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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. Translational repression by a miniature inverted-repeat transposable element in the 3′ untranslated region

    PubMed Central

    Shen, Jianqiang; Liu, Juhong; Xie, Kabin; Xing, Feng; Xiong, Fang; Xiao, Jinghua; Li, Xianghua; Xiong, Lizhong

    2017-01-01

    Transposable elements constitute a substantial portion of eukaryotic genomes and contribute to genomic variation, function, and evolution. Miniature inverted-repeat transposable elements (MITEs), as DNA transposons, are widely distributed in plant and animal genomes. Previous studies have suggested that retrotransposons act as translational regulators; however, it remains unknown how host mRNAs are influenced by DNA transposons. Here we report a translational repression mechanism mediated by a stowaway-like MITE (sMITE) embedded in the 3′-untranslated region (3′-UTR) of Ghd2, a member of the CCT (CONSTANS [CO], CO-LIKE and TIMING OF CAB1) gene family in rice. Ghd2 regulates important agronomic traits, including grain number, plant height and heading date. Interestingly, the translational repression of Ghd2 by the sMITE mainly relies on Dicer-like 3a (OsDCL3a). Furthermore, other MITEs in the 3′-UTRs of different rice genes exhibit a similar effect on translational repression, thus suggesting that MITEs may exert a general regulatory function at the translational level. PMID:28256530

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

    PubMed Central

    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

  6. A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation

    PubMed Central

    2012-01-01

    Background Miniature inverted repeat transposable element (MITE) is one type of transposable element (TE), which is largely found in eukaryotic genomes and involved in a wide variety of biological events. However, only few MITEs were proved to be currently active and their physiological function remains largely unknown. Results We found that the amplicon discrepancy of a gene locus LOC_Os01g0420 in different rice cultivar genomes was resulted from the existence of a member of Gaijin-like MITEs (mGing). This result indicated that mGing transposition was occurred at this gene locus. By using a modified transposon display (TD) analysis, the active transpositions of mGing were detected in rice Jiahua No. 1 genome under three conditions: in seedlings germinated from the seeds received a high dose γ-ray irradiation, in plantlets regenerated from anther-derived calli and from scutellum-derived calli, and were confirmed by PCR validation and sequencing. Sequence analysis revealed that single nucleotide polymorphisms (SNPs) or short additional DNA sequences at transposition sites post mGing transposition. It suggested that sequence modification was possibly taken place during mGing transposition. Furthermore, cell re-differentiation experiment showed that active transpositions of both mGing and mPing (another well studied MITE) were identified only in regenerated plantlets. Conclusions It is for the first time that mGing active transposition was demonstrated under γ-ray irradiation or in cell re-differentiation process in rice. This newly identified active MITE will provide a foundation for further analysis of the roles of MITEs in biological process. PMID:22500940

  7. 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.

  8. Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae).

    PubMed

    Osborne, P W; Luke, G N; Holland, P W H; Ferrier, D E K

    2006-01-01

    As the sister group to vertebrates, amphioxus is consistently used as a model of genome evolution for understanding the invertebrate/vertebrate transition. The amphioxus genome has not undergone massive duplications like those in the vertebrates or disruptive rearrangements like in the genome of Ciona, a urochordate, making it an ideal evolutionary model. Transposable elements have been linked to many genomic evolutionary changes including increased genome size, modified gene expression, massive gene rearrangements, and possibly intron evolution. Despite their importance in genome evolution, few previous examples of transposable elements have been identified in amphioxus. We report five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence, which we have named LanceleTn-1, LanceleTn-2, LanceleTn-3a, LanceleTn-3b and LanceleTn-4. Several of the LanceleTn elements were identified in the amphioxus ParaHox cluster, and we suggest these have had important implications for the evolution of this highly conserved gene cluster. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome.

  9. The origin and evolution of six miniature inverted-repeat transposable elements in Bombyx mori and Rhodnius prolixus.

    PubMed

    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.

  10. iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects

    PubMed Central

    Han, Min-Jin; Zhou, Qiu-Zhong; Zhang, Hua-Hao; Tong, Xiaoling; Lu, Cheng; Zhang, Ze; Dai, Fangyin

    2016-01-01

    Miniature inverted-repeat transposable elements (MITEs) have attracted much attention due to their widespread occurrence and high copy numbers in eukaryotic genomes. However, the systematic knowledge about MITEs in insects and other animals is still lacking. In this study, we identified 6012 MITE families from 98 insect species genomes. Comparison of these MITEs with known MITEs in the NCBI non-redundant database and Repbase showed that 5701(∼95%) of 6012 MITE families are novel. The abundance of MITEs varies drastically among different insect species, and significantly correlates with genome size. In general, larger genomes contain more MITEs than small genomes. Furthermore, all identified MITEs were included in a newly constructed database (iMITEdb) (http://gene.cqu.edu.cn/iMITEdb/), which has functions such as browse, search, BLAST and download. Overall, our results not only provide insight on insect MITEs but will also improve assembly and annotation of insect genomes. More importantly, the results presented in this study will promote studies of MITEs function, evolution and application in insects. Database URL: http://gene.cqu.edu.cn/iMITEdb/ PMID:28025339

  11. 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.

  12. PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements.

    PubMed Central

    Zhang, Xiaoyu; Jiang, Ning; Feschotte, Cédric; Wessler, Susan R

    2004-01-01

    Miniature inverted-repeat transposable elements (MITEs) are short, nonautonomous DNA elements that are widespread and abundant in plant genomes. Most of the hundreds of thousands of MITEs identified to date have been divided into two major groups on the basis of shared structural and sequence characteristics: Tourist-like and Stowaway-like. Since MITEs have no coding capacity, they must rely on transposases encoded by other elements. Two active transposons, the maize P Instability Factor (PIF) and the rice Pong element, have recently been implicated as sources of transposase for Tourist-like MITEs. Here we report that PIF- and Pong-like elements are widespread, diverse, and abundant in eukaryotes with hundreds of element-associated transposases found in a variety of plant, animal, and fungal genomes. The availability of virtually the entire rice genome sequence facilitated the identification of all the PIF/Pong-like elements in this organism and permitted a comprehensive analysis of their relationship with Tourist-like MITEs. Taken together, our results indicate that PIF and Pong are founding members of a large eukaryotic transposon superfamily and that members of this superfamily are responsible for the origin and amplification of Tourist-like MITEs. PMID:15020481

  13. Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon.

    PubMed

    Feschotte, C; Mouchès, C

    2000-05-01

    Sequence similarities exist between terminal inverted repeats (TIRs) of some miniature inverted-repeat transposable element (MITE) families isolated from a wide range of organisms, including plants, insects, and humans, and TIRs of DNA transposons from the pogo family. We present here evidence that one of these MITE families, previously described for Arabidopsis thaliana, is derived from a larger element encoding a putative transposase. We have named this novel class II transposon Lemi1. We show that its putative product is related to transposases of the Tc1/mariner superfamily, being closer to the pogo family. A similar truncated element was found in a tomato DNA sequence, indicating an ancient origin and/or horizontal transfer for this family of elements. These results are reminiscent of those recently reported for the human genome, where other members of the pogo family, named Tiggers, are believed to be responsible for the generation of abundant MITE-like elements in an early primate ancestor. These results further suggest that some MITE families, which are highly reiterated in plant, insect, and human genomes, could have arisen from a similar mechanism, implicating pogo-like elements.

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

    PubMed

    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.

  15. A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)n microsatellites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The insertion of transposable elements results in the modification of genome structure and gene expression, and also facilitates the propagation of derived internal sequences. We show that (GTCY)n microsatellite loci within genomes of Lepidoptera are mobile and multilocus due to hitchhiking within ...

  16. The rice miniature inverted repeat transposable element mPing is an effective insertional mutagen in soybean.

    PubMed

    Hancock, C Nathan; Zhang, Feng; Floyd, Kristen; Richardson, Aaron O; Lafayette, Peter; Tucker, Donna; Wessler, Susan R; Parrott, Wayne A

    2011-10-01

    Insertional mutagenesis of legume genomes such as soybean (Glycine max) should aid in identifying genes responsible for key traits such as nitrogen fixation and seed quality. The relatively low throughput of soybean transformation necessitates the use of a transposon-tagging strategy where a single transformation event will produce many mutations over a number of generations. However, existing transposon-tagging tools being used in legumes are of limited utility because of restricted transposition (Ac/Ds: soybean) or the requirement for tissue culture activation (Tnt1: Medicago truncatula). A recently discovered transposable element from rice (Oryza sativa), mPing, and the genes required for its mobilization, were transferred to soybean to determine if it will be an improvement over the other available transposon-tagging tools. Stable transformation events in soybean were tested for mPing transposition. Analysis of mPing excision at early and late embryo developmental stages revealed increased excision during late development in most transgenic lines, suggesting that transposition is developmentally regulated. Transgenic lines that produced heritable mPing insertions were identified, with the plants from the highest activity line producing at least one new insertion per generation. Analysis of the mPing insertion sites in the soybean genome revealed that features displayed in rice were retained including transposition to unlinked sites and a preference for insertion within 2.5 kb of a gene. Taken together these findings indicate that mPing has the characteristics necessary for an effective transposon-tagging resource.

  17. TamiR1123 originated from a family of miniature inverted-repeat transposable elements (MITE) including one inserted in the Vrn-A1a promoter in wheat.

    PubMed

    Yu, Ming; Carver, Brett F; Yan, Liuling

    2014-02-01

    More than half of spring wheat cultivars have a dominant Vrn-A1a allele that has an insertion of a miniature inverted-repeat transposable element (MITE) in its promoter. In this study, we found that the MITE present in the Vrn-A1a gene (MITE_VRN) is a nearly perfect palindrome and it can form highly stable hairpin loops when expressed as RNA. MITE_VRN also possessed sequences of a microRNA in Triticum aestivum (TamiR1123). The P(32) labeled TamiR1123 probe detected two RNA molecules on a small RNA gel blot, one expected for MITE_VRN, and the other expected for TamiR1123. These results demonstrated that MITE_VRN was expressed as RNAs and TamiR1123 was originated from the MITE_VRN family. The isogenic line TDD carrying the dominant Vrn-A1a allele with MITE_VRN showed higher TamiR1123 and Vrn-A1a transcript levels than the isogenic line TDE carrying the recessive vrn-A1a allele without MITE_VRN. TamiR1123 were greatly up-regulated by plant age but slightly down-regulated by low temperature and short days. These findings have pointed to alternative regulatory mechanisms for plant development governed by Vrn-A1a in spring wheat.

  18. Pegasus, a small terminal inverted repeat transposable element found in the white gene of Anopheles gambiae.

    PubMed

    Besansky, N J; Mukabayire, O; Bedell, J A; Lusz, H

    1996-10-01

    Pegasus, a novel transposable element, was discovered as a length polymorphism in the white gene of Anopheles gambiae. Sequence analysis revealed that this 535 bp element was flanked by 8 bp target site duplications and 8 bp perfect terminal inverted repeats similar to those found in many members of the Tc1 family. Its small size and lack of long open reading frames preclude protein coding capacity. Southern analysis and in situ hybridization to polytene chromosomes demonstrated that Pegasus occurs in approximately 30 copies in the genomes of An. gambiae and its sibling species and is homogenous in structure but polymorphic in chromosomal location. Characterization of five additional elements by sequencing revealed nucleotide identities of 95% to 99%. Of 30 Pegasus-containing phage clones examined by PCR, only one contained an element exceeding 535 bp in length, due to the insertion of another transposable element-like sequence. Thus, the majority, if not all, extant Pegasus elements may be defective copies of a complete element whose contemporary existence in An. gambiae is uncertain. No Pegasus-hybridizing sequences were detected in nine other anophelines and three culicines examined, suggesting a very limited taxonomic distribution.

  19. 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

  20. Mobility and generation of mosaic non-autonomous transposons by Tn3-derived inverted-repeat miniature elements (TIMEs).

    PubMed

    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, not

  1. 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.

  2. 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, ...

  3. 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...

  4. Distribution and evolutionary dynamics of Stowaway Miniature Inverted repeat Transposable Elements (MITEs) in grasses.

    PubMed

    Minaya, Miguel; Pimentel, Manuel; Mason-Gamer, Roberta; Catalan, Pilar

    2013-07-01

    The occurrence of Stowaway MITEs and their potential footprints in the grasses was assessed within an explicit phylogenetic framework. An organismal tree was used to analyze the distribution and evolutionary dynamics of these elements and their potential excision footprints in the fourth intron of the β-amylase gene and in other introns of several nuclear genes across the Poaceae. Megablast and discontiguous megablast searches in the Entrez nucleotide database were performed for the β-amylase, blz-1, dmc1, nuc, and xly genes MITEs. These elements and their potential footprints were distributed in introns and intergenic spacers of many other nuclear genes throughout the BEP lineages; however, they were absent in the studied PACCMAD lineages. A plausible underlying dynamic of successive acquisitions and deletions of β-amylase Stowaway MITEs in the temperate grasses could be explained by three alternative hypotheses: (i) a single early acquisition of a palindrome element, similar to Tc1-Mariner, in the fourth intron of the β-amylase gene in the ancestor of the Pooideae, followed by multiple independent losses, (ii) multiple independent acquisitions of MITEs in non-related pooid lineages or (iii) different waves of acquisition of MITEs, followed by multiple losses and horizontal transfers in the temperate grasses. This last hypothesis seems to fit best with the evidence found to date.

  5. Mutagenic inverted repeat assisted genome engineering (MIRAGE).

    PubMed

    Nair, Nikhil U; Zhao, Huimin

    2009-01-01

    Here we describe a one-step method to create precise modifications in the genome of Saccharomyces cerevisiae as a tool for synthetic biology, metabolic engineering, systems biology and genetic studies. Through homologous recombination, a mutagenesis cassette containing an inverted repeat of selection marker(s) is integrated into the genome. Due to its inherent instability in genomic DNA, the inverted repeat catalyzes spontaneous self-excision, resulting in precise genome modification. Since this excision occurs at very high frequencies, selection for the integration event can be followed immediately by counterselection, without the need for growth in permissive conditions. This is the first time a truly one-step method has been described for genome modification in any organism.

  6. Insertion sequence inversions mediated by ectopic recombination between terminal inverted repeats.

    PubMed

    Ling, Alison; Cordaux, Richard

    2010-12-20

    Transposable elements are widely distributed and diverse in both eukaryotes and prokaryotes, as exemplified by DNA transposons. As a result, they represent a considerable source of genomic variation, for example through ectopic (i.e. non-allelic homologous) recombination events between transposable element copies, resulting in genomic rearrangements. Ectopic recombination may also take place between homologous sequences located within transposable element sequences. DNA transposons are typically bounded by terminal inverted repeats (TIRs). Ectopic recombination between TIRs is expected to result in DNA transposon inversions. However, such inversions have barely been documented. In this study, we report natural inversions of the most common prokaryotic DNA transposons: insertion sequences (IS). We identified natural TIR-TIR recombination-mediated inversions in 9% of IS insertion loci investigated in Wolbachia bacteria, which suggests that recombination between IS TIRs may be a quite common, albeit largely overlooked, source of genomic diversity in bacteria. We suggest that inversions may impede IS survival and proliferation in the host genome by altering transpositional activity. They may also alter genomic instability by modulating the outcome of ectopic recombination events between IS copies in various orientations. This study represents the first report of TIR-TIR recombination within bacterial IS elements and it thereby uncovers a novel mechanism of structural variation for this class of prokaryotic transposable elements.

  7. Cloning and characterization of a transposable-like repeat in the heterochromatin of the darkling beetle Misolampus goudoti.

    PubMed

    Pons, Joan

    2004-08-01

    A long repeat unit of the PstI family in Misolampus goudoti (Coleoptera, Tenebrionodae) is characterized in this work. The 30 sequenced units have small differences in length (consensus 1169 bp), but very similar nucleotide composition (mean 61.1% A+T). PstI repeats contain a 36-bp-long inverted repeat at both the 5' and 3' ends, with a fully conserved 16-bp-long motif similar to those found in class II transposable elements. However, the transposable-like PstI repeats seems to be defective, since they do not encode for any protein related with transposition. Interestingly, energetically stable hairpins resembled the structure of a miniature interspersed transposable element, suggesting that the PstI satellite DNA family in M. goudoti may have originated from an ancestral active transposable element as also described in Drosophila guanche. The presence of transposable-like structure along with the non-detection of gene conversion or unequal crossing-over events suggest that transposition could be one of the putative molecular mechanisms involved in the strong amplification and (or) homogenization of these repeats. A putative transposition of PstI repeats allowing their genomic mobility also could explain why this satellite is widely distributed to all heterochromatic regions, telomeres, pericentromeric regions, and on the Y chromosome, whereas satellites of other tenebrionids lacking transposable-like structures are restricted only to pericentromeric regions.

  8. Mutator-Like Elements with Multiple Long Terminal Inverted Repeats in Plants

    PubMed Central

    Ferguson, Ann A.; Jiang, Ning

    2012-01-01

    Mutator-like transposable elements (MULEs) are widespread in plants and the majority have long terminal inverted repeats (TIRs), which distinguish them from other DNA transposons. It is known that the long TIRs of Mutator elements harbor transposase binding sites and promoters for transcription, indicating that the TIR sequence is critical for transposition and for expression of sequences between the TIRs. Here, we report the presence of MULEs with multiple TIRs mostly located in tandem. These elements are detected in the genomes of maize, tomato, rice, and Arabidopsis. Some of these elements are present in multiple copies, suggesting their mobility. For those elements that have amplified, sequence conservation was observed for both of the tandem TIRs. For one MULE family carrying a gene fragment, the elements with tandem TIRs are more prevalent than their counterparts with a single TIR. The successful amplification of this particular MULE demonstrates that MULEs with tandem TIRs are functional in both transposition and duplication of gene sequences. PMID:22474413

  9. Heterochromatin and molecular characterization of DsmarMITE transposable element in the beetle Dichotomius schiffleri (Coleoptera: Scarabaeidae).

    PubMed

    Xavier, Crislaine; Cabral-de-Mello, Diogo Cavalcanti; de Moura, Rita Cássia

    2014-12-01

    Cytogenetic studies of the Neotropical beetle genus Dichotomius (Scarabaeinae, Coleoptera) have shown dynamism for centromeric constitutive heterochromatin sequences. In the present work we studied the chromosomes and isolated repetitive sequences of Dichotomius schiffleri aiming to contribute to the understanding of coleopteran genome/chromosomal organization. Dichotomius schiffleri presented a conserved karyotype and heterochromatin distribution in comparison to other species of the genus with 2n = 18, biarmed chromosomes, and pericentromeric C-positive blocks. Similarly to heterochromatin distributional patterns, the highly and moderately repetitive DNA fraction (C 0 t-1 DNA) was detected in pericentromeric areas, contrasting with the euchromatic mapping of an isolated TE (named DsmarMITE). After structural analyses, the DsmarMITE was classified as a non-autonomous element of the type miniature inverted-repeat transposable element (MITE) with terminal inverted repeats similar to Mariner elements of insects from different orders. The euchromatic distribution for DsmarMITE indicates that it does not play a part in the dynamics of constitutive heterochromatin sequences.

