.5 mm wide, and 0.25 mm thick with an integrated diffused strain-gage bridge, located at the base of the beam, as the force measuring element. The dynamics of the beam are like those of a second-order system with a natural frequency of about 42 kHz and a damping coefficient of 0.007. The anemometer can be used in both forward and reversed flow. Measured flow characteristics up to Mach 0.6 are presented along with application examples including turbulence measurements.

  14. Miniature mechanical transfer optical coupler

    DOEpatents

    Abel, Philip; Watterson, Carl

    2011-02-15

    A miniature mechanical transfer (MT) optical coupler ("MMTOC") for optically connecting a first plurality of optical fibers with at least one other plurality of optical fibers. The MMTOC may comprise a beam splitting element, a plurality of collimating lenses, and a plurality of alignment elements. The MMTOC may optically couple a first plurality of fibers disposed in a plurality of ferrules of a first MT connector with a second plurality of fibers disposed in a plurality of ferrules of a second MT connector and a third plurality of fibers disposed in a plurality of ferrules of a third MT connector. The beam splitting element may allow a portion of each beam of light from the first plurality of fibers to pass through to the second plurality of fibers and simultaneously reflect another portion of each beam of light from the first plurality of fibers to the third plurality of fibers.

  15. Miniaturized flow injection analysis system

    DOEpatents

    Folta, James A.

    1997-01-01

    A chemical analysis technique known as flow injection analysis, wherein small quantities of chemical reagents and sample are intermixed and reacted within a capillary flow system and the reaction products are detected optically, electrochemically, or by other means. A highly miniaturized version of a flow injection analysis system has been fabricated utilizing microfabrication techniques common to the microelectronics industry. The microflow system uses flow capillaries formed by etching microchannels in a silicon or glass wafer followed by bonding to another wafer, commercially available microvalves bonded directly to the microflow channels, and an optical absorption detector cell formed near the capillary outlet, with light being both delivered and collected with fiber optics. The microflow system is designed mainly for analysis of liquids and currently measures 38.times.25.times.3 mm, but can be designed for gas analysis and be substantially smaller in construction.

  16. Miniaturization of Planar Horn Motors

    NASA Technical Reports Server (NTRS)

    Sherrit, Stewart; Ostlund, Patrick N.; Chang, Zensheu; Bao, Xiaoqi; Bar-Cohen, Yoseph; Widholm, Scott E.; Badescu, Mircea

    2012-01-01

    There is a great need for compact, efficient motors for driving various mechanisms including robots or mobility platforms. A study is currently underway to develop a new type of piezoelectric actuators with significantly more strength, low mass, small footprint, and efficiency. The actuators/motors utilize piezoelectric actuated horns which have a very high power density and high electromechanical conversion efficiency. The horns are fabricated using our recently developed novel pre-stress flexures that make them thermally stable and increases their coupling efficiency. The monolithic design and integrated flexures that pre-stresses the piezoelectric stack eliminates the use of stress bolt. This design allows embedding solid-state motors and actuators in any structure so that the only macroscopically moving parts are the rotor or the linear translator. The developed actuator uses a stack/horn actuation and has a Barth motor configuration, which potentially generates very large torque and speeds that do not require gearing. Finite element modeling and design tools were investigated to determine the requirements and operation parameters and the results were used to design and fabricate a motor. This new design offers a highly promising actuation mechanism that can potentially be miniaturized and integrated into systems and structures. It can be configured in many shapes to operate as multi-degrees of freedom and multi-dimensional motors/actuators including unidirectional, bidirectional, 2D and 3D. In this manuscript, we are reporting the experimental measurements from a bench top design and the results from the efforts to miniaturize the design using 2x2x2 mm piezoelectric stacks integrated into thin plates that are of the order of3 x 3x 0.2 cm.

  17. Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains.

    PubMed

    Baruch, Omer; Kashkush, Khalil

    2012-05-01

    Transposable elements (TEs) dominate the genetic capacity of most eukaryotes, especially plants, where they may compose up to 90% of the genome. Many studies, both in plants and animals reported that in fact non-autonomous elements that have lost their protein-coding sequences and became miniature elements were highly associated with genes, and showed a high level of transpositional activity such as mPing family in rice. In this study, we have investigated in detail the copy number, insertional polymorphism and the methylation status of the tiniest LTR retrotransposon family, termed TRIM, in nine rice strains, in comparison with mPing. While TRIM showed similar copy numbers (average of 79 insertions) in all the nine rice strains, the copy number of mPing varied dramatically (ranging from 6 to 203 insertions) in the same strains. Site-specific PCR analysis revealed that ~58% of the TRIM elements have identical insertion sites among the nine rice strains, while none of the mPing elements (100% polymorphism) have identical insertion sites in the same strains. Finally, over 65% of the TRIM insertion sites were cytosine methylated in all nine rice strains, while the level of the methylated mPing insertion sites ranged between 43 and 81.5%. The findings of this study indicate that unlike mPing, TRIM is most probably a fossil TE family in rice. In addition, the data shows that there might be a strong correlation between TE methylation and copy number. PMID:22183295

  18. Scanning Miniature Microscopes without Lenses

    NASA Technical Reports Server (NTRS)

    Wang, Yu

    2009-01-01

    The figure schematically depicts some alternative designs of proposed compact, lightweight optoelectronic microscopes that would contain no lenses and would generate magnified video images of specimens. Microscopes of this type were described previously in Miniature Microscope Without Lenses (NPO - 20218), NASA Tech Briefs, Vol. 22, No. 8 (August 1998), page 43 and Reflective Variants of Miniature Microscope Without Lenses (NPO 20610), NASA Tech Briefs, Vol. 26, No. 9 (September 1999), page 6a. To recapitulate: In the design and construction of a microscope of this type, the focusing optics of a conventional microscope are replaced by a combination of a microchannel filter and a charge-coupled-device (CCD) image detector. Elimination of focusing optics reduces the size and weight of the instrument and eliminates the need for the time-consuming focusing operation. The microscopes described in the cited prior articles contained two-dimensional CCDs registered with two-dimensional arrays of microchannels and, as such, were designed to produce full two-dimensional images, without need for scanning. The microscopes of the present proposal would contain one-dimensional (line image) CCDs registered with linear arrays of microchannels. In the operation of such a microscope, one would scan a specimen along a line perpendicular to the array axis (in other words, one would scan in pushbroom fashion). One could then synthesize a full two-dimensional image of the specimen from the line-image data acquired at one-pixel increments of position along the scan. In one of the proposed microscopes, a beam of unpolarized light for illuminating the specimen would enter from the side. This light would be reflected down onto the specimen by a nonpolarizing beam splitter attached to the microchannels at their lower ends. A portion of the light incident on the specimen would be reflected upward, through the beam splitter and along the microchannels, to form an image on the CCD. If the

  19. Computational imaging for miniature cameras

    NASA Astrophysics Data System (ADS)

    Salahieh, Basel

    Miniature cameras play a key role in numerous imaging applications ranging from endoscopy and metrology inspection devices to smartphones and head-mount acquisition systems. However, due to the physical constraints, the imaging conditions, and the low quality of small optics, their imaging capabilities are limited in terms of the delivered resolution, the acquired depth of field, and the captured dynamic range. Computational imaging jointly addresses the imaging system and the reconstructing algorithms to bypass the traditional limits of optical systems and deliver better restorations for various applications. The scene is encoded into a set of efficient measurements which could then be computationally decoded to output a richer estimate of the scene as compared with the raw images captured by conventional imagers. In this dissertation, three task-based computational imaging techniques are developed to make low-quality miniature cameras capable of delivering realistic high-resolution reconstructions, providing full-focus imaging, and acquiring depth information for high dynamic range objects. For the superresolution task, a non-regularized direct superresolution algorithm is developed to achieve realistic restorations without being penalized by improper assumptions (e.g., optimizers, priors, and regularizers) made in the inverse problem. An adaptive frequency-based filtering scheme is introduced to upper bound the reconstruction errors while still producing more fine details as compared with previous methods under realistic imaging conditions. For the full-focus imaging task, a computational depth-based deconvolution technique is proposed to bring a scene captured by an ordinary fixed-focus camera to a full-focus based on a depth-variant point spread function prior. The ringing artifacts are suppressed on three levels: block tiling to eliminate boundary artifacts, adaptive reference maps to reduce ringing initiated by sharp edges, and block-wise deconvolution or

  20. Miniature infrared data acquisition and telemetry system

    NASA Technical Reports Server (NTRS)

    Stokes, J. H.; Ward, S. M.

    1985-01-01

    The Miniature Infrared Data Acquisition and Telemetry (MIRDAT) Phase 1 study was performed to determine the technical and commercial feasibility of producing a miniaturized electro-optical telemetry system. This system acquires and transmits experimental data from aircraft scale models for realtime monitoring in wind tunnels. During the Phase 1 study, miniature prototype MIRDAT telemetry devices were constructed, successfully tested in the laboratory and delivered to the user for wind tunnel testing. A search was conducted for commercially available components and advanced hybrid techniques to further miniaturize the system during Phase 2 development. A design specification was generated from laboratory testing, user requirements and discussions with component manufacturers. Finally, a preliminary design of the proposed MIRDAT system was documented for Phase 2 development.

  1. Miniature capacitor functions as pressure sensor

    NASA Technical Reports Server (NTRS)

    Harrison, R. G.

    1967-01-01

    Miniature capacitor operates as a differential pressure telemetry sensor during free flight of test model in a hypersonic wind tunnel. The capacitor incorporates a beryllium copper diaphragm. It is also used as an absolute pressure sensor.

  2. Using Miniature Landforms in Teaching Geomorphology.

    ERIC Educational Resources Information Center

    Petersen, James F.

    1986-01-01

    This paper explores the uses of true landform miniatures and small-scale analogues and suggests ways to teach geomorphological concepts using small-scale relief features as illustrative examples. (JDH)

  3. On the processing of canonical word order during eye fixations in reading: Do readers process transposed word previews?

    PubMed

    Rayner, Keith; Angele, Bernhard; Schotter, Elizabeth R; Bicknell, Klinton

    2013-03-01

    Whether readers always identify words in the order they are printed is subject to considerable debate. In the present study, we used the gaze-contingent boundary paradigm (Rayner, 1975) to manipulate the preview for a two-word target region (e.g. white walls in My neighbor painted the white walls black). Readers received an identical (white walls), transposed (walls white), or unrelated preview (vodka clubs). We found that there was a clear cost of having a transposed preview compared to an identical preview, indicating that readers cannot or do not identify words out of order. However, on some measures, the transposed preview condition did lead to faster processing than the unrelated preview condition, suggesting that readers may be able to obtain some useful information from a transposed preview. Implications of the results for models of eye movement control in reading are discussed. PMID:24003322

  4. A family of transposable elements co-opted into developmental enhancers in the mouse neocortex

    PubMed Central

    Notwell, James H.; Chung, Tisha; Heavner, Whitney; Bejerano, Gill

    2015-01-01

    The neocortex is a mammalian-specific structure that is responsible for higher functions such as cognition, emotion, and perception. To gain insight into its evolution and the gene regulatory codes that pattern it, we studied the overlap of its active developmental enhancers with transposable element families and compared this overlap to uniformly shuffled enhancers. Here we show a striking enrichment of the MER130 repeat family among active enhancers in the mouse dorsal cerebral wall, which gives rise to the neocortex, at embryonic day 14.5 (E14.5). We show that MER130 instances preserve a common code of transcriptional regulatory logic, function as enhancers, and are adjacent to critical neocortical genes. MER130, a nonautonomous interspersed transposable element, originates in the tetrapod or possibly Sarcopterygii ancestor, which far predates the appearance of the neocortex. Our results show that MER130 elements were recruited, likely through their common regulatory logic, as neocortical enhancers. PMID:25806706

  5. Transposed-letter priming effects in reading aloud words and nonwords.

    PubMed

    Mousikou, Petroula; Kinoshita, Sachiko; Wu, Simon; Norris, Dennis

    2015-10-01

    A masked nonword prime generated by transposing adjacent inner letters in a word (e.g., jugde) facilitates the recognition of the target word (JUDGE) more than a prime in which the relevant letters are replaced by different letters (e.g., junpe). This transposed-letter (TL) priming effect has been widely interpreted as evidence that the coding of letter position is flexible, rather than precise. Although the TL priming effect has been extensively investigated in the domain of visual word recognition using the lexical decision task, very few studies have investigated this empirical phenomenon in reading aloud. In the present study, we investigated TL priming effects in reading aloud words and nonwords and found that these effects are of equal magnitude for the two types of items. We take this result as support for the view that the TL priming effect arises from noisy perception of letter order within the prime prior to the mapping of orthography to phonology. PMID:25665798

  6. Nonexistence of entangled continuous-variable Werner states with positive partial transpose

    NASA Astrophysics Data System (ADS)

    McNulty, Daniel; Tatham, Richard; Mišta, Ladislav

    2014-03-01

    We address an open question about the existence of entangled continuous-variable (CV) Werner states with positive partial transpose (PPT). We prove that no such state exists by showing that all PPT CV Werner states are separable. The separability follows by observing that these CV Werner states can be approximated by truncating the states into a finite-dimensional convex mixture of product states. In addition, the constituents of the product states comprise a generalized non-Gaussian measurement which gives, rather surprisingly, a strictly tighter upper bound on quantum discord than photon counting. These results uncover the presence of only negative partial transpose entanglement and illustrate the complexity of more general nonclassical correlations in this paradigmatic class of genuine non-Gaussian quantum states.

  7. A structured annotation frame for the transposable phages: a new proposed family "Saltoviridae" within the Caudovirales.

    PubMed

    Hulo, Chantal; Masson, Patrick; Le Mercier, Philippe; Toussaint, Ariane

    2015-03-01

    Enterobacteriophage Mu is the best studied and paradigm member of the transposable phages. Mu-encoded proteins have been annotated in detail in UniProtKB and linked to a controlled vocabulary describing the various steps involved in the phage lytic and lysogenic cycles. Transposable phages are ubiquitous temperate bacterial viruses with a dsDNA linear genome. Twenty-six of them, that infect α, β and γ-proteobacteria, have been sequenced. Their conserved properties are described. Based on these characteristics, we propose a reorganization of the Caudovirales, to allow for the inclusion of a "Saltoviridae" family and two newly proposed subfamilies, the "Myosaltovirinae" and "Siphosaltovirinae". The latter could temporarily be included in the existing Myoviridae and Siphoviridae families. PMID:25500185

  8. Structure and properties of the algebra of partially transposed permutation operators

    SciTech Connect

    Mozrzymas, Marek; Horodecki, Michał; Studziński, Michał

    2014-03-15

    We consider the structure of algebra of operators, acting in n-fold tensor product space, which are partially transposed on the last term. Using purely algebraical methods we show that this algebra is semi-simple and then, considering its regular representation, we derive basic properties of the algebra. In particular, we describe all irreducible representations of the algebra of partially transposed operators and derive expressions for matrix elements of the representations. It appears that there are two kinds of irreducible representations of the algebra. The first one is strictly connected with the representations of the group S(n − 1) induced by irreducible representations of the group S(n − 2). The second kind is structurally connected with irreducible representations of the group S(n − 1)

  9. Miniaturized GPS/MEMS IMU integrated board

    NASA Technical Reports Server (NTRS)

    Lin, Ching-Fang (Inventor)

    2012-01-01

    This invention documents the efforts on the research and development of a miniaturized GPS/MEMS IMU integrated navigation system. A miniaturized GPS/MEMS IMU integrated navigation system is presented; Laser Dynamic Range Imager (LDRI) based alignment algorithm for space applications is discussed. Two navigation cameras are also included to measure the range and range rate which can be integrated into the GPS/MEMS IMU system to enhance the navigation solution.

  10. Miniature Electrostatic Ion Thruster With Magnet

    NASA Technical Reports Server (NTRS)

    Hartley, Frank T.

    2006-01-01

    A miniature electrostatic ion thruster is proposed that, with one exception, would be based on the same principles as those of the device described in the previous article, "Miniature Bipolar Electrostatic Ion Thruster". The exceptional feature of this thruster would be that, in addition to using electric fields for linear acceleration of ions and electrons, it would use a magnetic field to rotationally accelerate slow electrons into the ion stream to neutralize the ions.

  11. Miniature electrically operated diaphragm valve

    DOEpatents

    Adkins, Douglas R.; Spletzer, Barry L.; Wong, Chungnin C.; Frye-Mason, Gregory C.; Fischer, Gary J.; Hesketh, Peter J.

    2001-01-01

    The present invention provides a miniature electrically operated valve that can stand off significant pressures, that can be inexpensively produced, and that can be made to operate without continuous electrical power. A valve according to the present invention comprises a housing and a beam mounted with the housing. A diaphragm mounted with the housing forms a sealed fluid volume. An electromagnetic energy source, such as an electromagnetic coil, mounts with the housing and when energized urges the beam in one direction. The beam can be urged in the opposing direction by passive means or by reversing the polarity of the electromagnetic energy source or by a second electromagnetic energy source. Two fluid ports mount with the housing. A first fluid port mounts so that, as the beam is urged in one direction or the opposite, the beam urges the diaphragm to move between engaging and substantially sealing the fluid port and disengaging and not substantially sealing the fluid port. A seat can be mounted with the diaphragm to aid in sealing the fluid port. Latching mechanisms such as permanent magnets can be mounted so that the valve remains in the open or closed positions without continuous electrical power input. Fluid can flow through the housing between the two fluid ports when the diaphragm does not seal the first fluid port, but can be prevented from flowing by urging the beam so that the diaphragm seals the first fluid port. Various embodiments accommodate various latching mechanisms, electromagnetic energy sources, number of fluid ports, and diaphragm design considerations.

  12. Miniature curved artificial compound eyes

    PubMed Central

    Floreano, Dario; Pericet-Camara, Ramon; Viollet, Stéphane; Ruffier, Franck; Brückner, Andreas; Leitel, Robert; Buss, Wolfgang; Menouni, Mohsine; Expert, Fabien; Juston, Raphaël; Dobrzynski, Michal Karol; L’Eplattenier, Geraud; Recktenwald, Fabian; Mallot, Hanspeter A.; Franceschini, Nicolas

    2013-01-01

    In most animal species, vision is mediated by compound eyes, which offer lower resolution than vertebrate single-lens eyes, but significantly larger fields of view with negligible distortion and spherical aberration, as well as high temporal resolution in a tiny package. Compound eyes are ideally suited for fast panoramic motion perception. Engineering a miniature artificial compound eye is challenging because it requires accurate alignment of photoreceptive and optical components on a curved surface. Here, we describe a unique design method for biomimetic compound eyes featuring a panoramic, undistorted field of view in a very thin package. The design consists of three planar layers of separately produced arrays, namely, a microlens array, a neuromorphic photodetector array, and a flexible printed circuit board that are stacked, cut, and curved to produce a mechanically flexible imager. Following this method, we have prototyped and characterized an artificial compound eye bearing a hemispherical field of view with embedded and programmable low-power signal processing, high temporal resolution, and local adaptation to illumination. The prototyped artificial compound eye possesses several characteristics similar to the eye of the fruit fly Drosophila and other arthropod species. This design method opens up additional vistas for a broad range of applications in which wide field motion detection is at a premium, such as collision-free navigation of terrestrial and aerospace vehicles, and for the experimental testing of insect vision theories. PMID:23690574

  13. Miniature curved artificial compound eyes.

    PubMed

    Floreano, Dario; Pericet-Camara, Ramon; Viollet, Stéphane; Ruffier, Franck; Brückner, Andreas; Leitel, Robert; Buss, Wolfgang; Menouni, Mohsine; Expert, Fabien; Juston, Raphaël; Dobrzynski, Michal Karol; L'Eplattenier, Geraud; Recktenwald, Fabian; Mallot, Hanspeter A; Franceschini, Nicolas

    2013-06-01

    In most animal species, vision is mediated by compound eyes, which offer lower resolution than vertebrate single-lens eyes, but significantly larger fields of view with negligible distortion and spherical aberration, as well as high temporal resolution in a tiny package. Compound eyes are ideally suited for fast panoramic motion perception. Engineering a miniature artificial compound eye is challenging because it requires accurate alignment of photoreceptive and optical components on a curved surface. Here, we describe a unique design method for biomimetic compound eyes featuring a panoramic, undistorted field of view in a very thin package. The design consists of three planar layers of separately produced arrays, namely, a microlens array, a neuromorphic photodetector array, and a flexible printed circuit board that are stacked, cut, and curved to produce a mechanically flexible imager. Following this method, we have prototyped and characterized an artificial compound eye bearing a hemispherical field of view with embedded and programmable low-power signal processing, high temporal resolution, and local adaptation to illumination. The prototyped artificial compound eye possesses several characteristics similar to the eye of the fruit fly Drosophila and other arthropod species. This design method opens up additional vistas for a broad range of applications in which wide field motion detection is at a premium, such as collision-free navigation of terrestrial and aerospace vehicles, and for the experimental testing of insect vision theories. PMID:23690574

  14. Miniature Ion-Array Spectrometer

    NASA Technical Reports Server (NTRS)

    Hartley, Frank T.

    2006-01-01

    A figure is shown that depicts a proposed miniature ion-mobility spectrometer that would share many features of design and operation of the instrument described in another article. The main differences between that instrument and this one would lie in the configuration and mode of operation of the filter and detector electrodes. A filter electrode and detector electrodes would be located along the sides of a drift tube downstream from the accelerator electrode. These electrodes would apply a combination of (1) a transverse AC electric field that would effect differential transverse dispersal of ions and (2) a transverse DC electric field that would drive the dispersed ions toward the detector electrodes at different distances along the drift tube. The electric current collected by each detector electrode would be a measure of the current, and thus of the abundance of the species of ions impinging on that electrode. The currents collected by all the detector electrodes could be measured simultaneously to obtain continuous readings of abundances of species. The downstream momentum of accelerated ions would be maintained through neutralization on the electrodes; the momentum of the resulting neutral atoms would serve to expel gases from spectrometer, without need for a pump.

  15. Miniature Quadrupole Mass Spectrometer Array

    NASA Technical Reports Server (NTRS)

    Karmon, D.; Darrech, M.; Chutjian, A.; Jan, D.

    1999-01-01

    JPL is funded by Code U to develop a Miniature QMSA for an EVA flight test. The initial intent was to fly an experiment internal to the astronaut suit during a shuttle EVA. Following discussions with JSC the suit application was abandoned in favor of other more urgent needs. The JSC EVA office was particularly interested in hydrazine detection on the astronaut suit. While discussing and exploring the implementation of such an experiment, managers at JSC suggested combining the interests of two JSC groups. The Life Support and Thermal Systems Branch, Crew and Thermal Systems Division has a need for an ammonia detection instrument, while the EVA office has a need for hydrazine detection. The two groups were pursuing separate single-purpose solutions. Instead, the JPL QMSA offers a single instrument solution via a portable instrument to be used by an astronaut on an EVA. Such an instrument would serve both the ammonia leak detection and the hydrazine contamination needs. The need for the QMSA was defined as urgent and targeted for a January 1999 flight. While the original JPL task (as funded by Code U) was for an experiment flight with JPL delivery in October 1998, this task was for a qualified flight instrument with a planned JPL delivery in August 1998. This schedule was very demanding and dictated a fast-tract implementation.

  16. Multipartite positive-partial-transpose inequalities exponentially stronger than local reality inequalities

    SciTech Connect

    Nagata, Koji

    2007-08-15

    We show that positivity of every partial transpose of N-partite quantum states implies inequalities on Bell correlations which are stronger than standard Bell inequalities by a factor of 2{sup (N-1)/2}. A violation of the inequality implies that the system is in a bipartite distillable entangled state. It turns out that a family of N-qubit bound entangled states proposed by Duer [Phys. Rev. Lett. 87, 230402 (2001)] violates the inequality for N{>=}4.

  17. The Holozoan Capsaspora owczarzaki Possesses a Diverse Complement of Active Transposable Element Families

    PubMed Central

    Carr, Martin; Suga, Hiroshi

    2014-01-01

    Capsaspora owczarzaki, a protistan symbiont of the pulmonate snail Biomphalaria glabrata, is the centre of much interest in evolutionary biology due to its close relationship to Metazoa. The whole genome sequence of this protist has revealed new insights into the ancestral genome composition of Metazoa, in particular with regard to gene families involved in the evolution of multicellularity. The draft genome revealed the presence of 23 families of transposable element, made up from DNA transposon as well as long terminal repeat (LTR) and non-LTR retrotransposon families. The phylogenetic analyses presented here show that all of the transposable elements identified in the C. owczarzaki genome have orthologous families in Metazoa, indicating that the ancestral metazoan also had a rich diversity of elements. Molecular evolutionary analyses also show that the majority of families has recently been active within the Capsaspora genome. One family now appears to be inactive and a further five families show no evidence of current transposition. Most individual element copies are evolutionarily young; however, a small proportion of inserts appear to have persisted for longer in the genome. The families present in the genome show contrasting population histories and appear to be in different stages of their life cycles. Transcriptome data have been analyzed from multiple stages in the C. owczarzaki life cycle. Expression levels vary greatly both between families and between different stages of the life cycle, suggesting an unexpectedly complex level of transposable element regulation in a single celled organism. PMID:24696401

  18. Transposable elements as a factor in the aging of Drosophila melanogaster.

    PubMed

    Driver, C J; McKechnie, S W

    1992-12-26

    We have considered the hypothesis that transposable elements may contribute to the aging process through somatic mutation. We have presented evidence to suggest that at least two elements, Copia and 412, are capable of somatic activity in adult Drosophila tissue. A strain harboring a third transposable element, P, was produced that showed eye color mosaicism and reversion to wild phenotype (red eyes) as a result of somatic and germ line transposition. A high-fat diet, known to accelerate aging, increased the frequency of eye color mosaicism and red eyes. We induced life span shortening by artificially activating somatic transposition of P elements, and the extent of reduction in life span was similar in both sexes. These data are consistent with the notion that some aspects of the age phenotype may be caused by mutational activity of transposable elements in somatic tissues. The hypothesis is readily tested in other organisms, including humans. It offers new dimensions in the understanding and management of age-associated changes. PMID:1336649

  19. The industrial melanism mutation in British peppered moths is a transposable element.

    PubMed

    Van't Hof, Arjen E; Campagne, Pascal; Rigden, Daniel J; Yung, Carl J; Lingley, Jessica; Quail, Michael A; Hall, Neil; Darby, Alistair C; Saccheri, Ilik J

    2016-06-01

    Discovering the mutational events that fuel adaptation to environmental change remains an important challenge for evolutionary biology. The classroom example of a visible evolutionary response is industrial melanism in the peppered moth (Biston betularia): the replacement, during the Industrial Revolution, of the common pale typica form by a previously unknown black (carbonaria) form, driven by the interaction between bird predation and coal pollution. The carbonaria locus has been coarsely localized to a 200-kilobase region, but the specific identity and nature of the sequence difference controlling the carbonaria-typica polymorphism, and the gene it influences, are unknown. Here we show that the mutation event giving rise to industrial melanism in Britain was the insertion of a large, tandemly repeated, transposable element into the first intron of the gene cortex. Statistical inference based on the distribution of recombined carbonaria haplotypes indicates that this transposition event occurred around 1819, consistent with the historical record. We have begun to dissect the mode of action of the carbonaria transposable element by showing that it increases the abundance of a cortex transcript, the protein product of which plays an important role in cell-cycle regulation, during early wing disc development. Our findings fill a substantial knowledge gap in the iconic example of microevolutionary change, adding a further layer of insight into the mechanism of adaptation in response to natural selection. The discovery that the mutation itself is a transposable element will stimulate further debate about the importance of 'jumping genes' as a source of major phenotypic novelty. PMID:27251284

  20. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

    PubMed Central

    Freeling, Michael; Lyons, Eric; Pedersen, Brent; Alam, Maqsudul; Ming, Ray; Lisch, Damon

    2008-01-01

    Previous to this work, typical genes were thought to move from one position to another infrequently. On the contrary, we now estimate that between one-fourth and three-fourths of the genes in Arabidopsis transposed in the Brassicales. We used the CoGe comparative genomics system to perform and visualize multiple orthologous chromosomal alignments. Using this tool, we found large differences between different categories of genes. Ten of the gene families examined, including genes in most transcription factor families, exhibited a median frequency of 5% transposed genes. In contrast, other gene families were composed largely of transposed genes: NB-LRR disease-resistance genes, genes encoding MADS-box and B3 transcription factors, and genes encoding F-box proteins. A unique method involving transposition-rich regions of genome allowed us to obtain an indirect estimate of the positional stability of the average gene. The observed differences between gene families raise important questions concerning the causes and consequences of gene transposition. PMID:18836034

  1. Periodontal Effects of a Transposed Versus a Conventional Flap in Mandibular Third Molar Extractions.

    PubMed

    Laurito, Domenica; Lollobrigida, Marco; Graziani, Filippo; Guerra, Fabrizio; Vestri, Annarita; De Biase, Alberto

    2016-05-01

    The aim of this study was to compare a transposed with a repositioned flap by assessing the periodontal effects on the second molar and primary healing after extraction of partially impacted lower third molars. A total of 24 patients requiring partially impacted mandibular wisdom tooth removal were enrolled in the study. The test group (n = 12) underwent a transposed flap procedure, whereas the control group (n = 12) underwent a repositioned flap procedure. Plaque index, probing depth, bleeding on probing, and width of keratinized tissue were recorded the day of surgery (T1) and after 60 days (T4). Wound dehiscence was assessed on the mesio-distal and bucco-lingual directions at days 2 (T2), 7 (T3), and T4. No significant differences have been observed in the periodontal parameters between the groups at T1 and T4 (P > 0.05). Similarly, no difference was found at T2, T3, and T4 in wound dehiscence incidence (P > 0.05). To date, no data exists on the use of transposed flaps in third molar surgery; thus a comparison of results cannot be done. Further studies with larger population are needed to investigate the potential advantages of this type of flap. PMID:27054424

  2. Transposing from the laboratory to the classroom to generate authentic research experiences for undergraduates.

    PubMed

    Burnette, James M; Wessler, Susan R

    2013-02-01

    Large lecture classes and standardized laboratory exercises are characteristic of introductory biology courses. Previous research has found that these courses do not adequately convey the process of scientific research and the excitement of discovery. Here we propose a model that provides beginning biology students with an inquiry-based, active learning laboratory experience. The Dynamic Genome course replicates a modern research laboratory focused on eukaryotic transposable elements where beginning undergraduates learn key genetics concepts, experimental design, and molecular biological skills. Here we report on two key features of the course, a didactic module and the capstone original research project. The module is a modified version of a published experiment where students experience how virtual transposable elements from rice (Oryza sativa) are assayed for function in transgenic Arabidopsis thaliana. As part of the module, students analyze the phenotypes and genotypes of transgenic plants to determine the requirements for transposition. After mastering the skills and concepts, students participate in an authentic research project where they use computational analysis and PCR to detect transposable element insertion site polymorphism in a panel of diverse maize strains. As a consequence of their engagement in this course, students report large gains in their ability to understand the nature of research and demonstrate that they can apply that knowledge to independent research projects. PMID:23172853

  3. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses.

    PubMed

    Pritham, Ellen J; Putliwala, Tasneem; Feschotte, Cédric

    2007-04-01

    We previously identified a group of atypical mobile elements designated Mavericks from the nematodes Caenorhabditis elegans and C. briggsae and the zebrafish Danio rerio. Here we present the results of comprehensive database searches of the genome sequences available, which reveal that Mavericks are widespread in invertebrates and non-mammalian vertebrates but show a patchy distribution in non-animal species, being present in the fungi Glomus intraradices and Phakopsora pachyrhizi and in several single-celled eukaryotes such as the ciliate Tetrahymena thermophila, the stramenopile Phytophthora infestans and the trichomonad Trichomonas vaginalis, but not detectable in plants. This distribution, together with comparative and phylogenetic analyses of Maverick-encoded proteins, is suggestive of an ancient origin of these elements in eukaryotes followed by lineage-specific losses and/or recurrent episodes of horizontal transmission. In addition, we report that Maverick elements have amplified recently to high copy numbers in T. vaginalis where they now occupy as much as 30% of the genome. Sequence analysis confirms that most Mavericks encode a retroviral-like integrase, but lack other open reading frames typically found in retroelements. Nevertheless, the length and conservation of the target site duplication created upon Maverick insertion (5- or 6-bp) is consistent with a role of the integrase-like protein in the integration of a double-stranded DNA transposition intermediate. Mavericks also display long terminal-inverted repeats but do not contain ORFs similar to proteins encoded by DNA transposons. Instead, Mavericks encode a conserved set of 5 to 9 genes (in addition to the integrase) that are predicted to encode proteins with homology to replication and packaging proteins of some bacteriophages and diverse eukaryotic double-stranded DNA viruses, including a DNA polymerase B homolog and putative capsid proteins. Based on these and other structural similarities, we

  4. Miniature Ion-Mobility Spectrometer

    NASA Technical Reports Server (NTRS)

    Hartley, Frank T.