  10. Small RNAs, DNA methylation and transposable elements in wheat

    PubMed Central

    2010-01-01

    Background More than 80% of the wheat genome is composed of transposable elements (TEs). Since active TEs can move to different locations and potentially impose a significant mutational load, their expression is suppressed in the genome via small non-coding RNAs (sRNAs). sRNAs guide silencing of TEs at the transcriptional (mainly 24-nt sRNAs) and post-transcriptional (mainly 21-nt sRNAs) levels. In this study, we report the distribution of these two types of sRNAs among the different classes of wheat TEs, the regions targeted within the TEs, and their impact on the methylation patterns of the targeted regions. Results We constructed an sRNA library from hexaploid wheat and developed a database that included our library and three other publicly available sRNA libraries from wheat. For five completely-sequenced wheat BAC contigs, most perfectly matching sRNAs represented TE sequences, suggesting that a large fraction of the wheat sRNAs originated from TEs. An analysis of all wheat TEs present in the Triticeae Repeat Sequence database showed that sRNA abundance was correlated with the estimated number of TEs within each class. Most of the sRNAs perfectly matching miniature inverted repeat transposable elements (MITEs) belonged to the 21-nt class and were mainly targeted to the terminal inverted repeats (TIRs). In contrast, most of the sRNAs matching class I and class II TEs belonged to the 24-nt class and were mainly targeted to the long terminal repeats (LTRs) in the class I TEs and to the terminal repeats in CACTA transposons. An analysis of the mutation frequency in potentially methylated sites revealed a three-fold increase in TE mutation frequency relative to intron and untranslated genic regions. This increase is consistent with wheat TEs being preferentially methylated, likely by sRNA targeting. Conclusions Our study examines the wheat epigenome in relation to known TEs. sRNA-directed transcriptional and post-transcriptional silencing plays important roles in

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

    PubMed Central

    Carvalho, Claudia M. B.; Ramocki, Melissa B.; Pehlivan, Davut; Franco, Luis M.; Gonzaga-Jauregui, Claudia; Fang, Ping; McCall, Alanna; Pivnick, Eniko Karman; Hines-Dowell, Stacy; Seaver, Laurie; Friehling, Linda; Lee, Sansan; Smith, Rosemarie; del Gaudio, Daniela; Withers, Marjorie; Liu, Pengfei; Cheung, Sau Wai; Belmont, John W.; Zoghbi, Huda Y.; Hastings, P. J.; Lupski, James R.

    2011-01-01

    We identified complex genomic rearrangements consisting of intermixed duplications and triplications of genomic segments at both the MECP2 and PLP1 loci. These complex rearrangements were characterized by a triplicated segment embedded within a duplication in 12 unrelated subjects. Interestingly, only two novel breakpoint junctions were generated during each rearrangement formation. Remarkably, all the complex rearrangement products share the common genomic organization duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) wherein the triplicated segment is inverted and located between directly oriented duplicated genomic segments. We provide evidence that the DUP-TRP/INV-DUP structures are mediated by inverted repeats that can be separated by over 300 kb; a genomic architecture that apparently leads to susceptibility to such complex rearrangements. A similar inverted repeat mediated mechanism may underlie structural variation in many other regions of the human genome. We propose a mechanism that involves both homology driven, via inverted repeats, and microhomologous/nonhomologous events. PMID:21964572

  12. FSM model correlation identification method based on invert-repeated m-sequence

    NASA Astrophysics Data System (ADS)

    Lei, Luo-lan; Wang, Qiang

    2014-09-01

    Fast steering mirror (FSM) is one of the most important components in electro-optical tracking system and access to FSM model is the basis for controlling and fault diagnosis. This paper presented a correlation identification method based on Invert-Repeated m-sequence which can be used in the electro-optical tracking system to achieve the model of FSM under low sampling rate. Firstly, this article discussed the properties of the Invert-Repeated m-sequence and program implemented in matlab language, then analyzed the principle of correlation identification method based on Invert-Repeated m-sequence by utilizing Wiener-Hopf equation which is simple to achieve with strong anti-jamming capability and small perturbations on the system. Finally, a FSM model with the experiment data got by Dynamic Signal Analyzer was built in Matlab/Simulink and identified by the method mentioned in the paper. The experiment showed that correlation identification method which has certain actual application value, based on Invert-Repeated m-sequence can obtain more accurate recognition results even if the FSM system's output signal contained large variance noise.

  13. 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.

  14. Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged.

    PubMed Central

    Strauss, S H; Palmer, J D; Howe, G T; Doerksen, A H

    1988-01-01

    Chloroplast genomes of Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] and radiata (Monterey) pine [Pinus radiata D. Don], two conifers from the widespread Pinaceae, were mapped and their genomes were compared to other land plants. Douglas-fir and radiata pine lack the large (20-25 kilobases) inverted repeat that characterizes most land plants. To our knowledge, this is only the second recorded loss of this ancient and highly conserved inverted repeat among all lineages of land plants thus far examined. Loss of the repeat largely accounts for the small size of the conifer genome, 120 kilobase, versus 140-160 kilobases in most land plants. Douglas-fir possesses a major inversion of 40-50 kilobases relative to radiata pine and nonconiferous plants. Nucleotide sequence differentiation between Douglas-fir and radiata pine was estimated to be 3.8%. Both conifer genomes possess a number of rearrangements relative to Osmunda, a fern, Ginkgo, a gymnosperm, and Petunia, an angiosperm. Among land plants, structural changes of this degree have occurred primarily within tribes of the legume family (Fabaceae) that have also lost the inverted repeat. These results support the hypothesis that the presence of the large inverted repeat stabilizes the chloroplast genome against major structural rearrangements. PMID:2836862

  15. 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.

  16. Gene organization in the UL region and inverted repeats of the canine herpesvirus genome.

    PubMed

    Rémond, M; Sheldrick, P; Lebreton, F; Nardeux, P; Foulon, T

    1996-01-01

    Restriction mapping and the determination of scattered nucleotide sequences have permitted a description of the global structure and evolutionary affinities of the canine herpesvirus (CHV) genome. The global structure closely resembles that of the totally sequenced genomes of varicella-zoster virus and equine herpesvirus 1 (EHV-1) in having a 37 bp inverted repeat flanking a long unique region (UL) of approximately 100,000 bp, and a 10,100-10,700 bp inverted repeat flanking a short unique region (U8) of roughly 7,400-8,600 bp. On the basis of the sequences obtained, 35 homologues to previously identified herpesvirus gene products were found in UL and the major inverted repeat, and the level of the similarities indicated that CHV belongs to the genus Varicellovirus. Within the genus, CHV appears to be most closely related to EHV-1, pseudorabies virus and feline herpesvirus. Surprisingly, genes for both subunits of the viral ribonucleotide reductase were found to be missing from their equivalent place in other herpesvirus genomes. Either they have been translocated to another position in the CHV genome or, we think more likely, they have been lost.

  17. 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

  18. Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges.

    PubMed

    Lavrov, Dennis V; Maikova, Olga O; Pett, Walker; Belikov, Sergey I

    2012-08-15

    Demosponges, the largest and most diverse class in the phylum Porifera, possess mitochondrial DNA (mtDNA) markedly different from that in other animals. Although several studies investigated evolution of demosponge mtDNA among major lineages of the group, the changes within these groups remain largely unexplored. Recently we determined mitochondrial genomic sequence of the Lake Baikal sponge Lubomirskia baicalensis and described proliferation of small inverted repeats (hairpins) that occurred in it since the divergence between L. baicalensis and the most closely related cosmopolitan freshwater sponge Ephydatia muelleri. Here we report mitochondrial genomes of three additional species of Lake Baikal sponges: Swartschewskia papyracea, Rezinkovia echinata and Baikalospongia intermedia morpha profundalis (Demospongiae, Haplosclerida, Lubomirskiidae) and from a more distantly related freshwater sponge Corvomeyenia sp. (Demospongiae, Haplosclerida, Metaniidae). We use these additional sequences to explore mtDNA evolution in Baikalian sponges, paying particular attention to the variation in the rates of nucleotide substitutions and the distribution of hairpins, abundant in these genomes. We show that most of the changes in Lubomirskiidae mitochondrial genomes are due to insertion/deletion/duplication of these elements rather than single nucleotide substitutions. Thus inverted repeats can act as an important force in evolution of mitochondrial genome architecture and be a valuable marker for population- and species-level studies in this group. In addition, we infer (((Rezinkovia+Lubomirskia)+Swartschewskia)+Baikalospongia) phylogeny for the family Lubomirskiidae based on the analysis of mitochondrial coding sequences from freshwater sponges.

  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. Nearby inverted repeats fuse to generate acentric and dicentric palindromic chromosomes by a replication template exchange mechanism.

    PubMed

    Mizuno, Ken'Ichi; Lambert, Sarah; Baldacci, Giuseppe; Murray, Johanne M; Carr, Antony M

    2009-12-15

    Gene amplification plays important roles in the progression of cancer and contributes to acquired drug resistance during treatment. Amplification can initiate via dicentric palindromic chromosome production and subsequent breakage-fusion-bridge cycles. Here we show that, in fission yeast, acentric and dicentric palindromic chromosomes form by homologous recombination protein-dependent fusion of nearby inverted repeats, and that these fusions occur frequently when replication forks arrest within the inverted repeats. Genetic and molecular analyses suggest that these acentric and dicentric palindromic chromosomes arise not by previously described mechanisms, but by a replication template exchange mechanism that does not involve a DNA double-strand break. We thus propose an alternative mechanism for the generation of palindromic chromosomes dependent on replication fork arrest at closely spaced inverted repeats.

  1. Checkpoint genes and Exo1 regulate nearby inverted repeat fusions that form dicentric chromosomes in Saccharomyces cerevisiae.

    PubMed

    Kaochar, Salma; Shanks, Lisa; Weinert, Ted

    2010-12-14

    Genomic rearrangements are common, occur by largely unknown mechanisms, and can lead to human diseases. We previously demonstrated that some genome rearrangements occur in budding yeast through the fusion of two DNA sequences that contain limited sequence homology, lie in inverted orientation, and are within 5 kb of one another. This inverted repeat fusion reaction forms dicentric chromosomes, which are well-known intermediates to additional rearrangements. We have previously provided evidence indicating that an error of stalled or disrupted DNA replication forks can cause inverted repeat fusion. Here we analyze how checkpoint protein regulatory pathways known to stabilize stalled forks affect this form of instability. We find that two checkpoint pathways suppress inverted repeat fusion, and that their activities are distinguishable by their interactions with exonuclease 1 (Exo1). The checkpoint kinase Rad53 (Chk2) and recombination protein complex MRX(MRN) inhibit Exo1 in one pathway, whereas in a second pathway the ATR-like kinases Mec1 and Tel1, adaptor protein Rad9, and effector kinases Chk1 and Dun1 act independently of Exo1 to prevent inverted repeat fusion. We provide a model that indicates how in Rad53 or MRX mutants, an inappropriately active Exo1 may facilitate faulty template switching between nearby inverted repeats to form dicentric chromosomes. We further investigate the role of Rad53, using hypomorphic alleles of Rad53 and null mutations in Rad9 and Mrc1, and provide evidence that only local, as opposed to global, activity of Rad53 is sufficient to prevent inverted repeat fusion.

  2. Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster

    PubMed Central

    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

  3. Long inverted repeats are an at-risk motif for recombination in mammalian cells.

    PubMed

    Waldman, A S; Tran, H; Goldsmith, E C; Resnick, M A

    1999-12-01

    Certain DNA sequence motifs and structures can promote genomic instability. We have explored instability induced in mouse cells by long inverted repeats (LIRs). A cassette was constructed containing a herpes simplex virus thymidine kinase (tk) gene into which was inserted an LIR composed of two inverted copies of a 1.1-kb yeast URA3 gene sequence separated by a 200-bp spacer sequence. The tk gene was introduced into the genome of mouse Ltk(-) fibroblasts either by itself or in conjunction with a closely linked tk gene that was disrupted by an 8-bp XhoI linker insertion; rates of intrachromosomal homologous recombination between the markers were determined. Recombination between the two tk alleles was stimulated 5-fold by the LIR, as compared to a long direct repeat (LDR) insert, resulting in nearly 10(-5) events per cell per generation. Of the tk(+) segregants recovered from LIR-containing cell lines, 14% arose from gene conversions that eliminated the LIR, as compared to 3% of the tk(+) segregants from LDR cell lines, corresponding to a >20-fold increase in deletions at the LIR hotspot. Thus, an LIR, which is a common motif in mammalian genomes, is at risk for the stimulation of homologous recombination and possibly other genetic rearrangements.

  4. 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

  5. Functional Organization of the Inverted Repeats of IS30▿ †

    PubMed Central

    Szabó, Mónika; Kiss, János; Olasz, Ferenc

    2010-01-01

    The mobile element IS30 has 26-bp imperfect terminal inverted repeats (IRs) that are indispensable for transposition. We have analyzed the effects of IR mutations on both major transposition steps, the circle formation and integration of the abutted ends, characteristic for IS30. Several mutants show strikingly different phenotypes if the mutations are present at one or both ends and differentially influence the transposition steps. The two IRs are equivalent in the recombination reactions and contain several functional regions. We have determined that positions 20 to 26 are responsible for binding of the N-terminal domain of the transposase and the formation of a correct 2-bp spacer between the abutted ends. However, integration is efficient without this region, suggesting that a second binding site for the transposase may exist, possibly within the region from 4 to 11 bp. Several mutations at this part of the IRs, which are highly conserved in the IS30 family, considerably affected both major transposition steps. In addition, positions 16 and 17 seem to be responsible for distinguishing the IRs of related insertion sequences by providing specificity for the transposase to recognize its cognate ends. Finally, we show both in vivo and in vitro that position 3 has a determining role in the donor function of the ends, especially in DNA cleavage adjacent to the IRs. Taken together, the present work provides evidence for a more complex organization of the IS30 IRs than was previously suggested. PMID:20418401

  6. ATP-dependent specific binding of Tn3 transposase to Tn3 inverted repeats

    NASA Astrophysics Data System (ADS)

    Wishart, W. L.; Broach, J. R.; Ohtsubo, E.

    1985-04-01

    Transposons are discrete segments of DNA which are capable of moving from one site in a genome to many different sites1,2. Tn3 is a prokaryotic transposon which is 4,957 base pairs (bp) long and encodes a transposase protein which is essential for transposition3-7. We report here a simple method for purifying Tn3 transposase and demonstrate that the transposase protein binds specifically to the ends of the Tn3 transposon in an ATP-dependent manner. The transposase protein binds to linear double-stranded DNA both nonspecifically and specifically; the nonspecific DNA binding activity is sensitive to challenge with heparin. Site-specific DNA binding to the ends (inverted repeats) of Tn3 is observed only when binding is performed in the presence of ATP; this ATP-dependent site-specific DNA binding activity is resistant to heparin challenge. Our results indicate that ATP qualitatively alters the DNA binding activity of the transposase protein so that the protein is able to bind specifically to the ends of the Tn3 transposon.

  7. Bioinformatic analyses of sense and antisense expression from terminal inverted repeat transposons in Drosophila somatic cells.

    PubMed

    Harrington, Andrew W; Steiniger, Mindy

    2016-01-02

    Understanding regulation of transposon movement in somatic cells is important as mobile elements can cause detrimental genomic rearrangements. Generally, transposons move via one of 2 mechanisms; retrotransposons utilize an RNA intermediate, therefore copying themselves and amplifying throughout the genome, while terminal inverted repeat transposons (TIR Tns) excise DNA sequences from the genome and integrate into a new location. Our recently published work indicates that retrotransposons in Drosophila tissue culture cells are actively transcribed in the antisense direction. Our data support a model in which convergent transcription of retrotransposons from intra element transcription start sites results in complementary RNAs that hybridize to form substrates for Dicer-2, the endogenous small interfering (esi)RNA generating enzyme. Here, we extend our previous analysis to TIR Tns. In contrast to retrotransposons, our data show that antisense TIR Tn RNAs result from transcription of intronic TIR Tns oriented antisense to their host genes. Also, disproportionately less esiRNAs are generated from TIR transcripts than from retrotransposons and transcription of very few individual TIR Tns could be confirmed. Collectively, these data support a model in which TIR Tns are regulated at the level of Transposase production while retrotransposons are regulated with esiRNA post-transcriptional mechanisms in Drosophila somatic cells.

  8. Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes.

    PubMed

    Weng, Mao-Lun; Ruhlman, Tracey A; Jansen, Robert K

    2017-04-01

    For species with minor inverted repeat (IR) boundary changes in the plastid genome (plastome), nucleotide substitution rates were previously shown to be lower in the IR than the single copy regions (SC). However, the impact of large-scale IR expansion/contraction on plastid nucleotide substitution rates among closely related species remains unclear. We included plastomes from 22 Pelargonium species, including eight newly sequenced genomes, and used both pairwise and model-based comparisons to investigate the impact of the IR on sequence evolution in plastids. Ten types of plastome organization with different inversions or IR boundary changes were identified in Pelargonium. Inclusion in the IR was not sufficient to explain the variation of nucleotide substitution rates. Instead, the rate heterogeneity in Pelargonium plastomes was a mixture of locus-specific, lineage-specific and IR-dependent effects. Our study of Pelargonium plastomes that vary in IR length and gene content demonstrates that the evolutionary consequences of retaining these repeats are more complicated than previously suggested.