    2006-01-01

    The figure depicts a proposed miniature ion-mobility spectrometer that would be fabricated by micromachining. Unlike prior ion-mobility spectrometers, the proposed instrument would not be based on a time-of-flight principle and, consequently, would not have some of the disadvantageous characteristics of prior time-of-flight ion-mobility spectrometers. For example, one of these characteristics is the need for a bulky carrier-gas-feeding subsystem that includes a shutter gate to provide short pulses of gas in order to generate short pulses of ions. For another example, there is need for a complex device to generate pulses of ions from the pulses of gas and the device is capable of ionizing only a fraction of the incoming gas molecules; these characteristics preclude miniaturization. In contrast, the proposed instrument would not require a carrier-gas-feeding subsystem and would include a simple, highly compact device that would ionize all the molecules passing through it. The ionization device in the proposed instrument would be a 0.1-micron-thick dielectric membrane with metal electrodes on both sides. Small conical holes would be micromachined through the membrane and electrodes. An electric potential of the order of a volt applied between the membrane electrodes would give rise to an electric field of the order of several megavolts per meter in the submicron gap between the electrodes. An electric field of this magnitude would be sufficient to ionize all the molecules that enter the holes. Ionization (but not avalanche arcing) would occur because the distance between the ionizing electrodes would be less than the mean free path of gas molecules at the operating pressure of instrument. An accelerating grid would be located inside the instrument, downstream from the ionizing membrane. The electric potential applied to this grid would be negative relative to the potential on the inside electrode of the ionizing membrane and would be of a magnitude sufficient to

  5. Miniaturized cathodic arc plasma source

    DOEpatents

    Anders, Andre; MacGill, Robert A.

    2003-04-15

    A cathodic arc plasma source has an anode formed of a plurality of spaced baffles which extend beyond the active cathode surface of the cathode. With the open baffle structure of the anode, most macroparticles pass through the gaps between the baffles and reflect off the baffles out of the plasma stream that enters a filter. Thus the anode not only has an electrical function but serves as a prefilter. The cathode has a small diameter, e.g. a rod of about 1/4 inch (6.25 mm) diameter. Thus the plasma source output is well localized, even with cathode spot movement which is limited in area, so that it effectively couples into a miniaturized filter. With a small area cathode, the material eroded from the cathode needs to be replaced to maintain plasma production. Therefore, the source includes a cathode advancement or feed mechanism coupled to cathode rod. The cathode also requires a cooling mechanism. The movable cathode rod is housed in a cooled metal shield or tube which serves as both a current conductor, thus reducing ohmic heat produced in the cathode, and as the heat sink for heat generated at or near the cathode. Cooling of the cathode housing tube is done by contact with coolant at a place remote from the active cathode surface. The source is operated in pulsed mode at relatively high currents, about 1 kA. The high arc current can also be used to operate the magnetic filter. A cathodic arc plasma deposition system using this source can be used for the deposition of ultrathin amorphous hard carbon (a-C) films for the magnetic storage industry.

  6. Miniature EVA Software Defined Radio

    NASA Technical Reports Server (NTRS)

    Pozhidaev, Aleksey

    2012-01-01

    As NASA embarks upon developing the Next-Generation Extra Vehicular Activity (EVA) Radio for deep space exploration, the demands on EVA battery life will substantially increase. The number of modes and frequency bands required will continue to grow in order to enable efficient and complex multi-mode operations including communications, navigation, and tracking applications. Whether conducting astronaut excursions, communicating to soldiers, or first responders responding to emergency hazards, NASA has developed an innovative, affordable, miniaturized, power-efficient software defined radio that offers unprecedented power-efficient flexibility. This lightweight, programmable, S-band, multi-service, frequency- agile EVA software defined radio (SDR) supports data, telemetry, voice, and both standard and high-definition video. Features include a modular design, an easily scalable architecture, and the EVA SDR allows for both stationary and mobile battery powered handheld operations. Currently, the radio is equipped with an S-band RF section. However, its scalable architecture can accommodate multiple RF sections simultaneously to cover multiple frequency bands. The EVA SDR also supports multiple network protocols. It currently implements a Hybrid Mesh Network based on the 802.11s open standard protocol. The radio targets RF channel data rates up to 20 Mbps and can be equipped with a real-time operating system (RTOS) that can be switched off for power-aware applications. The EVA SDR's modular design permits implementation of the same hardware at all Network Nodes concept. This approach assures the portability of the same software into any radio in the system. It also brings several benefits to the entire system including reducing system maintenance, system complexity, and development cost.

  7. Miniature Bipolar Electrostatic Ion Thruster

    NASA Technical Reports Server (NTRS)

    Hartley, Frank T.

    2006-01-01

    The figure presents a concept of a bipolar miniature electrostatic ion thruster for maneuvering a small spacecraft. The ionization device in the proposed thruster would be a 0.1-micron-thick dielectric membrane with metal electrodes on both sides. Small conical holes would be micromachined through the membrane and electrodes. An electric potential of the order of a volt applied between the membrane electrodes would give rise to an electric field of the order of several mega-volts per meter in the submicron gap between the electrodes. An electric field of this magnitude would be sufficient to ionize all the molecules that enter the holes. In a thruster-based on this concept, one or more propellant gases would be introduced into such a membrane ionizer. Unlike in larger prior ion thrusters, all of the propellant molecules would be ionized. This thruster would be capable of bipolar operation. There would be two accelerator grids - one located forward and one located aft of the membrane ionizer. In one mode of operation, which one could denote the forward mode, positive ions leaving the ionizer on the backside would be accelerated to high momentum by an electric field between the ionizer and an accelerator grid. Electrons leaving the ionizer on the front side would be ejected into free space by a smaller accelerating field. The equality of the ion and electron currents would eliminate the need for an additional electron- or ion-emitting device to keep the spacecraft charge-neutral. In another mode of operation, which could denote the reverse mode, the polarities of the voltages applied to the accelerator grids and to the electrodes of the membrane ionizer would be the reverse of those of the forward mode. The reversal of electric fields would cause the ion and electrons to be ejected in the reverse of their forward mode directions, thereby giving rise to thrust in the direction opposite that of the forward mode.

  8. Advances in miniature spectrometer and sensor development

    NASA Astrophysics Data System (ADS)

    Malinen, Jouko; Rissanen, Anna; Saari, Heikki; Karioja, Pentti; Karppinen, Mikko; Aalto, Timo; Tukkiniemi, Kari

    2014-05-01

    Miniaturization and cost reduction of spectrometer and sensor technologies has great potential to open up new applications areas and business opportunities for analytical technology in hand held, mobile and on-line applications. Advances in microfabrication have resulted in high-performance MEMS and MOEMS devices for spectrometer applications. Many other enabling technologies are useful for miniature analytical solutions, such as silicon photonics, nanoimprint lithography (NIL), system-on-chip, system-on-package techniques for integration of electronics and photonics, 3D printing, powerful embedded computing platforms, networked solutions as well as advances in chemometrics modeling. This paper will summarize recent work on spectrometer and sensor miniaturization at VTT Technical Research Centre of Finland. Fabry-Perot interferometer (FPI) tunable filter technology has been developed in two technical versions: Piezoactuated FPIs have been applied in miniature hyperspectral imaging needs in light weight UAV and nanosatellite applications, chemical imaging as well as medical applications. Microfabricated MOEMS FPIs have been developed as cost-effective sensor platforms for visible, NIR and IR applications. Further examples of sensor miniaturization will be discussed, including system-on-package sensor head for mid-IR gas analyzer, roll-to-roll printed Surface Enhanced Raman Scattering (SERS) technology as well as UV imprinted waveguide sensor for formaldehyde detection.

  9. A Laser Interferometric Miniature Sensor

    SciTech Connect

    Carr, Dustin W., PhD.; Baldwin, Patrick C.; Milburn, Howard; Robinson, David

    2011-09-12

    This is the second year of a Phase II Small Business Innovation Research (SBIR) contract geared towards the development of a new seismic sensor. Ground-based seismic monitoring systems have proven to be very capable in identifying nuclear tests, and can provide somewhat precise information on the location and yield of the explosive device. Making these measurements, however, currently requires very expensive and bulky seismometers that are difficult to deploy in places where they are most needed. A high performance, compact device can enable rapid deployment of large scale arrays, which can in turn be used to provide higher quality data during times of critical need. The use of a laser interferometer-based device has shown considerable promise, while also presenting significant challenges. The greatest strength of this optical readout technique is the ability to decouple the mechanical design from the transducer, thus enabling a miniaturized design that is not accessible with conventional sensing techniques. However, the nonlinearity in the optical response must be accounted for in the sensor output. Previously, we had proposed using a force-feedback approach to position the sensor at a point of maximum linearity. However, it can be shown that the combined nonlinearities of the optical response and the force-feedback curve necessarily results in a significant amount of unwanted noise at low frequencies. Having realized this, we have developed a new approach that eliminates force feedback, allowing the proof mass to move freely at all times. This takes advantage of some advanced optical spatial filtering that was developed at Symphony Acoustics for other types of sensors, and was recently adapted to this work. After processing the signals in real time, the digital output of the device is intrinsically linear, and the sensor can operate at any orientation with the same level of resolution, while instantly adapting to significant changes in orientation. Ultimately, we

  10. Miniature Long-life Space Cryocoolers

    NASA Technical Reports Server (NTRS)

    Tward, E.

    1993-01-01

    TRW has designed, built, and tested a miniature integral Stirling cooler and a miniature pulse tube cooler intended for long-life space application. Both efficient, low-vibration coolers were developed for cooling IR sensors to temperatures as low as 50 K on lightsats. The vibrationally balanced nonwearing design Stirling cooler incorporates clearance seals maintained by flexure springs for both the compressor and the drive displacer. The design achieved its performance goal of 0.25 W at 65 K for an input power to the compressor of 12 W. The cooler recently passed launch vibration tests prior to its entry into an extended life test and its first scheduled flight in 1995. The vibrationally balanced, miniature pulse tube cooler intended for a 10-year long-life space application incorporates a flexure bearing compressor vibrationally balanced by a motor-controlled balancer and a completely passive pulse tube cold head.

  11. Fabrication method for miniature plastic gripper

    DOEpatents

    Benett, W.J.; Krulevitch, P.A.; Lee, A.P.; Northrup, M.A.; Folta, J.A.

    1998-07-21

    A miniature plastic gripper is described actuated by inflation of a miniature balloon and method of fabricating same. The gripper is constructed of either heat-shrinkable or heat-expandable plastic tubing and is formed around a mandrel, then cut to form gripper prongs or jaws and the mandrel removed. The gripper is connected at one end with a catheter or tube having an actuating balloon at its tip, whereby the gripper is opened or dosed by inflation or deflation of the balloon. The gripper is designed to removably retain a member to which is connected a quantity or medicine, plugs, or micro-components. The miniature plastic gripper is inexpensive to fabricate and can be used for various applications, such as gripping, sorting, or placing of micron-scale particles for analysis. 8 figs.

  12. Fabrication method for miniature plastic gripper

    DOEpatents

    Benett, William J.; Krulevitch, Peter A.; Lee, Abraham P.; Northrup, Milton A.; Folta, James A.

    1998-01-01

    A miniature plastic gripper actuated by inflation of a miniature balloon and method of fabricating same. The gripper is constructed of either heat-shrinkable or heat-expandable plastic tubing and is formed around a mandrel, then cut to form gripper prongs or jaws and the mandrel removed. The gripper is connected at one end with a catheter or tube having an actuating balloon at its tip, whereby the gripper is opened or dosed by inflation or deflation of the balloon. The gripper is designed to removably retain a member to which is connected a quantity or medicine, plugs, or micro-components. The miniature plastic gripper is inexpensive to fabricate and can be used for various applications, such as gripping, sorting, or placing of micron-scale particles for analysis.

  13. Miniature plastic gripper and fabrication method

    DOEpatents

    Benett, W.J.; Krulevitch, P.A.; Lee, A.P.; Northrup, M.A.; Folta, J.A.

    1997-03-11

    A miniature plastic gripper actuated by inflation of a miniature balloon and method of fabricating same are disclosed. The gripper is constructed of either heat-shrinkable or heat-expandable plastic tubing and is formed around a mandrel, then cut to form gripper prongs or jaws and the mandrel removed. The gripper is connected at one end with a catheter or tube having an actuating balloon at its tip, whereby the gripper is opened or closed by inflation or deflation of the balloon. The gripper is designed to removably retain a member to which is connected a quantity or medicine, plugs, or micro-components. The miniature plastic gripper is inexpensive to fabricate and can be used for various applications, such as gripping, sorting, or placing of micron-scale particles for analysis. 8 figs.

  14. Miniature plastic gripper and fabrication method

    DOEpatents

    Benett, William J.; Krulevitch, Peter A.; Lee, Abraham P.; Northrup, Milton A.; Folta, James A.

    1997-01-01

    A miniature plastic gripper actuated by inflation of a miniature balloon and method of fabricating same. The gripper is constructed of either heat-shrinkable or heat-expandable plastic tubing and is formed around a mandrel, then cut to form gripper prongs or jaws and the mandrel removed. The gripper is connected at one end with a catheter or tube having an actuating balloon at its tip, whereby the gripper is opened or closed by inflation or deflation of the balloon. The gripper is designed to removably retain a member to which is connected a quantity or medicine, plugs, or micro-components. The miniature plastic gripper is inexpensive to fabricate and can be used for various applications, such as gripping, sorting, or placing of micron-scale particles for analysis.

  15. Goniometry and Limb Girth in Miniature Dachshunds

    PubMed Central

    Thomovsky, Stephanie A.; Chen, Annie V.; Kiszonas, Alecia M.; Lutskas, Lori A.

    2016-01-01

    Purpose. To report the mean and median pelvic limb joint angles and girth measurements in miniature Dachshunds presenting with varying degrees of pelvic limb weakness secondary to thoracolumbar intervertebral disc extrusion. Methods. 15 miniature Dachshunds who presented to WSU-VTH for thoracolumbar disc extrusion. Dachshunds varied in neurologic status from ambulatory paraparetic to paraplegic at the time of measurements. Results. There were no significant differences in joint angles or girth among the three groups (ambulatory paraparetic, nonambulatory paraparetic, or paraplegic) (P > 0.05). When group was disregarded and values for extension, flexion, and girth combined, no differences existed. Conclusions. Goniometry and limb girth measurements can successfully be made in the miniature Dachshund; however, the shape of the Dachshund leg makes obtaining these values challenging. There were no differences in joint angle or girth measurements between dogs with varying neurologic dysfunction at the time of measurement. PMID:27403455

  16. FY 2006 Miniature Spherical Retroreflectors Final Report

    SciTech Connect

    Anheier, Norman C.; Bernacki, Bruce E.; Krishnaswami, Kannan

    2006-12-28

    Research done by the Infrared Photonics team at Pacific Northwest National Laboratory (PNNL) is focused on developing miniature spherical retroreflectors using the unique optical and material properties of chalcogenide glass to reduce both performance limiting spherical aberrations. The optimized optical performance will provide efficient signal retroreflection that enables a broad range of remote detection scenarios for mid-wave infrared (MWIR) and long-wave infrared (LWIR) sensing applications. Miniature spherical retroreflectors can be developed to aid in the detection of signatures of nuclear proliferation or other chemical vapor or radiation signatures. Miniature spherical retroreflectors are not only well suited to traditional LIDAR methods for chemical plume detection and identification, but could enable remote detection of difficult semi-volatile chemical materials or low level radiation sources.

  17. Electronic systems miniaturization using programmable logic devices

    SciTech Connect

    Ashton, E.C.; Bergeson, G.C.

    1990-10-01

    This report describes the steps which were taken to miniaturize a target circuit using Erasable Programmable Logic Devices (EPLDs). The original objective of this project was to explore the miniaturization of a circuit using both Application Specific Integrated Circuits (ASICs) and EPLDs to meet the following goals: balance cost and circuit density; reduce fabrication time; improve quality control issues by keeping much of the design in-house; and eliminate security risks by partitioning the design into ASIC and PLD (EPLD) sections. Due to cost considerations, the target circuit was miniaturized using only PLDs. The results of this project indicate that PLDs are capable of realizing fairly dense circuitry, are considerably less expensive than ASICs (by a factor of 500--1000), and are able to eliminate security risks and reduce fabrication time by keeping the design completely in-house.

  18. Compact Miniaturized Antenna for 210 MHz RFID

    NASA Technical Reports Server (NTRS)

    Lee, Richard Q.; Chun, Kue

    2008-01-01

    This paper describes the design and simulation of a miniaturized square-ring antenna. The miniaturized antenna, with overall dimensions of approximately one tenth of a wavelength (0.1 ), was designed to operate at around 210 MHz, and was intended for radio-frequency identification (RFID) application. One unique feature of the design is the use of a parasitic element to improve the performance and impedance matching of the antenna. The use of parasitic elements to enhance the gain and bandwidth of patch antennas has been demonstrated and reported in the literature, but such use has never been applied to miniaturized antennas. In this work, we will present simulation results and discuss design parameters and their impact on the antenna performance.

  19. Method and system for assembling miniaturized devices

    DOEpatents

    Montesanti, Richard C.; Klingmann, Jeffrey L.; Seugling, Richard M.

    2013-03-12

    An apparatus for assembling a miniaturized device includes a manipulator system including six manipulators operable to position and orient components of the miniaturized device with submicron precision and micron-level accuracy. The manipulator system includes a first plurality of motorized axes, a second plurality of manual axes, and force and torque and sensors. Each of the six manipulators includes at least one translation stage, at least one rotation stage, tooling attached to the at least one translation stage or the at least one rotation stage, and an attachment mechanism disposed at a distal end of the tooling and operable to attach at least a portion of the miniaturized device to the tooling. The apparatus also includes an optical coordinate-measuring machine (OCMM) including a machine-vision system, a laser-based distance-measuring probe, and a touch probe. The apparatus also includes an operator control system coupled to the manipulator system and the OCMM.

  20. FY 2005 Miniature Spherical Retroreflectors Final Report

    SciTech Connect

    Anheier, Norman C.; Bernacki, Bruce E.; Johnson, Bradley R.; Riley, Brian J.; Sliger, William A.

    2005-12-01

    Research done by the Infrared Photonics team at Pacific Northwest National Laboratory (PNNL) is focused on developing miniature spherical retroreflectors using the unique optical and material properties of chalcogenide glass to reduce both performance limiting spherical and chromatic aberrations. The optimized optical performance will provide efficient signal retroreflection that enables a broad range of remote detection scenarios for mid-wave infrared (MWIR) and long-wave infrared (LWIR) sensing applications. Miniature spherical retroreflectors can be developed to aid in the detection of signatures of nuclear proliferation or other chemical vapor or radiation signatures. Miniature spherical retroreflectors are not only well suited to traditional bistatic LIDAR methods for chemical plume detection and identification, but could enable remote detection of difficult semi-volatile chemical materials or low level radiation sources.

  1. Coulomb Repulsion in Miniature Ion Mobility Spectrometry

    SciTech Connect

    Xu, J.; Whitten, W.B.; Ramsey, J.M.

    1999-08-08

    We have undertaken a study of ion mobility resolution in a miniature ion mobility spectrometer with a drift channel 1.7 mm in diameter and 35 mm in length. The device attained a maximum resolution of 14 in separating ions of NO, O{sub 2}, and methyl iodine. The ions were generated by pulses from a frequency-quadrupled Nd:YAG laser. Broadening due to Coulomb repulsion was modeled theoretically and shown experimentally to have a major effect on the resolution of the miniature device.

  2. Miniature rotating transmissive optical drum scanner

    NASA Technical Reports Server (NTRS)

    Lewis, Robert (Inventor); Parrington, Lawrence (Inventor); Rutberg, Michael (Inventor)

    2013-01-01

    A miniature rotating transmissive optical scanner system employs a drum of small size having an interior defined by a circumferential wall rotatable on a drum axis, an optical element positioned within the interior of the drum, and a light-transmissive lens aperture provided at an angular position in the circumferential wall of the drum for scanning a light beam to or from the optical element in the drum along a beam azimuth angle as the drum is rotated. The miniature optical drum scanner configuration obtains a wide scanning field-of-view (FOV) and large effective aperture is achieved within a physically small size.

  3. Continuous flow nitration in miniaturized devices

    PubMed Central

    2014-01-01

    Summary This review highlights the state of the art in the field of continuous flow nitration with miniaturized devices. Although nitration has been one of the oldest and most important unit reactions, the advent of miniaturized devices has paved the way for new opportunities to reconsider the conventional approach for exothermic and selectivity sensitive nitration reactions. Four different approaches to flow nitration with microreactors are presented herein and discussed in view of their advantages, limitations and applicability of the information towards scale-up. Selected recent patents that disclose scale-up methodologies for continuous flow nitration are also briefly reviewed. PMID:24605161

  4. Batch fabrication of precision miniature permanent magnets

    DOEpatents

    Christenson, Todd R.; Garino, Terry J.; Venturini, Eugene L.

    2002-01-01

    A new class of processes for fabrication of precision miniature rare earth permanent magnets is disclosed. Such magnets typically have sizes in the range 0.1 to 10 millimeters, and dimensional tolerances as small as one micron. Very large magnetic fields can be produced by such magnets, lending to their potential application in MEMS and related electromechanical applications, and in miniature millimeter-wave vacuum tubes. This abstract contains simplifications, and is supplied only for purposes of searching, not to limit or alter the scope or meaning of any claims herein.

  5. Research on miniature gas analysis systems

    NASA Technical Reports Server (NTRS)

    Angell, J. B.

    1974-01-01

    Technology for fabricating very small valves, whose function will be to introduce a small sample of the gas to be analyzed into the main carrier gas stream flowing through the chromatograph column is described. In addition, some analyses were made of the factors governing the resolution of gas chromatographs, particularly those with miniature columns. These analyses show how important the column lining thickness is in governing the ability of a miniature column to separate components of an unknown gas. A brief description of column lining factors is included. Preliminary work on a super small thermistor detector is included.

  6. Miniature biotelemeter gives multichannel wideband biomedical data

    NASA Technical Reports Server (NTRS)

    Carraway, J. B.

    1972-01-01

    A miniature biotelemeter was developed for sensing and transmitting multiple channels of biomedical data over a radio link. The design of this miniature, 10-channel, wideband (5 kHz/channel), pulse amplitude modulation/ frequency modulation biotelemeter takes advantage of modern device technology (e.g., integrated circuit operational amplifiers, complementary symmetry/metal oxide semiconductor logic, and solid state switches) and hybrid packaging techniques. The telemeter is being used to monitor 10 channels of neuron firings from specific regions of the brain in rats implanted with chronic electrodes. Design, fabrication, and testing of an engineering model biotelemeter are described.

  7. Orthographic Reading Deficits in Dyslexic Japanese Children: Examining the Transposed-Letter Effect in the Color-Word Stroop Paradigm

    PubMed Central

    Ogawa, Shino; Shibasaki, Masahiro; Isomura, Tomoko; Masataka, Nobuo

    2016-01-01

    In orthographic reading, the transposed-letter effect (TLE) is the perception of a transposed-letter position word such as “cholocate” as the correct word “chocolate.” Although previous studies on dyslexic children using alphabetic languages have reported such orthographic reading deficits, the extent of orthographic reading impairment in dyslexic Japanese children has remained unknown. This study examined the TLE in dyslexic Japanese children using the color-word Stroop paradigm comprising congruent and incongruent Japanese hiragana words with correct and transposed-letter positions. We found that typically developed children exhibited Stroop effects in Japanese hiragana words with both correct and transposed-letter positions, thus indicating the presence of TLE. In contrast, dyslexic children indicated Stroop effects in correct letter positions in Japanese words but not in transposed, which indicated an absence of the TLE. These results suggest that dyslexic Japanese children, similar to dyslexic children using alphabetic languages, may also have a problem with orthographic reading. PMID:27303331

  8. Transposable elements in the mammalian embryo: pioneers surviving through stealth and service.

    PubMed

    Gerdes, Patricia; Richardson, Sandra R; Mager, Dixie L; Faulkner, Geoffrey J

    2016-01-01

    Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomologous recombination, and other potentially deleterious processes can cause sporadic disease by disrupting genome integrity or inducing abrupt gene expression changes. Here, we discuss recent evidence suggesting that TEs may contribute regulatory innovation to mammalian embryonic and pluripotent states as a means to ward off complete repression by their host genome. PMID:27161170

  9. The effect of transposable elements on phenotypic variation: insights from plants to humans.

    PubMed

    Wei, Liya; Cao, Xiaofeng

    2016-01-01

    Transposable elements (TEs), originally discovered in maize as controlling elements, are the main components of most eukaryotic genomes. TEs have been regarded as deleterious genomic parasites due to their ability to undergo massive amplification. However, TEs can regulate gene expression and alter phenotypes. Also, emerging findings demonstrate that TEs can establish and rewire gene regulatory networks by genetic and epigenetic mechanisms. In this review, we summarize the key roles of TEs in fine-tuning the regulation of gene expression leading to phenotypic plasticity in plants and humans, and the implications for adaption and natural selection. PMID:26753674

  10. Germline transformation of Aedes fluviatilis (Diptera:Culicidae) with the piggyBac transposable element.

    PubMed

    Rodrigues, Flávia Guimarães; Oliveira, Sabrina Barbosa; Rocha, Bruno Coelho; Moreira, Luciano Andrade

    2006-11-01

    The technique to generate transgenic mosquitoes requires adaptation for each target species because of aspects related to species biology, sensitivity to manipulation and rearing conditions. Here we tested different parameters on the microinjection procedure in order to obtain a transgenic Neotropical mosquito species. By using a transposon-based strategy we were able to successfully transform Aedes fluviatilis (Lutz), which can be used as an avian malaria model. These results demonstrate the usefulness of the piggyBac transposable element as a transformation vector for Neotropical mosquito species and opens up new research frontiers for South American mosquito vectors. PMID:17160283

  11. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

    PubMed Central

    Burlet, Nelly

    2016-01-01

    While the evolutionary mechanisms driving eukaryote genome size evolution are still debated, repeated element content appears to be crucial. Here, we reconstructed the phylogeny and identified repeats in the genome of 26 Drosophila exhibiting a twofold variation in genome size. The content in transposable elements (TEs) is highly correlated to genome size evolution among these closely related species. We detected a strong phylogenetic signal on the evolution of both genome size and TE content, and a genome contraction in the Drosophila melanogaster subgroup. PMID:27576524

  12. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies.

    PubMed

    Sessegolo, Camille; Burlet, Nelly; Haudry, Annabelle

    2016-08-01

    While the evolutionary mechanisms driving eukaryote genome size evolution are still debated, repeated element content appears to be crucial. Here, we reconstructed the phylogeny and identified repeats in the genome of 26 Drosophila exhibiting a twofold variation in genome size. The content in transposable elements (TEs) is highly correlated to genome size evolution among these closely related species. We detected a strong phylogenetic signal on the evolution of both genome size and TE content, and a genome contraction in the Drosophila melanogaster subgroup. PMID:27576524

  13. Two Views of Islam: Ceramic Tile Design and Miniatures.

    ERIC Educational Resources Information Center

    Macaulay, Sara Grove

    2001-01-01

    Describes an art project focusing on Islamic art that consists of two parts: (1) ceramic tile design; and (2) Islamic miniatures. Provides background information on Islamic art and step-by-step instructions for designing the Islamic tile and miniature. Includes learning objectives and resources on Islamic tile miniatures. (CMK)

  14. A miniature mass spectrometer for hydrazine detection

    NASA Technical Reports Server (NTRS)

    Houseman, J.; Sinha, M. P.

    2003-01-01

    A Miniature Mass Spectrometer (MMS) with a focal plane (Mattauch-Herzog) geometry has been developed at the Jet Propulsion Laboratory. The MMS has the potential to meet the NASA requirements of 10 parts per billion sensitivity for Hydrazine detection, as well as the requirements for instant response, portability, and low maintenance.

  15. Miniaturization of EISCAP sensor for triglyceride detection.

    PubMed

    Vemulachedu, Hareesh; Fernandez, Renny Edwin; Bhattacharya, Enakshi; Chadha, Anju

    2009-12-01

    In this paper we discuss the fabrication and characterization of miniaturized triglyceride biosensors on crystalline silicon and porous silicon (PS) substrates. The sensors are miniaturized Electrolyte Insulator Semiconductor Capacitors (mini-EISCAPs), which primarily sense the pH variation of the electrolyte used. The lipase enzyme, which catalyses the hydrolysis of triglycerides, was immobilized on the sensor surface. Triglyceride solutions introduced into the enzyme immobilized sensor produced butyric acid which causes the change in pH of the electrolyte. Miniaturized EISCAP sensors were fabricated using bulk micromachining technique and have silicon nitride as the pH sensitive dielectric layer. The sensors are cubical pits of dimensions 1,500 microm x 1,500 microm x 100 microm which can hold an electrolyte volume of 0.1 microl. The pH changes in the solution can be sensed through the EISCAP sensors by monitoring the flatband voltage shift in the Capacitance-Voltage (C-V) characteristics taken during the course of the reaction. The reaction rate is found to be quite high in the miniature cells when compared to the sensors of bigger dimensions. PMID:18649048

  16. Miniature pulse tube cooler at 100HZ

    NASA Astrophysics Data System (ADS)

    Chen, Houlei; Xu, Nana; Yin, Chuanlin; Cai, Jinghui; Liang, Jingtao

    2012-06-01

    Miniature pulse tube coolers operating at 100Hz have been designed and manufactured. The regenerator is designed by REGEN 3.2, and the inertance tube is simulated by DeltaE. An in-line prototype is manufactured according to the theoretical design parameters initially. On that basis, a coaxial cooler is developed and with double inlet it gains higher cooling performance.

  17. Miniaturized symmetrization optics for junction laser

    NASA Technical Reports Server (NTRS)

    Hammer, Jacob M. (Inventor); Kaiser, Charlie J. (Inventor); Neil, Clyde C. (Inventor)

    1982-01-01

    Miniaturized optics comprising transverse and lateral cylindrical lenses composed of millimeter-sized rods with diameters, indices-of-refraction and spacing such that substantially all the light emitted as an asymmetrical beam from the emitting junction of the laser is collected and translated to a symmetrical beam.

  18. Miniature Marimbas: Migrant Workers' Memories of Home.

    ERIC Educational Resources Information Center

    Howell, Jayne

    1995-01-01

    Three Mexican migrant workers attending classes at Geneseo (New York) Migrant Center used leftover art materials to represent their home village in miniature. A spontaneous artistic expression, the objects allowed the men an opportunity to reminisce and reinforce cultural and interpersonal ties, and gave insight about their background and culture…

  19. Miniature Housings for Electronics With Standard Interfaces

    NASA Technical Reports Server (NTRS)

    Howard, David E.; Smith, Dennis A.; Alhorn, Dean C.

    2006-01-01

    A family of general-purpose miniature housings has been designed to contain diverse sensors, actuators, and drive circuits plus associated digital electronic readout and control circuits. The circuits contained in the housings communicate with the external world via standard RS-485 interfaces.

  20. MINIATURE ACID CONDENSATION SYSTEM: DESIGN AND OPERATION

    EPA Science Inventory

    An extractive source sampling system was designed and constructed. The sampling system measures gaseous sulfuric acid and sulfur dioxide in combustion emissions. The miniature acid condensation system (MACS) includes a high-temperature quartz probe and quartz-filter holder. Since...