  9. Intraspecific Variability of the Terminal Inverted Repeats of the Linear Chromosome of Streptomyces ambofaciens

    PubMed Central

    Choulet, Frédéric; Gallois, Alexandre; Aigle, Bertrand; Mangenot, Sophie; Gerbaud, Claude; Truong, Chantal; Francou, François-Xavier; Borges, Frédéric; Fourrier, Céline; Guérineau, Michel; Decaris, Bernard; Barbe, Valérie; Pernodet, Jean-Luc; Leblond, Pierre

    2006-01-01

    The sequences of the terminal inverted repeats (TIRs) ending the linear chromosomal DNA of two Streptomyces ambofaciens strains, ATCC23877 and DSM40697 (198 kb and 213 kb, respectively), were determined from two sets of recombinant cosmids. Among the 215 coding DNA sequences (CDSs) predicted in the TIRs of strain DSM40697, 65 are absent in the TIRs of strain ATCC23877. Reciprocally, 45 of the 194 predicted CDSs are specific to the ATCC23877 strain. The strain-specific CDSs are located mainly at the terminal end of the TIRs. Indeed, although TIRs appear almost identical over 150 kb (99% nucleotide identity), large regions of DNA of 60 kb (DSM40697) and 48 kb (ATCC23877), mostly spanning the ends of the chromosome, are strain specific. These regions are rich in plasmid-associated genes, including genes encoding putative conjugal transfer functions. The strain-specific regions also share a G+C content (68%) lower than that of the rest of the genome (from 71% to 73%), a percentage that is more typical of Streptomyces plasmids and mobile elements. These data suggest that exchanges of replicon extremities have occurred, thereby contributing to the terminal variability observed at the intraspecific level. In addition, the terminal regions include many mobile genetic element-related genes, pseudogenes, and genes related to adaptation. The results give insight into the mechanisms of evolution of the TIRs: integration of new information and/or loss of DNA fragments and subsequent homogenization of the two chromosomal extremities. PMID:16952952

  10. Intraspecific variability of the terminal inverted repeats of the linear chromosome of Streptomyces ambofaciens.

    PubMed

    Choulet, Frédéric; Gallois, Alexandre; Aigle, Bertrand; Mangenot, Sophie; Gerbaud, Claude; Truong, Chantal; Francou, François-Xavier; Borges, Frédéric; Fourrier, Céline; Guérineau, Michel; Decaris, Bernard; Barbe, Valérie; Pernodet, Jean-Luc; Leblond, Pierre

    2006-09-01

    The sequences of the terminal inverted repeats (TIRs) ending the linear chromosomal DNA of two Streptomyces ambofaciens strains, ATCC23877 and DSM40697 (198 kb and 213 kb, respectively), were determined from two sets of recombinant cosmids. Among the 215 coding DNA sequences (CDSs) predicted in the TIRs of strain DSM40697, 65 are absent in the TIRs of strain ATCC23877. Reciprocally, 45 of the 194 predicted CDSs are specific to the ATCC23877 strain. The strain-specific CDSs are located mainly at the terminal end of the TIRs. Indeed, although TIRs appear almost identical over 150 kb (99% nucleotide identity), large regions of DNA of 60 kb (DSM40697) and 48 kb (ATCC23877), mostly spanning the ends of the chromosome, are strain specific. These regions are rich in plasmid-associated genes, including genes encoding putative conjugal transfer functions. The strain-specific regions also share a G+C content (68%) lower than that of the rest of the genome (from 71% to 73%), a percentage that is more typical of Streptomyces plasmids and mobile elements. These data suggest that exchanges of replicon extremities have occurred, thereby contributing to the terminal variability observed at the intraspecific level. In addition, the terminal regions include many mobile genetic element-related genes, pseudogenes, and genes related to adaptation. The results give insight into the mechanisms of evolution of the TIRs: integration of new information and/or loss of DNA fragments and subsequent homogenization of the two chromosomal extremities.

  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 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.

  13. Fusion of nearby inverted repeats by a replication-based mechanism leads to formation of dicentric and acentric chromosomes that cause genome instability in budding yeast.

    PubMed

    Paek, Andrew L; Kaochar, Salma; Jones, Hope; Elezaby, Aly; Shanks, Lisa; Weinert, Ted

    2009-12-15

    Large-scale changes (gross chromosomal rearrangements [GCRs]) are common in genomes, and are often associated with pathological disorders. We report here that a specific pair of nearby inverted repeats in budding yeast fuse to form a dicentric chromosome intermediate, which then rearranges to form a translocation and other GCRs. We next show that fusion of nearby inverted repeats is general; we found that many nearby inverted repeats that are present in the yeast genome also fuse, as does a pair of synthetically constructed inverted repeats. Fusion occurs between inverted repeats that are separated by several kilobases of DNA and share >20 base pairs of homology. Finally, we show that fusion of inverted repeats, surprisingly, does not require genes involved in double-strand break (DSB) repair or genes involved in other repeat recombination events. We therefore propose that fusion may occur by a DSB-independent, DNA replication-based mechanism (which we term "faulty template switching"). Fusion of nearby inverted repeats to form dicentrics may be a major cause of instability in yeast and in other organisms.

  14. 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

  15. Functional Angucycline-Like Antibiotic Gene Cluster in the Terminal Inverted Repeats of the Streptomyces ambofaciens Linear Chromosome

    PubMed Central

    Pang, Xiuhua; Aigle, Bertrand; Girardet, Jean-Michel; Mangenot, Sophie; Pernodet, Jean-Luc; Decaris, Bernard; Leblond, Pierre

    2004-01-01

    Streptomyces ambofaciens has an 8-Mb linear chromosome ending in 200-kb terminal inverted repeats. Analysis of the F6 cosmid overlapping the terminal inverted repeats revealed a locus similar to type II polyketide synthase (PKS) gene clusters. Sequence analysis identified 26 open reading frames, including genes encoding the β-ketoacyl synthase (KS), chain length factor (CLF), and acyl carrier protein (ACP) that make up the minimal PKS. These KS, CLF, and ACP subunits are highly homologous to minimal PKS subunits involved in the biosynthesis of angucycline antibiotics. The genes encoding the KS and ACP subunits are transcribed constitutively but show a remarkable increase in expression after entering transition phase. Five genes, including those encoding the minimal PKS, were replaced by resistance markers to generate single and double mutants (replacement in one and both terminal inverted repeats). Double mutants were unable to produce either diffusible orange pigment or antibacterial activity against Bacillus subtilis. Single mutants showed an intermediate phenotype, suggesting that each copy of the cluster was functional. Transformation of double mutants with a conjugative and integrative form of F6 partially restored both phenotypes. The pigmented and antibacterial compounds were shown to be two distinct molecules produced from the same biosynthetic pathway. High-pressure liquid chromatography analysis of culture extracts from wild-type and double mutants revealed a peak with an associated bioactivity that was absent from the mutants. Two additional genes encoding KS and CLF were present in the cluster. However, disruption of the second KS gene had no effect on either pigment or antibiotic production. PMID:14742212

  16. Functional angucycline-like antibiotic gene cluster in the terminal inverted repeats of the Streptomyces ambofaciens linear chromosome.

    PubMed

    Pang, Xiuhua; Aigle, Bertrand; Girardet, Jean-Michel; Mangenot, Sophie; Pernodet, Jean-Luc; Decaris, Bernard; Leblond, Pierre

    2004-02-01

    Streptomyces ambofaciens has an 8-Mb linear chromosome ending in 200-kb terminal inverted repeats. Analysis of the F6 cosmid overlapping the terminal inverted repeats revealed a locus similar to type II polyketide synthase (PKS) gene clusters. Sequence analysis identified 26 open reading frames, including genes encoding the beta-ketoacyl synthase (KS), chain length factor (CLF), and acyl carrier protein (ACP) that make up the minimal PKS. These KS, CLF, and ACP subunits are highly homologous to minimal PKS subunits involved in the biosynthesis of angucycline antibiotics. The genes encoding the KS and ACP subunits are transcribed constitutively but show a remarkable increase in expression after entering transition phase. Five genes, including those encoding the minimal PKS, were replaced by resistance markers to generate single and double mutants (replacement in one and both terminal inverted repeats). Double mutants were unable to produce either diffusible orange pigment or antibacterial activity against Bacillus subtilis. Single mutants showed an intermediate phenotype, suggesting that each copy of the cluster was functional. Transformation of double mutants with a conjugative and integrative form of F6 partially restored both phenotypes. The pigmented and antibacterial compounds were shown to be two distinct molecules produced from the same biosynthetic pathway. High-pressure liquid chromatography analysis of culture extracts from wild-type and double mutants revealed a peak with an associated bioactivity that was absent from the mutants. Two additional genes encoding KS and CLF were present in the cluster. However, disruption of the second KS gene had no effect on either pigment or antibiotic production.

  17. 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

  18. 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

  19. Cruciform-forming inverted repeats appear to have mediated many of the microinversions that distinguish the human and chimpanzee genomes.

    PubMed

    Kolb, Jessica; Chuzhanova, Nadia A; Högel, Josef; Vasquez, Karen M; Cooper, David N; Bacolla, Albino; Kehrer-Sawatzki, Hildegard

    2009-01-01

    Submicroscopic inversions have contributed significantly to the genomic divergence between humans and chimpanzees over evolutionary time. Those microinversions which are flanked by segmental duplications (SDs) are presumed to have originated via non-allelic homologous recombination between SDs arranged in inverted orientation. However, the nature of the mechanisms underlying those inversions which are not flanked by SDs remains unclear. We have investigated 35 such inversions, ranging in size from 51-nt to 22056-nt, with the goal of characterizing the DNA sequences in the breakpoint-flanking regions. Using the macaque genome as an outgroup, we determined the lineage specificity of these inversions and noted that the majority (N = 31; 89%) were associated with deletions (of length between 1-nt and 6754-nt) immediately adjacent to one or both inversion breakpoints. Overrepresentations of both direct and inverted repeats, >or= 6-nt in length and capable of non-B DNA structure formation, were noted in the vicinity of breakpoint junctions suggesting that these repeats could have contributed to double strand breakage. Inverted repeats capable of cruciform structure formation were also found to be a common feature of the inversion breakpoint-flanking regions, consistent with these inversions having originated through the resolution of Holliday junction-like cruciforms. Sequences capable of non-B DNA structure formation have previously been implicated in promoting gross deletions and translocations causing human genetic disease. We conclude that non-B DNA forming sequences may also have promoted the occurrence of mutations in an evolutionary context, giving rise to at least some of the inversion/deletions which now serve to distinguish the human and chimpanzee genomes.

  20. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue

    PubMed Central

    El Kafsi, Hela; Loux, Valentin; Mariadassou, Mahendra; Blin, Camille; Chiapello, Hélène; Abraham, Anne-Laure; Maguin, Emmanuelle; van de Guchte, Maarten

    2017-01-01

    The first Lactobacillus delbrueckii ssp. bulgaricus genome sequence revealed the presence of a very large inverted repeat (IR), a DNA sequence arrangement which thus far seemed inconceivable in a non-manipulated circular bacterial chromosome, at the replication terminus. This intriguing observation prompted us to investigate if similar IRs could be found in other bacteria. IRs with sizes varying from 38 to 76 kbp were found at the replication terminus of all 5 L. delbrueckii ssp. bulgaricus chromosomes analysed, but in none of 1373 other chromosomes. They represent the first naturally occurring very large IRs detected in circular bacterial genomes. A comparison of the L. bulgaricus replication terminus regions and the corresponding regions without IR in 5 L. delbrueckii ssp. lactis genomes leads us to propose a model for the formation and evolution of the IRs. The DNA sequence data are consistent with a novel model of chromosome rescue after premature replication termination or irreversible chromosome damage near the replication terminus, involving mechanisms analogous to those proposed in the formation of very large IRs in human cancer cells. We postulate that the L. delbrueckii ssp. bulgaricus-specific IRs in different strains derive from a single ancestral IR of at least 93 kbp. PMID:28281695

  1. Long inverted repeat transiently stalls DNA replication by forming hairpin structures on both leading and lagging strands.

    PubMed

    Lai, Pey Jiun; Lim, Chew Theng; Le, Hang Phuong; Katayama, Tsutomu; Leach, David R F; Furukohri, Asako; Maki, Hisaji

    2016-02-01

    Long inverted repeats (LIRs), often found in eukaryotic genomes, are unstable in Escherichia coli where they are recognized by the SbcCD (the bacterial Mre11/Rad50 homologue), an endonuclease/exonuclease capable of cleaving hairpin DNA. It has long been postulated that LIRs form hairpin structures exclusively on the lagging-strand template during DNA replication, and SbcCD cleaves these hairpin-containing lagging strands to generate DNA double-strand breaks. Using a reconstituted oriC plasmid DNA replication system, we have examined how a replication fork behaves when it meets a LIR on DNA. We have shown that leading-strand synthesis stalls transiently within the upstream half of the LIR. Pausing of lagging-strand synthesis at the LIR was not clearly observed, but the pattern of priming sites for Okazaki fragment synthesis was altered within the downstream half of the LIR. We have found that the LIR on a replicating plasmid was cleaved by SbcCD with almost equal frequency on both the leading- and lagging-strand templates. These data strongly suggest that the LIR is readily converted to a cruciform DNA, before the arrival of the fork, creating SbcCD-sensitive hairpin structures on both leading and lagging strands. We propose a model for the replication-dependent extrusion of LIRs to form cruciform structures that transiently impede replication fork movement.

  2. Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue.

    PubMed

    El Kafsi, Hela; Loux, Valentin; Mariadassou, Mahendra; Blin, Camille; Chiapello, Hélène; Abraham, Anne-Laure; Maguin, Emmanuelle; van de Guchte, Maarten

    2017-03-10

    The first Lactobacillus delbrueckii ssp. bulgaricus genome sequence revealed the presence of a very large inverted repeat (IR), a DNA sequence arrangement which thus far seemed inconceivable in a non-manipulated circular bacterial chromosome, at the replication terminus. This intriguing observation prompted us to investigate if similar IRs could be found in other bacteria. IRs with sizes varying from 38 to 76 kbp were found at the replication terminus of all 5 L. delbrueckii ssp. bulgaricus chromosomes analysed, but in none of 1373 other chromosomes. They represent the first naturally occurring very large IRs detected in circular bacterial genomes. A comparison of the L. bulgaricus replication terminus regions and the corresponding regions without IR in 5 L. delbrueckii ssp. lactis genomes leads us to propose a model for the formation and evolution of the IRs. The DNA sequence data are consistent with a novel model of chromosome rescue after premature replication termination or irreversible chromosome damage near the replication terminus, involving mechanisms analogous to those proposed in the formation of very large IRs in human cancer cells. We postulate that the L. delbrueckii ssp. bulgaricus-specific IRs in different strains derive from a single ancestral IR of at least 93 kbp.

  3. 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

  4. Integration of promoters, inverted repeat sequences and proteomic data into a model for high silencing efficiency of coeliac disease related gliadins in bread wheat

    PubMed Central

    2013-01-01

    Background Wheat gluten has unique nutritional and technological characteristics, but is also a major trigger of allergies and intolerances. One of the most severe diseases caused by gluten is coeliac disease. The peptides produced in the digestive tract by the incomplete digestion of gluten proteins trigger the disease. The majority of the epitopes responsible reside in the gliadin fraction of gluten. The location of the multiple gliadin genes in blocks has to date complicated their elimination by classical breeding techniques or by the use of biotechnological tools. As an approach to silence multiple gliadin genes we have produced 38 transgenic lines of bread wheat containing combinations of two endosperm-specific promoters and three different inverted repeat sequences to silence three fractions of gliadins by RNA interference. Results The effects of the RNA interference constructs on the content of the gluten proteins, total protein and starch, thousand seed weights and SDSS quality tests of flour were analyzed in these transgenic lines in two consecutive years. The characteristics of the inverted repeat sequences were the main factor that determined the efficiency of silencing. The promoter used had less influence on silencing, although a synergy in silencing efficiency was observed when the two promoters were used simultaneously. Genotype and the environment also influenced silencing efficiency. Conclusions We conclude that to obtain wheat lines with an optimum reduction of toxic gluten epitopes one needs to take into account the factors of inverted repeat sequences design, promoter choice and also the wheat background used. PMID:24044767

  5. 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.

  6. The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species.

    PubMed

    Zhang, Yanzhen; Ma, Ji; Yang, Bingxian; Li, Ruyi; Zhu, Wei; Sun, Lianli; Tian, Jingkui; Zhang, Lin

    2014-05-01

    Taxus chinensis var. mairei (Taxaceae) is a domestic variety of yew species in local China. This plant is one of the sources for paclitaxel, which is a promising antineoplastic chemotherapy drugs during the last decade. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of T. chinensis var. mairei. The T. chinensis var. mairei cp genome is 129,513 bp in length, with 113 single copy genes and two duplicated genes (trnI-CAU, trnQ-UUG). Among the 113 single copy genes, 9 are intron-containing. Compared to other land plant cp genomes, the T. chinensis var. mairei cp genome has lost one of the large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperm such as Cycas revoluta and Ginkgo biloba L. Compared to related species, the gene order of T. chinensis var. mairei has a large inversion of ~110kb including 91 genes (from rps18 to accD) with gene contents unarranged. Repeat analysis identified 48 direct and 2 inverted repeats 30 bp long or longer with a sequence identity greater than 90%. Repeated short segments were found in genes rps18, rps19 and clpP. Analysis also revealed 22 simple sequence repeat (SSR) loci and almost all are composed of A or T.

  7. Evolutionary relationship between 5+5 and 7+7 inverted repeat folds within the amino acid-polyamine-organocation superfamily.

    PubMed

    Västermark, Åke; Saier, Milton H

    2014-02-01

    Evidence has been presented that 5+5 TMS and 7+7 TMS inverted repeat fold transporters are members of a single superfamily named the Amino acid-Polyamine-organoCation (APC) superfamily. However, the evolutionary relationship between the 5+5 and the 7+7 topological types has not been established. We have identified a common fold, consisting of a spiny membrane helix/sheet, followed by a U-like structure and a V-like structure that is recurrent between domain duplicated units of 5+5 and 7+7 inverted repeat folds. This fold is found in the following protein structures: AdiC, ApcT, LeuT, Mhp1, BetP, CaiT, and SglT (all 5+5 TMS repeats), as well as UraA and SulP (7+7 TMS repeats). AdiC, LeuT and Mhp1 have two extra TMSs after the second duplicated domain, SglT has four extra C-terminal TMSs, and BetP has two extra TMSs before the first duplicated domain. UraA and SulP on the other hand have two extra TMSs at the N-terminus of each duplicated domain unit. These observations imply that multiple hairpin and domain duplication events occurred during the evolution of the APC superfamily. We suggest that the five TMS architecture was primordial and that families gained two TMSs on either side of this basic structure via dissimilar hairpin duplications either before or after intragenic duplication. Evidence for homology between TMSs 1-2 of AdiC and TMSs 1-2 and 3-4 of UraA suggests that the 7+7 topology arose via an internal duplication of the N-terminal hairpin loop within the five TMS repeat unit followed by duplication of the 7 TMS domain.

  8. Interactions between WHITE Genes Carried by a Large Transposing Element and the ZESTE1 Allele in DROSOPHILA MELANOGASTER

    PubMed Central

    Gubb, D.; Roote, J.; McGill, S.; Shelton, M.; Ashburner, M.