  1. A brief history of the status of transposable elements: from junk DNA to major players in evolution.

    PubMed

    Biémont, Christian

    2010-12-01

    The idea that some genetic factors are able to move around chromosomes emerged more than 60 years ago when Barbara McClintock first suggested that such elements existed and had a major role in controlling gene expression and that they also have had a major influence in reshaping genomes in evolution. It was many years, however, before the accumulation of data and theories showed that this latter revolutionary idea was correct although, understandably, it fell far short of our present view of the significant influence of what are now known as "transposable elements" in evolution. In this article, I summarize the main events that influenced my thinking about transposable elements as a young scientist and the influence and role of these specific genomic elements in evolution over subsequent years. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. PMID:21156958

  2. A candidate autonomous version of the wheat MITE Hikkoshi is present in the rice genome.

    PubMed

    Saito, M; Yonemaru, J; Ishikawa, G; Nakamura, T

    2005-06-01

    A miniature inverted-repeat transposable element (MITE), designated as Hikkoshi, was previously identified in the null Wx-A1 allele of Turkish bread wheat lines. This MITE is 165 bp in size and has 12-bp terminal inverted repeats (TIRs) flanked by 8-bp target site duplications (TSDs). Southern and PCR analyses demonstrated the presence of multiple copies of Hikkoshi in the wheat genome. Database searches indicated that Hikkoshi MITEs are also present in barley, rice and maize. A 3.4-kb element that has Hikkoshi-like TIRs flanked by 8-bp TSDs has now been identified in the rice genome. This element shows high similarity to the 5' subterminal region of the wheat Hikkoshi MITE and contains a transposase (TPase) coding region. The TPase has two conserved domains, ZnF_TTF and hATC, and its amino acid sequence shows a high degree of homology to TPases encoded by Tip100 transposable elements belonging to the hAT superfamily. We designated the 3.4-kb element as OsHikkoshi. Several wheat clones deposited in EST databases showed sequence similarity to the TPase ORF of OsHikkoshi. The sequence information from the TPase of OsHikkoshi will thus be useful in isolating the autonomous element of the Hikkoshi system from wheat. PMID:15883824

  3. Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements

    PubMed Central

    Levy, Asaf; Schwartz, Schraga; Ast, Gil

    2010-01-01

    Throughout evolution, eukaryotic genomes have been invaded by transposable elements (TEs). Little is known about the factors leading to genomic proliferation of TEs, their preferred integration sites and the molecular mechanisms underlying their insertion. We analyzed hundreds of thousands nested TEs in the human genome, i.e. insertions of TEs into existing ones. We first discovered that most TEs insert within specific ‘hotspots’ along the targeted TE. In particular, retrotransposed Alu elements contain a non-canonical single nucleotide hotspot for insertion of other Alu sequences. We next devised a method for identification of integration sequence motifs of inserted TEs that are conserved within the targeted TEs. This method revealed novel sequences motifs characterizing insertions of various important TE families: Alu, hAT, ERV1 and MaLR. Finally, we performed a global assessment to determine the extent to which young TEs tend to nest within older transposed elements and identified a 4-fold higher tendency of TEs to insert into existing TEs than to insert within non-TE intergenic regions. Our analysis demonstrates that TEs are highly biased to insert within certain TEs, in specific orientations and within specific targeted TE positions. TE nesting events also reveal new characteristics of the molecular mechanisms underlying transposition. PMID:20008508

  4. The role of transposable elements in health and diseases of the central nervous system.

    PubMed

    Reilly, Matthew T; Faulkner, Geoffrey J; Dubnau, Joshua; Ponomarev, Igor; Gage, Fred H

    2013-11-01

    First discovered in maize by Barbara McClintock in the 1940s, transposable elements (TEs) are DNA sequences that in some cases have the ability to move along chromosomes or "transpose" in the genome. This revolutionary finding was initially met with resistance by the scientific community and viewed by some as heretical. A large body of knowledge has accumulated over the last 60 years on the biology of TEs. Indeed, it is now known that TEs can generate genomic instability and reconfigure gene expression networks both in the germline and somatic cells. This review highlights recent findings on the role of TEs in health and diseases of the CNS, which were presented at the 2013 Society for Neuroscience meeting. The work of the speakers in this symposium shows that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings on TE expression and function in the CNS have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in shaping individual behavior and contribute to vulnerability to disease. PMID:24198348

  5. Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species.

    PubMed

    Stapley, Jessica; Santure, Anna W; Dennis, Stuart R

    2015-05-01

    Rapid adaptation of invasive species to novel habitats has puzzled evolutionary biologists for decades, especially as this often occurs in the face of limited genetic variability. Although some ecological traits common to invasive species have been identified, little is known about the possible genomic/genetic mechanisms that may underlie their success. A common scenario in many introductions is that small founder population sizes will often lead to reduced genetic diversity, but that invading populations experience large environmental perturbations, such as changes in habitat and environmental stress. Although sudden and intense stress is usually considered in a negative context, these perturbations may actually facilitate rapid adaptation by affecting genome structure, organization and function via interactions with transposable elements (TEs), especially in populations with low genetic diversity. Stress-induced changes in TE activity can alter gene action and can promote structural variation that may facilitate the rapid adaptation observed in new environments. We focus here on the adaptive potential of TEs in relation to invasive species and highlight their role as powerful mutational forces that can rapidly create genetic diversity. We hypothesize that activity of transposable elements can explain rapid adaptation despite low genetic variation (the genetic paradox of invasive species), and provide a framework under which this hypothesis can be tested using recently developed and emerging genomic technologies. PMID:25611725

  6. An efficient tensor transpose algorithm for multicore CPU, Intel Xeon Phi, and NVidia Tesla GPU

    NASA Astrophysics Data System (ADS)

    Lyakh, Dmitry I.

    2015-04-01

    An efficient parallel tensor transpose algorithm is suggested for shared-memory computing units, namely, multicore CPU, Intel Xeon Phi, and NVidia GPU. The algorithm operates on dense tensors (multidimensional arrays) and is based on the optimization of cache utilization on x86 CPU and the use of shared memory on NVidia GPU. From the applied side, the ultimate goal is to minimize the overhead encountered in the transformation of tensor contractions into matrix multiplications in computer implementations of advanced methods of quantum many-body theory (e.g., in electronic structure theory and nuclear physics). A particular accent is made on higher-dimensional tensors that typically appear in the so-called multireference correlated methods of electronic structure theory. Depending on tensor dimensionality, the presented optimized algorithms can achieve an order of magnitude speedup on x86 CPUs and 2-3 times speedup on NVidia Tesla K20X GPU with respect to the naïve scattering algorithm (no memory access optimization). The tensor transpose routines developed in this work have been incorporated into a general-purpose tensor algebra library (TAL-SH).

  7. Frequent transpositions of Drosophila melanogaster HeT-A transposable elements to receding chromosome ends.

    PubMed Central

    Biessmann, H; Champion, L E; O'Hair, M; Ikenaga, K; Kasravi, B; Mason, J M

    1992-01-01

    HeT-A elements are a new family of transposable elements in Drosophila that are found exclusively in telomeric regions and in the pericentric heterochromatin. Transposition of these elements onto broken chromosome ends has been implicated in chromosome healing. To monitor the fate of HeT-A elements that had attached to broken ends of the X chromosome, we examined individual X chromosomes from a defined population over a period of 17 generations. The ends of the X chromosomes with new HeT-A additions receded at the same rate as the broken ends before the HeT-A elements attached. In addition, some chromosomes, approximately 1% per generation, had acquired new HeT-A sequences of an average of 6 kb at their ends with oligo(A) tails at the junctions. Thus, the rate of addition of new material per generation matches the observed rate of terminal loss (70-75 bp) caused by incomplete replication at the end of the DNA molecule. One such recently transposed HeT-A element which is at least 12 kb in length has been examined in detail. It contains a single open reading frame of 2.8 kb which codes for a gag-like protein. Images PMID:1330538

  8. TRANSPOSED LETTER EFFECTS IN PREFIXED WORDS: IMPLICATIONS FOR MORPHOLOGICAL DECOMPOSITION1

    PubMed Central

    Masserang, Kathleen M.; Pollatsek, Alexander

    2012-01-01

    A crucial issue in word encoding is whether morphemes are involved in early stages. One paradigm that tests for this employs the transposed letter (TL) effect – the difference in the times to process a word (misfile) when it is preceded by a TL prime (mifsile) and when it is preceded by a substitute letter (SL) prime (mintile) – and examines whether the TL effect is smaller when the two adjacent letters cross a morpheme boundary. The evidence from prior studies is not consistent. Experiments 1 and 2 employed a parafoveal preview paradigm in which the transposed letters either crossed the prefix-stem boundary or did not, and found a clear TL effect regardless of whether the two letters crossed the morpheme boundary. Experiment 3 replicated this finding employing a masked priming lexical-decision paradigm. It thus appears that morphemes are not involved in early processes in English that are sensitive to letter order. There is some evidence for morphemic modulation of the TL effect in other languages; thus, the properties of the language may modulate when morphemes influence early letter position encoding. PMID:23082239

  9. Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

    PubMed Central

    Castanera, Raúl; López-Varas, Leticia; Borgognone, Alessandra; LaButti, Kurt; Lapidus, Alla; Schmutz, Jeremy; Grimwood, Jane; Pisabarro, Antonio G.; Grigoriev, Igor V.; Ramírez, Lucía

    2016-01-01

    Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation. PMID:27294409

  10. Inhibition of RNA interference and modulation of transposable element expression by cell death in Drosophila.

    PubMed

    Xie, Weiwu; Liang, Chengzhi; Birchler, James A

    2011-08-01

    RNA interference (RNAi) regulates gene expression by sequence-specific destruction of RNA. It acts as a defense mechanism against viruses and represses the expression of transposable elements (TEs) and some endogenous genes. We report that mutations and transgene constructs that condition cell death suppress RNA interference in adjacent cells in Drosophila melanogaster. The reversal of RNAi is effective for both the white (w) eye color gene and green fluorescent protein (GFP), indicating the generality of the inhibition. Antiapoptotic transgenes that reverse cell death will also reverse the inhibition of RNAi. Using GFP and a low level of cell death produced by a heat shock-head involution defective (hs-hid) transgene, the inhibition appears to occur by blocking the conversion of double-stranded RNA (dsRNA) to short interfering RNA (siRNA). We also demonstrate that the mus308 gene and endogenous transposable elements, which are both regularly silenced by RNAi, are increased in expression and accompanied by a reduced level of siRNA, when cell death occurs. The finding that chronic ectopic cell death affects RNAi is critical for an understanding of the application of the technique in basic and applied studies. These results also suggest that developmental perturbations, disease states, or environmental insults that cause ectopic cell death would alter transposon and gene expression patterns in the organism by the inhibition of small RNA silencing processes. PMID:21596898

  11. An efficient tensor transpose algorithm for multicore CPU, Intel Xeon Phi, and NVidia Tesla GPU

    SciTech Connect

    Lyakh, Dmitry I.

    2015-01-05

    An efficient parallel tensor transpose algorithm is suggested for shared-memory computing units, namely, multicore CPU, Intel Xeon Phi, and NVidia GPU. The algorithm operates on dense tensors (multidimensional arrays) and is based on the optimization of cache utilization on x86 CPU and the use of shared memory on NVidia GPU. From the applied side, the ultimate goal is to minimize the overhead encountered in the transformation of tensor contractions into matrix multiplications in computer implementations of advanced methods of quantum many-body theory (e.g., in electronic structure theory and nuclear physics). A particular accent is made on higher-dimensional tensors that typically appear in the so-called multireference correlated methods of electronic structure theory. Depending on tensor dimensionality, the presented optimized algorithms can achieve an order of magnitude speedup on x86 CPUs and 2-3 times speedup on NVidia Tesla K20X GPU with respect to the na ve scattering algorithm (no memory access optimization). Furthermore, the tensor transpose routines developed in this work have been incorporated into a general-purpose tensor algebra library (TAL-SH).

  12. An efficient tensor transpose algorithm for multicore CPU, Intel Xeon Phi, and NVidia Tesla GPU

    DOE PAGESBeta

    Lyakh, Dmitry I.

    2015-01-05

    An efficient parallel tensor transpose algorithm is suggested for shared-memory computing units, namely, multicore CPU, Intel Xeon Phi, and NVidia GPU. The algorithm operates on dense tensors (multidimensional arrays) and is based on the optimization of cache utilization on x86 CPU and the use of shared memory on NVidia GPU. From the applied side, the ultimate goal is to minimize the overhead encountered in the transformation of tensor contractions into matrix multiplications in computer implementations of advanced methods of quantum many-body theory (e.g., in electronic structure theory and nuclear physics). A particular accent is made on higher-dimensional tensors that typicallymore » appear in the so-called multireference correlated methods of electronic structure theory. Depending on tensor dimensionality, the presented optimized algorithms can achieve an order of magnitude speedup on x86 CPUs and 2-3 times speedup on NVidia Tesla K20X GPU with respect to the na ve scattering algorithm (no memory access optimization). Furthermore, the tensor transpose routines developed in this work have been incorporated into a general-purpose tensor algebra library (TAL-SH).« less

  13. Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles.

    PubMed

    Castanera, Raúl; López-Varas, Leticia; Borgognone, Alessandra; LaButti, Kurt; Lapidus, Alla; Schmutz, Jeremy; Grimwood, Jane; Pérez, Gúmer; Pisabarro, Antonio G; Grigoriev, Igor V; Stajich, Jason E; Ramírez, Lucía

    2016-06-01

    Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation. PMID:27294409

  14. Miniature Scroll Pumps Fabricated by LIGA

    NASA Technical Reports Server (NTRS)

    Wiberg, Dean; Shcheglov, Kirill; White, Victor; Bae, Sam

    2009-01-01

    Miniature scroll pumps have been proposed as roughing pumps (low - vacuum pumps) for miniature scientific instruments (e.g., portable mass spectrometers and gas analyzers) that depend on vacuum. The larger scroll pumps used as roughing pumps in some older vacuum systems are fabricated by conventional machining. Typically, such an older scroll pump includes (1) an electric motor with an eccentric shaft to generate orbital motion of a scroll and (2) conventional bearings to restrict the orbital motion to a circle. The proposed miniature scroll pumps would differ from the prior, larger ones in both design and fabrication. A miniature scroll pump would include two scrolls: one mounted on a stationary baseplate and one on a flexure stage (see figure). An electromagnetic actuator in the form of two pairs of voice coils in a push-pull configuration would make the flexure stage move in the desired circular orbit. The capacitance between the scrolls would be monitored to provide position (gap) feedback to a control system that would adjust the drive signals applied to the voice coils to maintain the circular orbit as needed for precise sealing of the scrolls. To minimize power consumption and maximize precision of control, the flexure stage would be driven at the frequency of its mechanical resonance. The miniaturization of these pumps would entail both operational and manufacturing tolerances of <1 m. Such tight tolerances cannot be achieved easily by conventional machining of high-aspect-ratio structures like those of scroll-pump components. In addition, the vibrations of conventional motors and ball bearings exceed these tight tolerances by an order of magnitude. Therefore, the proposed pumps would be fabricated by the microfabrication method known by the German acronym LIGA ( lithographie, galvanoformung, abformung, which means lithography, electroforming, molding) because LIGA has been shown to be capable of providing the required tolerances at large aspect ratios.

  15. Genomic distribution of copia-like transposable elements in somatic tissues and during development of Drosophila melanogaster.

    PubMed

    Di Franco, C; Pisano, C; Dimitri, P; Gigliotti, S; Junakovic, N

    1989-12-01

    The genomic distribution of elements of the copia, 412, B 104, mdg 1, mdg 4 and 1731 transposon families was compared by the Southern technique in DNA preparations extracted from brains, salivary glands and adult flies of two related Drosophila lines. The copia, 412 and mdg 1 sequences were also probed in DNA from sperm, embryos, and 1st and 2nd instar larvae. The homogeneity of the patterns observed shows that somatic transposition is unlikely to occur frequently. A correlation between mobility and the euchromatic or heterochromatic location of transposable elements is discussed. In addition, an explanation of the variable band intensities of transposable elements in Southern autoradiographs is proposed. PMID:2560696

  16. Miniature Heat Transport System for Nanosatellite Technology

    NASA Technical Reports Server (NTRS)

    Douglas, Donya M,

    1999-01-01

    The scientific understanding of key physical processes between the Sun and the Earth require simultaneous measurements from many vantage points in space. Nano-satellite technologies will enable a class of constellation missions for the NASA Space Science Sun-Earth Connections. This recent emphasis on the implementation of smaller satellites leads to a requirement for development of smaller subsystems in several areas. Key technologies under development include: advanced miniaturized chemical propulsion; miniaturized sensors; highly integrated, compact electronics; autonomous onboard and ground operations; miniatures low power tracking techniques for orbit determination; onboard RF communications capable of transmitting data to the ground from far distances; lightweight efficient solar array panels; lightweight, high output battery cells; lightweight yet strong composite materials for the nano-spacecraft and deployer-ship structures. These newer smaller systems may have higher power densities and higher thermal transport requirements than seen on previous small satellites. Furthermore, the small satellites may also have a requirement to maintain thermal control through extended earth shadows, possibly up to 8 hours long. Older thermal control technology, such as heaters, thermostats, and heat pipes, may not be sufficient to meet the requirements of these new systems. Conversely, a miniature two-phase heat transport system (Mini-HTS) such as a Capillary Pumped Loop (CPL) or Loop Heat Pipe (LBP) is a viable alternative. A Mini-HTS can provide fine temperature control, thermal diode action, and a highly efficient means of heat transfer. The Mini-HTS would have power capabilities in the range of tens of watts or less and provide thermal control over typical spacecraft ranges. The Mini-HTS would allow the internal portion of the spacecraft to be thermally isolated from the external radiator, thus protecting the internal components from extreme cold temperatures during an

  17. Genomic patterns associated with paternal/maternal distribution of transposable elements

    NASA Astrophysics Data System (ADS)

    Jurka, Jerzy

    2003-03-01

    Transposable elements (TEs) are specialized DNA or RNA fragments capable of surviving in intragenomic niches. They are commonly, perhaps unjustifiably referred to as "selfish" or "parasitic" elements. TEs can be divided in two major classes: retroelements and DNA transposons. The former include non-LTR retrotransposons and retrovirus-like elements, using reverse transriptase for their reproduction prior to integration into host DNA. The latter depend mostly on host DNA replication, with possible exception of rolling-circle transposons recently discovered by our team. I will review basic information on TEs, with emphasis on human Alu and L1 retroelements discussed in the context of genomic organization. TEs are non-randomly distributed in chromosomal DNA. In particular, human Alu elements tend to prefer GC-rich regions, whereas L1 accumulate in AT-rich regions. Current explanations of this phenomenon focus on the so called "target effects" and post-insertional selection. However, the proposed models appear to be unsatisfactory and alternative explanations invoking "channeling" to different chromosomal regions will be a major focus of my presentation. Transposable elements (TEs) can be expressed and integrated into host DNA in the male or female germlines, or both. Different models of expression and integration imply different proportions of TEs on sex chromosomes and autosomes. The density of recently retroposed human Alu elements is around three times higher on chromosome Y than on chromosome X, and over two times higher than the average density for all human autosomes. This implies Alu activity in paternal germlines. Analogous inter-chromosomal proportions for other repeat families should determine their compatibility with one of the three basic models describing the inheritance of TEs. Published evidence indicates that maternally and paternally imprinted genes roughly correspond to GC-rich and AT-rich DNA. This may explain the observed chromosomal distribution of

  18. Miniature synthetic-aperture radar system

    NASA Astrophysics Data System (ADS)

    Stockton, Wayne; Stromfors, Richard D.

    1990-11-01

    Loral Defense Systems-Arizona has developed a high-performance synthetic-aperture radar (SAR) for small aircraft and unmanned aerial vehicle (UAV) reconnaissance applications. This miniature radar, called Miniature Synthetic-Aperture Radar (MSAR), is packaged in a small volume and has low weight. It retains key features of large SAR systems, including high-resolution imaging and all-weather operation. The operating frequency of MSAR can optionally be selected to provide foliage penetration capability. Many imaging radar configurations can be derived using this baseline system. MSAR with a data link provides an attractive UAV sensor. MSAR with a real-time image formation processor is well suited to installations where onboard processing and immediate image analysis are required. The MSAR system provides high-resolution imaging for short-to-medium range reconnaissance applications.

  19. Miniaturization of holographic Fourier-transform spectrometers.

    PubMed

    Agladze, Nikolay I; Sievers, Albert J

    2004-12-20

    Wave propagation equations in the stationary-phase approximation have been used to identify the theoretical bounds of a miniature holographic Fourier-transform spectrometer (HFTS). It is demonstrated that the HFTS throughput can be larger than for a scanning Fourier-transform spectrometer. Given room- or a higher-temperature constraint, a small HFTS has the potential to outperform a small multichannel dispersive spectrograph with the same resolving power because of the size dependence of the signal-to-noise ratio. These predictions are used to analyze the performance of a miniature HFTS made from simple optical components covering a broad spectral range from the UV to the near IR. The importance of specific primary aberrations in limiting the HFTS performance has been both identified and verified. PMID:15646777

  20. Design considerations for miniaturized PEM fuel cells

    NASA Astrophysics Data System (ADS)

    Meyers, Jeremy P.; Maynard, Helen L.

    In this paper, we consider the design of a miniaturized proton-exchange membrane (PEM) fuel cell for powering 0.5-20 W portable telecommunication and computing devices. Our design is implemented on a silicon substrate to take advantage of advanced silicon processing technology in order to minimize production costs. The reduced length scales afforded by silicon processing allow us to consider designs that would be prohibited by excessive Ohmic losses in larger systems. We employ a mathematical model to quantify the effects of the secondary current distribution on two competing cell designs. In addition to the design of the cell itself, we discuss key integration issues and engineering trade-offs relevant to all miniaturized fuel cell systems: air movement, fuel delivery and water balance, thermal management and load handling.

  1. Miniaturized Wilkinson Power Dividers Utilizing Capacitive Loading

    NASA Technical Reports Server (NTRS)

    Scardelletti, Maximilian C.; Ponchak, George E.; Weller, Thomas M.

    2001-01-01

    This letter reports the miniaturization of a planar Wilkinson power divider by capacitive loading of the quarter wave transmission lines employed in conventional Wilkinson power dividers. Reduction of the transmission line segments from lambda/4 to between lambda/5 and lambda/12 are reported here. The input and output lines at the three ports and the lines comprising the divider itself are coplanar waveguide (CPW) and asymmetric coplanar stripline (ACPS), respectively. The 10 GHZ power dividers are fabricated on high resistivity silicon (HRS) and alumina wafers. These miniaturized dividers are 74% smaller than conventional Wilkinson power dividers, and have a return loss better than +30 dB and an insertion loss less than 0.55 dB. Design equations and a discussion about the effect of parasitic reactance on the isolation are presented for the first time.

  2. Skeletal atavism in a miniature horse.

    PubMed

    Tyson, Reid; Graham, John P; Colahan, Patrick T; Berry, Clifford R

    2004-01-01

    An 8-month-old miniature horse filly was presented for evaluation of severe rotational and angular limb deformities of the thoracic and pelvic limbs. On radiographic examination, complete ulnas and fibulas were identified. These findings are consistent with a condition previously described as a form of atavism. The term atavism is used to describe the reappearance of a trait or character that was seen in all earlier evolutionary specimens of a particular species, but has not been seen in recent ancestors. The atavistic traits of complete ulnas and fibulas have previously been described in Welsh and Shetland Ponies, all of which had severe rotational and angular limb deformities. In this horse, bilateral osteochondritis dissecans of the medial trochlear ridge of the talii were also identified. To the authors' knowledge, this is the first report of the atavistic traits of complete ulnas and fibulas seen in the miniature horse. PMID:15373256

  3. Miniature sensor suitable for electronic nose applications

    NASA Astrophysics Data System (ADS)

    Pinnaduwage, Lal A.; Gehl, Anthony C.; Allman, Steve L.; Johansson, Alicia; Boisen, Anja

    2007-05-01

    A major research effort has been devoted over the years for the development of chemical sensors for the detection of chemical and explosive vapors. However, the deployment of such chemical sensors will require the use of multiple sensors (probably tens of sensors) in a sensor package to achieve selective detection. In order to keep the overall detector unit small, miniature sensors with sufficient sensitivity of detection will be needed. We report sensitive detection of dimethyl methylphosphonate (DMMP), a stimulant for the nerve agents, using a miniature sensor unit based on piezoresistive microcantilevers. The sensor can detect parts-per-trillion concentrations of DMMP within 10s exposure times. The small size of the sensor makes it ideally suited for electronic nose applications.

  4. Raytheon Advanced Miniature Cryocooler Characterization Testing

    NASA Astrophysics Data System (ADS)

    Conrad, T.; Yates, R.; Schaefer, B.; Bellis, L.; Pillar, M.; Barr, M.

    2015-12-01

    The Raytheon Advanced Miniature (RAM) cryocooler is a flight packaged, high frequency pulse tube cooler with an integrated surge volume and inertance tube. Its design has been fully optimized to make use of the Raytheon Advanced Regenerator, resulting in improved efficiency relative to previous Raytheon pulse tube coolers. In this paper, thermodynamic characterization data for the RAM cryocooler is presented along with details of its design specifications.

  5. Miniature tilting pad gas lubricated bearing

    SciTech Connect

    Sixsmith, H.; Swift, W.L.

    1983-12-01

    This paper describes the design and development of a miniature tilting pad gas bearing developed for use in very small turbomachines. The bearings have been developed for cryogenic turboexpanders with shaft diameters down to about 0.3 cm and rotational speeds up to one million rpm. Cryogenic expansion turbines incorporating this type of bearing should be suitable for refrigeration rates down to about 10 w.

  6. High Q Miniature Sapphire Acoustic Resonator

    NASA Technical Reports Server (NTRS)

    Wang, Rabi T.; Tjoelker, R. L.

    2010-01-01

    We have demonstrated high Q measurements in a room temperature Miniature Sapphire Acoustic Resonator (MSAR). Initial measurements of bulk acoustic modes in room temperature sapphire at 39 MHz have demonstrated a Q of 8.8 x 10(exp 6). The long term goal of this work is to integrate such a high Q resonator with small, low noise quartz oscillator electronics, providing a fractional frequency stability better than 1 x 10(exp -14) @ 1s.

  7. A miniature tilting pad gas lubricated bearing

    NASA Astrophysics Data System (ADS)

    Sixsmith, H.; Swift, W. L.

    1983-12-01

    This paper describes the design and development of a miniature tilting pad gas bearing developed for use in very small turbomachines. The bearings have been developed for cryogenic turboexpanders with shaft diameters down to about 0.3 cm and rotational speeds up to one million rpm. Cryogenic expansion turbines incorporating this type of bearing should be suitable for refrigeration rates down to about 10 w.

  8. A miniature tilting pad gas lubricated bearing

    NASA Technical Reports Server (NTRS)

    Sixsmith, H.; Swift, W. L.

    1983-01-01

    This paper describes the design and development of a miniature tilting pad gas bearing developed for use in very small turbomachines. The bearings have been developed for cryogenic turboexpanders with shaft diameters down to about 0.3 cm and rotational speeds up to one million rpm. Cryogenic expansion turbines incorporating this type of bearing should be suitable for refrigeration rates down to about 10 w.

  9. Miniature Reversal Electron-Attachment Detector

    NASA Technical Reports Server (NTRS)

    Chutjian, Ara

    1994-01-01

    Miniature reversal electron-attachment detector (miniREAD) enables direct injection of air or vapor at atmospheric pressure from monitored area into mass-spectrometric instrument to detect explosives, narcotics, or other substances, vapors of which suspected of being present in low concentrations. In comparison with older reversal electron-attachment detector, miniREAD simpler in design; more rugged; and easier to build, repair, and maintain. In addition, probably more sensitive.

  10. Imaging performance of a miniature integrated microendoscope

    PubMed Central

    Rogers, Jeremy D.; Landau, Sara; Tkaczyk, Tomasz S.; Descour, Michael R.; Rahman, Mohammed S.; Richards-Kortum, Rebecca; Kärkäinen, Ari H. O.; Christenson, Todd

    2011-01-01

    An integrated miniature multi-modal microscope (4M device) for microendoscopy was built and tested. Imaging performance is evaluated and imaging results are presented for both fluorescence and reflectance samples. Images of biological samples show successful imaging of both thin layers of fixed cells prepared on a slide as well as thick samples of excised fixed porcine epithelial tissue, thus demonstrating the potential for in vivo use. PMID:19021400

  11. Miniature, Variable-Speed Control Moment Gyroscope

    NASA Technical Reports Server (NTRS)

    Bilski, Steve; Kline-Schoder, Robert; Sorensen, Paul

    2011-01-01

    The Miniature Variable-Speed Control Moment Gyroscope (MVS-CMG) was designed for small satellites (mass from less than 1 kg up to 500 kg). Currently available CMGs are too large and heavy, and available miniature CMGs do not provide sufficient control authority for use on practical satellites. This primarily results from the need to greatly increase the speed of rotation of the flywheel in order to reduce the flywheel size and mass. This goal was achieved by making use of a proprietary, space-qualified, high-speed (100,000 rpm) motor technology to spin the flywheel at a speed ten times faster than other known miniature CMGs under development. NASA is supporting innovations in propulsion, power, and guidance and navigation systems for low-cost small spacecraft. One of the key enabling technologies is attitude control mechanisms. CMGs are particularly attractive for spacecraft attitude control since they can achieve higher torques with lower mass and power than reaction wheels, and they provide continuous torque capability that enables precision pointing (in contrast to on-off thruster control). The aim of this work was to develop a miniature, variable-speed CMG that is sized for use on small satellites. To achieve improved agility, these spacecraft must be able to slew at high rate, which requires attitude control actuators that can apply torques on the order of 5 N-m. The MVS-CMG is specifically designed to achieve a high-torque output with a minimum flywheel and system mass. The flywheel can be run over a wide range of speeds, which is important to help reduce/eliminate potential gimbal lock, and can be used to optimize the operational envelope of the CMG.

  12. Moving from Science to Service: Transposing and Sustaining the Early Risers Prevention Program in a Community Service System

    ERIC Educational Resources Information Center

    Bloomquist, Michael L.; August, Gerald J.; Horowitz, Jason L.; Lee, Susanne S.; Jensen, Cheryl

    2008-01-01

    This paper summarizes an effort to transpose and sustain the evidence-based Early Risers "Skills for Success" conduct problems prevention program in a real world community service system. The Early Risers program had previously been implemented by a local agency within the context of research-based operations. In the current initiative,…

  13. Genotype dependent burst of transposable element expression in crowns of hexaploid wheat (Triticum aestivum L.) during cold acclimation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The expression of 1,613 transposable elements (TEs) represented in the Affymetix Wheat Genome Chip was examined during cold treatment in crowns of 4 hexaploid wheat genotypes that vary in tolerance to cold and in flowering time. The TE expression profiles showed a constant level of expression throug...

  14. Substituted-Letter and Transposed-Letter Effects in a Masked Priming Paradigm with French Developing Readers and Dyslexics

    ERIC Educational Resources Information Center

    Lete, Bernard; Fayol, Michel

    2013-01-01

    The aim of the study was to undertake a behavioral investigation of the development of automatic orthographic processing during reading acquisition in French. Following Castles and colleagues' 2007 study ("Journal of Experimental Child Psychology, 97," 165-182) and their lexical tuning hypothesis framework, substituted-letter and transposed-letter…

  15. A new hobo, Ac, Tam3 transposable element, hopper, from Bactrocera dorsalis is distantly related to hobo and Ac

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new transposable element from the hobo, Ac, TamJ transposon family was isolated as a genomic clone from the oriental fruit fly, BactrOCi!ro dorsalis. It is approximately 3.1 kb in length with 19-bp inverted terminal repeat sequences having a single mismatch.Though sharing several amino acid sequen...