    1986-01-01

    TE146, a large transposing element of Drosophila melanogaster, carries two copies of the white and roughest genes in tandem. In consequence, z1 w 11E4; TE146(Z)/+ flies have a zeste (lemon-yellow) eye color. However, one in 103 TE146 chromosomes mutates to a red-eyed form. The majority of these "spontaneous red" (SR) derivatives of TE146 have only one copy of the white gene and are, cytologically, two- to three-banded elements, rather than six-banded as their progenitor. The SR forms of TE146 are also unstable and give zeste-colored forms with a frequency of about one in 104. One such "spontaneous zeste" (SZ) derivative carries duplicated white genes as an inverted, rather than a tandem, repeat. The genetic instability of this inverted repeat form of TE146 is different from that of the original tandem repeat form. In particular, the inverted repeat form frequently produces derivatives with internal rearrangements of the TE and gives a much lower frequency of SR forms. In addition, two novel features of the interaction between w+ alleles in a zeste background have been found. First, copies of w + can become insensitive to suppression by zeste even when paired. Second, an inversion breakpoint may disrupt the pairing between two adjacent w+ alleles, necessary for their suppression by zeste, without physically separating them. PMID:17246318

  9. Structural features of transposed human VK genes and implications for the mechanism of their transpositions.

    PubMed

    Borden, P; Jaenichen, R; Zachau, H G

    1990-04-25

    The genes encoding the variable, joining and constant regions of human immunoglobulin light chains have been localized to the short arm of chromosome 2. However, several VK genes lie outside of the locus: a single copy cluster of five VK genes is located on chromosome 22; an isolated but amplified VkI gene is found on chromosome 1; and several isolated VkI genes are on as-yet-unidentified chromosomes other than chromosome 2. Vk genes not contained within the kappa locus are termed orphons. We have attempted to gain insight into the mechanism of transposition of both the chromosome 22 cluster and the several amplified VkI genes by searching in the kappa locus for a parent copy of the former, and by analyzing the junctions between transposed VKI-containing segments and adjacent non-amplified regions. The chromosome 22 orphon cluster must have been non-duplicatively transposed. Sequence features at the junctions of this and other orphon regions are direct and inverted repeats, and, in one case, an Alu repeat. These unusual features may have predisposed the orphon regions to transposition by serving as target sites for enzymes involved in recombination.

  10. The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms.

    PubMed

    Ma, Ji; Yang, Bingxian; Zhu, Wei; Sun, Lianli; Tian, Jingkui; Wang, Xumin

    2013-10-10

    Mahonia bealei (Berberidaceae) is a frequently-used traditional Chinese medicinal plant with efficient anti-inflammatory ability. This plant is one of the sources of berberine, a new cholesterol-lowering drug with anti-diabetic activity. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of M. bealei. The complete cp genome of M. bealei is 164,792 bp in length, and has a typical structure with large (LSC 73,052 bp) and small (SSC 18,591 bp) single-copy regions separated by a pair of inverted repeats (IRs 36,501 bp) of large size. The Mahonia cp genome contains 111 unique genes and 39 genes are duplicated in the IR regions. The gene order and content of M. bealei are almost unarranged which is consistent with the hypothesis that large IRs stabilize cp genome and reduce gene loss-and-gain probabilities during evolutionary process. A large IR expansion of over 12 kb has occurred in M. bealei, 15 genes (rps19, rpl22, rps3, rpl16, rpl14, rps8, infA, rpl36, rps11, petD, petB, psbH, psbN, psbT and psbB) have expanded to have an additional copy in the IRs. The IR expansion rearrangement occurred via a double-strand DNA break and subsequence repair, which is different from the ordinary gene conversion mechanism. Repeat analysis identified 39 direct/inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Analysis also revealed 75 simple sequence repeat (SSR) loci and almost all are composed of A or T, contributing to a distinct bias in base composition. Comparison of protein-coding sequences with ESTs reveals 9 putative RNA edits and 5 of them resulted in non-synonymous modifications in rpoC1, rps2, rps19 and ycf1. Phylogenetic analysis using maximum parsimony (MP) and maximum likelihood (ML) was performed on a dataset composed of 65 protein-coding genes from 25 taxa, which yields an identical tree topology as previous plastid-based trees, and provides strong support for the sister relationship between Ranunculaceae and Berberidaceae

  11. Composite transposable elements in the Xenopus laevis genome.

    PubMed Central

    Garrett, J E; Knutzon, D S; Carroll, D

    1989-01-01

    Members of two related families of transposable elements, Tx1 and Tx2, were isolated from the genome of Xenopus laevis and characterized. In both families, two versions of the elements were found. The smaller version in each family (Tx1d and Tx2d) consisted largely of two types of 400-base-pair tandem internal repeats. These elements had discrete ends and short inverted terminal repeats characteristic of mobile DNAs that are presumed to move via DNA intermediates, e.g., Drosophila P and maize Ac elements. The longer versions (Tx1c and Tx2c) differed from Tx1d and Tx2d by the presence of a 6.9-kilobase-pair internal segment that included two long open reading frames (ORFs). ORF1 had one cysteine-plus-histidine-rich sequence of the type found in retroviral gag proteins. ORF2 showed more substantial homology to retroviral pol genes and particularly to the analogs of pol found in a subclass of mobile DNAs that are supposed retrotransposons, such as mammalian long interspersed repetitive sequences, Drosophila I factors, silkworm R1 elements, and trypanosome Ingi elements. Thus, the Tx1 elements present a paradox by exhibiting features of two classes of mobile DNAs that are thought to have very different modes of transposition. Two possible resolutions are considered: (i) the composite versions are actually made up of two independent elements, one of the retrotransposon class, which has a high degree of specificity for insertion into a target within the other, P-like element; and (ii) the composite elements are intact, autonomous mobile DNAs, in which the pol-like gene product collaborates with the terminal inverted repeats to cause transposition of the entire unit. Images PMID:2550791

  12. Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides1

    PubMed Central

    Czernic, Pierre; Gully, Djamel; Cartieaux, Fabienne; Moulin, Lionel; Guefrachi, Ibtissem; Patrel, Delphine; Pierre, Olivier; Fardoux, Joël; Chaintreuil, Clémence; Nguyen, Phuong; Gressent, Frédéric; Da Silva, Corinne; Poulain, Julie; Wincker, Patrick; Rofidal, Valérie; Hem, Sonia; Barrière, Quentin; Arrighi, Jean-François; Mergaert, Peter; Giraud, Eric

    2015-01-01

    Nutritional symbiotic interactions require the housing of large numbers of microbial symbionts, which produce essential compounds for the growth of the host. In the legume-rhizobium nitrogen-fixing symbiosis, thousands of rhizobium microsymbionts, called bacteroids, are confined intracellularly within highly specialized symbiotic host cells. In Inverted Repeat-Lacking Clade (IRLC) legumes such as Medicago spp., the bacteroids are kept under control by an arsenal of nodule-specific cysteine-rich (NCR) peptides, which induce the bacteria in an irreversible, strongly elongated, and polyploid state. Here, we show that in Aeschynomene spp. legumes belonging to the more ancient Dalbergioid lineage, bacteroids are elongated or spherical depending on the Aeschynomene spp. and that these bacteroids are terminally differentiated and polyploid, similar to bacteroids in IRLC legumes. Transcriptome, in situ hybridization, and proteome analyses demonstrated that the symbiotic cells in the Aeschynomene spp. nodules produce a large diversity of NCR-like peptides, which are transported to the bacteroids. Blocking NCR transport by RNA interference-mediated inactivation of the secretory pathway inhibits bacteroid differentiation. Together, our results support the view that bacteroid differentiation in the Dalbergioid clade, which likely evolved independently from the bacteroid differentiation in the IRLC clade, is based on very similar mechanisms used by IRLC legumes. PMID:26286718

  13. Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides.

    PubMed

    Czernic, Pierre; Gully, Djamel; Cartieaux, Fabienne; Moulin, Lionel; Guefrachi, Ibtissem; Patrel, Delphine; Pierre, Olivier; Fardoux, Joël; Chaintreuil, Clémence; Nguyen, Phuong; Gressent, Frédéric; Da Silva, Corinne; Poulain, Julie; Wincker, Patrick; Rofidal, Valérie; Hem, Sonia; Barrière, Quentin; Arrighi, Jean-François; Mergaert, Peter; Giraud, Eric

    2015-10-01

    Nutritional symbiotic interactions require the housing of large numbers of microbial symbionts, which produce essential compounds for the growth of the host. In the legume-rhizobium nitrogen-fixing symbiosis, thousands of rhizobium microsymbionts, called bacteroids, are confined intracellularly within highly specialized symbiotic host cells. In Inverted Repeat-Lacking Clade (IRLC) legumes such as Medicago spp., the bacteroids are kept under control by an arsenal of nodule-specific cysteine-rich (NCR) peptides, which induce the bacteria in an irreversible, strongly elongated, and polyploid state. Here, we show that in Aeschynomene spp. legumes belonging to the more ancient Dalbergioid lineage, bacteroids are elongated or spherical depending on the Aeschynomene spp. and that these bacteroids are terminally differentiated and polyploid, similar to bacteroids in IRLC legumes. Transcriptome, in situ hybridization, and proteome analyses demonstrated that the symbiotic cells in the Aeschynomene spp. nodules produce a large diversity of NCR-like peptides, which are transported to the bacteroids. Blocking NCR transport by RNA interference-mediated inactivation of the secretory pathway inhibits bacteroid differentiation. Together, our results support the view that bacteroid differentiation in the Dalbergioid clade, which likely evolved independently from the bacteroid differentiation in the IRLC clade, is based on very similar mechanisms used by IRLC legumes.

  14. 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

  15. The Agrocybe aegerita mitochondrial genome contains two inverted repeats of the nad4 gene arisen by duplication on both sides of a linear plasmid integration site.

    PubMed

    Ferandon, C; Chatel, S El Kirat; Castandet, B; Castroviejo, M; Barroso, G

    2008-03-01

    The Agrocybe aegerita mitochondrial genome possesses two polB genes with linear plasmid origin. The cloning and sequencing of the regions flanking Aa-polB P1 revealed two large inverted repeats (higher than 2421 nt) separated by a single copy region of 5834 nt. Both repeats contain identical copies of the nad4 gene. The single copy region contains two disrupted genes with plasmid origin Aa-polB P1 and a small ORF homologous to a small gene described in two basidiomycete linear plasmids. The phylogenetic analyses argue in favor of a same plasmid origin for both genes but, surprisingly, these genes were separated by a mitochondrial tRNA-Met. Both strands of the complete region containing the two nad4 inverted copies and the tRNA-Met appear to be transcribed on large polycistronic mRNAs. A model summarizing the events that would have occurred is proposed: (1) capture of the tRNA by the plasmid before its integration in the mtDNA or acquisition of the tRNA gene by recombination after the plasmid integration, (2) integration of the plasmid in the mtDNA, accompanied by a large duplication containing the nad4 gene and (3) erosion of the plasmid sequences by large deletions and mutations.

  16. The β-conglycinin deficiency in wild soybean is associated with the tail-to-tail inverted repeat of the α-subunit genes.

    PubMed

    Tsubokura, Yasutaka; Hajika, Makita; Kanamori, Hiroyuki; Xia, Zhengjun; Watanabe, Satoshi; Kaga, Akito; Katayose, Yuichi; Ishimoto, Masao; Harada, Kyuya

    2012-02-01

    β-conglycinin, a major seed protein in soybean, is composed of α, α', and β subunits sharing a high homology among them. Despite its many health benefits, β-conglycinin has a lower amino acid score and lower functional gelling properties compared to glycinin, another major soybean seed protein. In addition, the α, α', and β subunits also contain major allergens. A wild soybean (Glycine soja Sieb et Zucc.) line, 'QT2', lacks all of the β-conglycinin subunits, and the deficiency is controlled by a single dominant gene, Scg-1 (Suppressor of β-conglycinin). This gene was characterized using a soybean cultivar 'Fukuyutaka', 'QY7-25', (its near-isogenic line carrying the Scg-1 gene), and the F₂ population derived from them. The physical map of the Scg-1 region covered by lambda phage genomic clones revealed that the two α-subunit genes, a β-subunit gene, and a pseudo α-subunit gene were closely organized. The two α-subunit genes were arranged in a tail-to-tail orientation, and the genes were separated by 197 bp in Scg-1 compared to 3.3 kb in the normal allele (scg-1). In addition, small RNA was detected in immature seeds of the mutants by northern blot analysis using an RNA probe of the α subunit. These results strongly suggest that β-conglycinin deficiency in QT2 is controlled by post-transcriptional gene silencing through the inverted repeat of the α subunits.

  17. 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...

  18. 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%),...

  19. Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny.

    PubMed

    Wu, Chung-Shien; Wang, Ya-Nan; Hsu, Chi-Yao; Lin, Ching-Ping; Chaw, Shu-Miaw

    2011-01-01

    The relationships among the extant five gymnosperm groups--gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads--remain equivocal. To clarify this issue, we sequenced the chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana and Taiwania cryptomerioides, and 53 common chloroplast protein-coding genes from another three cupressophytes, Agathis dammara, Nageia nagi, and Sciadopitys verticillata, and a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed that Pinaceae and cupressophytes each lost a different copy of inverted repeats (IRs), which contrasts with the view that the same IR has been lost in all conifers. Based on our structural finding, the character of an IR loss no longer conflicts with the "gnepines" hypothesis (gnetophytes sister to Pinaceae). Chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, we demonstrated that high heterotachous genes (genes that have highly different rates in different lineages) contributed to the long-branch attraction (LBA) artifact, resulting in incongruence of phylogenomic estimates. Additionally, amino acid compositions appear more heterogeneous in high than low heterotachous genes among the five gymnosperm groups. Removal of high heterotachous genes alleviated the LBA artifact and yielded congruent and robust tree topologies in which gnetophytes and Pinaceae formed a sister clade to cupressophytes (the gnepines hypothesis) and Ginkgo clustered with cycads. Adding more cupressophyte taxa could not improve the accuracy of chloroplast phylogenomics for the five gymnosperm groups. In contrast, removal of high heterotachous genes from data sets is simple and can increase confidence in evaluating the phylogeny of gymnosperms.

  20. Specific binding of the replication protein of plasmid pPS10 to direct and inverted repeats is mediated by an HTH motif.

    PubMed Central

    García de Viedma, D; Serrano-López, A; Díaz-Orejas, R

    1995-01-01

    The initiator protein of the plasmid pPS10, RepA, has a putative helix-turn-helix (HTH) motif at its C-terminal end. RepA dimers bind to an inverted repeat at the repA promoter (repAP) to autoregulate RepA synthesis. [D. García de Viedma, et al. (1996) EMBO J. in press]. RepA monomers bind to four direct repeats at the origin of replication (oriV) to initiate pPS10 replication This report shows that randomly generated mutations in RepA, associated with defficiencies in autoregulation, map either at the putative HTH motif or in its vicinity. These mutant proteins do not promote pPS10 replication and are severely affected in binding to both the repAP and oriV regions in vitro. Revertants of a mutant that map in the vicinity of the HTH motif have been obtained and correspond to a second amino acid substitution far upstream of the motif. However, reversion of mutants that map in the helices of the motif occurs less frequently, at least by an order of magnitude. All these data indicate that the helices of the HTH motif play an essential role in specific RepA-DNA interactions, although additional regions also seem to be involved in DNA binding activity. Some mutations have slightly different effects in replication and autoregulation, suggesting that the role of the HTH motif in the interaction of RepA dimers or monomers with their respective DNA targets (IR or DR) is not the same. Images PMID:8559664

  1. Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species

    PubMed Central

    Sun, Yan-xia; Moore, Michael J.; Meng, Ai-ping; Soltis, Pamela S.; Soltis, Douglas E.; Li, Jian-qiang; Wang, Heng-chang

    2013-01-01

    The early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core eudicots), but complete plastome analyses do not resolve the relationships among these groups with strong support. However, plastid phylogenomic analyses have not included data for Tetracentron. To better resolve basal eudicot relationships and to clarify when the two extant genera of Trochodendrales diverged, we sequenced the complete plastid genome of Tetracentron sinense using Illumina technology. The Tetracentron and Trochodendron plastomes possess the typical gene content and arrangement that characterize most angiosperm plastid genomes, but both genomes have the same unusual ∼4 kb expansion of the inverted repeat region to include five genes (rpl22, rps3, rpl16, rpl14, and rps8) that are normally found in the large single-copy region. Maximum likelihood analyses of an 83-gene, 88 taxon angiosperm data set yield an identical tree topology as previous plastid-based trees, and moderately support the sister relationship between Buxaceae and Gunneridae. Molecular dating analyses suggest that Tetracentron and Trochodendron diverged between 44-30 million years ago, which is congruent with the fossil record of Trochodendrales and with previous estimates of the divergence time of these two taxa. We also characterize 154 simple sequence repeat loci from the Tetracentron sinense and Trochodendron aralioides plastomes that will be useful in future studies of population genetic structure for these relict species, both of which are of conservation concern. PMID:23577110

  2. Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny

    PubMed Central

    Wu, Chung-Shien; Wang, Ya-Nan; Hsu, Chi-Yao; Chaw, Shu-Miaw

    2011-01-01

    The relationships among the extant five gymnosperm groups—gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads—remain equivocal. To clarify this issue, we sequenced the chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana and Taiwania cryptomerioides, and 53 common chloroplast protein-coding genes from another three cupressophytes, Agathis dammara, Nageia nagi, and Sciadopitys verticillata, and a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed that Pinaceae and cupressophytes each lost a different copy of inverted repeats (IRs), which contrasts with the view that the same IR has been lost in all conifers. Based on our structural finding, the character of an IR loss no longer conflicts with the “gnepines” hypothesis (gnetophytes sister to Pinaceae). Chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, we demonstrated that high heterotachous genes (genes that have highly different rates in different lineages) contributed to the long-branch attraction (LBA) artifact, resulting in incongruence of phylogenomic estimates. Additionally, amino acid compositions appear more heterogeneous in high than low heterotachous genes among the five gymnosperm groups. Removal of high heterotachous genes alleviated the LBA artifact and yielded congruent and robust tree topologies in which gnetophytes and Pinaceae formed a sister clade to cupressophytes (the gnepines hypothesis) and Ginkgo clustered with cycads. Adding more cupressophyte taxa could not improve the accuracy of chloroplast phylogenomics for the five gymnosperm groups. In contrast, removal of high heterotachous genes from data sets is simple and can increase confidence in evaluating the phylogeny of gymnosperms. PMID:21933779

  3. Transposable elements and circular DNAs

    PubMed Central

    2016-01-01

    ABSTRACT Circular DNAs are extra-chromosomal fragments that become circularized by genomic recombination events. We have recently shown that yeast LTR elements generate circular DNAs through recombination events between their flanking long terminal repeats (LTRs). Similarly, circular DNAs can be generated by recombination between LTRs residing at different genomic loci, in which case the circular DNA will contain the intervening sequence. In yeast, this can result in gene copy number variations when circles contain genes and origins of replication. Here, I speculate on the potential and implications of circular DNAs generated through recombination between human transposable elements. PMID:28090380

  4. Characterization of new hAT transposable elements in 12 Drosophila genomes.

    PubMed

    de Freitas Ortiz, Mauro; Loreto, Elgion Lucio Silva

    2009-01-01

    In silico searches for sequences homologous to hAT elements in 12 Drosophila genomes have allowed us to identify 37 new hAT elements (8 in D. ananassae, 11 in D. mojavensis, 2 in D. sechellia, 1 in D. simulans, 2 in D. virilis, 3 in D. yakuba, 3 in D. persimilis, 1 in D. grimshawi, 5 in D. willistoni and 1 in D. pseudobscura). The size of these elements varies from 2,359 to 4,962 bp and the terminal inverted repeats (TIRs) show lengths ranging from 10 to 24 bp. Several elements show intact transposase ORFs, suggesting that they are active. Conserved amino acid motifs were identified that correspond to those important for transposase activity. These elements are highly variable and phylogenetic analysis showed that they can be clustered into four different families. Incongruencies were observed between the phylogenies of the transposable elements and those of their hosts, suggesting that horizontal transfer may have occurred between some of the species.