  16. Miniature Robotic Spacecraft for Inspecting Other Spacecraft

    NASA Technical Reports Server (NTRS)

    Fredrickson, Steven; Abbott, Larry; Duran, Steve; Goode, Robert; Howard, Nathan; Jochim, David; Rickman, Steve; Straube, Tim; Studak, Bill; Wagenknecht, Jennifer; Lemke, Matthew; Wade, Randall; Wheeler, Scott; Baggerman, Clinton

    2004-01-01

    A report discusses the Miniature Autonomous Extravehicular Robotic Camera (Mini AERCam)-- a compact robotic spacecraft intended to be released from a larger spacecraft for exterior visual inspection of the larger spacecraft. The Mini AERCam is a successor to the AERCam Sprint -- a prior miniature robotic inspection spacecraft that was demonstrated in a space-shuttle flight experiment in 1997. The prototype of the Mini AERCam is a demonstration unit having approximately the form and function of a flight system. The Mini AERCam is approximately spherical with a diameter of about 7.5 in. (.19 cm) and a weight of about 10 lb (.4.5 kg), yet it has significant additional capabilities, relative to the 14-in. (36-cm), 35-lb (16-kg) AERCam Sprint. The Mini AERCam includes miniaturized avionics, instrumentation, communications, navigation, imaging, power, and propulsion subsystems, including two digital video cameras and a high-resolution still camera. The Mini AERCam is designed for either remote piloting or supervised autonomous operations, including station keeping and point-to-point maneuvering. The prototype has been tested on an air-bearing table and in a hardware-in-the-loop orbital simulation of the dynamics of maneuvering in proximity to the International Space Station.

  17. Stability-Augmentation Devices for Miniature Aircraft

    NASA Technical Reports Server (NTRS)

    Wood, RIchard M.

    2005-01-01

    Non-aerodynamic mechanical devices are under consideration as means to augment the stability of miniature autonomous and remotely controlled aircraft. Such aircraft can be used for diverse purposes, including military reconnaissance, radio communications, and safety-related monitoring of wide areas. The need for stability-augmentation devices arises because adverse meteorological conditions generally affect smaller aircraft more strongly than they affect larger aircraft: Miniature aircraft often become uncontrollable under conditions that would not be considered severe enough to warrant grounding of larger aircraft. The need for the stability-augmentation devices to be non-aerodynamic arises because there is no known way to create controlled aerodynamic forces sufficient to counteract the uncontrollable meteorological forces on miniature aircraft. A stability-augmentation device of the type under consideration includes a mass pod (a counterweight) at the outer end of a telescoping shaft, plus associated equipment to support the operation of the aircraft. The telescoping shaft and mass pod are stowed in the rear of the aircraft. When deployed, they extend below the aircraft. Optionally, an antenna for radio communication can be integrated into the shaft. At the time of writing this article, the deployment of the telescoping shaft and mass pod was characterized as passive and automatic, but information about the deployment mechanism(s) was not available. The feasibility of this stability-augmentation concept was demonstrated in flights of hand-launched prototype aircraft.

  18. Micro-Miniature Split Stirling Linear Crycooler

    NASA Astrophysics Data System (ADS)

    Veprik, A.; Zehtzer, S.; Vilenchik, H.; Pundak, N.

    2010-04-01

    Novel tactics for rescue, surveillance, reconnaissance, force protection, perimeter security, navigation and targeting often involve the use of miniature infrared imagers, where the cooled imaging systems are known to be superior to their uncooled rivals in terms of working range, resolution and ability to distinguish/track fast moving objects in dynamic infrared scenes. The latest technological advances in industrial applications of high-temperature infrared detectors have spurred the development of linearly driven, long life, dynamically quiet and aurally undetectable micro-miniature split Stirling linear cryogenic coolers. Recent progress in designing highly efficient "moving magnet" resonant linear actuators and dedicated smart electronics have enabled further improvements to the cooler's size, weight, power consumption, cooldown time and ownership costs. The authors report on the development of a novel micro-miniature split Stirling linear cryogenic cooler, where, by means of increasing the driving frequency up to 90 Hz, it appeared possible to shorten the cold finger to 19 mm. The cooler was specifically designed to cool a new generation of 130 K infrared detectors for portable infrared imagers, where compactness, low steady-state power consumption, fast cool-down time, vibration export and aural stealth are of primary concern.

  19. Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues.

    PubMed

    De Cecco, Marco; Criscione, Steven W; Peterson, Abigail L; Neretti, Nicola; Sedivy, John M; Kreiling, Jill A

    2013-12-01

    Transposable elements (TEs) were discovered by Barbara McClintock in maize and have since been found to be ubiquitous in all living organisms. Transposition is mutagenic and organisms have evolved mechanisms to repress the activity of their endogenous TEs. Transposition in somatic cells is very low, but recent evidence suggests that it may be derepressed in some cases, such as cancer development. We have found that during normal aging several families of retrotransposable elements (RTEs) start being transcribed in mouse tissues. In advanced age the expression culminates in active transposition. These processes are counteracted by calorie restriction (CR), an intervention that slows down aging. Retrotransposition is also activated in age-associated, naturally occurring cancers in the mouse. We suggest that somatic retrotransposition is a hitherto unappreciated aging process. Mobilization of RTEs is likely to be an important contributor to the progressive dysfunction of aging cells. PMID:24323947

  20. Altering genomic integrity: heavy metal exposure promotes trans-posable element-mediated damage

    PubMed Central

    Morales, Maria E.; Servant, Geraldine; Ade, Catherine; Roy-Enge, Astrid M.

    2015-01-01

    Maintenance of genomic integrity is critical for cellular homeostasis and survival. The active transposable elements (TEs) composed primarily of three mobile element lineages LINE-1, Alu, and SVA comprise approximately 30% of the mass of the human genome. For the past two decades, studies have shown that TEs significantly contribute to genetic instability and that TE-caused damages are associated with genetic diseases and cancer. Different environmental exposures, including several heavy metals, influence how TEs interact with its host genome increasing their negative impact. This mini-review provides some basic knowledge on TEs, their contribution to disease and an overview of the current knowledge on how heavy metals influence TE-mediated damage. PMID:25774044

  1. The developmental control of transposable elements and the evolution of higher species.

    PubMed

    Friedli, Marc; Trono, Didier

    2015-01-01

    Transposable elements (TEs) account for at least 50% of the human genome. They constitute essential motors of evolution through their ability to modify genomic architecture, mutate genes and regulate gene expression. Accordingly, TEs are subject to tight epigenetic control during the earliest phases of embryonic development via histone and DNA methylation. Key to this process is recognition by sequence-specific RNA- and protein-based repressors. Collectively, these mediators are responsible for silencing a very broad range of TEs in an evolutionarily dynamic fashion. As a consequence, mobile elements and their controllers exert a marked influence on transcriptional networks in embryonic stem cells and a variety of adult tissues. The emerging picture is not that of a simple arms race but rather of a massive and sophisticated enterprise of TE domestication for the evolutionary benefit of the host. PMID:26393776

  2. Role of transposable elements in genomic rearrangement, evolution, gene regulation and epigenetics in primates.

    PubMed

    Lee, Hee-Eun; Ayarpadikannan, Selvam; Kim, Heui-Soo

    2016-03-23

    The Human Genome Project revealed that almost half of the human genome consists of transposable elements (TEs), which are also abundant in non-human primates. Various studies have confirmed the roles of different TE families in primate evolution. TEs such as endogenous retroviruses (ERVs), long terminal repeats (LTRs), long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) all have numerous effects on the primate genome, including genomic rearrangement, regulatory functions and epigenetic mechanisms. This review offers an overview of research on TEs, including our current understanding of their presence in modern primate lineages, their evolutionary origins, and their regulatory and modifying effects on primate as well as human genomes. The information provided here should be useful for the study of primate genomics. PMID:26781081

  3. A family of transposable elements co-opted into developmental enhancers in the mouse neocortex.

    PubMed

    Notwell, James H; Chung, Tisha; Heavner, Whitney; Bejerano, Gill

    2015-01-01

    The neocortex is a mammalian-specific structure that is responsible for higher functions such as cognition, emotion and perception. To gain insight into its evolution and the gene regulatory codes that pattern it, we studied the overlap of its active developmental enhancers with transposable element (TE) families and compared this overlap to uniformly shuffled enhancers. Here we show a striking enrichment of the MER130 repeat family among active enhancers in the mouse dorsal cerebral wall, which gives rise to the neocortex, at embryonic day 14.5. We show that MER130 instances preserve a common code of transcriptional regulatory logic, function as enhancers and are adjacent to critical neocortical genes. MER130, a nonautonomous interspersed TE, originates in the tetrapod or possibly Sarcopterygii ancestor, which far predates the appearance of the neocortex. Our results show that MER130 elements were recruited, likely through their common regulatory logic, as neocortical enhancers. PMID:25806706

  4. Transposable element islands facilitate adaptation to novel environments in an invasive species

    PubMed Central

    Schrader, Lukas; Kim, Jay W.; Ence, Daniel; Zimin, Aleksey; Klein, Antonia; Wyschetzki, Katharina; Weichselgartner, Tobias; Kemena, Carsten; Stökl, Johannes; Schultner, Eva; Wurm, Yannick; Smith, Christopher D.; Yandell, Mark; Heinze, Jürgen; Gadau, Jürgen; Oettler, Jan

    2014-01-01

    Adaptation requires genetic variation, but founder populations are generally genetically depleted. Here we sequence two populations of an inbred ant that diverge in phenotype to determine how variability is generated. Cardiocondyla obscurior has the smallest of the sequenced ant genomes and its structure suggests a fundamental role of transposable elements (TEs) in adaptive evolution. Accumulations of TEs (TE islands) comprising 7.18% of the genome evolve faster than other regions with regard to single-nucleotide variants, gene/exon duplications and deletions and gene homology. A non-random distribution of gene families, larvae/adult specific gene expression and signs of differential methylation in TE islands indicate intragenomic differences in regulation, evolutionary rates and coalescent effective population size. Our study reveals a tripartite interplay between TEs, life history and adaptation in an invasive species. PMID:25510865

  5. Plant regeneration methods for rapid generation of a large scale Ds transposant population in rice.

    PubMed

    Xuan, Yuan Hu; Huang, Jin; Yi, Gihwan; Park, Dong-Soo; Park, Soo Kwon; Eun, Moo Young; Yun, Doh Won; Lee, Gang-Seob; Kim, Tae Ho; Han, Chang-deok

    2013-01-01

    To mutagenize rice genomes, a two-element system is utilized. This system comprises an immobile Ac element driven by the CaMV 35S promoter, and a gene trap Ds carrying a partial intron with alternative splice acceptors fused to the GUS coding region. Rapid, large-scale generation of a Ds transposant population was achieved using a plant regeneration procedure involving the tissue culture of seed-derived calli carrying Ac and Ds elements. During tissue cultures, Ds mobility accompanies changes in methylation patterns of a terminal region of Ds, where over 70% of plants contained independent Ds insertions. In the transposon population, around 12% of plants expressed GUS at the early seedling stage. A flanking-sequence-tag (FST) database has been established by cloning over 19,968 Ds insertion sites and the Ds map shows relatively uniform distribution across the rice chromosomes. PMID:23918423

  6. Transposable elements in cancer as a by-product of stress-induced evolvability

    PubMed Central

    Mourier, Tobias; Nielsen, Lars P.; Hansen, Anders J.; Willerslev, Eske

    2014-01-01

    Transposable elements (TEs) are ubiquitous in eukaryotic genomes. Barbara McClintock’s famous notion of TEs acting as controlling elements modifying the genetic response of an organism upon exposure to stressful environments has since been solidly supported in a series of model organisms. This requires the TE activity response to possess an element of specificity and be targeted toward certain parts of the genome. We propose that a similar TE response is present in human cells, and that this stress response may drive the onset of human cancers. As such, TE-driven cancers may be viewed as an evolutionary by-product of organisms’ abilities to genetically adapt to environmental stress. PMID:24910642

  7. Association of a Drosophila transposable element of the roo family with chromosomal deletion breakpoints.

    PubMed Central

    McGinnis, W; Beckendorf, S K

    1983-01-01

    A 9.3 kb transposable element of the roo family has been found inserted 3' to the Sgs-4 glue protein gene of Drosophila. The X chromosome which carries this insert also carries wDZL, a dominant, unstable allele of the white locus caused by the insertion of the 13 kb wDZL element. Three deletions isolated from the wDZL strain have molecular breakpoints 3' to Sgs-4 that are associated with the roo element. Though the deletions eliminate much of the DNA between white and Sgs-4, none of the distal breakpoints fall at or near the wDZL element. The results suggest that this copia-like element, which is structurally similar to an integrated retrovirus, is capable of promoting chromosomal deletions. Images PMID:6300765

  8. An inhibitory influence of transposed-letter neighbors on eye movements during reading.

    PubMed

    Pagán, Ascensión; Paterson, Kevin B; Blythe, Hazel I; Liversedge, Simon P

    2016-02-01

    Previous research has shown that prior exposure to a word's substitution neighbor earlier in the same sentence can disrupt processing of that word, indicating that interword lexical priming occurs naturally during reading, due to the competition between lexical candidates during word identification. Through the present research, we extended these findings by investigating the effects of prior exposure to a word's transposed-letter neighbor (TLN) earlier in a sentence. TLNs are constituted from the same letters, but in different orders. The findings revealed an inhibitory TLN effect, with longer total reading times for target words, and increased regressions to prime and target words, when the target followed a TLN rather than a control word. These findings indicate that prior exposure to a TLN can disrupt word identification during reading. We suggest that this is caused by a failure of word identification, due to the initial misidentification of the target word (potentially as its TLN) triggering postlexical checking. PMID:26032225

  9. Mutational analysis of the N terminus of the protein of maize transposable element Ac.

    PubMed Central

    Li, M G; Starlinger, P

    1990-01-01

    Mutations of transposable element Ac were tested for their capability to excise themselves from their location autonomously, to be excised by an active Ac, or to act in trans in the excision of an Ac delta element. Removal of 101 amino acids from the N terminus of the Ac protein does not decrease excision. A cis-acting site between base pairs 186 and 207 is important for excision by the wild-type protein but is not necessary for excision by the truncated protein. Improvement of the sequence context of the first AUG does not have a significant effect. Mutations in a small open reading frame of Ac encoding a 102-amino acid protein do not visibly alter excision frequency. Images PMID:2166942

  10. Control of excision frequency of maize transposable element Ds in Petunia protoplasts.

    PubMed Central

    Becker, D; Lütticke, R; Li, M; Starlinger, P

    1992-01-01

    The complete coding region of maize transposable element Ac and truncated but active derivatives of it were placed under the control of promoters of different strength and tested for the ability to excise transposable element Ds from a beta-glucuronidase reporter gene in a cotransfection assay in Petunia protoplasts. The highest excision values (5% of the protoplasts able to express the beta-glucuronidase gene in a control experiment) were observed with a truncated version of the Ac coding region under the control of the 2' promoter. The weak Ac promoter is sufficient to give rise to excision values not much lower than those found with much stronger promoters such as the 2' and nos promoters. A decrease in excision frequency was observed when translation of the Ac coding region was hindered by out-of-frame ATG codons in addition to the use of weak promoters. Increasing the level of Ac transposase thus does not seem to be sufficient to raise the level of Ds excision observed in this system and possibly also in maize. Therefore another factor limits the excision of Ds elements. Previously, it was reported that in tobacco cells the deletion of Ds sequence between base pairs 186 and 245 led to a decrease of the Ds excision frequency by the full-length but not by the truncated Ac product. In the Petunia assay system, however, deletion of these sequences decreased the excision rate with both the full length and the truncated Ac coding region. A cDNA construct was found similarly active as the corresponding genomic DNA. PMID:11607300

  11. Transposable Element ISHp608 of Helicobacter pylori: Nonrandom Geographic Distribution, Functional Organization, and Insertion Specificity

    PubMed Central

    Kersulyte, Dangeruta; Velapatiño, Billie; Dailide, Giedrius; Mukhopadhyay, Asish K.; Ito, Yoshiyuki; Cahuayme, Lizbeth; Parkinson, Alan J.; Gilman, Robert H.; Berg, Douglas E.

    2002-01-01

    A new member of the IS605 transposable element family, designated ISHp608, was found by subtractive hybridization in Helicobacter pylori. Like the three other insertion sequences (ISs) known in this gastric pathogen, it contains two open reading frames (orfA and orfB), each related to putative transposase genes of simpler (one-gene) elements in other prokaryotes; orfB is also related to the Salmonella virulence gene gipA. PCR and hybridization tests showed that ISHp608 is nonrandomly distributed geographically: it was found in 21% of 194 European and African strains, 14% of 175 Bengali strains, 43% of 131 strains from native Peruvians and Alaska natives, but just 1% of 223 East Asian strains. ISHp608 also seemed more abundant in Peruvian gastric cancer strains than gastritis strains (9 of 14 versus 15 of 45, respectively; P = 0.04). Two ISHp608 types differing by ∼11% in DNA sequence were identified: one was widely distributed geographically, and the other was found only in Peruvian and Alaskan strains. Isolates of a given type differed by ≤2% in DNA sequence, but several recombinant elements were also found. ISHp608 marked with a resistance gene was found to (i) transpose in Escherichia coli; (ii) generate simple insertions during transposition, not cointegrates; (iii) insert downstream of the motif 5"-TTAC without duplicating target sequences; and (iv) require orfA but not orfB for its transposition. ISHp608 represents a widespread family of novel chimeric mobile DNA elements whose further analysis should provide new insights into transposition mechanisms and into microbial population genetic structure and genome evolution. PMID:11807059

  12. Rapid, large-scale generation of Ds transposant lines and analysis of the Ds insertion sites in rice.

    PubMed

    Kim, Chul Min; Piao, Hai Long; Park, Soon Ju; Chon, Nam Soo; Je, Byoung Il; Sun, Bingyao; Park, Sung Han; Park, Jin Young; Lee, Eun Jin; Kim, Min Jung; Chung, Woo Sik; Lee, Kon Ho; Lee, Young Suk; Lee, Jeung Joo; Won, Yong Jae; Yi, GiHwan; Nam, Min Hee; Cha, Young Soon; Yun, Doh Won; Eun, Moo Young; Han, Chang-deok

    2004-07-01

    Rapid, large-scale generation of a Ds transposant population was achieved using a regeneration procedure involving tissue culture of seed-derived calli carrying Ac and inactive Ds elements. In the F(2) progeny from genetic crosses between the same Ds and Ac starter lines, most of the crosses produced an independent germinal transposition frequency of 10-20%. Also, many Ds elements underwent immobilization even though Ac was expressed. By comparison, in a callus-derived regenerated population, over 70% of plants carried independent Ds insertions, indicating transposition early in callus formation. In the remaining population, the majority of plants carried only Ac. Most of the new Ds insertions were stably transmitted to a subsequent generation. An exceptionally high proportion of independent transposants in the regenerated population means that selection markers for transposed Ds and continual monitoring of Ac/Ds activities may not necessarily be required. By analyzing 1297 Ds-flanking DNA sequences, a genetic map of 1072 Ds insertion sites was developed. The map showed that Ds elements were transposed onto all of the rice chromosomes, with preference not only near donor sites (36%) but also on certain physically unlinked arms. Populations from both genetic crossing and tissue culture showed the same distribution patterns of Ds insertion sites. The information of these mapped Ds insertion sites was deposited in GenBank. Among them, 55% of Ds elements were on predicted open-reading frame (ORF) regions. Thus, we propose an optimal strategy for the rapid generation of a large population of Ds transposants in rice. PMID:15225289

  13. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We identified complex genomic rearrangements consisting of intermixed duplications and triplications of genomic segments at the MECP2 and PLP1 loci. These complex rearrangements were characterized by a triplicated segment embedded within a duplication in 11 unrelated subjects. Notably, only two brea...

  14. Fabrication of miniaturized electrostatic deflectors using LIGA

    SciTech Connect

    Jackson, K.H.; Khan-Malek, C.; Muray, L.P.

    1997-04-01

    Miniaturized electron beam columns ({open_quotes}microcolumns{close_quotes}) have been demonstrated to be suitable candidates for scanning electron microscopy (SEM), e-beam lithography and other high resolution, low voltage applications. In the present technology, microcolumns consist of {open_quotes}selectively scaled{close_quotes} micro-sized lenses and apertures, fabricated from silicon membranes with e-beam lithography, reactive ion beam etching and other semiconductor thin-film techniques. These miniaturized electron-optical elements provide significant advantages over conventional optics in performance and ease of fabrication. Since lens aberrations scale roughly with size, it is possible to fabricate simple microcolumns with extremely high brightness sources and electrostatic objective lenses, with resolution and beam current comparable to conventional e-beam columns. Moreover since microcolumns typically operate at low voltages (1 KeV), the proximity effects encountered in e-beam lithography become negligible. For high throughput applications, batch fabrication methods may be used to build large parallel arrays of microcolumns. To date, the best reported performance with a 1 keV cold field emission cathode, is 30 nm resolution at a working distance of 2mm in a 3.5mm column. Fabrication of the microcolumn deflector and stigmator, however, have remained beyond the capabilities of conventional machining operations and semiconductor processing technology. This work examines the LIGA process as a superior alternative to fabrication of the deflectors, especially in terms of degree of miniaturization, dimensional control, placement accuracy, run-out, facet smoothness and choice of suitable materials. LIGA is a combination of deep X-ray lithography, electroplating, and injection molding processes which allow the fabrication of microstructures.

  15. Miniaturized Mid-Infrared Sensor Technologies

    SciTech Connect

    Kim, S; Young, C; Mizaikoff, B

    2007-08-16

    Fundamental vibrational and rotational modes associated with most inorganic and organic molecules are spectroscopically accessible within the mid-infrared (MIR; 3-20 {micro}m) regime of the electromagnetic spectrum. The interaction between MIR photons and organic molecules provides particularly sharp transitions, which - despite the wide variety of organic molecules - provide unique MIR absorption spectra reflecting the molecularly characteristic arrangement of chemical bonds within the probed molecules via the frequency position of the associated vibrational and rotational transitions. Given the inherent molecular selectivity and achievable sensitivity, MIR spectroscopy provides an ideal platform for optical sensing applications. Despite this potential, early MIR sensing applications were limited to localized applications due to the size of the involved instrumentation, and limited availability of appropriately compact MIR optical components including light sources, detectors, waveguides, and spectrometers. During the last decades, engineering advances in photonics and optical engineering have facilitated the translation of benchtop-style MIR spectroscopy into miniaturized optical sensing schemes providing a footprint compatible with portable instrumentation requirements for field deployable analytical tools. In this trend article, we will discuss recent advances and future strategies for miniaturizing MIR sensor technology. The Beer-Lambert law implies that achievable limit of detection (LOD) for any optical sensor system improves by increasing the interaction length between photons and target analyte species such as e.g., folding the optical path multiple times as in multi-pass gas phase sensing; however, this governing paradigm naturally leads to an increase in system dimensions. Hence, miniaturization of optical sensing system requires scaling down of each optical component, yet improving the performance of each optical element within a smaller form factor for

  16. Chromosome Evolution and Genome Miniaturization in Minifish

    PubMed Central

    Liu, Shaojun; Hui, Tan Heok; Tan, Sze Ley; Hong, Yunhan

    2012-01-01

    Background Paedocypris is a newly established genus of fish in Southeast Asia. Paedocypris is characterized by several unique features, including a tiny adult size (thus named miniature fish or minifish), fragmentary habitats of acidic peat blackwater swamps, an unusual reproduction mode and truncated development. These peculiarities lend themselves excellent for studying chromosome evolution and rapid speciation in vertebrates but also make them highly controversial for the phylogenetic position. Methodology and Principal Findings We have established an organ procedure to prepare chromosome spreads from tiny organs of minifish and performed a cytogenetic study on two species of the genus Paedocypris, namely P. carbunculus (Pc) and P. sp. “Singkep” (Ps). We found 30 and 34 chromosomes in diploid cells of Pc and Ps, respectively, which are unusual in teleost fishes. The diploid metaphase has 5 pairs of metacentrics and 7 pairs of subtelocentrics in Pc compared to 3 pairs of metacentrics and 11 pairs of subtelocentrics in Ps, whereas the haploid metaphase contains 5 metacentrics and 7 subtelocentrics in Pc compared to 3 metacentrics and 11 subtelocentrics Ps. Chromosome behavior in first meiosis revealed the presence of a chromosomal ring consisting of 2 metacentrics in Pc, suggesting that centric fusion rather than fission was responsible for the karyotypic evolution from Ps to Pc. Flow cytometry revealed that Pc had a 45% nuclear staining intensity relative to medaka whose genome is 700 Mb in size and contains 0.81 pg DNA. The Pc genome should have 315 Mb in length and 0.36 pg of DNA, which represent one of the smallest values in vertebrates, suggesting genome miniaturization in this organism. Conclusions Our data demonstrate that gross chromosome rearrangements and genome miniaturization have accompanied the evolution of Paedocypris fishes. Our data also place Paedocypris outside currently described taxa of the Cypriniformes. PMID:22615970

  17. Development of Californium-252 Miniature Source Assemblies

    SciTech Connect

    Notspecified, N. A.

    2007-06-26

    The purpose of this CRADA between ORNL and lsotron, Inc. is to develop miniature californium-252 sources configured for remote handling that can be used in neutron brachytherapy for treatment of cancer. Brachytherapy places the · radioactive source at or near the site of the tumor, using a catheter. The CRADA ran from late 1999 through November 2005. The heart of a Cf-252 source is the radioactive core wire, which is sealed inside a metallic source capsule. Previous Cf-252 medical sources were based on a cermet wire with californium oxide dispersed in palladium, typically >1-mm diameter and <0.1% Cf-252 by weight. Previously, the standard medical source in the U.S. was the Applicator Tube (AT) source. 23-mm long, 2.8-mm diameter, with ~30 {micro}g of Cf-252, and which required manual loading into patients by medical staff. The goal of this work was to develop capabilities and technology to fabricate higher-intensity Cf-252 sources attached to a positioning cable, with overall diameter approaching that of exist ing photon (iridium-192) brachytherapy sources (i.e., ~1.1 mm). This work was successful in developing and demonstrating new technologies and procedures for the fabrication of miniaturized Cf-252 sources. CRADA-designed equipment reduced the wire diameters significantly (patent pending). Short wire segments were cut and successfully welded inside capsules meeting the miniaturization goals. A batch of seven prototype sources was prepared that met fabrication specifications. Although their neutron emissions were not maximized, they were still several times more intense than the previous AT sources. Very robust source-to-cable attachment methods were demonstrated (patent issued). A shipping canister was designed and built to contain the completed source assembly. lsotron designed and built a computer-controlled remote afterloader system to deliver the new sources for treatments.

  18. Collaborating miniature drones for surveillance and reconnaissance

    NASA Astrophysics Data System (ADS)

    Bürkle, Axel

    2009-09-01

    The use of miniature Unmanned Aerial Vehicles (UAVs), e.g. quadrocopters, has gained great popularity over the last years. Some complex application scenarios for micro UAVs call for the formation of swarms of multiple drones. In this paper a platform for the creation of such swarms is presented. It consists of commercial quadrocopters enhanced with on-board processing and communication units enabling autonomy of individual drones. Furthermore, a generic ground control station has been realized. Different co-operation strategies for teams of UAVs are currently evaluated with an agent based simulation tool. Finally, complex application scenarios for multiple micro UAVs are presented.

  19. Miniature laser direct-detection radar

    NASA Astrophysics Data System (ADS)

    Acharekar, Madhu; Lebeau, Robert

    1992-06-01

    A miniature laser with a total volume less than 15 cu cm and weight less than 100 g has been designed, fabricated, and assembled. The laser uses a composite rod consisting of Nd:Cr:GSGG material rod cladded with an Er:Cr:YSGG tube. The laser provides output at 1 and 3 micron wavelengths. The size and weight reduction is obtained by chemical pumping which eliminates the prime power and the power supply. The laser is used as an illuminator in a direct detection radar.

  20. Miniature integrated-optical wavelength analyzer chip

    NASA Astrophysics Data System (ADS)

    Kunz, R. E.; Dübendorfer, J.

    1995-11-01

    A novel integrated-optical chip suitable for realizing compact miniature wavelength analyzers with high linear dispersion is presented. The chip performs the complete task of converting the spectrum of an input beam into a corresponding spatial irradiance distribution without the need for an imaging function. We demonstrate the feasibility of this approach experimentally by monitoring the changes in the mode spectrum of a laser diode on varying its case temperature. Comparing the results with simultaneous measurements by a commercial spectrometer yielded a rms wavelength deviation of 0.01 nm.

  1. Miniature Robotic Submarine for Exploring Harsh Environments

    NASA Technical Reports Server (NTRS)

    Behar, Alberto; Bruhn, Fredrik; Carsey, Frank

    2004-01-01

    The miniature autonomous submersible explorer (MASE) has been proposed as a means of scientific exploration -- especially, looking for signs of life -- in harsh, relatively inaccessible underwater environments. Basically, the MASE would be a small instrumented robotic submarine (see figure) that could launch itself or could be launched from another vehicle. Examples of environments that might be explored by use of the MASE include subglacial lakes, deep-ocean hydrothermal vents, acidic or alkaline lakes, brine lenses in permafrost, and ocean regions under Antarctic ice shelves.

  2. Miniature interferometer terminals for earth surveying

    NASA Technical Reports Server (NTRS)

    Counselman, C. C., III; Shapiro, I. I.

    1978-01-01

    A system of miniature radio interferometer terminals was proposed for the measurement of vector baselines with uncertainties ranging from the millimeter to the centimeter level for baseline lengths ranging, respectively, from a few to a few hundred kilometers. Each terminal would have no moving parts, could be packaged in a volume of less than 0.1 cu m, and would operate unattended. These units would receive radio signals from low-power (10 w) transmitters on earth-orbiting satellites. The baselines between units could be determined virtually instantaneously and monitored continuously as long as at least four satellites were visible simultaneously.

  3. Miniaturized bendable 400 MHz artificial magnetic conductor

    NASA Astrophysics Data System (ADS)

    Presse, Anthony; Tarot, Anne-Claude

    2016-04-01

    A bendable artificial magnetic conductor (AMC) with a resonant frequency of 400 MHz is proposed. The dimensions of the unit cell are 50 × 50 mm2 or 0.07 × 0.07 λ0. The miniaturization is achieved with closely coupled patches printed on each side of a 0.127-mm-thick dielectric substrate. This last one is stacked on a flexible 3-mm-thick silicone over a ground plane. An AMC prototype is simulated and manufactured. Also, a printed inverted-F antenna is used to highlight the bandwidth of the AMC.

  4. A miniature solid propellant rocket motor

    SciTech Connect

    Grubelich, M.C.; Hagan, M.; Mulligan, E.

    1997-08-01

    A miniature solid-propellant rocket motor has been developed to impart a specific motion to an object deployed in space. This rocket motor effectively eliminated the need for a cold-gas thruster system or mechanical spin-up system. A low-energy igniter, an XMC4397, employing a semiconductor bridge was used to ignite the rocket motor. The rocket motor was ground-tested in a vacuum tank to verify predicted space performance and successfully flown in a Sandia National Laboratories flight vehicle program.