  5. Three transposed elements in the intron of a human VK immunoglobulin gene.

    PubMed

    Straubinger, B; Osterholzer, E; Zachau, H G

    1987-11-25

    Two gene segments coding for the variable region of human immunoglobulin light chains of the kappa type (VK genes, ref. 2) were found to have unusual structures. The two genes which are called A6 and A22 are located in duplicated gene clusters. Their restriction maps are very similar. About 4 kb of the A22 gene region were sequenced. It turned out that the intron contains an insert with the characteristics of a transposed element. The inserted DNA of 1.2 kb length contains imperfect direct and inverted repeats at its ends; at the insertion site a duplication of five nucleotides was found. Within the inserted DNA one copy each of an Alu element and of the simple sequence motif (T-G)17 were identified. Also these two repetitive sequences are themselves flanked by short direct repeats. The major inserted DNA has no significant homology to published human nucleic acid sequences. The whole structure is interpreted best by assuming a sequential insertion of the three elements. The coding region of the VK gene itself has several mutations which by themselves would render it a pseudogene; we assume that the insertion event(s) occurred prior to the mutations. According to mapping and hybridization data A6 is very similar to A22.

  6. A dispersed family of repetitive DNA sequences exhibits characteristics of a transposable element in the genus Lycopersicon.

    PubMed

    Young, R J; Francis, D M; St Clair, D A; Taylor, B H

    1994-06-01

    A segment of DNA 5' to the transcribed region of an auxin-regulated gene, ARPI, from Lycopersicon esculentum Mill. cv. VFN8 contains a sequence with the structural characteristics of a transposable element. The putative element (Lyt1) is 1340 bp long, has terminal inverted repeats of approximately 235 bp and is flanked by 9-bp direct repeats. Lyt1 has a structure similar to the Robertson's Mutator (Mu) family from maize. The terminal inverted repeats are 80% AT-rich, are 96.6% identical, and define a larger family of repetitive elements. Southern analysis and genomic dot-blot reconstructions detected at least 41 copies of Lyt1-hybridizing sequences in red-fruited Lycopersicon spp. (L. esculentum, L. pimpinellifolium and L. cheesmanii), and 2-8 copies in the green-fruited species (L. hirsutum, L. pennellii, L. peruvianum, L. chilense and L. chmielewskii). There were two to four copies in the Solanum spp. closely allied with the genus Lycopersicon (S. lycopersicoides, S. ochranthum and S. juglandifolium), while the more distantly related Solanum spp. showed little (one to two copies in S. tuberosum) to no (S. quitoense) detectable hybridization under stringent conditions. Linkage analysis in the F2 progeny of a cross between L. esculentum and L. cheesmanii indicated that at least six loci that hybridize to the Lyt1 sequence are dispersed in the genome. Polymerase chain reaction and Southern analyses revealed that some red-fruited accessions and L. chmielewskii lacked Lyt1 5' to the transcribed region of ARPI. Subsequent sequence analysis indicated that only one copy of the 9-bp direct repeat (target site) was present, suggesting that transposition of the element into the ARPI gene occurred after the divergence of the red-fruited and green-fruited Lycopersicon species.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. Tana1, a new putatively active Tc1-like transposable element in the genome of sturgeons.

    PubMed

    Pujolar, José Martin; Astolfi, Laura; Boscari, Elisa; Vidotto, Michele; Barbisan, Federica; Bruson, Alice; Congiu, Leonardo

    2013-01-01

    We report the discovery of a new putatively active Tc1-like transposable element (Tana1) in the genome of sturgeons, an ancient group of fish considered as living fossils. The complete sequence of Tana1 was first characterized in the 454-sequenced transcriptome of the Adriatic sturgeon (Acipenser naccarii) and then isolated from the genome of the same species and from 12 additional sturgeons including three genera of the Acipenseridae (Acipenser, Huso, Scaphirhynchus). The element has a total length of 1588bp and presents inverted repeats of 210bp, one of which partially overlapping the 3' region of the transposase gene. The spacing of the DDE motif within the catalytic domain in Tana1 is unique (DD38E) and indicates that Tana1 can be considered as the first representative of a new Tc1 subfamily. The integrity of the native form (with no premature termination codons within the transposase), the presence of all expected functional domains and its occurrence in the sturgeon transcriptome suggest a current or recent activity of Tana1. The presence of Tana1 in the genome of the 13 sturgeon species in our study points to an ancient origin of the element that existed before the split of the group 170 million years ago. The dissemination of Tana1 across sturgeon genomes could be interpreted by postulating vertical transmission from an ancestral Tana1 with a particularly slow evolutionary rate Horizontal transmission might have also played a role in the dissemination of Tana1 as evidenced by the presence of a complete copy in the genome of Atlantic salmon. Vertical and horizontal transmission are not mutually exclusive and may have concurred in shaping the evolution of Tana1.

  12. Partial transpose criteria for symmetric states

    NASA Astrophysics Data System (ADS)

    Bohnet-Waldraff, F.; Braun, D.; Giraud, O.

    2016-10-01

    We express the positive-partial-transpose (PPT) separability criterion for symmetric states of multiqubit systems in terms of matrix inequalities based on the recently introduced tensor representation for spin states. We construct a matrix from the tensor representation of the state and show that it is similar to the partial transpose of the density matrix written in the computational basis. Furthermore, the positivity of this matrix is equivalent to the positivity of a correlation matrix constructed from tensor products of Pauli operators. This allows for a more transparent experimental interpretation of the PPT criteria for an arbitrary spin-j state. The unitary matrices connecting our matrix to the partial transpose of the state generalize the so-called magic basis that plays a central role in Wootters' explicit formula for the concurrence of a two-qubit system and the Bell bases used for the teleportation of a one- or two-qubit state.

  13. 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)

  14. Mammary Cancer and Activation of Transposable Elements

    DTIC Science & Technology

    2014-09-01

    AD_________________ AWARD NUMBER: W81XWH-11-1-0401 TITLE: Mammary Cancer and Activation of Transposable Elements PRINCIPAL INVESTIGATOR...way as transcripts from the regular gene promoter. Transcriptional activation of retrotransposons is strongly linked with their CpG DNA methylation

  15. Mammary Cancer and Activation of Transposable Elements

    DTIC Science & Technology

    2014-09-01

    AD_________________ Award Number: W81XWH-11-1-0402 TITLE: Mammary Cancer and Activation...TYPE Annual 3. DATES COVERED 1 Sep 2013 – 31 Aug 2014 4. TITLE AND SUBTITLE Mammary Cancer and Activation of Transposable Elements 5a. CONTRACT...investigate molecular events occurring in the preclinical stages of mammary cancer. Specifically, the project investigates the intersection between the

  16. 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

  17. 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

    Kim, Hyoung Tae; Kim, Jung Sung; 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.

  18. 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.

  19. Miniaturized autonomous robot

    NASA Astrophysics Data System (ADS)

    Ishihara, Hidenori; Fukuda, Toshio

    1998-01-01

    Many projects developing the miniaturized autonomous robot have been carried out in the whole world. This paper deals with our challenges developing a miniaturized autonomous robot. The miniaturized autonomous robot is defined as the miniaturized closed-loop system with micro processor, microactuators and microsensors. We have developed the micro autonomous robotic system (MARS) consisting of the microprocessor, microsensors, microactuators, communication units and batteries. The MARS controls itself by the downloaded program supplied through the IR communication system. In this paper, we demonstrate several performance of the MARS, and discuss the properties of the miniaturized autonomous robot.

  20. Transposed Paternò-Büchi Reaction.

    PubMed

    Kumarasamy, Elango; Raghunathan, Ramya; Kandappa, Sunil Kumar; Sreenithya, A; Jockusch, Steffen; Sunoj, Raghavan B; Sivaguru, J

    2017-01-18

    A complementary strategy of utilizing ππ* excited state of alkene instead of nπ* excited state of the carbonyl chromophore in a "transposed Paternò-Büchi" reaction is evaluated with atropisomeric enamides as the model system. Based on photophysical investigations, the nature of excited states and the reactive pathway was deciphered leading to atropselective reaction. This new concept of switching of excited-state configuration should pave the way to control the stereochemical course of photoreaction due to the orbital approaches required for photochemical reactivity.

  1. 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.

  2. Computing Partial Transposes and Related Entanglement Functions

    NASA Astrophysics Data System (ADS)

    Maziero, Jonas

    2016-12-01

    The partial transpose (PT) is an important function for entanglement testing and quantification and also for the study of geometrical aspects of the quantum state space. In this article, considering general bipartite and multipartite discrete systems, explicit formulas ready for the numerical implementation of the PT and of related entanglement functions are presented and the Fortran code produced for that purpose is described. What is more, we obtain an analytical expression for the Hilbert-Schmidt entanglement of two-qudit systems and for the associated closest separable state. In contrast to previous works on this matter, we only use the properties of the PT, not applying Lagrange multipliers.

  3. FB-NOF is a non-autonomous transposable element, expressed in Drosophila melanogaster and present only in the melanogaster group.

    PubMed

    Badal, Martí; Xamena, Noel; Cabré, Oriol

    2013-09-10

    Most foldback elements are defective due to the lack of coding sequences but some are associated with coding sequences and may represent the entire element. This is the case of the NOF sequences found in the FB of Drosophila melanogaster, formerly considered as an autonomous TE and currently proposed as part of the so-called FB-NOF element, the transposon that would be complete and fully functional. NOF is always associated with FB and never seen apart from the FB inverted repeats (IR). This is the reason why the FB-NOF composite element can be considered the complete element. At least one of its ORFs encodes a protein that has always been considered its transposase, but no detailed studies have been carried out to verify this. In this work we test the hypothesis that FB-NOF is an active transposon nowadays. We search for its expression product, obtaining its cDNA, and propose the ORF and the sequence of its potential protein. We found that the NOF protein is not a transposase as it lacks any of the motifs of known transposases and also shows structural homology with hydrolases, therefore FB-NOF cannot belong to the superfamily MuDR/foldback, as up to now it has been classified, and can be considered as a non-autonomous transposable element. The alignment with the published genomes of 12 Drosophila species shows that NOF presence is restricted only to the 6 Drosophila species belonging to the melanogaster group.

  4. Transcriptional activity of transposable elements in coelacanth.

    PubMed

    Forconi, Mariko; Chalopin, Domitille; Barucca, Marco; Biscotti, Maria Assunta; De Moro, Gianluca; Galiana, Delphine; Gerdol, Marco; Pallavicini, Alberto; Canapa, Adriana; Olmo, Ettore; Volff, Jean-Nicolas

    2014-09-01

    The morphological stasis of coelacanths has long suggested a slow evolutionary rate. General genomic stasis might also imply a decrease of transposable elements activity. To evaluate the potential activity of transposable elements (TEs) in "living fossil" species, transcriptomic data of Latimeria chalumnae and its Indonesian congener Latimeria menadoensis were compared through the RNA-sequencing mapping procedures in three different organs (liver, testis, and muscle). The analysis of coelacanth transcriptomes highlights a significant percentage of transcribed TEs in both species. Major contributors are LINE retrotransposons, especially from the CR1 family. Furthermore, some particular elements such as a LF-SINE and a LINE2 sequences seem to be more expressed than other elements. The amount of TEs expressed in testis suggests possible transposition burst in incoming generations. Moreover, significant amount of TEs in liver and muscle transcriptomes were also observed. Analyses of elements displaying marked organ-specific expression gave us the opportunity to highlight exaptation cases, that is, the recruitment of TEs as new cellular genes, but also to identify a new Latimeria-specific family of Short Interspersed Nuclear Elements called CoeG-SINEs. Overall, transcriptome results do not seem to be in line with a slow-evolving genome with poor TE activity.

  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. 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…

  7. 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.

  8. Transposable Elements: No More 'Junk DNA'.

    PubMed

    Kim, Yun-Ji; Lee, Jungnam; Han, Kyudong

    2012-12-01

    Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA) elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.

  9. Genomic impact of eukaryotic transposable elements

    PubMed Central

    2012-01-01

    The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come. PMID:23171443

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Chemistry "en Miniature"

    NASA Astrophysics Data System (ADS)

    Roesky, Herbert W.

    1997-04-01

    By using the video camera projector system we are improving the techniques which are employed in various schools. This is an important reason for employing "Chemistry en Miniature", as this method provides a new means of demonstrating chemical experiments in a lecture hall.

  17. 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.

  18. Transposed-Letter Priming across Inflectional Morpheme Boundaries

    ERIC Educational Resources Information Center

    Zargar, Ehsan Shafiee; Witzel, Naoko

    2017-01-01

    This study reports findings from two experiments testing whether a transposed-letter (TL) priming effect can be obtained when the transposition occurs across morphological boundaries. Previous studies have primarily tested derivationally complex words or compound words, but have not examined a more rule-based and productive morphological…

  19. 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.

  20. Cross-Regulation between Transposable Elements and Host DNA Replication

    PubMed Central

    Zaratiegui, Mikel

    2017-01-01

    Transposable elements subvert host cellular functions to ensure their survival. Their interaction with the host DNA replication machinery indicates that selective pressures lead them to develop ancestral and convergent evolutionary adaptations aimed at conserved features of this fundamental process. These interactions can shape the co-evolution of the transposons and their hosts. PMID:28335567

  1. 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.

  2. 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

  3. Miniaturized photoacoustic spectrometer

    DOEpatents

    Okandan, Murat; Robinson, Alex; Nielson, Gregory N.; Resnick, Paul J.

    2016-08-09

    A low-power miniaturized photoacoustic sensor uses an optical microphone made by semiconductor fabrication techniques, and optionally allows for all-optical communication to and from the sensor. This allows integration of the photoacoustic sensor into systems with special requirements, such as those that would be reactive in an electrical discharge condition. The photoacoustic sensor can also be operated in various other modes with wide application flexibility.

  4. 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.

  5. Miniature Airflow Sensor

    NASA Technical Reports Server (NTRS)

    Kershner, D. D.

    1984-01-01

    Miniature flow-angle and airspeed sensor quickly mounted on light aircraft wing with two-sided tape since conventional sensors are restricted to large aircraft. Sensor operates as free-trailing wind vane selfalineing in airstream through two independent axes. Vane attached to wing surface through hollow mounting boom that fits on mounting plate attached to wing with two-sided neoprene-foam tape. Method shown strong enough for loads of low-speed flight.

  6. 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.

  7. 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

  8. Horizontal transfers of transposable elements in eukaryotes: The flying genes.

    PubMed

    Panaud, Olivier

    2016-01-01

    Transposable elements (TEs) are the major components of eukaryotic genomes. Their propensity to densely populate and in some cases invade the genomes of plants and animals is in contradiction with the fact that transposition is strictly controlled by several molecular pathways acting at either transcriptional or post-transcriptional levels. Horizontal transfers, defined as the transmission of genetic material between sexually isolated species, have long been considered as rare phenomena. Here, we show that the horizontal transfers of transposable elements (HTTs) are very frequent in ecosystems. The exact mechanisms of such transfers are not well understood, but species involved in close biotic interactions, like parasitism, show a propensity to exchange genetic material horizontally. We propose that HTTs allow TEs to escape the silencing machinery of their host genome and may therefore be an important mechanism for their survival and their dissemination in eukaryotes.

  9. R-strippled maize as a transposable element system

    SciTech Connect

    Williams, W.M.; Satyanarayana, K.V.; Kermicle, J.L.

    1984-07-01

    The I-R element at the R locus destabilizes kernel pigmentation giving the variegated pattern known as stippled (R-st). In trans linkage phase with R-st the element was shown to act as a modifier of stippled, intensifying seed spotting in parallel with effects of the dominant linked modifier M-st. Presence of I-R in the genome was, therefore, shown to be detectable as a modifier of R-st. When this test was used, new modifiers resembling M-st were often detected following mutations of R-st to the stable allele R-sc. Such mutations evidently occurred by transposition of I-R away from the R locus to a site where it was identifiable as a modifier. M-st may be such a transposed I-R. Analysis of mutations to R-sc during the second (sperm-forming) mitosis in pollen grains showed that some of the transposed I-R elements were linked with R, whereas others assorted independently. Their strengths varied from barely discernible to a level equal to M-st. Overreplication frequently accompanied transposition at the sperm-forming mitosis, leading to transposed I-R elements in both the mutant and nonmutant sperm.

  10. 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).

  11. 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.

  12. 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.

  13. Miniaturized optical wavelength sensors

    NASA Astrophysics Data System (ADS)

    Kung, Helen Ling-Ning

    Recently semiconductor processing technology has been applied to the miniaturization of optical wavelength sensors. Compact sensors enable new applications such as integrated diode-laser wavelength monitors and frequency lockers, portable chemical and biological detection, and portable and adaptive hyperspectral imaging arrays. Small sensing systems have trade-offs between resolution, operating range, throughput, multiplexing and complexity. We have developed a new wavelength sensing architecture that balances these parameters for applications involving hyperspectral imaging spectrometer arrays. In this thesis we discuss and demonstrate two new wavelength-sensing architectures whose single-pixel designs can easily be extended into spectrometer arrays. The first class of devices is based on sampling a standing wave. These devices are based on measuring the wavelength-dependent period of optical standing waves formed by the interference of forward and reflected waves at a mirror. We fabricated two different devices based on this principle. The first device is a wavelength monitor, which measures the wavelength and power of a monochromatic source. The second device is a spectrometer that can also act as a selective spectral coherence sensor. The spectrometer contains a large displacement piston-motion MEMS mirror and a thin GaAs photodiode flip-chip bonded to a quartz substrate. The performance of this spectrometer is similar to that of a Michelson in resolution, operating range, throughput and multiplexing but with the added advantages of fewer components and one-dimensional architecture. The second class of devices is based on the Talbot self-imaging effect. The Talbot effect occurs when a periodic object is illuminated with a spatially coherent wave. Periodically spaced self-images are formed behind the object. The spacing of the self-images is proportional to wavelength of the incident light. We discuss and demonstrate how this effect can be used for spectroscopy

  14. Miniature cold gas thrusters

    NASA Astrophysics Data System (ADS)

    Bzibziak, R. J., Sr.