  5. A miniature chemiresistor sensor for carbon dioxide.

    PubMed

    Srinives, Sira; Sarkar, Tapan; Hernandez, Raul; Mulchandani, Ashok

    2015-05-18

    A carpet-like nanostructure of polyaniline (PANI) nanothin film functionalized with poly(ethyleneimine), PEI, was used as a miniature chemiresistor sensor for detection of CO2 at room temperature. Good sensing performance was observed upon exposing the PEI-PANI device to 50-5000 ppm CO2 in presence of humidity with negligible interference from ammonia, carbon monoxide, methane and nitrogen dioxide. The sensing mechanism relied on acid-base reaction, CO2 dissolution and amine-catalyzed hydration that yielded carbamates and carbonic acid for a subsequent pH detection. The sensing device showed reliable results in detecting an unknown concentration of CO2 in air. PMID:25910446

  6. De novo origin of VCY2 from autosome to Y-transposed amplicon.

    PubMed

    Cao, Peng-Rong; Wang, Lei; Jiang, Yu-Chao; Yi, Yin-Sha; Qu, Fang; Liu, Tao-Cheng; Lv, Yuan

    2015-01-01

    The formation of new genes is a primary driving force of evolution in all organisms. The de novo evolution of new genes from non-protein-coding genomic regions is emerging as an important additional mechanism for novel gene creation. Y chromosomes underlie sex determination in mammals and contain genes that are required for male-specific functions. In this study, a search was undertaken for Y chromosome de novo genes derived from non-protein-coding sequences. The Y chromosome orphan gene variable charge, Y-linked (VCY)2, is an autosome-derived gene that has sequence similarity to large autosomal fragments but lacks an autosomal protein-coding homolog. VCY2 locates in the amplicon containing long DNA fragments that were transposed from autosomes to the Y chromosome before the ape-monkey split. We confirmed that VCY2 cannot be encoded by autosomes due to the presence of multiple disablers that disrupt the open reading frame, such as the absence of start or stop codons and the presence of premature stop codons. Similar observations have been made for homologs in the autosomes of the chimpanzee, gorilla, rhesus macaque, baboon and out-group marmoset, which suggests that there was a non-protein-coding ancestral VCY2 that was common to apes and monkeys that predated the transposition event. Furthermore, while protein-coding orthologs are absent, a putative non-protein-coding VCY2 with conserved disablers was identified in the rhesus macaque Y chromosome male-specific region. This finding implies that VCY2 might have not acquired its protein-coding ability before the ape-monkey split. VCY2 encodes a testis-specific expressed protein and is involved in the pathologic process of male infertility, and the acquisition of this gene might improve male fertility. This is the first evidence that de novo genes can be generated from transposed autosomal non-protein-coding segments, and this evidence provides novel insights into the evolutionary history of the Y chromosome. PMID

  7. Miniature acoustic guidance system for endotracheal tubes

    NASA Astrophysics Data System (ADS)

    Juan, Eduardo J.

    Ensuring that the distal end of an endotracheal tube is properly located within the trachea, and that the tube is not obstructed by mucous deposition, is a major clinical concern in patients that require mechanical ventilation. A novel acoustic system was developed to allow for the continuous monitoring of endotracheal tube position and patency. A miniature sound source and two sensing microphones are placed in-line between the ventilator hose and the proximal end of the endotracheal tube. Reflections of an acoustic pulse from the endotracheal tube lumen and the airways are digitally analyzed to estimate the location and degree of obstruction, as well as the position of the distal end of the tube in the airway. The system was evaluated through computer simulations, in vitro studies, and in a rabbit model. The system noninvasively estimated tube position in vivo to within roughly 4.5 mm, and differentiated between proper tracheal, and erroneous bronchial or esophageal intubation in all cases. In addition, the system estimated the area and location of lumen obstructions in vitro to within 14% and 3.5 mm, respectively. These findings indicate that this miniature technology could improve the quality of care provided to the ventilated adult and infant.

  8. Maximizing strain in miniaturized dielectric elastomer actuators

    NASA Astrophysics Data System (ADS)

    Rosset, Samuel; Araromi, Oluwaseun; Shea, Herbert

    2015-04-01

    We present a theoretical model to optimise the unidirectional motion of a rigid object bonded to a miniaturized dielectric elastomer actuator (DEA), a configuration found for example in AMI's haptic feedback devices, or in our tuneable RF phase shifter. Recent work has shown that unidirectional motion is maximized when the membrane is both anistropically prestretched and subjected to a dead load in the direction of actuation. However, the use of dead weights for miniaturized devices is clearly highly impractical. Consequently smaller devices use the membrane itself to generate the opposing force. Since the membrane covers the entire frame, one has the same prestretch condition in the active (actuated) and passive zones. Because the passive zone contracts when the active zone expands, it does not provide a constant restoring force, reducing the maximum achievable actuation strain. We have determined the optimal ratio between the size of the electrode (active zone) and the passive zone, as well as the optimal prestretch in both in-plane directions, in order to maximize the absolute displacement of the rigid object placed at the active/passive border. Our model and experiments show that the ideal active ratio is 50%, with a displacement twice smaller than what can be obtained with a dead load. We expand our fabrication process to also show how DEAs can be laser-post-processed to remove carefully chosen regions of the passive elastomer membrane, thereby increasing the actuation strain of the device.

  9. Miniature Linear Actuator for Small Spacecraft

    NASA Technical Reports Server (NTRS)

    Willey, Cliff E.; Hill, Stuart W.

    2004-01-01

    A report discusses the development of a kit of mechanisms intended for use aboard future spacecraft having masses between 10 and 100 kg. The report focuses mostly on two prototypes of one of the mechanisms: a miniature linear actuator based on a shape-memory-alloy (SMA) wire. In this actuator, as in SMA-wire actuators described previously in NASA Tech Briefs, a spring biases a moving part toward one limit of its stroke and is restrained or pulled toward the other limit of the stroke by an SMA wire, which assumes a slightly lesser or greater "remembered" length, depending on whether or not an electric current is applied to the wire to heat it above a transition temperature. Topics addressed in the report include the need to develop mechanisms like these, the general approach to be taken in designing SMA actuators, tests of the two prototypes of the miniature linear actuators, and improvements in the second prototype over the first prototype resulting in reduced mass and increased stroke. The report also presents recommendations for future development, briefly discusses problems of tolerances and working with small parts, states a need for better understanding of behaviors of SMAs, and presents conclusions.

  10. Miniaturized kappa goniometer for macromolecular crystallography

    SciTech Connect

    Rosenbaum, G.; Westbrook, E. M.

    1997-07-01

    A goniometer with kappa geometry has been designed and built specifically for macromolecular crystallography. The main feature is a miniaturized kappa stage made possible by the small weight of specimen and specimen holder. The design goal was to: 1) eliminate interference between stage and area detector for specimen-to-detector distances of 100 mm and more; 2) minimize the sphere of confusion on expectation of dealing with very small crystals at third generation sources; 3) minimize the solid angle of shadow and inaccessible positioning of the sample due to interference of the stage with other objects in the sample area; 4) achieve a rotation speed of 10 degree/s at 0.5% constancy and 0.4 s acceleration time for 0.05 s exposures of 0.2 degree fine slice frames every 2 seconds, and 5) to achieve precise synchronization between rotation angle and shutter opening and closing. The kappa stage is mounted on a commercial high precision rotary table, designed for use in both horizontal and vertical orientation. This table provides the high precision rotation for data acquisition. The required crisp response and constant speed is delivered by a high output direct drive DC-motor, controlled by a closed-loop controller using feedback from a precision angular encoder. The kappa- and phi-motions are used for sample positioning only and are driven by miniature DC-motors equipped with integral encoders.

  11. Miniaturized kappa goniometer for macromolecular crystallography

    SciTech Connect

    Rosenbaum, G.; Westbrook, E.M.

    1997-07-01

    A goniometer with kappa geometry has been designed and built specifically for macromolecular crystallography. The main feature is a miniaturized kappa stage made possible by the small weight of specimen and specimen holder. The design goal was to: 1) eliminate interference between stage and area detector for specimen-to-detector distances of 100 mm and more; 2) minimize the sphere of confusion on expectation of dealing with very small crystals at third generation sources; 3) minimize the solid angle of shadow and inaccessible positioning of the sample due to interference of the stage with other objects in the sample area; 4) achieve a rotation speed of 10 degree/s at 0.5{percent} constancy and 0.4 s acceleration time for 0.05 s exposures of 0.2 degree fine slice frames every 2 seconds, and 5) to achieve precise synchronization between rotation angle and shutter opening and closing. The kappa stage is mounted on a commercial high precision rotary table, designed for use in both horizontal and vertical orientation. This table provides the high precision rotation for data acquisition. The required crisp response and constant speed is delivered by a high output direct drive DC-motor, controlled by a closed-loop controller using feedback from a precision angular encoder. The kappa- and phi-motions are used for sample positioning only and are driven by miniature DC-motors equipped with integral encoders.{copyright} {ital 1997 American Institute of Physics.}

  12. Miniature bioreactors: current practices and future opportunities

    PubMed Central

    Betts, Jonathan I; Baganz, Frank

    2006-01-01

    This review focuses on the emerging field of miniature bioreactors (MBRs), and examines the way in which they are used to speed up many areas of bioprocessing. MBRs aim to achieve this acceleration as a result of their inherent high-throughput capability, which results from their ability to perform many cell cultivations in parallel. There are several applications for MBRs, ranging from media development and strain improvement to process optimisation. The potential of MBRs for use in these applications will be explained in detail in this review. MBRs are currently based on several existing bioreactor platforms such as shaken devices, stirred-tank reactors and bubble columns. This review will present the advantages and disadvantages of each design together with an appraisal of prototype and commercialised devices developed for parallel operation. Finally we will discuss how MBRs can be used in conjunction with automated robotic systems and other miniature process units to deliver a fully-integrated, high-throughput (HT) solution for cell cultivation process development. PMID:16725043

  13. Miniature Free-Space Electrostatic Ion Thrusters

    NASA Technical Reports Server (NTRS)

    Hartley, Frank T.; Stephens, James B.

    2006-01-01

    A miniature electrostatic ion thruster is proposed for maneuvering small spacecraft. In a thruster based on this concept, one or more propellant gases would be introduced into an ionizer based on the same principles as those of the device described in an earlier article, "Miniature Bipolar Electrostatic Ion Thruster". On the front side, positive ions leaving an ionizer element would be accelerated to high momentum by an electric field between the ionizer and an accelerator grid around the periphery of the concave laminate structure. On the front side, electrons leaving an ionizer element would be ejected into free space by a smaller accelerating field. The equality of the ion and electron currents would eliminate the need for an additional electron- or ion-emitting device to keep the spacecraft charge-neutral. In a thruster design consisting of multiple membrane ionizers in a thin laminate structure with a peripheral accelerator grid, the direction of thrust could then be controlled (without need for moving parts in the thruster) by regulating the supply of gas to specific ionizer.

  14. Miniaturized integration of a fluorescence microscope

    PubMed Central

    Ghosh, Kunal K.; Burns, Laurie D.; Cocker, Eric D.; Nimmerjahn, Axel; Ziv, Yaniv; Gamal, Abbas El; Schnitzer, Mark J.

    2013-01-01

    The light microscope is traditionally an instrument of substantial size and expense. Its miniaturized integration would enable many new applications based on mass-producible, tiny microscopes. Key prospective usages include brain imaging in behaving animals towards relating cellular dynamics to animal behavior. Here we introduce a miniature (1.9 g) integrated fluorescence microscope made from mass-producible parts, including semiconductor light source and sensor. This device enables high-speed cellular-level imaging across ∼0.5 mm2 areas in active mice. This capability allowed concurrent tracking of Ca2+ spiking in >200 Purkinje neurons across nine cerebellar microzones. During mouse locomotion, individual microzones exhibited large-scale, synchronized Ca2+ spiking. This is a mesoscopic neural dynamic missed by prior techniques for studying the brain at other length scales. Overall, the integrated microscope is a potentially transformative technology that permits distribution to many animals and enables diverse usages, such as portable diagnostics or microscope arrays for large-scale screens. PMID:21909102

  15. Miniaturized optical neuroimaging in unrestrained animals.

    PubMed

    Yu, Hang; Senarathna, Janaka; Tyler, Betty M; Thakor, Nitish V; Pathak, Arvind P

    2015-06-01

    The confluence of technological advances in optics, miniaturized electronic components and the availability of ever increasing and affordable computational power have ushered in a new era in functional neuroimaging, namely, an era in which neuroimaging of cortical function in unrestrained and unanesthetized rodents has become a reality. Traditional optical neuroimaging required animals to be anesthetized and restrained. This greatly limited the kinds of experiments that could be performed in vivo. Now one can assess blood flow and oxygenation changes resulting from functional activity and image functional response in disease models such as stroke and seizure, and even conduct long-term imaging of tumor physiology, all without the confounding effects of anesthetics or animal restraints. These advances are shedding new light on mammalian brain organization and function, and helping to elucidate loss of this organization or 'dysfunction' in a wide array of central nervous system disease models. In this review, we highlight recent advances in the fabrication, characterization and application of miniaturized head-mounted optical neuroimaging systems pioneered by innovative investigators from a wide array of disciplines. We broadly classify these systems into those based on exogenous contrast agents, such as single- and two-photon microscopy systems; and those based on endogenous contrast mechanisms, such as multispectral or laser speckle contrast imaging systems. Finally, we conclude with a discussion of the strengths and weaknesses of these approaches along with a perspective on the future of this exciting new frontier in neuroimaging. PMID:25791782

  16. Somatic variegation and germinal mutability reflect the position of transposable element dissociation within the maize R gene

    SciTech Connect

    Alleman, M.; Kermicle, J.L. )

    1993-09-01

    The R gene regulates the timing and tissue-specificity of anthocyanin deposition during maize development. The Ac/Ds system of transposable elements was used to induce insertional mutants of the R-sc:124 allele during two cycles of mutagenesis. Of 43 unstable, spotted-aleurone mutants generated, 42 contain inserts of the Ds6 transposable element differing only in the position and orientation of the element. The remaining mutant, r-sc;ml, contained an insert of a Ds element of the approximate size of the Ds1 transposable element. The patterns of somatic variegation of these mutants, resulting from excision of Ds, define a spectrum of phenotypes ranging from sparse to dense variegation. The sparsely variegated mutants produce many germinal revertants and few stable null derivatives. Molecular analysis shows that the sparsely variegated alleles are caused by Ds6 insertions in protein coding regions of R-sc:124 whereas the densely variegated mutants result from insertions in introns or in flanking regions of the gene. The excision rate of Ds6 from R, estimated as the proportion of R genomic DNA restriction fragments lacking the element, was uniform regardless of position, orientation or whether the element was inserted in R-sc:124 or another R allele. The excision rate was greater, however, for the mutable alleles involving the Ds element from r-sc:m1. These data indicate that, although the excision rates are uniform for a given Ds element, the somatic and germinal mutability patterns of alleles associated with that element vary widely and depend primarily on the position of the transposable element within coding or noncoding regions of the gene.

  17. Miniature spinning as a fiber quality assessment tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Miniature spinning has long been used to assess cotton varieties in a timely manner. It has been an accepted fact that the quality of miniature spinning is less than optimal, but that it allows a direct comparison between cottons during varietal studies. Recently, researchers have made processing ...

  18. Congenital urethral stenosis in a male miniature piglet

    PubMed Central

    Pouleur-Larrat, Bénédicte; Maccolini, Edouard; Carmel, Eric Norman; Hélie, Pierre

    2014-01-01

    A 2-month-old male miniature pig showed progressive abdominal pain, pollakiuria, and stranguria that progressed to complete urinary obstruction. Postmortem examination revealed idiopathic urethral stenosis at the level of the recess, of probable congenital origin. Urinary tract malformations should be included in the differential diagnosis of miniature piglets with urinary disorders. PMID:24891635

  19. The Miniature Job Training and Evaluation Approach: Additional Findings.

    ERIC Educational Resources Information Center

    Siegel, Arthur I.

    1983-01-01

    Describes miniature job training and evaluation situations administered to 1,034 "low aptitude" Navy recruits. Checklist criterion data describing the on-the-job performance of the sample were collected after the recruits were on their fleet assignments. The results confirmed the predictive validity of the miniature job training approach.…

  20. Enhancer/Suppressor mutator (En/Spm)-like transposable elements of cassava (Manihot esculenta) are transcriptionally inactive.

    PubMed

    Gbadegesin, M A; Beeching, J R

    2010-01-01

    Transposable elements contribute to the size, structure, variation, and diversity of the genome and have major effects on gene function. Sequencing projects have revealed the diversity of transposable elements in many organisms and have shown that they constitute a high percentage of the genome. PCR-based techniques using degenerate primers designed from conserved enzyme domains of transposable elements can provide quick and extensive surveys, making study of diversity and abundance and their applications possible in species where full genome sequence data are not yet available. We studied cassava (Manihot esculenta) En/Spm-like transposons (Meens) with regard to genomic distribution, sequence diversity and methylation status. Cassava transposase fragments characteristic of En/Spm-like transposons were isolated, cloned and characterized. Sequence analysis showed that cassava En/Spm-like elements are highly conserved, with overall identity in the range of 68-98%. Southern hybridization supports the presence of multiple copies of En/Spm-like transposons integrated in the genome of all cassava cultivars that we tested. Hybridization patterns of HpaII- and MspI-digested cassava genomic DNA revealed highly methylated sequences. There were no clear differences in hybridization pattern between the cultivars. We did not detect RNA transcripts of Meens by Northern procedures. We examined the possibility of recent transposition activities of the cassava En/Spm-like elements. PMID:20449796

  1. A Recent Adaptive Transposable Element Insertion Near Highly Conserved Developmental Loci in Drosophila melanogaster

    PubMed Central

    González, Josefa; Macpherson, J. Michael; Petrov, Dmitri A.

    2009-01-01

    A recent genomewide screen identified 13 transposable elements that are likely to have been adaptive during or after the spread of Drosophila melanogaster out of Africa. One of these insertions, Bari-Juvenile hormone epoxy hydrolase (Bari-Jheh), was associated with the selective sweep of its flanking neutral variation and with reduction of expression of one of its neighboring genes: Jheh3. Here, we provide further evidence that Bari-Jheh insertion is adaptive. We delimit the extent of the selective sweep and show that Bari-Jheh is the only mutation linked to the sweep. Bari-Jheh also lowers the expression of its other flanking gene, Jheh2. Subtle consequences of Bari-Jheh insertion on life-history traits are consistent with the effects of reduced expression of the Jheh genes. Finally, we analyze molecular evolution of Jheh genes in both the long- and the short-term and conclude that Bari-Jheh appears to be a very rare adaptive event in the history of these genes. We discuss the implications of these findings for the detection and understanding of adaptation. PMID:19458110

  2. High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster

    PubMed Central

    González, Josefa; Lenkov, Kapa; Lipatov, Mikhail; Macpherson, J. Michael; Petrov, Dmitri A

    2008-01-01

    Although transposable elements (TEs) are known to be potent sources of mutation, their contribution to the generation of recent adaptive changes has never been systematically assessed. In this work, we conduct a genome-wide screen for adaptive TE insertions in Drosophila melanogaster that have taken place during or after the spread of this species out of Africa. We determine population frequencies of 902 of the 1,572 TEs in Release 3 of the D. melanogaster genome and identify a set of 13 putatively adaptive TEs. These 13 TEs increased in population frequency sharply after the spread out of Africa. We argue that many of these TEs are in fact adaptive by demonstrating that the regions flanking five of these TEs display signatures of partial selective sweeps. Furthermore, we show that eight out of the 13 putatively adaptive elements show population frequency heterogeneity consistent with these elements playing a role in adaptation to temperate climates. We conclude that TEs have contributed considerably to recent adaptive evolution (one TE-induced adaptation every 200–1,250 y). The majority of these adaptive insertions are likely to be involved in regulatory changes. Our results also suggest that TE-induced adaptations arise more often from standing variants than from new mutations. Such a high rate of TE-induced adaptation is inconsistent with the number of fixed TEs in the D. melanogaster genome, and we discuss possible explanations for this discrepancy. PMID:18942889

  3. Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication

    PubMed Central

    Johnson, Rory; Gamblin, Richard J.; Ooi, Lezanne; Bruce, Alexander W.; Donaldson, Ian J.; Westhead, David R.; Wood, Ian C.; Jackson, Richard M.; Buckley, Noel J.

    2006-01-01

    The genome-wide mapping of gene-regulatory motifs remains a major goal that will facilitate the modelling of gene-regulatory networks and their evolution. The repressor element 1 is a long, conserved transcription factor-binding site which recruits the transcriptional repressor REST to numerous neuron-specific target genes. REST plays important roles in multiple biological processes and disease states. To map RE1 sites and target genes, we created a position specific scoring matrix representing the RE1 and used it to search the human and mouse genomes. We identified 1301 and 997 RE1s inhuman and mouse genomes, respectively, of which >40% are novel. By employing an ontological analysis we show that REST target genes are significantly enriched in a number of functional classes. Taking the novel REST target gene CACNA1A as an experimental model, we show that it can be regulated by multiple RE1s of different binding affinities, which are only partially conserved between human and mouse. A novel BLAST methodology indicated that many RE1s belong to closely related families. Most of these sequences are associated with transposable elements, leading us to propose that transposon-mediated duplication and insertion of RE1s has led to the acquisition of novel target genes by REST during evolution. PMID:16899447

  4. Transposable elements, polydactyl proteins and the genesis of human-specific transcription networks

    PubMed Central

    Trono, Didier

    2016-01-01

    Transposable elements (TEs) may account for up to two-thirds of the human genome, and as genomic threats they are subjected to epigenetic control mechanisms engaged from the earliest stages of embryonic development. We previously determined that an important component of this process is the sequence-specific recognition of TEs by KRAB-containing zinc finger proteins (KRAB-ZFPs), a large family of tetrapod-restricted transcription factors that act by recruiting inducers of heterochromatin formation and DNA methylation. We further demonstrated that KRAB-ZFPs and their cofactor KAP1 exert a marked influence on the transcription dynamics of embryonic stem cells via their docking of repressor complexes at TE-contained regulatory sequences. It is generally held that, beyond this early embryonic period, TEs become permanently silenced, and that the evolutionary selection of KRAB-ZFPs and other TE controllers is the result of a simple evolutionary arms race between the host and these genetics invaders. Here, I discuss recent evidence that invalidates this dual assumption, and instead suggests that KRAB-ZFPs are the instruments of a massive enterprise of TE domestication, whereby transposon-based regulatory sequences and their cellular ligands establish species-specific transcription regulation networks that influence multiple aspects of human development and physiology. PMID:26763983

  5. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi.

    PubMed

    Tycowski, Kazimierz T; Shu, Mei-Di; Steitz, Joan A

    2016-05-10

    The ENE (element for nuclear expression) is a cis-acting RNA structure that protects viral or cellular noncoding RNAs (ncRNAs) from nuclear decay through triple-helix formation with the poly(A) tail or 3'-terminal A-rich tract. We expanded the roster of nine known ENEs by bioinformatic identification of ∼200 distinct ENEs that reside in transposable elements (TEs) of numerous non-metazoan and one fish species and in four Dicistrovirus genomes. Despite variation within the ENE core, none of the predicted triple-helical stacks exceeds five base triples. Increased accumulation of reporter transcripts in human cells demonstrated functionality for representative ENEs. Location close to the poly(A) tail argues that ENEs are active in TE transcripts. Their presence in intronless, but not intron-containing, hAT transposase genes supports the idea that TEs acquired ENEs to counteract the RNA-destabilizing effects of intron loss, a potential evolutionary consequence of TE horizontal transfer in organisms that couple RNA silencing to splicing deficits. PMID:27134163

  6. Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements

    PubMed Central

    Joly-Lopez, Zoé; Hoen, Douglas R.; Blanchette, Mathieu; Bureau, Thomas E.

    2016-01-01

    Once perceived as merely selfish, transposable elements (TEs) are now recognized as potent agents of adaptation. One way TEs contribute to evolution is through TE exaptation, a process whereby TEs, which persist by replicating in the genome, transform into novel host genes, which persist by conferring phenotypic benefits. Known exapted TEs (ETEs) contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet little is known about this process. To better understand TE exaptation, we designed an approach to resolve the phylogenetic context and timing of exaptation events and subsequent patterns of ETE diversification. Starting with known ETEs, we search in diverse genomes for basal ETEs and closely related TEs, carefully curate the numerous candidate sequences, and infer detailed phylogenies. To distinguish TEs from ETEs, we also weigh several key genomic characteristics including repetitiveness, terminal repeats, pseudogenic features, and conserved domains. Applying this approach to the well-characterized plant ETEs MUG and FHY3, we show that each group is paraphyletic and we argue that this pattern demonstrates that each originated in not one but multiple exaptation events. These exaptations and subsequent ETE diversification occurred throughout angiosperm evolution including the crown group expansion, the angiosperm radiation, and the primitive evolution of angiosperms. In addition, we detect evidence of several putative novel ETE families. Our findings support the hypothesis that TE exaptation generates novel genes more frequently than is currently thought, often coinciding with key periods of evolution. PMID:27189548

  7. Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

    PubMed Central

    Platt, Roy N.; Blanco-Berdugo, Laura; Ray, David A.

    2016-01-01

    Transposable elements (TEs) are mobile genetic elements with the ability to replicate themselves throughout the host genome. In some taxa TEs reach copy numbers in hundreds of thousands and can occupy more than half of the genome. The increasing number of reference genomes from nonmodel species has begun to outpace efforts to identify and annotate TE content and methods that are used vary significantly between projects. Here, we demonstrate variation that arises in TE annotations when less than optimal methods are used. We found that across a variety of taxa, the ability to accurately identify TEs based solely on homology decreased as the phylogenetic distance between the queried genome and a reference increased. Next we annotated repeats using homology alone, as is often the case in new genome analyses, and a combination of homology and de novo methods as well as an additional manual curation step. Reannotation using these methods identified a substantial number of new TE subfamilies in previously characterized genomes, recognized a higher proportion of the genome as repetitive, and decreased the average genetic distance within TE families, implying recent TE accumulation. Finally, these finding—increased recognition of younger TEs—were confirmed via an analysis of the postman butterfly (Heliconius melpomene). These observations imply that complete TE annotation relies on a combination of homology and de novo–based repeat identification, manual curation, and classification and that relying on simple, homology-based methods is insufficient to accurately describe the TE landscape of a newly sequenced genome. PMID:26802115

  8. A Snapshot of Histone Modifications within Transposable Elements in Drosophila Wild Type Strains

    PubMed Central

    Rebollo, Rita; Horard, Béatrice; Begeot, Flora; Delattre, Marion; Gilson, Eric; Vieira, Cristina

    2012-01-01

    Transposable elements (TEs) are a major source of genetic variability in genomes, creating genetic novelty and driving genome evolution. Analysis of sequenced genomes has revealed considerable diversity in TE families, copy number, and localization between different, closely related species. For instance, although the twin species Drosophila melanogaster and D. simulans share the same TE families, they display different amounts of TEs. Furthermore, previous analyses of wild type derived strains of D. simulans have revealed high polymorphism regarding TE copy number within this species. Several factors may influence the diversity and abundance of TEs in a genome, including molecular mechanisms such as epigenetic factors, which could be a source of variation in TE success. In this paper, we present the first analysis of the epigenetic status of four TE families (roo, tirant, 412 and F) in seven wild type strains of D. melanogaster and D. simulans. Our data shows intra- and inter-specific variations in the histone marks that adorn TE copies. Our results demonstrate that the chromatin state of common TEs varies among TE families, between closely related species and also between wild type strains. PMID:22962605

  9. Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species.

    PubMed

    Roncal, Julissa; Guyot, Romain; Hamon, Perla; Crouzillat, Dominique; Rigoreau, Michel; Konan, Olivier N'Guessan; Rakotomalala, Jean-Jacques; Nowak, Michael D; Davis, Aaron P; de Kochko, Alexandre

    2016-02-01

    The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascar were divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution. PMID:26231981

  10. Biogeography revealed by mariner-like transposable element sequences via a Bayesian coalescent approach.

    PubMed

    Nakagome, Shigeki; Nakajima, Yumiko; Mano, Shuhei

    2013-09-01

    Genetic diversity of natural populations is useful in biogeographical studies. Here, we apply a Bayesian method based on the coalescent model to dating biogeographical events by using published DNA sequences of wild silkworms, Bombyx mandarina, and the domesticated model organisms B. mori, both of which categorized into the order of Lepidoptera, sampled from China, Korea, and Japan. The sequences consist of the BmTNML locus and the flanking intergenic regions. The BmTNML locus is composed of cecropia-type mariner-like element (MLE) with inverted terminal repeats, and three different transposable elements (TE), including L1BM, BMC1 retrotransposons, and BmamaT1, are inserted into the MLE. Based on the genealogy defined by TE insertions/deletions (indels), we estimated times to the most recent common ancestor and these indels events using the flanking, MLE, and indels sequences, respectively. These estimates by using MLE sequences strongly correlated with those by using flanking sequences, implying that cecropia-type MLEs can be used as a molecular clock. MLEs are thought to have transmitted horizontally among different species. By using a pair of published cecropia-type MLE sequences from lepidopteran insect, an emperor moth, and a coral in Ryukyu Islands, we demonstrated dating of horizontal transmission between species which are distantly related but inhabiting geographically close region. PMID:23989494

  11. Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes

    PubMed Central

    Kannan, Sivakumar; Chernikova, Diana; Rogozin, Igor B.; Poliakov, Eugenia; Managadze, David; Koonin, Eugene V.; Milanesi, Luciano

    2015-01-01

    Transposable elements (TEs) are abundant in mammalian genomes and appear to have contributed to the evolution of their hosts by providing novel regulatory or coding sequences. We analyzed different regions of long intergenic non-coding RNA (lincRNA) genes in human and mouse genomes to systematically assess the potential contribution of TEs to the evolution of the structure and regulation of expression of lincRNA genes. Introns of lincRNA genes contain the highest percentage of TE-derived sequences (TES), followed by exons and then promoter regions although the density of TEs is not significantly different between exons and promoters. Higher frequencies of ancient TEs in promoters and exons compared to introns implies that many lincRNA genes emerged before the split of primates and rodents. The content of TES in lincRNA genes is substantially higher than that in protein-coding genes, especially in exons and promoter regions. A significant positive correlation was detected between the content of TEs and evolutionary rate of lincRNAs indicating that inserted TEs are preferentially fixed in fast-evolving lincRNA genes. These results are consistent with the repeat insertion domains of LncRNAs hypothesis under which TEs have substantially contributed to the origin, evolution, and, in particular, fast functional diversification, of lincRNA genes. PMID:26106594

  12. Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

    PubMed Central

    de Souza, Flávio S.J.; Franchini, Lucía F.; Rubinstein, Marcelo

    2013-01-01

    Transposable elements (TEs) are mobile genetic sequences that can jump around the genome from one location to another, behaving as genomic parasites. TEs have been particularly effective in colonizing mammalian genomes, and such heavy TE load is expected to have conditioned genome evolution. Indeed, studies conducted both at the gene and genome levels have uncovered TE insertions that seem to have been co-opted—or exapted—by providing transcription factor binding sites (TFBSs) that serve as promoters and enhancers, leading to the hypothesis that TE exaptation is a major factor in the evolution of gene regulation. Here, we critically review the evidence for exaptation of TE-derived sequences as TFBSs, promoters, enhancers, and silencers/insulators both at the gene and genome levels. We classify the functional impact attributed to TE insertions into four categories of increasing complexity and argue that so far very few studies have conclusively demonstrated exaptation of TEs as transcriptional regulatory regions. We also contend that many genome-wide studies dealing with TE exaptation in recent lineages of mammals are still inconclusive and that the hypothesis of rapid transcriptional regulatory rewiring mediated by TE mobilization must be taken with caution. Finally, we suggest experimental approaches that may help attributing higher-order functions to candidate exapted TEs. PMID:23486611

  13. The mechanism of ageing: primary role of transposable elements in genome disintegration.

    PubMed

    Sturm, Ádám; Ivics, Zoltán; Vellai, Tibor

    2015-05-01

    Understanding the molecular basis of ageing remains a fundamental problem in biology. In multicellular organisms, while the soma undergoes a progressive deterioration over the lifespan, the germ line is essentially immortal as it interconnects the subsequent generations. Genomic instability in somatic cells increases with age, and accumulating evidence indicates that the disintegration of somatic genomes is accompanied by the mobilisation of transposable elements (TEs) that, when mobilised, can be mutagenic by disrupting coding or regulatory sequences. In contrast, TEs are effectively silenced in the germ line by the Piwi-piRNA system. Here, we propose that TE repression transmits the persistent proliferation capacity and the non-ageing phenotype (e.g., preservation of genomic integrity) of the germ line. The Piwi-piRNA pathway also operates in tumorous cells and in somatic cells of certain organisms, including hydras, which likewise exhibit immortality. However, in somatic cells lacking the Piwi-piRNA pathway, gradual chromatin decondensation increasingly allows the mobilisation of TEs as the organism ages. This can explain why the mortality rate rises exponentially throughout the adult life in most animal species, including humans. PMID:25837999

  14. On the time-course of adjacent and non-adjacent transposed-letter priming

    PubMed Central

    Ktori, Maria; Kingma, Brechtsje; Hannagan, Thomas; Holcomb, Phillip J.; Grainger, Jonathan

    2014-01-01

    We compared effects of adjacent (e.g., atricle-ARTICLE) and non-adjacent (e.g., actirle-ARTICLE) transposed-letter (TL) primes in an ERP study using the sandwich priming technique. TL priming was measured relative to the standard double-substitution condition. We found significantly stronger priming effects for adjacent transpositions than non-adjacent transpositions (with 2 intervening letters) in behavioral responses (lexical decision latencies), and the adjacent priming effects emerged earlier in the ERP signal, at around 200 ms post-target onset. Non-adjacent priming effects emerged about 50 ms later and were short-lived, being significant only in the 250-300 ms time-window. Adjacent transpositions on the other hand continued to produce priming in the N400 time-window (300-500 ms post-target onset). This qualitatively different pattern of priming effects for adjacent and non-adjacent transpositions is discussed in the light of different accounts of letter transposition effects, and the utility of drawing a distinction between positional flexibility and positional noise. PMID:25364497

  15. Patterns of repeat-induced point mutation in transposable elements of basidiomycete fungi.

    PubMed

    Horns, Felix; Petit, Elsa; Yockteng, Roxana; Hood, Michael E

    2012-01-01

    Transposable elements (TEs) are ubiquitous genomic parasites that have prompted the evolution of genome defense systems that restrict their activity. Repeat-induced point mutation (RIP) is a homology-dependent genome defense that introduces C-to-T transition mutations in duplicated DNA sequences and is thought to control the proliferation of selfish repetitive DNA. Here, we determine the taxonomic distribution of hypermutation patterns indicative of RIP among basidiomycetes. We quantify C-to-T transition mutations in particular di- and trinucleotide target sites for TE-like sequences from nine fungal genomes. We find evidence of RIP-like patterns of hypermutation at TpCpG trinucleotide sites in repetitive sequences from all species of the Pucciniomycotina subphylum of the Basidiomycota, Microbotryum lychnidis-dioicae, Puccinia graminis, Melampsora laricis-populina, and Rhodotorula graminis. In contrast, we do not find evidence for RIP-like hypermutation in four species of the Agaricomycotina and Ustilaginomycotina subphyla of the Basidiomycota. Our results suggest that a RIP-like process and the specific nucleotide context for mutations are conserved within the Pucciniomycotina subphylum. These findings imply that coevolutionary interactions between TEs and a hypermutating genome defense are stable over long evolutionary timescales. PMID:22250128

  16. No evidence that sex and transposable elements drive genome size variation in evening primroses.

    PubMed

    Ågren, J Arvid; Greiner, Stephan; Johnson, Marc T J; Wright, Stephen I

    2015-04-01

    Genome size varies dramatically across species, but despite an abundance of attention there is little agreement on the relative contributions of selective and neutral processes in governing this variation. The rate of sex can potentially play an important role in genome size evolution because of its effect on the efficacy of selection and transmission of transposable elements (TEs). Here, we used a phylogenetic comparative approach and whole genome sequencing to investigate the contribution of sex and TE content to genome size variation in the evening primrose (Oenothera) genus. We determined genome size using flow cytometry for 30 species that vary in genetic system and find that variation in sexual/asexual reproduction cannot explain the almost twofold variation in genome size. Moreover, using whole genome sequences of three species of varying genome sizes and reproductive system, we found that genome size was not associated with TE abundance; instead the larger genomes had a higher abundance of simple sequence repeats. Although it has long been clear that sexual reproduction may affect various aspects of genome evolution in general and TE evolution in particular, it does not appear to have played a major role in genome size evolution in the evening primroses. PMID:25690700

  17. Mobility properties of the Hermes transposable element in transgenic lines of Aedes aegypti.

    PubMed

    Smith, Ryan C; Atkinson, Peter W

    2011-01-01

    The Hermes transposable element has been used to genetically transform a wide range of insect species, including the mosquito, Aedes aegypti, a vector of several important human pathogens. Hermes integrations into the mosquito germline are characterized by the non-canonical integration of the transposon and flanking plasmid and, once integrated, Hermes is stable in the presence of its transposase. In an effort to improve the post-integration mobility of Hermes in the germline of Ae. aegypti, a transgenic helper Mos1 construct expressing Hermes transposase under the control of a testis-specific promoter was crossed to a separate transgenic strain containing a target Hermes transposon. In less than 1% of the approximately 1,500 progeny from jumpstarter lines analyzed, evidence of putative Hermes germline remobilizations were detected. These recovered transposition events occur through an aberrant mechanism and provide insight into the non-canonical cut-and-paste transposition of Hermes in the germ line of Ae. aegypti. PMID:20596755

  18. Mobility properties of the Hermes transposable element in transgenic lines of Aedes aegypti

    PubMed Central

    Smith, Ryan C.

    2010-01-01

    The Hermes transposable element has been used to genetically transform a wide range of insect species, including the mosquito, Aedes aegypti, a vector of several important human pathogens. Hermes integrations into the mosquito germline are characterized by the non-canonical integration of the transposon and flanking plasmid and, once integrated, Hermes is stable in the presence of its transposase. In an effort to improve the post-integration mobility of Hermes in the germline of Ae. aegypti, a transgenic helper Mos1 construct expressing Hermes transposase under the control of a testis-specific promoter was crossed to a separate transgenic strain containing a target Hermes transposon. In less than 1% of the approximately 1,500 progeny from jumpstarter lines analyzed, evidence of putative Hermes germline remobilizations were detected. These recovered transposition events occur through an aberrant mechanism and provide insight into the non-canonical cut-and-paste transposition of Hermes in the germ line of Ae. aegypti. PMID:20596755

  19. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi

    PubMed Central

    Tycowski, Kazimierz T.; Shu, Mei-Di; Steitz, Joan A.

    2016-01-01

    SUMMARY The ENE (element for nuclear expression) is a cis-acting RNA structure that protects viral or cellular noncoding (nc)RNAs from nuclear decay through triple-helix formation with the poly(A) tail or 3′-terminal A-rich tract. We expanded the roster of 9 known ENEs by bioinformatic identification of ~200 distinct ENEs that reside in transposable elements (TEs) of numerous non-metazoan and one fish species, and in four Dicistrovirus genomes. Despite variation within the ENE core, none of the predicted triple-helical stacks exceeds five base triples. Increased accumulation of reporter transcripts in human cells demonstrated functionality for representative ENEs. Location close to the poly(A) tail argues that ENEs are active in TE transcripts. Their presence in intronless but not intron-containing hAT transposase genes supports the idea that TEs acquired ENEs to counteract the RNA-destabilizing effects of intron loss, a potential evolutionary consequence of TE horizontal transfer in organisms that couple RNA silencing to splicing deficits. PMID:27134163

  20. New insights into helitron transposable elements in the mesopolyploid species Brassica rapa.

    PubMed

    Fu, Donghui; Wei, Lijuan; Xiao, Meili; Hayward, Alice

    2013-12-15

    Helitrons are DNA transposable elements that are widely present in the genomes of diverse eukaryotic taxa. Helitrons are distinct from other transposons in their ability to capture gene fragments and their rolling-replication mechanism. Brassica rapa is a mesopolyploid species and one of the most important vegetable and oil crops globally. A total of 787 helitrons were identified in the B. rapa genome and were assigned to 662 families and 700 subfamilies. More than 21,806 repetitive sequences were found within the helitrons, whose G+C content correlated negatively to that of the host helitron. Each helitron contained an average of 2.9 gene fragments and 1.9 intact genes, of which the majority were annotated with binding functions in metabolic processes. In addition, a set of 114 nonredundant microRNAs were detected within 174 helitrons and predicted to regulate a set of 787 nonredundant target genes. These results suggest that helitrons contribute to genomic structural and transcriptional variation by capturing gene fragments and generating microRNAs. PMID:24055723

  1. Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.

    PubMed

    Iranzo, Jaime; Gómez, Manuel J; López de Saro, Francisco J; Manrubia, Susanna

    2014-06-01

    Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events-punctuations-during which the state of coexistence of IS and host becomes perturbated. PMID:24967627

  2. Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements.

    PubMed

    Joly-Lopez, Zoé; Hoen, Douglas R; Blanchette, Mathieu; Bureau, Thomas E

    2016-08-01

    Once perceived as merely selfish, transposable elements (TEs) are now recognized as potent agents of adaptation. One way TEs contribute to evolution is through TE exaptation, a process whereby TEs, which persist by replicating in the genome, transform into novel host genes, which persist by conferring phenotypic benefits. Known exapted TEs (ETEs) contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet little is known about this process. To better understand TE exaptation, we designed an approach to resolve the phylogenetic context and timing of exaptation events and subsequent patterns of ETE diversification. Starting with known ETEs, we search in diverse genomes for basal ETEs and closely related TEs, carefully curate the numerous candidate sequences, and infer detailed phylogenies. To distinguish TEs from ETEs, we also weigh several key genomic characteristics including repetitiveness, terminal repeats, pseudogenic features, and conserved domains. Applying this approach to the well-characterized plant ETEs MUG and FHY3, we show that each group is paraphyletic and we argue that this pattern demonstrates that each originated in not one but multiple exaptation events. These exaptations and subsequent ETE diversification occurred throughout angiosperm evolution including the crown group expansion, the angiosperm radiation, and the primitive evolution of angiosperms. In addition, we detect evidence of several putative novel ETE families. Our findings support the hypothesis that TE exaptation generates novel genes more frequently than is currently thought, often coinciding with key periods of evolution. PMID:27189548

  3. Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data.

    PubMed

    Li, Shu-Fen; Gao, Wu-Jun; Zhao, Xin-Peng; Dong, Tian-Yu; Deng, Chuan-Liang; Lu, Long-Dou

    2014-01-01

    Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant. PMID:24810432

  4. Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana

    PubMed Central

    Le, Tu N.; Miyazaki, Yuji; Takuno, Shohei; Saze, Hidetoshi

    2015-01-01

    Genomes of higher eukaryotes, including plants, contain numerous transposable elements (TEs), that are often silenced by epigenetic mechanisms, such as histone modifications and DNA methylation. Although TE silencing adversely affects expression of nearby genes, recent studies reveal the presence of intragenic TEs marked by repressive heterochromatic epigenetic marks within transcribed genes. However, even for the well-studied plant model Arabidopsis thaliana, the abundance of intragenic TEs, how they are epigenetically regulated, and their potential impacts on host gene expression, remain unexplored. In this study, we comprehensively analyzed genome-wide distribution and epigenetic regulation of intragenic TEs in A. thaliana. Our analysis revealed that about 3% of TEs are located within gene bodies, dominantly at intronic regions. Most of them are shorter and less methylated than intergenic TEs, but they are still targeted by RNA-directed DNA methylation-dependent and independent pathways. Surprisingly, the heterochromatic epigenetic marks at TEs are maintained within actively transcribed genes. Moreover, the heterochromatic state of intronic TEs is critical for proper transcription of associated genes. Our study provides the first insight into how intragenic TEs affect the transcriptional landscape of the A. thaliana genome, and suggests the importance of epigenetic mechanisms for regulation of TEs within transcriptional gene units. PMID:25813042

  5. The Role of Transposable Elements in Health and Diseases of the Central Nervous System

    PubMed Central

    Faulkner, Geoffrey J.; Dubnau, Joshua; Ponomarev, Igor

    2013-01-01

    First discovered in maize by Barbara McClintock in the 1940s, transposable elements (TEs) are DNA sequences that in some cases have the ability to move along chromosomes or “transpose” in the genome. This revolutionary finding was initially met with resistance by the scientific community and viewed by some as heretical. A large body of knowledge has accumulated over the last 60 years on the biology of TEs. Indeed, it is now known that TEs can generate genomic instability and reconfigure gene expression networks both in the germline and somatic cells. This review highlights recent findings on the role of TEs in health and diseases of the CNS, which were presented at the 2013 Society for Neuroscience meeting. The work of the speakers in this symposium shows that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings on TE expression and function in the CNS have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in shaping individual behavior and contribute to vulnerability to disease. PMID:24198348

  6. A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads.

    PubMed

    Kang, Houxiang; Zhu, Dan; Lin, Runmao; Opiyo, Stephen Obol; Jiang, Ning; Shiu, Shin-Han; Wang, Guo-Liang

    2016-06-01

    Identification of polymorphic transposable elements (TEs) is important because TE polymorphism creates genetic diversity and influences the function of genes in the host genome. However, de novo scanning of polymorphic TEs remains a challenge. Here, we report a novel computational method, called PTEMD (polymorphic TEs and their movement detection), for de novo discovery of genome-wide polymorphic TEs. PTEMD searches highly identical sequences using reads supported breakpoint evidences. Using PTEMD, we identified 14 polymorphic TE families (905 sequences) in rice blast fungus Magnaporthe oryzae, and 68 (10,618 sequences) in maize. We validated one polymorphic TE family experimentally, MoTE-1; all MoTE-1 family members are located in different genomic loci in the three tested isolates. We found that 57.1% (8 of 14) of the PTEMD-detected polymorphic TE families in M. oryzae are active. Furthermore, our data indicate that there are more polymorphic DNA transposons in maize than their counterparts of retrotransposons despite the fact that retrotransposons occupy largest fraction of genomic mass. We demonstrated that PTEMD is an effective tool for identifying polymorphic TEs in M. oryzae and maize genomes. PTEMD and the genome-wide polymorphic TEs in M. oryzae and maize are publically available at http://www.kanglab.cn/blast/PTEMD_V1.02.htm. PMID:27098848

  7. Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes.

    PubMed

    Mirouze, Marie; Vitte, Clémentine

    2014-06-01

    In the past decade, plant biologists and breeders have developed a growing interest in the field of epigenetics, which is defined as the study of heritable changes in gene expression that cannot be explained by changes in the DNA sequence. Epigenetic marks can be responsive to the environment, and evolve faster than genetic changes. Therefore, epigenetic diversity may represent an unexplored resource of natural variation that could be used in plant breeding programmes. On the other hand, crop genomes are largely populated with transposable elements (TEs) that are efficiently targeted by epigenetic marks, and part of the epigenetic diversity observed might be explained by TE polymorphisms. Characterizing the degree to which TEs influence epigenetic variation in crops is therefore a major goal to better use epigenetic variation. To date, epigenetic analyses have been mainly focused on the model plant Arabidopsis thaliana, and have provided clues on epigenome features, components that silence pathways, and effects of silencing impairment. But to what extent can Arabidopsis be used as a model for the epigenomics of crops? In this review, we discuss the similarities and differences between the epigenomes of Arabidopsis and crops. We explore the relationship between TEs and epigenomes, focusing on TE silencing control and escape, and the impact of TE mobility on epigenomic variation. Finally, we provide insights into challenges to tackle, and future directions to take in the route towards using epigenetic diversity in plant breeding programmes. PMID:24744427

  8. Target site choice of the related transposable elements Tc1 and Tc3 of Caenorhabditis elegans.

    PubMed Central

    van Luenen, H G; Plasterk, R H

    1994-01-01

    We have investigated the target choice of the related transposable elements Tc1 and Tc3 of the nematode C. elegans. The exact locations of 204 independent Tc1 insertions and 166 Tc3 insertions in an 1 kbp region of the genome were determined. There was no phenotypic selection for the insertions. All insertions were into the sequence TA. Both elements have a strong preference for certain positions in the 1 kbp region. Hot sites for integration are not clustered or regularly spaced. The orientation of the integrated transposon has no effect on the distribution pattern. We tested several explanations for the target site preference. If simple structural features of the DNA (e.g. bends) would mark hot sites, we would expect the patterns of the two related transposons Tc1 and Tc3 to be similar; however we found them to be completely different. Furthermore we found that the sequence at the donor site has no effect on the choice of the new insertion site, because the insertion pattern of a transposon that jumps from a transgenic donor site is identical to the insertion pattern of transposons jumping from endogenous genomic donor sites. The most likely explanation for the target choice is therefore that the primary sequence of the target site is recognized by the transposase. However, alignment of the Tc1 and Tc3 integration sites does not reveal a strong consensus sequence for either transposon. PMID:8127662

  9. Transposable elements and their KRAB-ZFP controllers regulate gene expression in adult tissues

    PubMed Central

    Ecco, Gabriela; Cassano, Marco; Kauzlaric, Annamaria; Duc, Julien; Coluccio, Andrea; Offner, Sandra; Imbeault, Michaël; Rowe, Helen M.; Turelli, Priscilla; Trono, Didier

    2016-01-01

    Summary KRAB-containing zinc finger proteins (KRAB-ZFPs) are early embryonic controllers of transposable elements (TEs), which they repress with their cofactor KAP1 through histone and DNA methylation, a process thought to result in irreversible silencing. Using a target-centered functional screen, we matched murine TEs with their cognate KRAB-ZFP. We found the paralogs ZFP932 and Gm15446 to bind overlapping but distinguishable subsets of ERVK (endogenous retrovirus K), to repress these elements in embryonic stem cells, and to regulate secondarily the expression of neighboring genes. Most importantly, we uncovered that these KRAB-ZFPs and KAP1 control TEs in adult tissues, in cell culture and in vivo, where they partner up to modulate cellular genes. Therefore, TEs and KRAB-ZFPs establish transcriptional networks that regulate not only development but probably many physiological events. Given the high degree of species-specificity of TEs and KRAB-ZFPs, these results have important implications for understanding the biology of higher vertebrates, including humans. PMID:27003935

  10. A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads

    PubMed Central

    Kang, Houxiang; Zhu, Dan; Lin, Runmao; Opiyo, Stephen Obol; Jiang, Ning; Shiu, Shin-Han; Wang, Guo-Liang

    2016-01-01

    Identification of polymorphic transposable elements (TEs) is important because TE polymorphism creates genetic diversity and influences the function of genes in the host genome. However, de novo scanning of polymorphic TEs remains a challenge. Here, we report a novel computational method, called PTEMD (polymorphic TEs and their movement detection), for de novo discovery of genome-wide polymorphic TEs. PTEMD searches highly identical sequences using reads supported breakpoint evidences. Using PTEMD, we identified 14 polymorphic TE families (905 sequences) in rice blast fungus Magnaporthe oryzae, and 68 (10,618 sequences) in maize. We validated one polymorphic TE family experimentally, MoTE-1; all MoTE-1 family members are located in different genomic loci in the three tested isolates. We found that 57.1% (8 of 14) of the PTEMD-detected polymorphic TE families in M. oryzae are active. Furthermore, our data indicate that there are more polymorphic DNA transposons in maize than their counterparts of retrotransposons despite the fact that retrotransposons occupy largest fraction of genomic mass. We demonstrated that PTEMD is an effective tool for identifying polymorphic TEs in M. oryzae and maize genomes. PTEMD and the genome-wide polymorphic TEs in M. oryzae and maize are publically available at http://www.kanglab.cn/blast/PTEMD_V1.02.htm. PMID:27098848

  11. Codon usage biases of transposable elements and host nuclear genes in Arabidopsis thaliana and Oryza sativa.

    PubMed

    Jia, Jia; Xue, Qingzhong

    2009-12-01

    Transposable elements (TEs) are mobile genetic entities ubiquitously distributed in nearly all genomes. High frequency of codons ending in A/T in TEs has been previously observed in some species. In this study, the biases in nucleotide composition and codon usage of TE transposases and host nuclear genes were investigated in the AT-rich genome of Arabidopsis thaliana and the GC-rich genome of Oryza sativa. Codons ending in A/T are more frequently used by TEs compared with their host nuclear genes. A remarkable positive correlation between highly expressed nuclear genes and C/G-ending codons were detected in O. sativa (r=0.944 and 0.839, respectively, P<0.0001) but not in A. thaliana, indicating a close association between the GC content and gene expression level in monocot species. In both species, TE codon usage biases are similar to that of weakly expressed genes. The expression and activity of TEs may be strictly controlled in plant genomes. Mutation bias and selection pressure have simultaneously acted on the TE evolution in A. thaliana and O. sativa. The consistently observed biases of nucleotide composition and codon usage of TEs may also provide a useful clue to accurately detect TE sequences in different species. PMID:20172490

  12. Pseudomonas aeruginosa transposable bacteriophages D3112 and B3 require pili and surface growth for adsorption.

    PubMed Central

    Roncero, C; Darzins, A; Casadaban, M J

    1990-01-01

    Pseudomonas aeruginosa transposable bacteriophages D3112 and B3 were found to require pili for infection. Seventy mutants of P. aeruginosa PAO selected by resistance to D3112 or B3 were also resistant to the phage not used in the selection and suggested that the receptors of these two phages are identical. Of five resistant mutants examined, all were defective in the production of pili and did not adsorb either phage. P. aeruginosa PAK strains altered in pilus expression, such as hyperpiliated or nonpiliated mutants, adsorbed the phage but were not productively infected, implying that an additional host function was required for infection. The cell-associated lipopolysaccharide was not required for D3112 or B3 infection, since mutants deficient in O side-chain and core biosynthesis were still capable of adsorption and productive infection. This is in contrast to Escherichia coli mutator phages Mu and D108, which are dependent on lipopolysaccharide for adsorption. The P. aeruginosa phages adsorbed only to cells grown on solid media or in liquid media supplemented with agents that increase the macroviscosity, such as polyvinylpyrrolidone. Adsorption time course studies of D3112 and B3 using cells grown in solid media revealed similar but not identical adsorption patterns. These studies suggested that expression of the D3112 and B3 cell receptor is induced by growth on solid media. Images FIG. 2 PMID:1969404

  13. Population dynamics of an Ac-like transposable element in self- and cross-pollinating arabidopsis.

    PubMed Central

    Wright, S I; Le, Q H; Schoen, D J; Bureau, T E

    2001-01-01

    Theoretical models predict that the mating system should be an important factor driving the dynamics of transposable elements in natural populations due to differences in selective pressure on both element and host. We used a PCR-based approach to examine the abundance and levels of insertion polymorphism of Ac-III, a recently identified Ac-like transposon family, in natural populations of the selfing plant Arabidopsis thaliana and its close outcrossing relative, Arabidopsis lyrata. Although several insertions appeared to be ancient and shared between species, there is strong evidence for recent activity of this element family in both species. Sequences of the regions flanking insertions indicate that all Ac-III transposons segregating in natural populations are in noncoding regions and provide no evidence for local transposition events. Transposon display analysis suggests the presence of slightly higher numbers of insertion sites per individual but fewer total polymorphic insertions in the self-pollinating A. thaliana than A. lyrata. Element insertions appear to be segregating at significantly lower frequencies in A. lyrata than A. thaliana, which is consistent with a reduction in transposition rate, reduction in effective population size, or reduced efficacy of natural selection against element insertions in selfing populations. PMID:11454774

  14. Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus.

    PubMed

    Valente, Guilherme; Kocher, Thomas; Eickbush, Thomas; Simões, Rafael P; Martins, Cesar

    2016-06-01

    Integration of cytogenetics and genomics has become essential to a better view of architecture and function of genomes. Although the advances on genomic sequencing have contributed to study genes and genomes, the repetitive DNA fraction of the genome is still enigmatic and poorly understood. Among repeated DNAs, transposable elements (TEs) are major components of eukaryotic chromatin and their investigation has been hindered even after the availability of whole sequenced genomes. The cytogenetic mapping of TEs in chromosomes has proved to be of high value to integrate information from the micro level of nucleotide sequence to a cytological view of chromosomes. Different TEs have been cytogenetically mapped in cichlids; however, neither details about their genomic arrangement nor appropriated copy number are well defined by these approaches. The current study integrates TEs distribution in Nile tilapia Oreochromis niloticus genome based on cytogenetic and genomics/bioinformatics approach. The results showed that some elements are not randomly distributed and that some are genomic dependent on each other. Moreover, we found extensive overlap between genomics and cytogenetics data and that tandem duplication may be the major mechanism responsible for the genomic dynamics of TEs here analyzed. This paper provides insights in the genomic organization of TEs under an integrated view based on cytogenetics and genomics. PMID:26860923

  15. Identification of NbME MITE families: potential molecular markers in the microsporidia Nosema bombycis.

    PubMed

    Xu, Jinshan; Wang, Min; Zhang, Xiaoyan; Tang, Fahui; Pan, Guoqing; Zhou, Zeyang

    2010-01-01

    Six novel families of miniature inverted-repeat transposable elements (MITEs) were characterized in the microsporidia Nosema bombycis and were named NbMEs. The structural characteristics and the distribution of NbME copies in the N. bombycis genome were investigated, and it was found that portions of NbMEs are associated with gene sections. Potential molecular markers for various N. bombycis strains were identified in this study through utilization of the MITE-AFLP technique. Three distinct pathogenic isolates collected from different areas were distinguished, and polymorphisms were detected using the NbME5 marker, thereby establishing this NbME as a potential marker for studying isolate variation in N. bombycis. PMID:19861130

  16. Miniature LED endoilluminators for vitreoretinal surgery

    NASA Astrophysics Data System (ADS)

    Hessling, M.; Koelbl, P. S.; Lingenfelder, C.; Koch, F.

    2015-07-01

    Two innovative approaches for intraocular illumination during vitreoretinal surgery by application of white LEDs are being developed. Both techniques are less harmful to the patient, more convenient for the surgeon and smaller and cheaper compared to conventional illumination by Xenon light sources and optical fibers. These two novel approaches are: I) The miniature LED chandelier endoilluminator consisting of a single white LED with a "light probe" on top of the LED housing that fits in a small incision in the wall of the eye. II) The alternative transscleral LED endoilluminator is integrated into an eye speculum that presses the flat LED top against the eye. The intraocular space is only illuminated by light transmitted through the sclera. In contrast to conventional illumination techniques for vitreoretinal surgery no incision is necessary. Both approaches are evaluated with regard to potential photochemical and thermal risks for the patient's retina and they are tested on porcine eyes.

  17. Miniature fiber optic surface plasmon resonance biosensors

    NASA Astrophysics Data System (ADS)

    Slavik, Radan; Brynda, Eduard; Homola, Jiri; Ctyroky, Jiri

    1999-01-01

    A novel design of surface plasmon resonance fiber optic sensor is reported which leads to a compact, highly miniaturized sensing element with excellent sensitivity. The sensing device is based on a side-polished single-mode optical fiber with a thin metal overlayer supporting surface plasmon waves. The strength of interaction between a fiber mode and a surface plasmon wave depends strongly on the refractive index near the sensing surface. Therefore, refractive index changes associated with biospecific interaction between antibodies immobilized on the sensor and antigen molecules can be monitored by measuring light intensity variations. Detection of horse radish peroxidase (HRP) of the concentration of 100 ng/ml has been accomplished using the fiber optic sensor with a matrix of monoclonal antibodies against HRP immobilized on the sensor surface.

  18. Miniature Ring-Shaped Peristaltic Pump

    NASA Technical Reports Server (NTRS)

    Bar-Cohen, Yoseph; Chang, Zensheu; Bao, Xiaoqi; Lih, Shyh-Shiuh

    2004-01-01

    An experimental miniature peristaltic pump exploits piezoelectrically excited flexural waves that travel around a ring: A fluid is carried in the containers formed in the valleys between the peaks of the flexural waves, What sets the present pump apart from other pumps that exploit piezoelectrically excited flexural waves is the ring shape, which makes it possible to take advantage of some of the desirable characteristics of previously developed piezoelectric rotary motors. A major advantage of the circular (in contradistinction to a straight-line) wave path is that the flexural waves do not come to a stop and, instead, keep propagating around the ring. Hence, a significant portion of the excitation energy supplied during each cycle is reused during the next cycle, with the result that the pump operates more effectively than it otherwise would.

  19. Gallbladder lymphoma in a miniature dachshund.

    PubMed

    Nagata, Nao; Shibata, Sanae; Sakai, Hiroki; Konno, Hiroaki; Takashima, Satoshi; Kawabe, Mifumi; Mori, Takashi; Kitagawa, Hitoshi; Washizu, Makoto

    2015-01-01

    A 7-year-old, miniature dachshund was referred for examination and treatment of persistent anorexia, deep yellow-coloured urine and leucocytosis. The clinical sign of jaundice, results from a serum biochemistry profile and ultrasonographic images suggested a biliary tract obstruction. A cholecystectomy was performed to remove the obstruction. Histopathological assessment of the resected gallbladder and partial common bile duct indicated diffuse large B-cell lymphoma. Twelve days after the initial operation, a second procedure was performed due to bile leakage into the abdominal cavity. Chemotherapy was administered twice after the second operation but discontinued, because the dog showed adverse effects. The dog is still alive 24 months after the surgery. To the authors' knowledge, this is the first description of canine gallbladder lymphoma. PMID:25311915

  20. Power Electronics for a Miniaturized Arcjet

    NASA Technical Reports Server (NTRS)

    Pinero, Luis R.; Bowers, Glen E.

    1997-01-01

    A 0.3 kW Power Processing Unit (PPU) was designed, tested on resistive loads, and then integrated with a miniaturized arcjet. The main goal of the design was to minimize size and mass while maintaining reasonable efficiency. In order to obtain the desired reductions in mass, simple topologies and control methods were considered. The PPU design incorporates a 50 kHz, current-mode-control, pulse-width-modulated (PWM), push-pull topology. An input voltage of 28 +/- 4V was chosen for compatibility with typical unregulated low voltage busses anticipated for smallsats. An efficiency of 0.90 under nominal operating conditions was obtained. The component mass of the PPU was 0.475 kg and could be improved by optimization of the output filter design. The estimated mass for a flight PPU based on this design is less than a kilogram.

  1. An automated miniature robotic vehicle inspection system

    SciTech Connect

    Dobie, Gordon; Summan, Rahul; MacLeod, Charles; Pierce, Gareth; Galbraith, Walter

    2014-02-18

    A novel, autonomous reconfigurable robotic inspection system for quantitative NDE mapping is presented. The system consists of a fleet of wireless (802.11g) miniature robotic vehicles, each approximately 175 × 125 × 85 mm with magnetic wheels that enable them to inspect industrial structures such as storage tanks, chimneys and large diameter pipe work. The robots carry one of a number of payloads including a two channel MFL sensor, a 5 MHz dry coupled UT thickness wheel probe and a machine vision camera that images the surface. The system creates an NDE map of the structure overlaying results onto a 3D model in real time. The authors provide an overview of the robot design, data fusion algorithms (positioning and NDE) and visualization software.

  2. Miniature piezo electric vacuum inlet valve

    DOEpatents

    Keville, Robert F.; Dietrich, Daniel D.

    1998-03-24

    A miniature piezo electric vacuum inlet valve having a fast pulse rate and is battery operated with variable flow capability. The low power (<1.6 watts), high pulse rate (<2 milliseconds), variable flow inlet valve is utilized for mass spectroscopic applications or other applications where pulsed or continuous flow conditions are needed. The inlet valve also has a very minimal dead volume of less than 0.01 std/cc. The valve can utilize, for example, a 12 Vdc input/750 Vdc, 3 mA output power supply compared to conventional piezo electric valves which require preloading of the crystal drive mechanism and 120 Vac, thus the valve of the present invention is smaller by a factor of three.

  3. Miniature piezo electric vacuum inlet valve

    DOEpatents

    Keville, R.F.; Dietrich, D.D.

    1998-03-24

    A miniature piezo electric vacuum inlet valve having a fast pulse rate and is battery operated with variable flow capability is disclosed. The low power (<1.6 watts), high pulse rate (<2 milliseconds), variable flow inlet valve is utilized for mass spectroscopic applications or other applications where pulsed or continuous flow conditions are needed. The inlet valve also has a very minimal dead volume of less than 0.01 std/cc. The valve can utilize, for example, a 12 Vdc input/750 Vdc, 3 mA output power supply compared to conventional piezo electric valves which require preloading of the crystal drive mechanism and 120 Vac, thus the valve of the present invention is smaller by a factor of three. 6 figs.

  4. A miniaturized pointing mount for Spacelab missions

    NASA Technical Reports Server (NTRS)

    Fritz, C. G.; Howell, T., Jr.; Nicaise, P. D.; Parker, J. R.