    1992-07-01

    Cold gas thrusters provide a safe, inexpensive, lightweight and reliable means of propulsive control for small satellites, projectiles and maneuvering control systems. Moog Inc. has designed and developed a family of miniature cold gas thrusters for use on Strategic Defense Iniative flight simulation experiments, sounding rockets, small satellite applications, astronaut control systems, and close proximity maneuvering systems for Space System. Construction features such as coil assembly, core assembly, armature assembly, external housing and valve body are discussed. The design approach, performance characteristics and functional description of cold gas thrusters designed for various applications are presented.

  15. 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.

  16. Miniature snapshot multispectral imager

    NASA Astrophysics Data System (ADS)

    Gupta, Neelam; Ashe, Philip R.; Tan, Songsheng

    2011-03-01

    We present a miniature snapshot multispectral imager based on using a monolithic filter array that operates in the short wavelength infrared spectral region and has a number of defense and commercial applications. The system is low-weight, portable with a miniature platform, and requires low power. The imager uses a 4×4 Fabry-Pérot filter array operating from 1487 to 1769 nm with a spectral bandpass ~10 nm. The design of the filters is based on using a shadow mask technique to fabricate an array of Fabry-Pérot etalons with two multilayer dielectric mirrors. The filter array is installed in a commercial handheld InGaAs camera, replacing the imaging lens with a custom designed 4×4 microlens assembly with telecentric imaging performance in each of the 16 subimaging channels. We imaged several indoor and outdoor scenes. The microlens assembly and filter design is quite flexible and can be tailored for any wavelength region from the ultraviolet to the longwave infrared, and the spectral bandpass can also be customized to meet sensing requirements. In this paper we discuss the design and characterization of the filter array, the microlens optical assembly, and imager and present imaging results.

  17. Miniature spectrally selective dosimeter

    NASA Astrophysics Data System (ADS)

    Adams, R. R.; MacConochie, I. O.; Poole, B. D., Jr.

    1980-10-01

    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.

  18. 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.

  19. 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.

  20. 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.

  1. Miniaturized fundus camera

    NASA Astrophysics Data System (ADS)

    Gliss, Christine; Parel, Jean-Marie A.; Flynn, John T.; Pratisto, Hans S.; Niederer, Peter F.

    2003-07-01

    We present a miniaturized version of a fundus camera. The camera is designed for the use in screening for retinopathy of prematurity (ROP). There, but also in other applications a small, light weight, digital camera system can be extremely useful. We present a small wide angle digital camera system. The handpiece is significantly smaller and lighter then in all other systems. The electronics is truly portable fitting in a standard boardcase. The camera is designed to be offered at a compatible price. Data from tests on young rabbits' eyes is presented. The development of the camera system is part of a telemedicine project screening for ROP. Telemedical applications are a perfect application for this camera system using both advantages: the portability as well as the digital image.

  2. 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.

  3. Argonautes team up to silence transposable elements in Arabidopsis.

    PubMed

    Underwood, Charles J; Martienssen, Robert A

    2015-03-04

    The de novo silencing of transposable elements in plants and animals is mediated in part by RNA-directed chromatin modification. In flowering plants, AGO4 has been seen as the key argonauteprotein in the RNA-directed DNA methylation pathway that links the plant-specific RNA polymerase V with the de novo DNA methyltransferase DRM2 (Zhong et al,2014). Two recent papers in The EMBO Journal strongly implicate a role for the AGO6 protein in the process of de novo silencing.

  4. Transpose symmetry of the Jones matrix and topological phases.

    PubMed

    Bhandari, Rajendra

    2008-04-15

    The transmission Jones matrix of an arbitrary stack of reciprocal plane-parallel plates that has been turned through 180 degrees about an axis in the plane of the stack is, in an appropriate basis, the transpose of the transmission matrix of the unturned slab with a change in the sign of the off-diagonal elements. We prove this convention-free result for the case where reflection at the interfaces can be ignored and use it to devise an experimental scheme to separate isotropic and topological phase changes in a reciprocal optical medium.

  5. Heavy-ion radiation induces both activation of multiple endogenous transposable elements and alterations in DNA methylation in rice

    NASA Astrophysics Data System (ADS)

    Zhang, Meng; Sun, Yeqing; Li, Xishan; Xiaolin, Cui; Li, Xiang

    2012-07-01

    Space radiation represents a complex environmental condition in which several interacting factors such as electron, neutron, proton, heavy-ion are involved, which may provoke stress responses and jeopardize genome integrity. Given the inherent property of epigenetic modifications to respond to intrinsic aswell as external perturbations, it is conceivable that epigenetic markers like DNA methylation and transposition may undergo alterations in response to space radiation. Cytosine DNA methylation plays important roles in maintaining genome stability and controlling gene expression. A predominant means for Transposable elements (TEs) to cause genetic instability is via their transpositional activation. To find the detailed molecular characterization of the nature of genomic changes induced by space radiation, the seeds of rice were exposed to 0.02, 0.2, 1, 2 and 20 Gy dose of ^{12}C heavy-ion radiation, respectively. We found that extensive alteration in both DNA methylation and gene expression occurred in rice plants after different dose of heavy-ion radiation. Here we shown that heavy-ion radiation has induced transposition of mPing and Tos17 in rice, which belong to distinct classes including the miniature inverted terminal repeat TEs (MITEs) and long-terminal repeat (LTR) retrotransposons, respectively. mPing and Tos17 mobility were found to correlate with cytosine methylation alteration detected by MSAP and genetic variation detected by AFLP. The result showed that at least in some cases transposition of TEs was associated with cytosine demethylation within the elements. Our results implicate that the heavy-ion radiation represents a potent mutagenic agent that can cause genomic instabilities by eliciting transposition of endogenous TEs in rice. Keywords: Heavy-ion radiation, DNA methylation, Transposable elements, mPing, Tos17

  6. Rates of movement of transposable elements in Drosophila melanogaster.

    PubMed

    Domínguez, A; Albornoz, J

    1996-05-23

    Mobilization rates of nine families of transposable elements (P, hobo, FB, gypsy, 412, copia, blood, 297, and jockey) were estimated by using 182 lines. Lines were started from a completely isogenic population of Drosophila melanogaster, carrying the marker sepia as an indicator of possible contamination, and have been accumulating spontaneous mutations independently for 80 generations of brother-sister (or two double-first-cousin) matings. Transposable element movements have been analyzed in complete genomes by the Southern technique. Mobilization was a rare event, with an average rate of 10(-5) per site per generation. The most active element was FB. In contrast, the retroelements gypsy and blood did not move at all. Most changes in restriction patterns were consistent with rearrangements rather than with true transposition. The euchromatic or heterochromatic location of elements was tested by comparing insertion patterns from adults and salivary glands. Certain putative rearrangements involved heterochromatic copies of the retroelements 412, copia or 297. Clustering of movement across families was observed, suggesting that movement of different families may be non-independent. As association between modified insertion patterns and mutant effects on quantitative traits shows that spontaneous transposition events cause continuous variation.

  7. Gene vector and transposable element behavior in mosquitoes.

    PubMed

    O'Brochta, David A; Sethuraman, Nagaraja; Wilson, Raymond; Hice, Robert H; Pinkerton, Alexandra C; Levesque, Cynthia S; Bideshi, Dennis K; Jasinskiene, Nijole; Coates, Craig J; James, Anthony A; Lehane, Michael J; Atkinson, Peter W

    2003-11-01

    The development of efficient germ-line transformation technologies for mosquitoes has increased the ability of entomologists to find, isolate and analyze genes. The utility of the currently available systems will be determined by a number of factors including the behavior of the gene vectors during the initial integration event and their behavior after chromosomal integration. Post-integration behavior will determine whether the transposable elements being employed currently as primary gene vectors will be useful as gene-tagging and enhancer-trapping agents. The post-integration behavior of existing insect vectors has not been extensively examined. Mos1 is useful as a primary germ-line transformation vector in insects but is inefficiently remobilized in Drosophila melanogaster and Aedes aegypti. Hermes transforms D. melanogaster efficiently and can be remobilized in this species. This element is also useful for creating transgenic A. aegypti, but its mode of integration in mosquitoes results in the insertion of flanking plasmid DNA. Hermes can be remobilized in the soma of A. aegypti and transposes using a common cut-and-paste mechanism; however, the element does not remobilize in the germ line. piggyBac can be used to create transgenic mosquitoes and occasionally integrates using a mechanism other than a simple cut-and-paste mechanism. Preliminary data suggest that remobilization is infrequent. Minos also functions in mosquitoes and, like the other gene vectors, appears to remobilize inefficiently following integration. These results have implications for future gene vector development efforts and applications.

  8. Transposable elements and early evolution of sex chromosomes in fish.

    PubMed

    Chalopin, Domitille; Volff, Jean-Nicolas; Galiana, Delphine; Anderson, Jennifer L; Schartl, Manfred

    2015-09-01

    In many organisms, the sex chromosome pair can be recognized due to heteromorphy; the Y and W chromosomes have often lost many genes due to the absence of recombination during meiosis and are frequently heterochromatic. Repetitive sequences are found at a high proportion on such heterochromatic sex chromosomes and the evolution and emergence of sex chromosomes has been connected to the dynamics of repeats and transposable elements. With an amazing plasticity of sex determination mechanisms and numerous instances of independent emergence of novel sex chromosomes, fish represent an excellent lineage to investigate the early stages of sex chromosome differentiation, where sex chromosomes often are homomorphic and not heterochromatic. We have analyzed the composition, distribution, and relative age of TEs from available sex chromosome sequences of seven teleost fish. We observed recent bursts of TEs and simple repeat accumulations around young sex determination loci. More strikingly, we detected transposable element (TE) amplifications not only on the sex determination regions of the Y and W sex chromosomes, but also on the corresponding regions of the X and Z chromosomes. In one species, we also clearly demonstrated that the observed TE-rich sex determination locus originated from a TE-poor genomic region, strengthening the link between TE accumulation and emergence of the sex determination locus. Altogether, our results highlight the role of TEs in the initial steps of differentiation and evolution of sex chromosomes.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. [Transposition of the maize transposable element dSpm in transgenic sugar beets].

    PubMed

    Kishchenko, E M; Komarnitskiĭ, I K; Kuchuk, N V

    2010-01-01

    Transgenic sugar beet plants carrying maize Spmn/dSpm transposable elements system have been constructed. Heterologous system of maize transposable elements Spm/dSpm was active in transgenic sugar beets that permits transposon-based gene tagging and obtaining of marker-free transgenic sugar beet.

  15. The Effect of Neighborhood Frequency in Reading: Evidence with Transposed-Letter Neighbors

    ERIC Educational Resources Information Center

    Acha, Joana; Perea, Manuel

    2008-01-01

    Transposed-letter effects (e.g., jugde activates judge) pose serious models for models of visual-word recognition that use position-specific coding schemes. However, even though the evidence of transposed-letter effects with nonword stimuli is strong, the evidence for word stimuli is scarce and inconclusive. The present experiment examined the…

  16. Resident aliens: the Tc1/mariner superfamily of transposable elements.

    PubMed

    Plasterk, R H; Izsvák, Z; Ivics, Z

    1999-08-01

    Transgenic technology is currently applied to several animal species of agricultural or medical importance, such as fish, cattle, mosquitos and parasitic worms. However, the repertoire of genetic tools used for molecular analyses of mice and Drosophila is not always applicable to other species. For example, while retroviral enhancer-trap experiments in mice can be based on embryonic stem (ES) cell technology, this is not currently an option with other animals. Similarly, the germline transformation of Drosophila depends on the use of the P-element transposon, which does not jump in other genera. This article analyses the main characteristics of Tc1/mariner transposable elements, examines some of the factors that have contributed to their evolutionary success, and describes their potential, as well as their limitations, for transgenesis and insertional mutagenesis in diverse animals.

  17. The impact of transposable elements on mammalian development.

    PubMed

    Garcia-Perez, Jose L; Widmann, Thomas J; Adams, Ian R

    2016-11-15

    Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that have a significant impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and discuss how the somatic activity of TEs can influence gene regulatory networks.

  18. 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.

  19. Transposable elements and small RNAs: Genomic fuel for species diversity

    PubMed Central

    Hoffmann, Federico G; McGuire, Liam P; Counterman, Brian A; Ray, David A

    2015-01-01

    While transposable elements (TE) have long been suspected of involvement in species diversification, identifying specific roles has been difficult. We recently found evidence of TE-derived regulatory RNAs in a species-rich family of bats. The TE-derived small RNAs are temporally associated with the burst of species diversification, suggesting that they may have been involved in the processes that led to the diversification. In this commentary, we expand on the ideas that were briefly touched upon in that manuscript. Specifically, we suggest avenues of research that may help to identify the roles that TEs may play in perturbing regulatory pathways. Such research endeavors may serve to inform evolutionary biologists of the ways that TEs have influenced the genomic and taxonomic diversity around us. PMID:26904375

  20. Evolution and Diversity of Transposable Elements in Vertebrate Genomes

    PubMed Central

    Sotero-Caio, Cibele G.; Platt, Roy N.; Suh, Alexander

    2017-01-01

    Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4–60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes. PMID:28158585

  1. Transposable elements in cancer and other human diseases.

    PubMed

    Chenais, Benoit

    2015-01-01

    Transposable elements (TEs) are mobile DNA sequences representing a substantial fraction of most genomes. Through the creation of new genes and functions, TEs are important elements of genome plasticity and evolution. However TE insertion in human genomes may be the cause of genetic dysfunction and alteration of gene expression contributing to cancer and other human diseases. Besides the chromosome rearrangements induced by TE repeats, this mini-review shows how gene expression may be altered following TE insertion, for example by the creation of new polyadenylation sites, by the creation of new exons (exonization), by exon skipping and by other modification of alternative splicing, and also by the alteration of regulatory sequences. Through the correlation between TE mobility and the methylation status of DNA, the importance of chromatin regulation is evident in several diseases. Finally this overview ends with a brief presentation of the use of TEs as biotechnology tools for insertional mutagenesis screening and gene therapy with DNA transposons.

  2. Transposable elements and small RNAs: Genomic fuel for species diversity.

    PubMed

    Hoffmann, Federico G; McGuire, Liam P; Counterman, Brian A; Ray, David A

    2015-01-01

    While transposable elements (TE) have long been suspected of involvement in species diversification, identifying specific roles has been difficult. We recently found evidence of TE-derived regulatory RNAs in a species-rich family of bats. The TE-derived small RNAs are temporally associated with the burst of species diversification, suggesting that they may have been involved in the processes that led to the diversification. In this commentary, we expand on the ideas that were briefly touched upon in that manuscript. Specifically, we suggest avenues of research that may help to identify the roles that TEs may play in perturbing regulatory pathways. Such research endeavors may serve to inform evolutionary biologists of the ways that TEs have influenced the genomic and taxonomic diversity around us.

  3. A blessing in disguise: Transposable elements are more than parasites.

    PubMed

    Martin, Antoine; Bendahmane, Abdelhafid

    2010-07-01

    Transposable elements (TEs) are various DNA fragments inserted throughout genomes, which are able to move or duplicate themselves. Recent advances in genomics have placed them back at the center of genome dynamics. One of the emerging observations, especially in plants, is the importance of interactions between TEs and genes to generate or to participate in relevant functions essential for development, adaptation and/or life cycle. A recent publication illustrates the influence of TEs epigenetic control on the expression of a neighboring gene crucial for reproduction. Different reports lately showed that a fundamental mechanism such as imprinting is likely to be closely linked to the dynamics of TEs epigenetic control. Here we discuss and bring together these and others recent findings, to underline that the cis-vicinity or the trans-relation between TEs and genes could bring unexpected but positive outcomes.

  4. 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

  5. Transposable elements: from DNA parasites to architects of metazoan evolution.

    PubMed

    Piskurek, Oliver; Jackson, Daniel J

    2012-07-12

    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.

  6. Useful parasites: the evolutionary biology and biotechnology applications of transposable elements.

    PubMed

    Bonchev, Georgi N

    2016-12-01

    Transposable elements usually comprise the most abundant nongenic fraction of eukaryotic genomes. Because of their capacity to selfreplicate and to induce a wide range of mutations, transposable elements have long been considered as 'parasitic' or 'selfish'. 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. Numerous studies have provided evidences that mobile elements have the potential to act as agents of evolution by increasing, rearranging and diversifying the genetic repertoire of their hosts. With large-scale sequencing becoming increasingly available, more and more scientists come across transposable element sequences in their data. I will provide examples that transposable elements, although having signatures of 'selfish' DNA, play a significant biological role in the maintainance of genome integrity and providing novel regulatoty networks. These features, along with the transpositional and mutagenic capacity to produce a raw genetic diversity, make the genome mobile fraction, a key player in species adaptation and microevolution. The last but not least, transposable elements stand as informative DNA markers that may complement other conventional DNA markers. Altogether, transposable elements represent a promising, but still largely unexplored research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.

  7. Miniaturized Cassegrainian concentrator concept demonstration

    NASA Astrophysics Data System (ADS)

    Patterson, R. E.; Rauschenbach, H. S.

    High concentration ratio photovoltaic systems for space applications have generally been considered impractical because of perceived difficulties in controlling solar cell temperatures to reasonably low values. A miniaturized concentrator system is now under development which surmounts this objection by providing acceptable solar cell temperatures using purely passive cell cooling methods. An array of identical miniaturized, rigid Cassegrainian optical systems having a low f-number with resulting short dimensions along their optical axes are rigidly mounted into a frame to form a relatively thin concentrator solar array panel. A number of such panels, approximately 1.5 centimeters thick, are wired as an array and are folded against one another for launch in a stowed configuration. Deployment on orbit is similar to the deployment of conventional planar honeycomb panel arrays or flexible blanket arrays. The miniaturized concept was conceived and studied in the 1978-80 time frame. Progress in the feasibility demonstration to date is reported.

  8. Miniature information displays: primary applications

    NASA Astrophysics Data System (ADS)

    Alvelda, Phillip; Lewis, Nancy D.