    1975-01-01

    A Miniaturized Pointing Mount (MPM) for Spacelab missions is defined and simulation results are described. This mount is proposed to complement the Spacelab Instrument Pointing System (IPS). It uses the same mount isolator concept as the Spacelab IPS but is much more efficient and economical for the accommodation of small shuttle payloads. The MPM is built from star tracker assemblies left over from the Apollo Telescope Mount program thereby assuring low cost and development risk. Simulation results indicate a high level of instrument stability can be expected. The short development time of the MPM would permit it to serve as a precursor to the Spacelab IPS for verifying critical new concepts such as the mount isolation and hold down mechanisms.

  5. Miniature Trailing Edge Effector for Aerodynamic Control

    NASA Technical Reports Server (NTRS)

    Lee, Hak-Tae (Inventor); Bieniawski, Stefan R. (Inventor); Kroo, Ilan M. (Inventor)

    2008-01-01

    Improved miniature trailing edge effectors for aerodynamic control are provided. Three types of devices having aerodynamic housings integrated to the trailing edge of an aerodynamic shape are presented, which vary in details of how the control surface can move. A bucket type device has a control surface which is the back part of a C-shaped member having two arms connected by the back section. The C-shaped section is attached to a housing at the ends of the arms, and is rotatable about an axis parallel to the wing trailing edge to provide up, down and neutral states. A flip-up type device has a control surface which rotates about an axis parallel to the wing trailing edge to provide up, down, neutral and brake states. A rotating type device has a control surface which rotates about an axis parallel to the chord line to provide up, down and neutral states.

  6. A miniaturized fibrinolytic assay for plasminogen activators

    NASA Technical Reports Server (NTRS)

    Lewis, M. L.; Nachtwey, D. S.; Damron, K. L.

    1991-01-01

    This report describes a micro-clot lysis assay (MCLA) for evaluating fibrinolytic activity of plasminogen activators (PA). Fibrin clots were formed in wells of microtiter plates. Lysis of the clots by PA, indicated by change in turbidity (optical density, OD), was monitored with a microplate reader at five minutes intervals. Log-log plots of PA dilution versus endpoint, the time at which the OD value was halfway between the maximum and minimum value for each well, were linear over a broad range of PA concentrations (2-200 International units/ml). The MCLA is a modification and miniaturization of well established fibrinolytic methods. The significant practical advantages of the MCLA are that it is a simple, relatively sensitive, non-radioactive, quantitative, kinetic, fibrinolytic micro-technique which can be automated.

  7. Miniaturized attitude control system for nanosatellites

    NASA Astrophysics Data System (ADS)

    Candini, Gian Paolo; Piergentili, Fabrizio; Santoni, Fabio

    2012-12-01

    A miniaturized attitude control system suitable for nanosatellites, developed using only commercial off-the-shelf components, is described in the paper. It is a complete and independent system to be used on board nanosatellites, allowing automated attitude control. To integrate this system into nanosatellites such as Cubesats its size has been reduced down to a cube of side about 5 cm. The result is a low cost attitude control system built with terrestrial components, integrating three micro magnetotorquers, three micro reaction wheels, three magnetometers and redundant control electronics, capable of performing automatics operations on request from the ground. The system can operate as a real time maneuvering system, executing commands sent from the ground or as a standalone attitude control system receiving the solar array status from a hosting satellite and the satellite ephemeris transmitted from the ground station. The main characteristics of the developed system and test results are depicted in this paper.

  8. Miniature linear-to-rotary motion actuator

    NASA Technical Reports Server (NTRS)

    Sorokach, Michael R., Jr.

    1993-01-01

    A miniature hydraulic actuation system capable of converting linear actuator motion to control surface rotary motion has been designed for application to active controls on dynamic wind tunnel models. Due to space constraints and the torque requirements of an oscillating control surface at frequencies up to 50 Hertz, a new actuation system was developed to meet research objectives. This new actuation system was designed and developed to overcome the output torque limitations and fluid loss/sealing difficulties associated with an existing vane type actuator. Static control surface deflections and dynamic control surface oscillations through a given angle are provided by the actuation system. The actuator design has been incorporated into a transonic flutter model with an active trailing edge flap and two active spoilers. The model is scheduled for testing in the LaRC 16 Foot Transonic Dynamics Tunnel during Summer 1993. This paper will discuss the actuation system, its design, development difficulties, test results, and application to aerospace vehicles.

  9. Miniature, sub-nanometer resolution Talbot spectrometer.

    PubMed

    Ye, Erika; Atabaki, Amir H; Han, Ningren; Ram, Rajeev J

    2016-06-01

    Miniaturization of optical spectrometers has a significant practical value as it can enable compact, affordable spectroscopic systems for chemical and biological sensing applications. For many applications, the spectrometer must gather light from sources that span a wide range of emission angles and wavelengths. Here, we report a lens-free spectrometer that is simultaneously compact (<0.6  cm3), of high resolution (<1  nm), and has a clear aperture (of 10×10  mm). The wavelength-scale pattern in the dispersive element strongly diffracts the input light to produce non-paraxial mid-field diffraction patterns that are then recorded using an optimally matched image sensor and processed to reconstruct the spectrum. PMID:27244382

  10. A pair of miniature helium expansion turbines

    SciTech Connect

    Sixsmith, H.; Swift, W.

    1982-01-01

    Two miniature cryogenic turboexpanders are discussed. These were developed to provide first and second stage expansion in small helium liquifiers or refrigerators. The design of each is virtually identical although the design operating conditions varied more than 30% in specific speed. The expanders run at high speeds in pressurized helium bearings with an integral brake heat exchanger. The vital components are contained in a cartridge, held in place by a single nut, which can be removed and replaced in less than one minute. Specifications and descriptions are discussed are parameters itemized. The assembly is diagramed with an photo of the brazed bearing assembly and titanium shaft. Expander operation is discussed. A subsequent discussion is recorded concerning the efficiency of the turbine, which is similar to that of an NBS turbine.

  11. Miniature Neutron-Alpha Activation Spectrometer

    NASA Astrophysics Data System (ADS)

    Rhodes, Edgar; Holloway, James Paul; He, Zhong; Goldsten, John

    2002-10-01

    We are developing a miniature neutron-alpha activation spectrometer for in-situ analysis of chem-bio samples, including rocks, fines, ices, and drill cores, suitable for a lander or Rover platform for Mars or outer-planet missions. In the neutron-activation mode, penetrating analysis will be performed of the whole sample using a γ spectrometer and in the α-activation mode, the sample surface will be analyzed using Rutherford-backscatter and x-ray spectrometers. Novel in our approach is the development of a switchable radioactive neutron source and a small high-resolution γ detector. The detectors and electronics will benefit from remote unattended operation capabilities resulting from our NEAR XGRS heritage and recent development of a Ge γ detector for MESSENGER. Much of the technology used in this instrument can be adapted to portable or unattended terrestrial applications for detection of explosives, chemical toxins, nuclear weapons, and contraband.

  12. Self-folding miniature elastic electric devices

    NASA Astrophysics Data System (ADS)

    Miyashita, Shuhei; Meeker, Laura; Tolley, Michael T.; Wood, Robert J.; Rus, Daniela

    2014-09-01

    Printing functional materials represents a considerable impact on the access to manufacturing technology. In this paper we present a methodology and validation of print-and-self-fold miniature electric devices. Polyvinyl chloride laminated sheets based on metalized polyester film show reliable self-folding processes under a heat application, and it configures 3D electric devices. We exemplify this technique by fabricating fundamental electric devices, namely a resistor, capacitor, and inductor. Namely, we show the development of a self-folded stretchable resistor, variable resistor, capacitive strain sensor, and an actuation mechanism consisting of a folded contractible solenoid coil. Because of their pre-defined kinematic design, these devices feature elasticity, making them suitable as sensors and actuators in flexible circuits. Finally, an RLC circuit obtained from the integration of developed devices is demonstrated, in which the coil based actuator is controlled by reading a capacitive strain sensor.

  13. Miniature reciprocating heat pumps and engines

    NASA Technical Reports Server (NTRS)

    Thiesen, Jack H. (Inventor); Willen, Gary S. (Inventor); Mohling, Robert A. (Inventor)

    2003-01-01

    The present invention discloses a miniature thermodynamic device that can be constructed using standard micro-fabrication techniques. The device can be used to provide cooling, generate power, compress gases, pump fluids and reduce pressure below ambient (operate as a vacuum pump). Embodiments of the invention relating to the production of a cooling effect and the generation of electrical power, change the thermodynamic state of the system by extracting energy from a pressurized fluid. Energy extraction is attained using an expansion process, which is as nearly isentropic as possible for the appropriately chosen fluid. An isentropic expansion occurs when a compressed gas does work to expand, and in the disclosed embodiments, the gas does work by overcoming either an electrostatic or a magnetic force.

  14. Integrated measurement system for miniature camera modules

    NASA Astrophysics Data System (ADS)

    Tervonen, Ari; Nivala, Ilkka; Ryytty, Pasi; Saari, Hannu; Ojanen, Harri; Viinikanoja, Jarkko

    2006-04-01

    Particularly for miniature camera modules, manufactured in high volumes, characterization and measurement approaches are needed that provide information on camera key properties efficiently. An integrated measurement system named has been developed that uses images taken on specifically designed test chart targets, which are then automatically analysed by software. The chart combines target elements for measurement of optoelectronic conversion function, resolution, noise, uniformity, distortion and colour reproduction. The software applies machine vision to recognize the various target elements from the images, and to register analysis locations properly. The actual analysis methods conform with existing standards. The software includes graphical user interface, and in addition to the automatic analysis, also user-defined analysis can be flexibly done. The software supports modifications in the chart layout, batch analysis of images and storing the results in spreadsheet report format.

  15. Miniature solid-state gas compressor

    DOEpatents

    Lawless, William N.; Cross, Leslie E.; Steyert, William A.

    1985-01-01

    A miniature apparatus for compressing gases is disclosed in which an elastomer disposed between two opposing electrostrictive or piezoelectric ceramic blocks, or between a single electrostrictive or piezoelectric ceramic block and a rigid surface, is caused to extrude into or recede from a channel defined adjacent to the elastomer in response to application or removal of an electric field from the blocks. Individual cells of blocks and elastomer are connected to effect a gas compression by peristaltic activation of the individual cells. The apparatus is self-valving in that the first and last cells operate as inlet and outlet valves, respectively. Preferred electrostrictive and piezoelectric ceramic materials are disclosed, and an alternative, non-peristaltic embodiment of the apparatus is described.

  16. Miniature solid-state gas compressor

    DOEpatents

    Lawless, W.N.; Cross, L.E.; Steyert, W.A.

    1985-05-07

    A miniature apparatus for compressing gases is disclosed in which an elastomer disposed between two opposing electrostrictive or piezoelectric ceramic blocks, or between a single electrostrictive or piezoelectric ceramic block and a rigid surface, is caused to extrude into or recede from a channel defined adjacent to the elastomer in response to application or removal of an electric field from the blocks. Individual cells of blocks and elastomer are connected to effect a gas compression by peristaltic activation of the individual cells. The apparatus is self-valving in that the first and last cells operate as inlet and outlet valves, respectively. Preferred electrostrictive and piezoelectric ceramic materials are disclosed, and an alternative, non-peristaltic embodiment of the apparatus is described. 9 figs.

  17. An automated miniature robotic vehicle inspection system

    NASA Astrophysics Data System (ADS)

    Dobie, Gordon; Summan, Rahul; MacLeod, Charles; Pierce, Gareth; Galbraith, Walter

    2014-02-01

    A novel, autonomous reconfigurable robotic inspection system for quantitative NDE mapping is presented. The system consists of a fleet of wireless (802.11g) miniature robotic vehicles, each approximately 175 × 125 × 85 mm with magnetic wheels that enable them to inspect industrial structures such as storage tanks, chimneys and large diameter pipe work. The robots carry one of a number of payloads including a two channel MFL sensor, a 5 MHz dry coupled UT thickness wheel probe and a machine vision camera that images the surface. The system creates an NDE map of the structure overlaying results onto a 3D model in real time. The authors provide an overview of the robot design, data fusion algorithms (positioning and NDE) and visualization software.

  18. Miniaturized Autonomous Extravehicular Robotic Camera (Mini AERCam)

    NASA Technical Reports Server (NTRS)

    Fredrickson, Steven E.

    2001-01-01

    The NASA Johnson Space Center (JSC) Engineering Directorate is developing the Autonomous Extravehicular Robotic Camera (AERCam), a low-volume, low-mass free-flying camera system . AERCam project team personnel recently initiated development of a miniaturized version of AERCam known as Mini AERCam. The Mini AERCam target design is a spherical "nanosatellite" free-flyer 7.5 inches in diameter and weighing 1 0 pounds. Mini AERCam is building on the success of the AERCam Sprint STS-87 flight experiment by adding new on-board sensing and processing capabilities while simultaneously reducing volume by 80%. Achieving enhanced capability in a smaller package depends on applying miniaturization technology across virtually all subsystems. Technology innovations being incorporated include micro electromechanical system (MEMS) gyros, "camera-on-a-chip" CMOS imagers, rechargeable xenon gas propulsion system , rechargeable lithium ion battery, custom avionics based on the PowerPC 740 microprocessor, GPS relative navigation, digital radio frequency communications and tracking, micropatch antennas, digital instrumentation, and dense mechanical packaging. The Mini AERCam free-flyer will initially be integrated into an approximate flight-like configuration for demonstration on an airbearing table. A pilot-in-the-loop and hardware-in-the-loop simulation to simulate on-orbit navigation and dynamics will complement the airbearing table demonstration. The Mini AERCam lab demonstration is intended to form the basis for future development of an AERCam flight system that provides beneficial on-orbit views unobtainable from fixed cameras, cameras on robotic manipulators, or cameras carried by EVA crewmembers.

  19. Miniaturized spectral imager for Aalto-1 nanosatellite

    NASA Astrophysics Data System (ADS)

    Mannila, Rami; Näsilä, Antti; Praks, Jaan; Saari, Heikki; Antila, Jarkko

    2011-11-01

    The Aalto-1 is a 3U-cubesat project coordinated by Aalto University. The satellite, Aalto-1, will be mainly built by students as project assignments and thesis works. VTT Technical Research Centre of Finland will develop the main Earth observation payload, a miniaturized spectral imager, for the satellite. It is a novel highly miniaturized tunable filter type spectral imager. Mass of the spectral imager will be less than 400 grams, and dimensions will be approximately 80 mm x 80 mm x 45 mm. The spectral imager is based on a tunable Fabry-Pérot interferometer (FPI) accompanied by an RGB CMOS image sensor. The FPI consists of two highly reflective surfaces separated by a tunable air gap and it is based either on a microelectromechanical (MEMS) or piezo-actuated structure. The MEMS FPI is a monolithic device, i.e. it is made entirely on one substrate in a batch process, without assembling separate pieces together. The gap is adjusted by moving the upper mirror with electrostatic force. Benefits of the MEMS FPI are low mass and small size. However, large aperture (2-10 mm) MEMS FPIs are currently under development, thus it is not yet known if their performance is adequate. The piezo-actuated FPI uses three piezo-actuators and is controlled in a closed capacitive feedback loop. The drawback of the piezo-actuated FPI is its higher mass. However, it has a large aperture which enables a shorter exposure times. Selection of the FPI type will be done after thorough evaluation. Depending on the selected FPI type, the spectral resolution of the imager will be 5 - 10 nm at full width at half maximum and it will operate in the visible and/or near infrared range.

  20. Miniature, Lightweight, One-Time-Opening Valve

    NASA Technical Reports Server (NTRS)

    Jones, Jack; Wu, Juinn Jenq; Leland, Robert

    2008-01-01

    The figure depicts the main parts of a prototype miniature, lightweight, onetime- opening valve. Like some other miniature one-time-opening valves reported in previous issues of NASA Tech Briefs, this valve is opened by melting a material that blocks the flow path. This valve is designed to remain closed at some temperature between room temperature and cryogenic temperature until the time of opening. The prototype valve includes a 1/8-in. (3-mm) aluminum tube, one end of which is plugged with a solder comprising about 37 weight percent of lead and 63 weight percent of tin. The tube and the solder both have a coefficient of thermal expansion of 23 micron/m-K at room temperature. Before plugging, the interior surface of the plug end of the tube is cleaned with a commercial flux paste developed specifically for preparing aluminum for bonding with lead/tin solder. The solder is then melted into the cleaned end of the tube, forming the plug. In a test, the plugged tube was pressurized to 1,000 psi (6.9 MPa) with helium and leak-tested. It was then cooled to a temperature of 77 K (about 196 C) and again leak-tested at the same pressure. Finally, at a lower pressure, the plugged end of the tube was heated to about 200 C (the melting temperature of the solder is 183 C), causing the solder plug to be ejected (see figure). It has been estimated that in a subsequent version of the valve, the plug could be melted by electrical heating, using a nichrome wire having a mass of only 10 g.

  1. Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila

    PubMed Central

    González, Josefa; Karasov, Talia L.; Messer, Philipp W.; Petrov, Dmitri A.

    2010-01-01

    Investigating spatial patterns of loci under selection can give insight into how populations evolved in response to selective pressures and can provide monitoring tools for detecting the impact of environmental changes on populations. Drosophila is a particularly good model to study adaptation to environmental heterogeneity since it is a tropical species that originated in sub-Saharan Africa and has only recently colonized the rest of the world. There is strong evidence for the adaptive role of Transposable Elements (TEs) in the evolution of Drosophila, and TEs might play an important role specifically in adaptation to temperate climates. In this work, we analyzed the frequency of a set of putatively adaptive and putatively neutral TEs in populations with contrasting climates that were collected near the endpoints of two known latitudinal clines in Australia and North America. The contrasting results obtained for putatively adaptive and putatively neutral TEs and the consistency of the patterns between continents strongly suggest that putatively adaptive TEs are involved in adaptation to temperate climates. We integrated information on population behavior, possible environmental selective agents, and both molecular and functional information of the TEs and their nearby genes to infer the plausible phenotypic consequences of these insertions. We conclude that adaptation to temperate environments is widespread in Drosophila and that TEs play a significant role in this adaptation. It is remarkable that such a diverse set of TEs located next to a diverse set of genes are consistently adaptive to temperate climate-related factors. We argue that reverse population genomic analyses, as the one described in this work, are necessary to arrive at a comprehensive picture of adaptation. PMID:20386746

  2. Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

    PubMed Central

    Makarevitch, Irina; Waters, Amanda J.; West, Patrick T.; Stitzer, Michelle; Hirsch, Candice N.; Ross-Ibarra, Jeffrey; Springer, Nathan M.

    2015-01-01

    Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as “junk” DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize. PMID:25569788

  3. Characterization of transposable element-associated mutations that alter yeast alcohol dehydrogenase II expression.

    PubMed Central

    Williamson, V M; Cox, D; Young, E T; Russell, D W; Smith, M

    1983-01-01

    Seven cis-dominant, constitutively expressed mutations of the normally glucose-repressible isozyme of alcohol dehydrogenase (ADHII) from the yeast Saccharomyces cerevisiae are caused by insertion of transposable elements from the Ty1 family in front of the ADHII structural gene (ADR2) (V. M. Williamson, E. T. Young, and M. Ciriacy, Cell 23:605-614, 1981). We cloned ADR2 with its associated Ty1 element from five S. cerevisiae strains carrying these mutations. Comparison of the Ty1 elements by heteroduplex studies and restriction enzyme analyses indicated that four were very similar; the fifth, although the same size as the others (about 5.6 kilobases), differed by the presence of two large substitutions of approximately 1 and 2 kilobases. The DNA sequences of the terminal direct repeats (deltas) were very homologous but not identical and were similar to previously reported Ty1 element direct repeats. We determined the 5'-flanking sequences of the ADR2 gene isolated from a wild-type strain and from five Ty1-associated mutations. The 5-base pair target sequence at the site of Ty1 insertion was present at both ends of each Ty1 element. The sites of insertion of the elements were all different and occurred from 125 to 210 base pairs in front of the coding region of ADR2. The 5' end of the major transcript as determined by S1 mapping was the same in wild-type cells and in Ty1-associated constitutive mutants and was approximately 54 base pairs upstream from the coding region. ADR2 transcripts were not detected when a solo delta sequence was present in the 5'-flanking region of this gene. Images PMID:6298605

  4. Gross deletions involving IGHM, BTK, or Artemis: a model for genomic lesions mediated by transposable elements.

    PubMed

    van Zelm, Menno C; Geertsema, Corinne; Nieuwenhuis, Nicole; de Ridder, Dick; Conley, Mary Ellen; Schiff, Claudine; Tezcan, Ilhan; Bernatowska, Ewa; Hartwig, Nico G; Sanders, Elisabeth A M; Litzman, Jiri; Kondratenko, Irina; van Dongen, Jacques J M; van der Burg, Mirjam

    2008-02-01

    Most genetic disruptions underlying human disease are microlesions, whereas gross lesions are rare with gross deletions being most frequently found (6%). Similar observations have been made in primary immunodeficiency genes, such as BTK, but for unknown reasons the IGHM and DCLRE1C (Artemis) gene defects frequently represent gross deletions ( approximately 60%). We characterized the gross deletion breakpoints in IGHM-, BTK-, and Artemis-deficient patients. The IGHM deletion breakpoints did not show involvement of recombination signal sequences or immunoglobulin switch regions. Instead, five IGHM, eight BTK, and five unique Artemis breakpoints were located in or near sequences derived from transposable elements (TE). The breakpoints of four out of five disrupted Artemis alleles were located in highly homologous regions, similar to Ig subclass deficiencies and Vh deletion polymorphisms. Nevertheless, these observations suggest a role for TEs in mediating gross deletions. The identified gross deletion breakpoints were mostly located in TE subclasses that were specifically overrepresented in the involved gene as compared to the average in the human genome. This concerned both long (LINE1) and short (Alu, MIR) interspersed elements, as well as LTR retrotransposons (ERV). Furthermore, a high total TE content (>40%) was associated with an increased frequency of gross deletions. Both findings were further investigated and confirmed in a total set of 20 genes disrupted in human disease. Thus, to our knowledge for the first time, we provide evidence that a high TE content, irrespective of the type of element, results in the increased incidence of gross deletions as gene disruption underlying human disease. PMID:18252213

  5. Gross Deletions Involving IGHM, BTK, or Artemis: A Model for Genomic Lesions Mediated by Transposable Elements

    PubMed Central

    van Zelm, Menno C.; Geertsema, Corinne; Nieuwenhuis, Nicole; de Ridder, Dick; Conley, Mary Ellen; Schiff, Claudine; Tezcan, Ilhan; Bernatowska, Ewa; Hartwig, Nico G.; Sanders, Elisabeth A.M.; Litzman, Jiri; Kondratenko, Irina; van Dongen, Jacques J.M.; van der Burg, Mirjam

    2008-01-01

    Most genetic disruptions underlying human disease are microlesions, whereas gross lesions are rare with gross deletions being most frequently found (6%). Similar observations have been made in primary immunodeficiency genes, such as BTK, but for unknown reasons the IGHM and DCLRE1C (Artemis) gene defects frequently represent gross deletions (∼60%). We characterized the gross deletion breakpoints in IGHM-, BTK-, and Artemis-deficient patients. The IGHM deletion breakpoints did not show involvement of recombination signal sequences or immunoglobulin switch regions. Instead, five IGHM, eight BTK, and five unique Artemis breakpoints were located in or near sequences derived from transposable elements (TE). The breakpoints of four out of five disrupted Artemis alleles were located in highly homologous regions, similar to Ig subclass deficiencies and Vh deletion polymorphisms. Nevertheless, these observations suggest a role for TEs in mediating gross deletions. The identified gross deletion breakpoints were mostly located in TE subclasses that were specifically overrepresented in the involved gene as compared to the average in the human genome. This concerned both long (LINE1) and short (Alu, MIR) interspersed elements, as well as LTR retrotransposons (ERV). Furthermore, a high total TE content (>40%) was associated with an increased frequency of gross deletions. Both findings were further investigated and confirmed in a total set of 20 genes disrupted in human disease. Thus, to our knowledge for the first time, we provide evidence that a high TE content, irrespective of the type of element, results in the increased incidence of gross deletions as gene disruption underlying human disease. PMID:18252213

  6. Introduction of the Transposable Element Mariner into the Germline of Drosophila Melanogaster

    PubMed Central

    Garza, D.; Medhora, M.; Koga, A.; Hartl, D. L.

    1991-01-01

    A chimeric white gene (w(pch)) and other constructs containing the transposable element mariner from Drosophila mauritiana were introduced into the germline of Drosophila melanogaster using transformation mediated by the P element. In the absence of other mariner elements, the w(pch) allele is genetically stable in both germ cells and somatic cells, indicating that the peach element (i.e., the particular copy of mariner inserted in the w(pch) allele) is inactive. However, in the presence of the active element Mos1, the w(pch) allele reverts, owing to excision of the peach element, yielding eye-color mosaics and a high rate of germline reversion. In strains containing Mos1 virtually every fly is an eye-color mosaic, and the rate of w(pch) germline reversion ranges from 10 to 25%, depending on temperature. The overall rates of mariner excision and transposition are approximately sixfold greater than the rates in comparable strains of Drosophila simulans. The activity of the Mos1 element is markedly affected by position effects at the site of Mos1 insertion. In low level mosaic lines, dosage effects of Mos1 are apparent in the heavier level of eye-color mosaicism in Mos1 homozygotes than in heterozygotes. However, saturation occurs in high level mosaic lines, and then dosage effects are not observed. A pBluescribe M13+ plasmid containing Mos1 was injected into the pole plasm of D. melanogaster embryos, and the Mos1 element spontaneously integrated into the germline at high efficiency. These transformed strains of D. melanogaster presently contain numerous copies of mariner and may be useful in transposon tagging and other applications. PMID:1649067

  7. Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression

    PubMed Central

    Zhang, Jie; Liu, Yuan; Xia, En-Hua; Yao, Qiu-Yang; Liu, Xiang-Dong; Gao, Li-Zhi

    2015-01-01

    Polyploidy, or whole-genome duplication (WGD), serves as a key innovation in plant evolution and is an important genomic feature for all eukaryotes. Neopolyploids have to overcome difficulties in meiosis, genomic alterations, changes of gene expression, and epigenomic reorganization. However, the underlying mechanisms for these processes are poorly understood. One of the most interesting aspects is that genome doubling events increase the dosage of all genes. Unlike allopolyploids entangled by both hybridization and polyploidization, autopolyploids, especially artificial lines, in relatively uniform genetic background offer a model system to understand mechanisms of genome-dosage effects. To investigate DNA methylation effects in response to WGD rather than hybridization, we produced autotetraploid rice with its diploid donor, Oryza sativa ssp. indica cv. Aijiaonante, both of which were independently self-pollinated over 48 generations, and generated and compared their comprehensive transcriptomes, base pair-resolution methylomes, and siRNAomes. DNA methylation variation of transposable elements (TEs) was observed as widespread in autotetraploid rice, in which hypermethylation of class II DNA transposons was predominantly noted in CHG and CHH contexts. This was accompanied by changes of 24-nt siRNA abundance, indicating the role of the RNA-directed DNA methylation pathway. Our results showed that the increased methylation state of class II TEs may suppress the expression of neighboring genes in autotetraploid rice that has obtained double alleles, leading to no significant differences in transcriptome alterations for most genes from its diploid donor. Collectively, our findings suggest that chromosome doubling induces methylation variation in TEs that affect gene expression and may become a “genome shock” response factor to help neoautopolyploids adapt to genome-dosage effects. PMID:26621743

  8. Widespread contribution of transposable elements to the innovation of gene regulatory networks.

    PubMed

    Sundaram, Vasavi; Cheng, Yong; Ma, Zhihai; Li, Daofeng; Xing, Xiaoyun; Edge, Peter; Snyder, Michael P; Wang, Ting

    2014-12-01

    Transposable elements (TEs) have been shown to contain functional binding sites for certain transcription factors (TFs). However, the extent to which TEs contribute to the evolution of TF binding sites is not well known. We comprehensively mapped binding sites for 26 pairs of orthologous TFs in two pairs of human and mouse cell lines (representing two cell lineages), along with epigenomic profiles, including DNA methylation and six histone modifications. Overall, we found that 20% of binding sites were embedded within TEs. This number varied across different TFs, ranging from 2% to 40%. We further identified 710 TF-TE relationships in which genomic copies of a TE subfamily contributed a significant number of binding peaks for a TF, and we found that LTR elements dominated these relationships in human. Importantly, TE-derived binding peaks were strongly associated with open and active chromatin signatures, including reduced DNA methylation and increased enhancer-associated histone marks. On average, 66% of TE-derived binding events were cell type-specific with a cell type-specific epigenetic landscape. Most of the binding sites contributed by TEs were species-specific, but we also identified binding sites conserved between human and mouse, the functional relevance of which was supported by a signature of purifying selection on DNA sequences of these TEs. Interestingly, several TFs had significantly expanded binding site landscapes only in one species, which were linked to species-specific gene functions, suggesting that TEs are an important driving force for regulatory innovation. Taken together, our data suggest that TEs have significantly and continuously shaped gene regulatory networks during mammalian evolution. PMID:25319995

  9. Widespread contribution of transposable elements to the innovation of gene regulatory networks

    PubMed Central

    Sundaram, Vasavi; Cheng, Yong; Ma, Zhihai; Li, Daofeng; Xing, Xiaoyun; Edge, Peter

    2014-01-01

    Transposable elements (TEs) have been shown to contain functional binding sites for certain transcription factors (TFs). However, the extent to which TEs contribute to the evolution of TF binding sites is not well known. We comprehensively mapped binding sites for 26 pairs of orthologous TFs in two pairs of human and mouse cell lines (representing two cell lineages), along with epigenomic profiles, including DNA methylation and six histone modifications. Overall, we found that 20% of binding sites were embedded within TEs. This number varied across different TFs, ranging from 2% to 40%. We further identified 710 TF–TE relationships in which genomic copies of a TE subfamily contributed a significant number of binding peaks for a TF, and we found that LTR elements dominated these relationships in human. Importantly, TE-derived binding peaks were strongly associated with open and active chromatin signatures, including reduced DNA methylation and increased enhancer-associated histone marks. On average, 66% of TE-derived binding events were cell type-specific with a cell type-specific epigenetic landscape. Most of the binding sites contributed by TEs were species-specific, but we also identified binding sites conserved between human and mouse, the functional relevance of which was supported by a signature of purifying selection on DNA sequences of these TEs. Interestingly, several TFs had significantly expanded binding site landscapes only in one species, which were linked to species-specific gene functions, suggesting that TEs are an important driving force for regulatory innovation. Taken together, our data suggest that TEs have significantly and continuously shaped gene regulatory networks during mammalian evolution. PMID:25319995

  10. The piRNA Pathway Guards the Germline Genome Against Transposable Elements

    PubMed Central

    Pezic, Dubravka; Stuwe, Evelyn; Webster, Alexandre

    2016-01-01

    Transposable elements (TEs) have the capacity to replicate and insert into new genomic locations. This contributed significantly to evolution of genomes, but can also result in DNA breaks and illegitimate recombination, and therefore posing a significant threat to genomic integrity. Excess damage to the germ cell genome results in sterility. A specific RNA silencing pathway, termed the piRNA pathway operates in germ cells of animals to control TE activity. At the core of the piRNA pathway is a ribonucleo-protein complex consisting of a small RNA, called piRNA, and a protein from the PIWI subfamily of Argonaute nucleases. The piRNA pathway relies on the specificity provided by the piRNAs to recognize TEs targets, while effector functions are provided by the PIWI protein. PIWI-piRNA complexes silence TEs both at the transcriptional level – by attracting repressive chromatin modifications to genomic targets – and at the post-transcriptional level – by cleaving TE transcripts in the cytoplasm. Impairment of the piRNA pathway leads to overexpression of TEs, significantly compromised genome structure and, invariably, germ cells death and sterility. The piRNA pathway is best understood in the fruit fly, Drosophila melanogaster, and in mouse. This Chapter gives an overview of current knowledge on piRNA biogenesis, and mechanistic details of both transcriptional and posttranscriptional TE silencing by the piRNA pathway. It further focuses on the importance of post-translational modifications and subcellular localization of the piRNA machinery. Finally, it provides a brief description of analogous pathways in other systems. PMID:26659487

  11. Transposable elements play an important role during cotton genome evolution and fiber cell development.

    PubMed

    Wang, Kun; Huang, Gai; Zhu, Yuxian

    2016-02-01

    Transposable elements (TEs) usually occupy largest fractions of plant genome and are also the most variable part of the structure. Although traditionally it is hallmarked as "junk and selfish DNA", today more and more evidence points out TE's participation in gene regulations including gene mutation, duplication, movement and novel gene creation via genetic and epigenetic mechanisms. The recently sequenced genomes of diploid cottons Gossypium arboreum (AA) and Gossypium raimondii (DD) together with their allotetraploid progeny Gossypium hirsutum (AtAtDtDt) provides a unique opportunity to compare genome variations in the Gossypium genus and to analyze the functions of TEs during its evolution. TEs accounted for 57%, 68.5% and 67.2%, respectively in DD, AA and AtAtDtDt genomes. The 1,694 Mb A-genome was found to harbor more LTR(long terminal repeat)-type retrotransposons that made cardinal contributions to the twofold increase in its genome size after evolution from the 775.2 Mb D-genome. Although the 2,173 Mb AtAtDtDt genome showed similar TE content to the A-genome, the total numbers of LTR-gypsy and LTR-copia type TEs varied significantly between these two genomes. Considering their roles on rewiring gene regulatory networks, we believe that TEs may somehow be involved in cotton fiber cell development. Indeed, the insertion or deletion of different TEs in the upstream region of two important transcription factor genes in At or Dt subgenomes resulted in qualitative differences in target gene expression. We suggest that our findings may open a window for improving cotton agronomic traits by editing TE activities. PMID:26687725

  12. The ant genomes have been invaded by several types of mariner transposable elements

    NASA Astrophysics Data System (ADS)

    Lorite, Pedro; Maside, Xulio; Sanllorente, Olivia; Torres, María I.; Periquet, Georges; Palomeque, Teresa

    2012-12-01

    To date, only three types of full-length mariner elements have been described in ants, each one in a different genus of the Myrmicinae subfamily: Sinvmar was isolated from various Solenopsis species, Myrmar from Myrmica ruginodis, and Mboumar from Messor bouvieri. In this study, we report the coexistence of three mariner elements ( Tnigmar- Si, Tnigmar- Mr, and Tnigmar- Mb) in the genome of a single species, Tapinoma nigerrimum (subfamily Dolichoderinae). Molecular evolutionary analyses of the nucleotide sequence data revealed a general agreement between the evolutionary history of most the elements and the ant species that harbour them, and suggest that they are at the vertical inactivation stage of the so-called Mariner Life Cycle. In contrast, significantly reduced levels of synonymous divergence between Mboumar and Tnigmar- Mb and between Myrmar and Botmar (a mariner element isolated from Bombus terrestris), relative to those observed between their hosts, suggest that these elements arrived to the species that host them by horizontal transfer, long after the species' split. The horizontal transfer events for the two pairs of elements could be roughly dated within the last 2 million years and about 14 million years, respectively. As would be expected under this scenario, the coding sequences of the youngest elements, Tnigmar- Mb and Mboumar, are intact and, thus, potentially functional. Each mariner element has a different chromosomal distribution pattern according to their stage within the Mariner Life Cycle. Finally, a new defective transposable element ( Azteca) has also been found inserted into the Tnigmar- Mr sequences showing that the ant genomes have been invaded by at least four different types of mariner elements.

  13. Scanning of Transposable Elements and Analyzing Expression of Transposase Genes of Sweet Potato [Ipomoea batatas

    PubMed Central

    Tao, Xiang; Lai, Xian-Jun; Zhang, Yi-Zheng; Tan, Xue-Mei; Wang, Haiyan

    2014-01-01

    Background Transposable elements (TEs) are the most abundant genomic components in eukaryotes and affect the genome by their replications and movements to generate genetic plasticity. Sweet potato performs asexual reproduction generally and the TEs may be an important genetic factor for genome reorganization. Complete identification of TEs is essential for the study of genome evolution. However, the TEs of sweet potato are still poorly understood because of its complex hexaploid genome and difficulty in genome sequencing. The recent availability of the sweet potato transcriptome databases provides an opportunity for discovering and characterizing the expressed TEs. Methodology/Principal Findings We first established the integrated-transcriptome database by de novo assembling four published sweet potato transcriptome databases from three cultivars in China. Using sequence-similarity search and analysis, a total of 1,405 TEs including 883 retrotransposons and 522 DNA transposons were predicted and categorized. Depending on mapping sets of RNA-Seq raw short reads to the predicted TEs, we compared the quantities, classifications and expression activities of TEs inter- and intra-cultivars. Moreover, the differential expressions of TEs in seven tissues of Xushu 18 cultivar were analyzed by using Illumina digital gene expression (DGE) tag profiling. It was found that 417 TEs were expressed in one or more tissues and 107 in all seven tissues. Furthermore, the copy number of 11 transposase genes was determined to be 1–3 copies in the genome of sweet potato by Real-time PCR-based absolute quantification. Conclusions/Significance Our result provides a new method for TE searching on species with transcriptome sequences while lacking genome information. The searching, identification and expression analysis of TEs will provide useful TE information in sweet potato, which are valuable for the further studies of TE-mediated gene mutation and optimization in asexual reproduction

  14. International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories

    PubMed Central

    2012-01-01

    An international conference on Transposable Elements (TEs) was held 21–24 April 2012 in Saint Malo, France. Organized by the French Transposition Community (GDR Elements Génétiques Mobiles et Génomes, CNRS) and the French Society of Genetics (SFG), the conference’s goal was to bring together researchers from around the world who study transposition in diverse organisms using multiple experimental approaches. The meeting drew more than 217 attendees and most contributed through poster presentations (117), invited talks and short talks selected from poster abstracts (48 in total). The talks were organized into four scientific sessions, focused on: impact of TEs on genomes, control of transposition, evolution of TEs and mechanisms of transposition. Here, we present highlights from the talks given during the platform sessions. The conference was sponsored by Alliance pour les sciences de la vie et de la santé (Aviesan), Centre national de la recherche scientifique (CNRS), Institut national de la santé et de la recherche médicale (INSERM), Institut de recherche pour le développement (IRD), Institut national de la recherche agronomique (INRA), Université de Perpignan, Université de Rennes 1, Région Bretagne and Mobile DNA. Chair of the organization committee Jean-Marc Deragon Organizers Abdelkader Ainouche, Mireille Bétermier, Mick Chandler, Richard Cordaux, Gaël Cristofari, Jean-Marc Deragon, Pascale Lesage, Didier Mazel, Olivier Panaud, Hadi Quesneville, Chantal Vaury, Cristina Vieira and Clémentine Vitte PMID:23110759

  15. Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

    PubMed Central

    da Silva, Carlos R. M.; Andrade, Alan C.; Marraccini, Pierre; Teixeira, João B.; Carazzolle, Marcelo F.; Pereira, Gonçalo A. G.; Pereira, Luiz Filipe P.; Vanzela, André L. L.; Wang, Lu; Jordan, I. King; Carareto, Claudia M. A.

    2013-01-01

    Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences. PMID:24244387

  16. A transposable element insertion in APOB causes cholesterol deficiency in Holstein cattle.

    PubMed

    Menzi, F; Besuchet-Schmutz, N; Fragnière, M; Hofstetter, S; Jagannathan, V; Mock, T; Raemy, A; Studer, E; Mehinagic, K; Regenscheit, N; Meylan, M; Schmitz-Hsu, F; Drögemüller, C

    2016-04-01

    Cholesterol deficiency, a new autosomal recessive inherited genetic defect in Holstein cattle, has been recently reported to have an influence on the rearing success of calves. The affected animals show unresponsive diarrhea accompanied by hypocholesterolemia and usually die within the first weeks or months of life. Here, we show that whole genome sequencing combined with the knowledge about the pedigree and inbreeding status of a livestock population facilitates the identification of the causative mutation. We resequenced the entire genomes of an affected calf and a healthy partially inbred male carrying one copy of the critical 2.24-Mb chromosome 11 segment in its ancestral state and one copy of the same segment with the cholesterol deficiency mutation. We detected a single structural variant, homozygous in the affected case and heterozygous in the non-affected carrier male. The genetic makeup of this key animal provides extremely strong support for the causality of this mutation. The mutation represents a 1.3kb insertion of a transposable LTR element (ERV2-1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing. This finding was further supported by RNA sequencing of the liver transcriptome of an affected calf. The encoded apolipoprotein B is an essential apolipoprotein on chylomicrons and low-density lipoproteins, and therefore, the mutation represents a loss of function mutation similar to autosomal recessive inherited familial hypobetalipoproteinemia-1 (FHBL1) in humans. Our findings provide a direct gene test to improve selection against this deleterious mutation in Holstein cattle. PMID:26763170

  17. Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

    PubMed Central

    Chalopin, Domitille; Naville, Magali; Plard, Floriane; Galiana, Delphine; Volff, Jean-Nicolas

    2015-01-01

    Transposable elements (TEs) are major components of vertebrate genomes, with major roles in genome architecture and evolution. In order to characterize both common patterns and lineage-specific differences in TE content and TE evolution, we have compared the mobilomes of 23 vertebrate genomes, including 10 actinopterygian fish, 11 sarcopterygians, and 2 nonbony vertebrates. We found important variations in TE content (from 6% in the pufferfish tetraodon to 55% in zebrafish), with a more important relative contribution of TEs to genome size in fish than in mammals. Some TE superfamilies were found to be widespread in vertebrates, but most elements showed a more patchy distribution, indicative of multiple events of loss or gain. Interestingly, loss of major TE families was observed during the evolution of the sarcopterygian lineage, with a particularly strong reduction in TE diversity in birds and mammals. Phylogenetic trends in TE composition and activity were detected: Teleost fish genomes are dominated by DNA transposons and contain few ancient TE copies, while mammalian genomes have been predominantly shaped by nonlong terminal repeat retrotransposons, along with the persistence of older sequences. Differences were also found within lineages: The medaka fish genome underwent more recent TE amplification than the related platyfish, as observed for LINE retrotransposons in the mouse compared with the human genome. This study allows the identification of putative cases of horizontal transfer of TEs, and to tentatively infer the composition of the ancestral vertebrate mobilome. Taken together, the results obtained highlight the importance of TEs in the structure and evolution of vertebrate genomes, and demonstrate their major impact on genome diversity both between and within lineages. PMID:25577199

  18. Malazy, a degenerate, species-specific transposable element in Cercospora zeae-maydis.

    PubMed

    Shim, Won-Bo; Dunkle, Larry D

    2005-01-01

    Two fungal pathogens, Cercospora zeae-maydis Groups I and II, cause gray leaf spot of maize. During the sequencing of a cosmid library from C. zeae-maydis Group I, we discovered a sequence with high similarity to Maggy, a transposable element from Magnaporthe grisea. The element from C. zeae-maydis, named Malazy, contained 194-base-pair terminal repeats and sequences with high similarity to reverse transcriptase and integrase, components of the POL gene in the gypsy-like retrotransposons in fungi. Sequences with similarity to other POL gene components, protease and ribonuclease, were not detected in Malazy. A single copy of the element was detected by PCR and Southern analyses in all six North American isolates of C. zeae-maydis Group I but was not detected in the four isolates of C. zeae-maydis Group II from three continents or in phylogenetically related species. Fragments of the core domains of reverse transcriptase and integrase contained a high frequency of stop codons that were conserved in all six isolates of Group I. Additional C:G to T:A transitions in occasional isolates usually were silent mutations, while two resulted in isolate-specific stop codons. The absence of Malazy from related species suggests that it was acquired after the divergence of C. zeae-maydis Groups I and II. The high frequency of stop codons and the presence of a single copy of the element suggest that it was inactivated soon after it was acquired. Because the element is inactive and because reading frames for other genes were not found in sequences flanking the element, Malazy does not appear to be the cause of differences leading to speciation or genetic diversity between C. zeae-maydis Groups I and II. PMID:16396343

  19. Achromatic miniature lens system for coherent Raman scattering microscopy

    PubMed Central

    Mittal, Richa; Balu, Mihaela; Wilder-Smith, Petra; Potma, Eric O.

    2013-01-01

    We discuss the design and performance of a miniature objective lens optimized for coherent Raman scattering microscopy. The packaged lens assembly has a numerical aperture of 0.51 in water and an outer diameter of 8 mm. The lens system exhibits minimum chromatic aberrations, and produces coherent Raman scattering images with sub-micrometer lateral resolution (0.648 μm) using near-infrared excitation pulses. We demonstrate that despite the small dimensions of the miniature objective, the performance of this lens system is comparable to standard microscope objective lenses, offering opportunities for miniaturizing coherent Raman scattering imaging probes without sacrificing the image quality. PMID:24156075

  20. A MEMS-based miniature DNA analysis system

    SciTech Connect

    Northrup, M.A.; Gonzalez, C.; Hadley, D.

    1995-04-25

    We detail the design and development of a miniature thermal cycling instrument for performing the polymerase chain reaction (PCR) that uses microfabricated, silicon-based reaction chambers. The MEMS-based, battery-operated instrument shows significant improvements over commercial thermal cycling instrumentation. Several different biological systems have been amplified and verified with the miniature PCR instrument including the Human Immunodeficiency Virus; both cloned and genomic DNA templates of {beta} globin; and the genetic disease, Cystic Fibrosis from human DNA. The miniaturization of a PCR thermal cycler is the initial module of a fully-integrated portable, low-power, rapid, and highly efficient bioanalytical instrument.

  1. Miniaturized Airborne Imaging Central Server System

    NASA Technical Reports Server (NTRS)

    Sun, Xiuhong

    2011-01-01

    In recent years, some remote-sensing applications require advanced airborne multi-sensor systems to provide high performance reflective and emissive spectral imaging measurement rapidly over large areas. The key or unique problem of characteristics is associated with a black box back-end system that operates a suite of cutting-edge imaging sensors to collect simultaneously the high throughput reflective and emissive spectral imaging data with precision georeference. This back-end system needs to be portable, easy-to-use, and reliable with advanced onboard processing. The innovation of the black box backend is a miniaturized airborne imaging central server system (MAICSS). MAICSS integrates a complex embedded system of systems with dedicated power and signal electronic circuits inside to serve a suite of configurable cutting-edge electro- optical (EO), long-wave infrared (LWIR), and medium-wave infrared (MWIR) cameras, a hyperspectral imaging scanner, and a GPS and inertial measurement unit (IMU) for atmospheric and surface remote sensing. Its compatible sensor packages include NASA s 1,024 1,024 pixel LWIR quantum well infrared photodetector (QWIP) imager; a 60.5 megapixel BuckEye EO camera; and a fast (e.g. 200+ scanlines/s) and wide swath-width (e.g., 1,920+ pixels) CCD/InGaAs imager-based visible/near infrared reflectance (VNIR) and shortwave infrared (SWIR) imaging spectrometer. MAICSS records continuous precision georeferenced and time-tagged multisensor throughputs to mass storage devices at a high aggregate rate, typically 60 MB/s for its LWIR/EO payload. MAICSS is a complete stand-alone imaging server instrument with an easy-to-use software package for either autonomous data collection or interactive airborne operation. Advanced multisensor data acquisition and onboard processing software features have been implemented for MAICSS. With the onboard processing for real time image development, correction, histogram-equalization, compression, georeference, and

  2. Pneumatically Actuated Miniature Peristaltic Vacuum Pumps

    NASA Technical Reports Server (NTRS)

    Feldman, Sabrina; Feldman, Jason; Svehla, Danielle

    2003-01-01

    Pneumatically actuated miniature peristaltic vacuum pumps have been proposed for incorporation into advanced miniature versions of scientific instruments that depend on vacuum for proper operation. These pumps are expected to be capable of reaching vacuum-side pressures in the torr to millitorr range (from .133 down to .0.13 Pa). Vacuum pumps that operate in this range are often denoted roughing pumps. In comparison with previously available roughing pumps, these pumps are expected to be an order of magnitude less massive and less power-hungry. In addition, they would be extremely robust, and would operate with little or no maintenance and without need for oil or other lubricants. Portable mass spectrometers are typical examples of instruments that could incorporate the proposed pumps. In addition, the proposed pumps could be used as roughing pumps in general laboratory applications in which low pumping rates could be tolerated. The proposed pumps could be designed and fabricated in conventionally machined and micromachined versions. A typical micromachined version (see figure) would include a rigid glass, metal, or plastic substrate and two layers of silicone rubber. The bottom silicone layer would contain shallow pump channels covered by silicone arches that could be pushed down pneumatically to block the channels. The bottom silicone layer would be covered with a thin layer of material with very low gas permeability, and would be bonded to the substrate everywhere except in the channel areas. The top silicone layer would be attached to the bottom silicone layer and would contain pneumatic- actuation channels that would lie crosswise to the pump channels. This version is said to be micromachined because the two silicone layers containing the channels would be fabricated by casting silicone rubber on micromachined silicon molds. The pneumatic-actuation channels would be alternately connected to a compressed gas and (depending on pump design) either to atmospheric

  3. A novel miniature thermomagnetic energy harvester

    NASA Astrophysics Data System (ADS)

    Chen, Chin-Chung; Chung, Tien-Kan; Cheng, Chi-Cheng; Tseng, Chia-Yuan

    2014-03-01

    Nowadays, thermal-energy-harvesting is an important research topic for powering wireless sensors. Among numerous thermal-energy-harvesting approaches, some researchers demonstrated novel thermomagnetic-energy harvesters to convert a thermal-energy from an ambient temperature-difference to an electrical-output to power the sensors. However, the harvesters are too bulky to be integrated with the sensors embedded in tiny mechanical-structures for some structuralhealth- monitoring applications. Therefore, miniaturized harvesters are needed. Hence, we demonstrate a miniature thermomagnetic-energy harvester. The harvester consists of CuBe-beams, PZT-piezoelectric-sheet, Gd-soft-magnet, NdFeB-hard-magnet, and mechanical-frame. The piezoelectric-sheet and soft-magnet is bounded at fixed-end and freeend of the beams, respectively. The mechanical-frame assembles the beams and hard-magnet. The length×width×thickness of the harvester is 2.5cm×1.7cm×1.5cm. According to this, our harvester is 20-times smaller than the other harvesters. In the initial-state of the energy-harvesting, the beams' free-end is near the cold-side. Thus, the soft-magnet is cooled lower than its curie temperature (Tc) and consequently changed from paramagnetic to ferromagnetic. Therefore, a magnetic-attractive force is produced between the soft-magnet and hard-magnet. Consequently, the beams/soft-magnet are down-pulled toward the hard-magnet fixed on the hot-side. The soft-magnet closing to the hot-side is heated higher than its Tc and subsequently changed to paramagnetic. Consequently, the magnetic-force is eliminated thus the beams are rebounded to the initial-state. Hence, when the harvester is under a temperature-difference, the beams' pulling-down/back process is cyclic. Due to the piezoelectric effect, the piezoelectric-sheet fixed on the beams continuously produces voltage-response. Under the temperature-difference of 29°C, the voltage-response of the harvester is 30.4 mV with an oscillating

  4. A Miniature Controllable Flapping Wing Robot

    NASA Astrophysics Data System (ADS)

    Arabagi, Veaceslav Gheorghe

    The agility and miniature size of nature's flapping wing fliers has long baffled researchers, inspiring biological studies, aerodynamic simulations, and attempts to engineer their robotic replicas. Flapping wing flight is characterized by complex reciprocating wing kinematics, transient aerodynamic effects, and very small body lengths. These characteristics render robotic flapping wing aerial vehicles ideal for surveillance and defense applications, search and rescue missions, and environment monitoring, where their ability to hover and high maneuverability is immensely beneficial. One of the many difficulties in creating flapping wing based miniature robotic aerial vehicles lies in generating a proper wing trajectory that would result in sufficient lift forces for hovering and maneuvering. Since design of a flapping wing system is a balance between overall weight and the number of actuated inputs, we take the approach of having minimal controlled inputs, allowing passive behavior wherever possible. Hence, we propose a completely passive wing pitch reversal design that relies on wing inertial dynamics, an elastic energy storage mechanism, and low Reynolds number aerodynamic effects. Theoretical models, compiling previous research on piezoelectric actuators, four-bar transmissions, and aerodynamics effects, are developed and used as basis for a complete numerical simulation. Limitations of the model are discussed in comparison to experimental results obtained from a working prototype of the proposed passive pitch reversal flapping wing mechanism. Given that the mechanism is under-actuated, methods to control lift force generation by actively varying system parameters are proposed, discussed, and tested experimentally. A dual wing aerial platform is developed based on the passive pitch reversal wing concept. Design considerations are presented, favoring controllability and structural rigidity of the final platform. Finite element analysis and experimental

  5. BuT2 Is a Member of the Third Major Group of hAT Transposons and Is Involved in Horizontal Transfer Events in the Genus Drosophila

    PubMed Central

    Rossato, Dirleane Ottonelli; Ludwig, Adriana; Deprá, Maríndia; Loreto, Elgion L. S.; Ruiz, Alfredo; Valente, Vera L. S.

    2014-01-01

    The hAT superfamily comprises a large and diverse array of DNA transposons found in all supergroups of eukaryotes. Here we characterized the Drosophila buzzatii BuT2 element and found that it harbors a five-exon gene encoding a 643-aa putatively functional transposase. A phylogeny built with 85 hAT transposases yielded, in addition to the two major groups already described, Ac and Buster, a third one comprising 20 sequences that includes BuT2, Tip100, hAT-4_BM, and RP-hAT1. This third group is here named Tip. In addition, we studied the phylogenetic distribution and evolution of BuT2 by in silico searches and molecular approaches. Our data revealed BuT2 was, most often, vertically transmitted during the evolution of genus Drosophila being lost independently in several species. Nevertheless, we propose the occurrence of three horizontal transfer events to explain its distribution and conservation among species. Another aspect of BuT2 evolution and life cycle is the presence of short related sequences, which contain similar 5′ and 3′ regions, including the terminal inverted repeats. These sequences that can be considered as miniature inverted repeat transposable elements probably originated by internal deletion of complete copies and show evidences of recent mobilization. PMID:24459285

  6. Characterization of active ribosomal RNA harboring MITEs insertion in microsporidian Nosema bombycis genome.

    PubMed

    Liu, Handeng; Pan, Guoqing; Dang, Xiaoqun; Li, Tian; Zhou, Zeyang

    2013-03-01

    Microsporidia are a group of obligate intracellular parasites of medical and agricultural importance, which can infect almost all animals, including human beings. Using the genome data of Nosema bombycis, four families of miniature inverted-repeat transposable elements (MITEs) in ribosomal DNA (rDNA) were characterized in the microsporidian N. bombycis and were named LSUME1, ITSME1, SSUME1, and SSUME2, respectively. The genome-wide investigation of these MITEs shows that these MITEs families distribute randomly in N. bombycis genome. All insertion sequences have conserved characteristics of MITEs, the direct repeat sequence and terminal inverted-repeat sequence at both ends of each MITEs sequence. Additionally, using the CLC RNA Workbench Software, secondary structures of rRNA containing MITEs sequence have been predicted and were located in variable region or expansion segment. Furthermore, using two different probes, one is prepared by MITE sequence only (short probe) and the other is prepared by MITE sequence flanking partial rDNA sequence (long probe); northern blotting and dot blotting have been performed to detect the transcriptional and functional activity of the rDNA containing MITEs insertion. Fortunately, we found that the rDNA, which harbors the MITE, not only can be transcripted but also can form a complete ribosome. This is an interesting thing that one gene can keep active even when it has been inserted with another sequence. But the biological and structural significance of this observation is not readily apparent. PMID:23254587

  7. The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE: consequences for the transposition mechanism of MITEs

    PubMed Central

    Loot, Céline; Santiago, Néstor; Sanz, Alicia; Casacuberta, Josep M.

    2006-01-01

    MITEs (miniature inverted-repeated transposable elements) are a particular class of defective DNA transposons usually present within genomes as high copy number populations of highly homogeneous elements. Although an active MITE, the mPing element, has recently been characterized in rice, the transposition mechanism of MITEs remains unknown. It has been proposed that transposases of related transposons could mobilize MITEs in trans. Moreover, it has also been proposed that the presence of conserved terminal inverted-repeated (TIR) sequences could be the only requirement of MITEs for mobilization, allowing divergent or unrelated elements to be mobilized by a particular transposase. We present here evidence for a recent mobility of the Arabidopsis Emigrant MITE and we report on the capacity of the proteins encoded by the related Lemi1 transposon, a pogo-related element, to specifically bind Emigrant elements. This suggests that Lemi1 could mobilize Emigrant elements and makes the Lemi1/Emigrant couple an ideal system to study the transposition mechanism of MITEs. Our results show that Lemi1 proteins bind Emigrant TIRs but also bind cooperatively to subterminal repeated motifs. The requirement of internal sequences for the formation of proper DNA/protein structure could affect the capacity of divergent MITEs to be mobilized by distantly related transposases. PMID:17003053

  8. An Investigation Into the Performance of a Miniature Diesel Engine

    ERIC Educational Resources Information Center

    Stevenson, P. W.

    1970-01-01

    Reports the procedures and results of a student investigation of the performance of a miniature diesel engine. The experiments include (1) torque measurement, (2) power measurement, and (3) variation of power output with applied load. Bibliography. (LC)

  9. Miniature oxygen-hydrogen cutting torch constructed from hypodermic needle

    NASA Technical Reports Server (NTRS)

    Shlichta, P.

    1964-01-01

    A miniature cutting torch consisting of a main body member, upon which the hydrogen and oxygen containers are mounted, valves for controlling gas flow, and a hypodermic needle that acts as a mixing tube and flame tip is constructed.

  10. Miniature Tractor Pull Helps Teach Mechanical Power Transmission.

    ERIC Educational Resources Information Center

    Waggoner, Todd C.

    1996-01-01

    A miniature tractor pull was developed as a high school activity, enabling students to assess a tractor's pulling capabilities and determine subsequent horsepower. The activity takes the textbook concept of horsepower and makes it come alive. (JOW)

  11. Miniature paint-spray gun for recessed areas

    NASA Technical Reports Server (NTRS)

    Vanasse, M. A.

    1968-01-01

    Miniature spray gun regulates paints and other liquids to spray at close range, facilitating spraying of remote or recessed areas. Individual valves for regulating air pressure and paint maximizes atomization for low pressure spraying.

  12. Miniaturized King furnace permits absorption spectroscopy of small samples

    NASA Technical Reports Server (NTRS)

    Ercoli, B.; Tompkins, F. S.

    1968-01-01

    Miniature King-type furnace, consisting of an inductively heated, small diameter tantalum tube supported in a radiation shield eliminates the disadvantages of the conventional furnace in obtaining absorption spectra of metal vapors.

  13. Miniature LIMS System for In Situ Detection of Biosignatures

    NASA Astrophysics Data System (ADS)

    Riedo, A.; Tulej, M.; Neuland, M. B.; Wurz, P.

    2016-05-01

    The current measurement capabilities of our miniature Laser Ablation Ionization Mass Spectrometer for sensitive and quantitative in situ chemical analyses (element, isotope and molecular) of solids on planetary surfaces will be presented.

  14. Personal communication system combines high performance with miniaturization

    NASA Technical Reports Server (NTRS)

    Atlas, N. D.

    1967-01-01

    Personal communication system provides miniaturized components that incorporate high level signal characteristics plus noise rejection in both microphone and earphone circuitry. The microphone is designed to overcome such spacecraft flight problems as size, ambient noise level, and RF interference.

  15. Miniaturized biological and electrochemical fuel cells: challenges and applications.

    PubMed

    Yang, Jie; Ghobadian, Sasan; Goodrich, Payton J; Montazami, Reza; Hashemi, Nastaran

    2013-09-14

    This paper discusses the fundamentals and developments of miniaturized fuel cells, both biological and electrochemical. An overview of microfluidic fuel cells, miniaturized microbial fuel cells, enzymatic biofuel cells, and implanted biofuel cells in an attempt to provide green energy and to power implanted microdevices is provided. Also, the challenges and applications of each type of fuel cell are discussed in detail. Most recent developments in fuel cell technologies such as novel catalysts, compact designs, and fabrication methods are reviewed. PMID:23503374

  16. MEMS mass spectrometers: the next wave of miniaturization

    NASA Astrophysics Data System (ADS)

    Syms, Richard R. A.; Wright, Steven

    2016-02-01

    This paper reviews mass spectrometers based on micro-electro-mechanical systems (MEMS) technology. The MEMS approach to integration is first briefly described, and the difficulties of miniaturizing mass spectrometers are outlined. MEMS components for ionization and mass filtering are then reviewed, together with additional components for ion detection, vacuum pressure measurement and pumping. Mass spectrometer systems containing MEMS sub-components are then described, applications for miniaturized and portable systems are discussed, and challenges and opportunities are presented.

  17. Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genera Drosophila and Zaprionus

    PubMed Central

    2011-01-01

    We have recently reported numerous cases of horizontal transfers of transposable elements between species of drosophilids. These studies revealed a substantial number of horizontal transfers between species of the subgroup melanogaster of the genus Drosophila and between these species and species of the genus Zaprionus. In this review, these transfers and similar, previously reported events are discussed and reanalysed to portray the interrelationships between the species that allowed the occurrence of so many horizontal transfers. The paper also addresses problems that may arise in drawing inferences about the time period during which the horizontal transfers occurred and the factors that may be associated with these transfers are discussed. PMID:22312591

  18. Product Vectors in the Ranges of Multi-Partite States with Positive Partial Transposes and Permanents of Matrices

    NASA Astrophysics Data System (ADS)

    Kiem, Young-Hoon; Kye, Seung-Hyeok; Na, Joohan

    2015-09-01

    In this paper, we consider a system of homogeneous algebraic equations in complex variables and their conjugates, which arise naturally from the range criterion for separability of PPT states. We examine systematically these equations to get sufficient conditions for the existence of nontrivial solutions. This gives us possible upper bounds of ranks of PPT entangled edge states and their partial transposes. We will focus on the multi-partite cases, which are much more delicate than the bi-partite cases. We use the notion of permanents of matrices as well as techniques from algebraic geometry through the discussion.

  19. Miniaturized Technologies for Enhancement of Motor Plasticity.

    PubMed

    Moorjani, Samira

    2016-01-01

    The idea that the damaged brain can functionally reorganize itself - so when one part fails, there lies the possibility for another to substitute - is an exciting discovery of the twentieth century. We now know that motor circuits once presumed to be hardwired are not, and motor-skill learning, exercise, and even mental rehearsal of motor tasks can turn genes on or off to shape brain architecture, function, and, consequently, behavior. This is a very significant alteration from our previously static view of the brain and has profound implications for the rescue of function after a motor injury. Presentation of the right cues, applied in relevant spatiotemporal geometries, is required to awaken the dormant plastic forces essential for repair. The focus of this review is to highlight some of the recent progress in neural interfaces designed to harness motor plasticity, and the role of miniaturization in development of strategies that engage diverse elements of the neuronal machinery to synergistically facilitate recovery of function after motor damage. PMID:27148525

  20. Recent Advances in Miniaturized Optical Gyroscopes

    NASA Astrophysics Data System (ADS)

    Dell'Olio, F.; Tatoli, T.; Ciminelli, C.; Armenise, M. N.

    2014-03-01

    Low-cost chip-scale optoelectronic gyroscopes having a resolution ≤ 10 °/h and a good reliability also in harsh environments could have a strong impact on the medium/high performance gyro market, which is currently dominated by well-established bulk optical angular velocity sensors. The R&D activity aiming at the demonstration of those miniaturized sensors is crucial for aerospace/defense industry, and thus it is attracting an increasing research effort and notably funds. In this paper the recent technological advances on the compact optoelectronic gyroscopes with low weight and high energy saving are reviewed. Attention is paid to both the so-called gyroscope-on-a-chip, which is a novel sensor, at the infantile stage, whose optical components are monolithically integrated on a single indium phosphide chip, and to a new ultra-high Q ring resonator for gyro applications with a configuration including a 1D photonic crystal in the resonant path. The emerging field of the gyros based on passive ring cavities, which have already shown performance comparable with that of optical fiber gyros, is also discussed.