    1998-04-01

    Positioned to replace current liquid crystal display technology in many applications, miniature information displays have evolved to provide several truly portable platforms for the world's growing personal computing and communication needs. The technology and functionality of handheld computer and communicator systems has finally surpassed many of the standards that were originally established for desktop systems. In these new consumer electronics, performance, display size, packaging, power consumption, and cost have always been limiting factors for fabricating genuinely portable devices. The rapidly growing miniature information display manufacturing industry is making it possible to bring a wide range of highly anticipated new products to new markets.

  9. 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.

  10. Marsupial-specific microRNAs evolved from marsupial-specific transposable elements.

    PubMed

    Devor, Eric J; Peek, Andrew S; Lanier, William; Samollow, Paul B

    2009-12-15

    Using a direct miRNA cloning strategy we previously identified fourteen marsupial- or species-specific microRNAs in the marsupial species Monodelphis domestica. In the present study we examined each of the pre-miRNAs and their flanking sequences and demonstrate that half of these miRNAs evolved from marsupial-specific transposable elements. These findings reinforce the view that transposable elements are a previously unappreciated source of new, lineage-specific microRNAs.

  11. 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

  12. 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

  13. Transposable element influences on gene expression in plants.

    PubMed

    Hirsch, Cory D; Springer, Nathan M

    2017-01-01

    Transposable elements (TEs) comprise a major portion of many plant genomes and bursts of TE movements cause novel genomic variation within species. In order to maintain proper gene function, plant genomes have evolved a variety of mechanisms to tolerate the presence of TEs within or near genes. Here, we review our understanding of the interactions between TEs and gene expression in plants by assessing three ways that transposons can influence gene expression. First, there is growing evidence that TE insertions within introns or untranslated regions of genes are often tolerated and have minimal impact on expression level or splicing. However, there are examples in which TE insertions within genes can result in aberrant or novel transcripts. Second, TEs can provide novel alternative promoters, which can lead to new expression patterns or original coding potential of an alternate transcript. Third, TE insertions near genes can influence regulation of gene expression through a variety of mechanisms. For example, TEs may provide novel cis-acting regulatory sites behaving as enhancers or insert within existing enhancers to influence transcript production. Alternatively, TEs may change chromatin modifications in regions near genes, which in turn can influence gene expression levels. Together, the interactions of genes and TEs provide abundant evidence for the role of TEs in changing basic functions within plant genomes beyond acting as latent genomic elements or as simple insertional mutagens. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

  14. 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.

  15. Expression of Transposable Elements in Neural Tissues during Xenopus Development

    PubMed Central

    Faunes, Fernando; Sanchez, Natalia; Moreno, Mauricio; Olivares, Gonzalo H.; Lee-Liu, Dasfne; Almonacid, Leonardo; Slater, Alex W.; Norambuena, Tomas; Taft, Ryan J.; Mattick, John S.; Melo, Francisco; Larrain, Juan

    2011-01-01

    Transposable elements comprise a large proportion of animal genomes. Transposons can have detrimental effects on genome stability but also offer positive roles for genome evolution and gene expression regulation. Proper balance of the positive and deleterious effects of transposons is crucial for cell homeostasis and requires a mechanism that tightly regulates their expression. Herein we describe the expression of DNA transposons of the Tc1/mariner superfamily during Xenopus development. Sense and antisense transcripts containing complete Tc1-2_Xt were detected in Xenopus embryos. Both transcripts were found in zygotic stages and were mainly localized in Spemann's organizer and neural tissues. In addition, the Tc1-like elements Eagle, Froggy, Jumpy, Maya, Xeminos and TXr were also expressed in zygotic stages but not oocytes in X. tropicalis. Interestingly, although Tc1-2_Xt transcripts were not detected in Xenopus laevis embryos, transcripts from other two Tc1-like elements (TXr and TXz) presented a similar temporal and spatial pattern during X. laevis development. Deep sequencing analysis of Xenopus tropicalis gastrulae showed that PIWI-interacting RNAs (piRNAs) are specifically derived from several Tc1-like elements. The localized expression of Tc1-like elements in neural tissues suggests that they could play a role during the development of the Xenopus nervous system. PMID:21818339

  16. What makes transposable elements move in the Drosophila genome?

    PubMed Central

    Guerreiro, M P García

    2012-01-01

    Transposable elements (TEs), by their capacity of moving and inducing mutations in the genome, are considered important drivers of species evolution. The successful invasions of TEs in genomes, despite their mutational properties, are an apparent paradox. TEs' transposition is usually strongly regulated to low value, but in some cases these elements can also show high transposition rates, which has been associated sometimes to changes in environmental conditions. It is evident that factors susceptible to induce transpositions in natural populations contribute to TE perpetuation. Different factors were proposed as causative agents of TE mobilization in a wide range of organisms: biotic and abiotic stresses, inter- and intraspecific crosses and populational factors. However, there is no clear evidence of the factors capable of inducing TE mobilization in Drosophila, and data on laboratory stocks show contradictory results. The aim of this review is to have an update critical revision about mechanisms promoting transposition of TEs in Drosophila, and to provide to the readers a global vision of the dynamics of these genomic elements in the Drosophila genome. PMID:21971178

  17. 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

  18. 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

  19. Toward a miniaturized fundus camera.

    PubMed

    Gliss, Christine; Parel, Jean-Marie; Flynn, John T; Pratisto, Hans; Niederer, Peter

    2004-01-01

    Retinopathy of prematurity (ROP) describes a pathological development of the retina in prematurely born children. In order to prevent severe permanent damage to the eye and enable timely treatment, the fundus of the eye in such children has to be examined according to established procedures. For these examinations, our miniaturized fundus camera is intended to allow the acquisition of wide-angle digital pictures of the fundus for on-line or off-line diagnosis and documentation. We designed two prototypes of a miniaturized fundus camera, one with graded refractive index (GRIN)-based optics, the other with conventional optics. Two different modes of illumination were compared: transscleral and transpupillary. In both systems, the size and weight of the camera were minimized. The prototypes were tested on young rabbits. The experiments led to the conclusion that the combination of conventional optics with transpupillary illumination yields the best results in terms of overall image quality.

  20. 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.

  1. Organic photodiodes for biosensor miniaturization.

    PubMed

    Wojciechowski, Jason R; Shriver-Lake, Lisa C; Yamaguchi, Mariko Y; Füreder, Erwin; Pieler, Roland; Schamesberger, Martin; Winder, Christoph; Prall, Hans Jürgen; Sonnleitner, Max; Ligler, Frances S

    2009-05-01

    Biosensors have successfully demonstrated the capability to detect multiple pathogens simultaneously at very low levels. Miniaturization of biosensors is essential for use in the field or at the point of care. While microfluidic systems reduce the footprint for biochemical processing devices and electronic components are continually becoming smaller, optical components suitable for integration--such as LEDs and CMOS chips--are generally still too expensive for disposable components. This paper describes the integration of polymer diodes onto a biosensor chip to create a disposable device that includes both the detector and the sensing surface coated with immobilized capture antibody. We performed a chemiluminescence immunoassay on the OPD substrate and measured the results using a hand-held reader attached to a laptop computer. The miniaturized biosensor with the disposable slide including the organic photodiode detected Staphylococcal enterotoxin B at concentrations as low as 0.5 ng/mL.

  2. 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.

  3. Organic Photodiodes for Biosensor Miniaturization

    DTIC Science & Technology

    2009-01-01

    1 pW/mm2. Using this system, sandwich immunoassays were performed on the OPD substrate for detection of Staphylococcal enterotoxin B (SEB). Results...demonstrated the capability to detect multiple pathogens simultaneously at very low levels. Miniaturization of biosensors is essential for use in the field or...the sensing surface coated with immobilized capture antibody. We performed a chemiluminescence immunoassay on the OPD substrate and measured the results

  4. 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.

  5. 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

  6. Transposable elements: powerful contributors to angiosperm evolution and diversity.

    PubMed

    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.

  7. Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes.

    PubMed

    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).

  8. Transposable elements belonging to the Tc1-Mariner superfamily are heavily mutated in Colletotrichum graminicola.

    PubMed

    Braga, Raíssa Mesquita; Santana, Mateus Ferreira; Veras da Costa, Rodrigo; Brommonschenkel, Sergio Herminio; de Araújo, Elza Fernandes; de Queiroz, Marisa Vieira

    2014-01-01

    Transposable elements are ubiquitous and constitute an important source of genetic variation in addition to generating deleterious mutations. Several filamentous fungi are able to defend against transposable elements using RIP(repeat-induced point mutation)-like mechanisms, which induce mutations in duplicated sequences. The sequenced Colletotrichum graminicola genome and the availability of transposable element databases provide an efficient approach for identifying and characterizing transposable elements in this fungus, which was the subject of this study. We identified 132 full-sized Tc1-Mariner transposable elements in the sequenced C. graminicola genome, which were divided into six families. Several putative transposases that have been found in these elements have conserved DDE motifs, but all are interrupted by stop codons. An in silico analysis showed evidence for RIP-generated mutations. The TCg1 element, which was cloned from the Brazilian 2908 m isolate, has a putative transposase sequence with three characteristic conserved motifs. However, this sequence is interrupted by five stop codons. Genomic DNA from various isolates was analyzed by hybridization with an internal region of TCg1. All of the isolates featured transposable elements that were similar to TCg1, and several hybridization profiles were identified. C. graminicola has many Tc1-Mariner transposable elements that have been degenerated by characteristic RIP mutations. It is unlikely that any of the characterized elements are autonomous in the sequenced isolate. The possible existence of active copies in field isolates from Brazil was shown. The TCg1 element is present in several C. graminicola isolates and is a potentially useful molecular marker for population studies of this phytopathogen.

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

    PubMed Central

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

    2016-01-01

    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

  10. TRANSPOSABLE REGULARIZED COVARIANCE MODELS WITH AN APPLICATION TO MISSING DATA IMPUTATION.

    PubMed

    Allen, Genevera I; Tibshirani, Robert

    2010-06-01

    Missing data estimation is an important challenge with high-dimensional data arranged in the form of a matrix. Typically this data matrix is transposable, meaning that either the rows, columns or both can be treated as features. To model transposable data, we present a modification of the matrix-variate normal, the mean-restricted matrix-variate normal, in which the rows and columns each have a separate mean vector and covariance matrix. By placing additive penalties on the inverse covariance matrices of the rows and columns, these so called transposable regularized covariance models allow for maximum likelihood estimation of the mean and non-singular covariance matrices. Using these models, we formulate EM-type algorithms for missing data imputation in both the multivariate and transposable frameworks. We present theoretical results exploiting the structure of our transposable models that allow these models and imputation methods to be applied to high-dimensional data. Simulations and results on microarray data and the Netflix data show that these imputation techniques often outperform existing methods and offer a greater degree of flexibility.

  11. TRANSPOSABLE REGULARIZED COVARIANCE MODELS WITH AN APPLICATION TO MISSING DATA IMPUTATION

    PubMed Central

    Allen, Genevera I.; Tibshirani, Robert

    2015-01-01

    Missing data estimation is an important challenge with high-dimensional data arranged in the form of a matrix. Typically this data matrix is transposable, meaning that either the rows, columns or both can be treated as features. To model transposable data, we present a modification of the matrix-variate normal, the mean-restricted matrix-variate normal, in which the rows and columns each have a separate mean vector and covariance matrix. By placing additive penalties on the inverse covariance matrices of the rows and columns, these so called transposable regularized covariance models allow for maximum likelihood estimation of the mean and non-singular covariance matrices. Using these models, we formulate EM-type algorithms for missing data imputation in both the multivariate and transposable frameworks. We present theoretical results exploiting the structure of our transposable models that allow these models and imputation methods to be applied to high-dimensional data. Simulations and results on microarray data and the Netflix data show that these imputation techniques often outperform existing methods and offer a greater degree of flexibility. PMID:26877823

  12. Novel non-autonomous transposable elements on W chromosome of the silkworm, Bombyx mori.

    PubMed

    Abe, Hiroaki; Fujii, Tsuguru; Shimada, Toru; Mita, Kazuei

    2010-09-01

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

  13. Novel non-autonomous transposable elements on W chromosome of the silkworm, Bombyx mori.

    PubMed

    Abe, Hiroaki; Fujii, Tsuguru; Shimada, Toru; Mita, Kazuei

    2010-01-01

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

  14. 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.

  15. Patterns of Transposable Element Expression and Insertion in Cancer

    PubMed Central

    Clayton, Evan A.; Wang, Lu; Rishishwar, Lavanya; Wang, Jianrong; McDonald, John F.; Jordan, I. King

    2016-01-01

    Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data. We applied these new sequence analysis techniques to matched normal and primary tumor patient samples from the Cancer Genome Atlas (TCGA) in order to analyze the patterns of TE expression and insertion for three cancer types: breast invasive carcinoma, head and neck squamous cell carcinoma, and lung adenocarcinoma. Our analysis focused on the three most abundant families of active human TEs: Alu, SVA, and L1. We found evidence for high levels of somatic TE activity for these three families in normal and cancer samples across diverse tissue types. Abundant transcripts for all three TE families were detected in both normal and cancer tissues along with an average of ~80 unique TE insertions per individual patient/tissue. We observed an increase in L1 transcript expression and L1 insertional activity in primary tumor samples for all three cancer types. Tumor-specific TE insertions are enriched for private mutations, consistent with a potentially causal role in tumorigenesis. We used genome feature analysis to investigate two specific cases of putative cancer-causing TE mutations in further detail. An Alu insertion in an upstream enhancer of the CBL tumor suppressor gene is associated with down-regulation of the gene in a single breast cancer patient, and an L1 insertion in the first exon of the BAALC gene also disrupts its expression in head and neck squamous cell carcinoma. Our results are consistent with

  16. 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.

  17. 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.

  18. 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.

  19. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen

    PubMed Central

    Slotkin, R. Keith; Vaughn, Matthew; Tanurdžic, Miloš; Borges, Filipe; Becker, Jörg D.; Feijó, José A.; Martienssen, Robert A.

    2009-01-01

    Summary The mutagenic activity of transposable elements (TEs) is suppressed by epigenetic silencing and small interfering RNAs (siRNAs), especially in gametes that would transmit transposed elements to the next generation. In pollen from the model plant Arabidopsis, we show that TEs are unexpectedly reactivated and transpose, but only in the pollen vegetative nucleus, which accompanies the sperm cells but does not provide DNA to the fertilized zygote. TE expression coincides with down-regulation of the heterochromatin remodeler DECREASE IN DNA METHYLATION 1 and of most TE siRNAs. However, 21 nucleotide siRNA from Athila retrotransposons is generated in pollen and accumulates in sperm, indicating that siRNA from TEs activated in the vegetative nucleus can target silencing in gametes. We propose a conserved role for reprogramming in germline companion cells, such as nurse cells in insects and vegetative nuclei in plants, to reveal intact TEs in the genome and regulate their activity in gametes. PMID:19203581

  20. Eye movements when reading transposed text: the importance of word-beginning letters.

    PubMed

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

    2008-10-01

    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.

  1. 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...

  2. 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...

  3. 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...

  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, 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...

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. Miniaturization of a Hydrogen Plant

    SciTech Connect

    Holladay, Jamie D.; Jones, Evan O.; Dagle, Robert A.; Xia, Gordon; Cao, Chunshe; Wang, Yong

    2005-09-01

    The development of a miniaturized hydrogen plant is discussed. The micro-scale system is capable of producing 1-5 sccm hydrogen that could be used as a fuel supply in a small fuel cell to produce <1 W power. The paper describes the developmental approach, significant unit operations, material selection, and reactor design. The final microscale fuel processing system is composed of a catalytic combustor, catalytic methanol reformer, selective methanation reactor, and the necessary vaporizers and heat exchangers. The fuel processing system is less than 0.3 cm3 and less than 1 gram mass. Thermal efficiencies as high as 33% for hydrogen production were achieved. When a methanation reactor was incorporated into the system, a carbon monoxide level of less than 100 ppm was reached, but at a reduced system efficiency. Further development work includes increasing efficiency through improved system integration.

  14. 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.

  15. 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.

  16. Overview of the miniaturization technologies

    NASA Astrophysics Data System (ADS)

    Warrington, Robert O., Jr.

    1995-09-01

    This overview paper will cover the miniaturization technologies as applied to microelectromechanical systems (MEMS) or micromanufacturing. Technologies reviewed will include bulk and surface micromachining of silicon, the high-aspect ratio technologies including deep X-ray lithography (LIGA) and photo sensitive polyimide, and the complementary processes which include micro-drilling, milling, turning, and electrical discharge machining, laser based micromachining and focussed ion beam micromachining. Examples of each of the process technologies will be given and a capabilities comparison among the technologies will be presented. A historical comparison of MEMS with the vlsi industry will be made and the current status and market forecast for these technologies will be presented. A brief comparison of US research with current research in Japan and Europe will be made along with comments about the status of US research, including current research projects at the Institute for Micromanufacturing.

  17. 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.

  18. 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.

  19. 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.

  20. Miniature laser ignited bellows motor

    NASA Technical Reports Server (NTRS)

    Renfro, Steven L.; Beckman, Tom M.

    1994-01-01

    A miniature optically ignited actuation device has been demonstrated using a laser diode as an ignition source. This pyrotechnic driven motor provides between 4 and 6 lbs of linear force across a 0.090 inch diameter surface. The physical envelope of the device is 1/2 inch long and 1/8 inch diameter. This unique application of optical energy can be used as a mechanical link in optical arming systems or other applications where low shock actuation is desired and space is limited. An analysis was performed to determine pyrotechnic materials suitable to actuate a bellows device constructed of aluminum or stainless steel. The aluminum bellows was chosen for further development and several candidate pyrotechnics were evaluated. The velocity profile and delivered force were quantified using an non-intrusive optical motion sensor.

  1. Miniature mechanical transfer optical coupler

    DOEpatents

    Abel, Philip [Overland Park, KS; Watterson, Carl [Kansas City, MO

    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.

  2. 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

  3. 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…

  4. The coelacanth: Can a "living fossil" have active transposable elements in its genome?

    PubMed

    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.

  5. 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…

  6. 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…

  7. 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…

  8. 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...

  9. 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...

  10. 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...

  11. Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates.

    PubMed

    Warren, Ian A; Naville, Magali; Chalopin, Domitille; Levin, Perrine; Berger, Chloé Suzanne; Galiana, Delphine; Volff, Jean-Nicolas

    2015-09-01

    Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.

  12. 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.

  13. 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...

  14. Eye Movements when Reading Transposed Text: The Importance of Word-Beginning Letters

    ERIC Educational Resources Information Center

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

    2008-01-01

    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…

  15. Miniaturization of planar horn motors

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

    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 a 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 2×2×2 mm piezoelectric stacks integrated into thin plates that are of the order of 3 × 3 × 0.2 cm.

  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. Discovery and characterization of a new transposable element, Tn4811, in Streptomyces lividans 66.

    PubMed Central

    Chen, C W; Yu, T W; Chung, H M; Chou, C F

    1992-01-01

    Transposition of a new 5.4-kb transposon, Tn4811, of Streptomyces lividans to the melC operon of Streptomyces antibioticus on plasmid pIJ702 was discovered. The nucleotide sequence of this copy of Tn4811, which contained an imperfect (9 of 11 bp) terminal inverted repeat, five putative Streptomyces coding sequences for an oxidoreductase and its transcription regulator, and three transposition-related proteins, was determined. SLP- strains of S. lividans contained one copy (A) of Tn4811, while SLP2+ strains contained an additional copy (B) on the SLP2 plasmid. The nucleotide sequences at three insertion junctions of Tn4811 were determined. Copy B lacked 41 bp from the left end. At the other five junctions the duplication of a putative 3-bp target sequence (TGA) was observed. A sequence of less than 3 kb homologous to Tn4811 was present in S. antibioticus. DNA homologous to Tn4811 was not detected in 14 other Streptomyces species. Images PMID:1332944

  18. 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.

  19. 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.

  20. 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

  1. Contact stresses calculated for miniature slip rings

    NASA Technical Reports Server (NTRS)

    Albright, F. G.; Domerest, K. E.; Horton, J. C.

    1965-01-01

    Using mathematical formulations to plot the graphs of the contact preload versus the Hertzian load, calculations of unit loading of the preloaded brushes on slip rings can be made. This optimizes the design of contact brushes and miniature slip rings.

  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. 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.

  4. Miniature robots can assist in laparoscopic cholecystectomy.

    PubMed

    Oleynikov, D; Rentschler, M; Hadzialic, A; Dumpert, J; Platt, S R; Farritor, S

    2005-04-01

    Laparoscopy reduces patient trauma but eliminates the surgeon's ability to directly view and touch the surgical environment. Although current robot-assisted laparoscopy improves the surgeon's ability to manipulate and visualize the target organs, the instruments and cameras remain constrained by the entry incision. This limits tool tip orientation and optimal camera placement. This article focuses on developing miniature in vivo robots to assist surgeons during laparoscopic surgery by providing an enhanced field of view from multiple angles and dexterous manipulators not constrained by the abdominal wall fulcrum effect. Miniature camera robots were inserted through a small incision into the insufflated abdominal cavity of an anesthetized pig. Trocar insertion and other laparoscopic tool placements were then viewed with these robotic cameras. The miniature robots provided additional camera angles that improved surgical visualization during a cholecystectomy. These successful prototype trials have demonstrated that miniature in vivo robots can provide surgeons with additional visual information that can increase procedural safety.

  5. Miniaturized Plasma and Neutral Diagnostics for JIMO

    NASA Technical Reports Server (NTRS)

    McHarg, M. G.; Enloe, C. L.; Krause, L. A.; Herrero, F. A.

    2003-01-01

    We describe a miniaturized suite of instruments which provides both bulk energy resolved plasma properties and coarse neutral mass spectroscopy suitable for measurements on the Jupiter Icy Moons Orbiter (JIMO). The suite is comprised of two instruments; the Miniaturized Electro-Static Analyzer (MESA), and the Flat Plasma Spectrometer (FLAPS), designed to measure the near earth environment on the Air Force Academy small satellite missions Falconsat-2 and 3.

  6. Metamaterials for Miniaturization of Optical Components

    DTIC Science & Technology

    2014-09-24

    AFRL-OSR-VA-TR-2014-0226 METAMATERIALS FOR MINIATURIZATION OF OPTICAL COMPONENTS Aleksandr Figotin UNIVERSITY OF CALIFORNIA IRVINE Final Report 09/24...8-98) v Prescribed by ANSI Std. Z39.18 10/09/2014 Final 30/06/2011-30/06/2014 METAMATERIALS FOR MINIATURIZATION OF OPTICAL COMPONENTS FA9550-11-1...relativistic and spinorial aspects of our neoclassical electromagnetic theory. Metamaterials , fundamentals of electromagnetic theory, dissipation, magnetic

  7. 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.

  8. 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.

  9. 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

  10. 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.

  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

    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

    2013-06-04

    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.

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

    PubMed Central

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

    2013-01-01

    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

  14. Transposable elements as a potential source for understanding the fish genome

    PubMed Central

    Porto-Foresti, Fabio; Oliveira, Claudio; Foresti, Fausto

    2011-01-01

    Transposable elements are repetitive sequences with the capacity tomove inside of the genome. They constitute the majority of the eukaryotic genomes, and are extensively present in the human genome, representing more than 45% of the genome sequences. The knowledge of the origin and function of these elements in the fish genome is still reduced and fragmented, mainly with regard to its structure and organization in the chromosomes of the representatives of this biological group, with data currently available for very few species that represent the great variety of forms and existing diversity. Comparative analyses ascertain differences in the organization of such elements in the species studied up to the present. They can be part of the heterochromatic regions in some species or be spread throughout the genome in others. The main objective of the present revision is to discuss the aspects of the organization of transposable elements in the fish genome. PMID:22016858

  15. 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.

  16. A proposal for the reference-based annotation of de novo transposable element insertions.

    PubMed

    Bergman, Casey M

    2012-01-01

    Understanding the causes and consequences of transposable element (TE) activity in the genomic era requires sophisticated bioinformatics approaches to accurately identify individual insertion sites. Next-generation sequencing technology now makes it possible to rapidly identify new TE insertions using resequencing data, opening up new possibilities to study the nature of TE-induced mutation and the target site preferences of different TE families. While the identification of new TE insertion sites is seemingly a simple task, the mechanisms of transposition present unique challenges for the annotation of de novo transposable element insertions mapped to a reference genome. Here I discuss these challenges and propose a framework for the annotation of de novo TE insertions that accommodates known mechanisms of TE insertion and established coordinate systems for genome annotation.

  17. 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

  18. The contribution of transposable elements to the evolution of regulatory networks

    PubMed Central

    Feschotte, Cédric

    2008-01-01

    Preface The control and coordination of eukaryotic gene expression rely on transcriptional and post-transcriptional regulatory networks. Although progress has been made in mapping the components and deciphering the function of these networks, the mechanisms by which such intricate circuits originate and evolve remain poorly understood. Here I revisit and expand earlier models proposing that genomic repeats, and in particular transposable elements, have been a rich source of material for the assembly and tinkering of eukaryotic gene regulatory systems. PMID:18368054

  19. Large-scale mapping of transposable element insertion sites using digital encoding of sample identity.

    PubMed

    Gohl, Daryl M; Freifeld, Limor; Silies, Marion; Hwa, Jennifer J; Horowitz, Mark; Clandinin, Thomas R

    2014-03-01

    Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools.

  20. 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.

  1. The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements.

    PubMed

    Staton, S Evan; Bakken, Bradley H; Blackman, Benjamin K; Chapman, Mark A; Kane, Nolan C; Tang, Shunxue; Ungerer, Mark C; Knapp, Steven J; Rieseberg, Loren H; Burke, John M

    2012-10-01

    Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well-documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain-containing Gypsy LTR retrotransposons ('chromoviruses'), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.

  2. Are chromosomal inversions induced by transposable elements? A paradigm from the malaria mosquito Anopheles gambiae.

    PubMed

    Mathiopoulos, K D; della Torre, A; Santolamazza, F; Predazzi, V; Petrarca, V; Coluzzi, M

    1999-09-01

    Chromosomal rearrangements abound in nature and can be studied in detail in organisms with polytene chromosomes. In Drosophila and in Anopheline mosquitoes most speciation processes seem to be associated with the establishment of chromosomal rearrangements, particularly of paracentric inversions. It is not known what triggers inversions in natural populations. In the laboratory inversions are commonly generated by X-rays, mutagens or after the activity of certain transposable elements (TEs). The Anopheles gambiae complex is comprised of six sibling species, each one characterized by the presence of fixed paracentric inversions on their chromosomes. Two of these, An. gambiae s.s. and An. arabiensis, are the most important vectors of human malaria and are structured into sub-populations, each carrying a characteristic set of polymorphic chromosomal inversions. We have cloned the breakpoints of the naturally occurring polymorphic inversion In(2R)d' of An. arabiensis. Analysis of the surrounding sequences demonstrated that adjacent to the distal breakpoint lies a transposable element that we called Odysseus. Characteristics of Odysseus' terminal region and its cytological distribution in different strains as well as within the same strain indicate that Odysseus is an actively transposing element. The presence of Odysseus at the junction of the naturally occurring inversion In(2R)d' suggests that the inversion may be the result of the TEs activity. Cytological evidence from Drosophila melanogaster has also implicated the hobo transposable element in the generation of certain Hawaiian endemic inversions. This picture supports the hypothesis of the important role of TEs in generating natural inversions.

  3. 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.

  4. 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.

  5. High torque miniature rotary actuator

    NASA Astrophysics Data System (ADS)

    Nalbandian, Ruben

    2005-07-01

    This paper summarizes the design and the development of a miniature rotary actuator (36 mm diameter by 100 mm length) used in spacecraft mechanisms requiring high torques and/or ultra-fine step resolution. This actuator lends itself to applications requiring high torque but with strict volume limitations which challenge the use of conventional rotary actuators. The design challenge was to develop a lightweight (less than 500 grams), very compact, high bandwidth, low power, thermally stable rotary actuator capable of producing torques in excess of 50 N.m and step resolutions as fine as 0.003 degrees. To achieve a relatively high torsional stiffness in excess of 1000 Nm/radian, the design utilizes a combination of harmonic drive and multistage planetary gearing. The unique design feature of this actuator that contributes to its light weight and extremely precise motion capability is a redundant stepper motor driving the output through a multistage reducing gearbox. The rotary actuator is powered by a high reliability space-rated stepper motor designed and constructed by Moog, Inc. The motor is a three-phase stepper motor of 15 degree step angle, producing twenty-four full steps per revolution. Since micro-stepping is not used in the design, and un-powered holding torque is exhibited at every commanded step, the rotary actuator is capable of reacting to torques as high as 35 Nm by holding position with the power off. The output is driven through a gear transmission having a total train ratio of 5120:1, resulting in a resolution of 0.003 degrees output rotation per motor step. The modular design of the multi-stage output transmission makes possible the addition of designs having different output parameters, such as lower torque and higher output speed capability. Some examples of an actuator family based on this growth capability will be presented in the paper.

  6. 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.

  7. Scattered organization of the histone multigene family and transposable elements in Synbranchus

    PubMed Central

    Utsunomia, Ricardo; Pansonato-Alves, José Carlos; Scacchetti, Priscilla Cardim; Oliveira, Claudio; Foresti, Fausto

    2014-01-01

    The fish species Synbranchus marmoratus is widely distributed throughout the Neotropical region and exhibits a significant karyotype differentiation. However, data concerning the organization and location of the repetitive DNA sequences in the genomes of these karyomorphs are still lacking. In this study we made a physical mapping of the H3 and H4 histone multigene family and the transposable elements Rex1 and Rex3 in the genome of three known S. marmoratus karyomorphs. The results indicated that both histone sequences seem to be linked with one another and are scattered all over the chromosomes of the complement, with a little compartmentalization in one acrocentric pair, which is different from observations in other fish groups. Likewise, the transposable elements Rex1 and Rex3 were also dispersed throughout the genome as small clusters. The data also showed that the histone sites are organized in a differentiated manner in the genomes of S. marmoratus, while the transposable elements Rex1 and Rex3 do not seem to be compartmentalized in this group. PMID:24688288

  8. 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

    2016-06-02

    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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. Superamphiphobic miniature boat fabricated by laser micromachining

    NASA Astrophysics Data System (ADS)

    Yin, Kai; Dong, Xinran; Zhang, Fan; Wang, Cong; Duan, Ji'an

    2017-03-01

    We fabricated a superamphiphobic miniature boat with marked drag reduction and excellent loading capacity using femtosecond laser direct writing technology. The as-prepared superamphiphobic surface of the boat exhibited apparent contact angles larger than 150° toward both water and oil. Miniature boats with the superamphiphobic surface slid effortlessly on both water and oil-polluted water surfaces, with an increase in sliding distance by up to 52% and load increase of up to 27% compared with those of a boat with an untreated surface. A potential mechanism that explains the excellent performance of the superamphiphobic miniature boat was also discussed. This work provides a simple and economically viable strategy to obtain advanced surfaces for use in microfluidics and marine engineering.

  14. 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.

  15. 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.

  16. Acral mutilation syndrome in a miniature pinscher.

    PubMed

    Bardagí, M; Montoliu, P; Ferrer, L; Fondevila, D; Pumarola, M

    2011-01-01

    Acral mutilation syndrome (AMS) is a rare canine hereditary sensory neuropathy that results in progressive mutilation of the distal extremities and which has been reported only in German short-haired pointers, English pointers, English springer spaniels and French spaniels. The present report describes a case of AMS in an 18-month-old female miniature pinscher with progressive self-mutilation of the hind feet. The dog did not respond to any treatment and was humanely destroyed at the age of 30 months. Microscopical findings post mortem were restricted to the nervous system and were compatible with AMS. This is the first case of AMS described in a miniature pinscher. It is not known if the disease was the result of a point mutation in this particular dog or if the miniature pinscher breed will evolve to become a breed predisposed to AMS.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Presynaptic miniature GABAergic currents in developing interneurons.

    PubMed

    Trigo, Federico F; Bouhours, Brice; Rostaing, Philippe; Papageorgiou, George; Corrie, John E T; Triller, Antoine; Ogden, David; Marty, Alain

    2010-04-29

    Miniature synaptic currents have long been known to represent random transmitter release under resting conditions, but much remains to be learned about their nature and function in central synapses. In this work, we describe a new class of miniature currents ("preminis") that arise by the autocrine activation of axonal receptors following random vesicular release. Preminis are prominent in gabaergic synapses made by cerebellar interneurons during the development of the molecular layer. Unlike ordinary miniature postsynaptic currents in the same cells, premini frequencies are strongly enhanced by subthreshold depolarization, suggesting that the membrane depolarization they produce belongs to a feedback loop regulating neurotransmitter release. Thus, preminis could guide the formation of the interneuron network by enhancing neurotransmitter release at recently formed synaptic contacts.

  4. 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

  5. Jarvik 2000 pump technology and miniaturization.

    PubMed

    Jarvik, Robert

    2014-01-01

    Blood-pump miniaturization has made amazing progress, reducing the pump diameter to one-tenth of the size of previous positive displacement pumps. In particular, axial-flow-pump technology allows tiny pumps running at high speeds to deliver from 2 to 10 L/min. A review of the background inventions of the Jarvik 2000 technology is presented, together with the reason that making pumps smaller than demanded by the particular application for which they are designed is counterproductive. Pump miniaturization is nearing its practical limit. The optimization of performance and patient outcomes should remain our primary design goal.

  6. 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.

  7. 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.

  8. 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.

  9. A miniature origami biofuel cell based on a consumed cathode.

    PubMed

    Yu, You; Han, Yujie; Lou, Baohua; Zhang, Lingling; Han, Lei; Dong, Shaojun

    2016-11-10

    Considerable interest has been focused on miniature biofuel cells (BFCs) because of their portability and possibility to be implantable. Origami devices with hollow channels will provide novel insight into the assembly methods of miniature BFCs. Herein a miniature origami BFC has been fabricated from a MnO2-graphite flake consumed solid-state cathode. For further practical applications, miniature origami BFCs can directly generate energy from soft drinks.

  10. 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)

  11. 21 CFR 890.1615 - Miniature pressure transducer.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Miniature pressure transducer. 890.1615 Section... Miniature pressure transducer. (a) Identification. A miniature pressure transducer is a device intended for medical purposes to measure the pressure between a device and soft tissue by converting mechanical...

  12. 21 CFR 890.1615 - Miniature pressure transducer.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Miniature pressure transducer. 890.1615 Section... Miniature pressure transducer. (a) Identification. A miniature pressure transducer is a device intended for medical purposes to measure the pressure between a device and soft tissue by converting mechanical...

  13. 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.

  14. The technology of miniature acoustic element arrays

    NASA Technical Reports Server (NTRS)

    Bom, N.; Lancee, C. T.; Ridder, J.; Ligtvoet, C.; Roelandt, J.

    1975-01-01

    Various aspects of miniature element array construction are discussed. Some initial results on optimization of lateral resolution with a special focusing technique in linear array design is presented, together with the constructional details. Furthermore the construction of a catheter tip array is treated in detail.

  15. Miniaturization of a biomedical gas sensor.

    PubMed

    Mirtaheri, Peyman; Omtveit, Tore; Klotzbuecher, Thomas; Grimnes, Sverre; Martinsen, Orjan G; Tønnessen, Tor Inge

    2004-12-01

    In a previous study, we concluded that a conductivity based PCO2 sensor is an attractive solution for early detection of ischemia and presented two design geometries. For organ surface measurements, the planar design was suitable but it was difficult to insert the sensor into the tissue. A cylindrical design solution was favored for insertion due to the large membrane contact area and easy placement in a medical catheter. Since the previous cylindrical prototype was large and could damage the tissue, a more miniaturized sensor was needed. In the current paper, we present a miniaturized sensor with an outer diameter of 1 mm. The applied technology for manufacturing the sensor was a combination of mechanical turning, excimer laser drilling and conventional molding technique. The materials applied were PEEK (polyetherether ketone), PI (polyimide) with gold layers and polysiloxane. The membrane had to be gas permeable while acting as a barrier for ion transport, and was made of polysiloxane and had a thickness of 100-150 microm. The miniaturized sensor was tested for calibration, response time, drifting and pressure sensitivity. The results show that the miniaturized PCO2 sensor is capable of rapid and stable measurements both in vitro and ex vivo. The result from this study will be applied for the industrial manufacturing of such a biomedical sensor as a clinical product.

  16. 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.

  17. Miniature Paintings: Small Size, Big Impact!

    ERIC Educational Resources Information Center

    Hicks, Bill

    2011-01-01

    This article describes a miniature painting project that allows students to research a master painter and then replicate the work on a smaller scale. This lesson focuses on the students' ability to learn to identify style, subject matter, themes, and content in painting through the study of historical paintings, and the application of various…

  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. Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths.

    PubMed

    Naville, Magali; Chalopin, Domitille; Volff, Jean-Nicolas

    2014-01-01

    Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.

  20. The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes

    PubMed Central

    Estill, James C; Bennetzen, Jeffrey L

    2009-01-01

    Background High quality annotation of the genes and transposable elements in complex genomes requires a human-curated integration of multiple sources of computational evidence. These evidences include results from a diversity of ab initio prediction programs as well as homology-based searches. Most of these programs operate on a single contiguous sequence at a time, and the results are generated in a diverse array of readable formats that must be translated to a standardized file format. These translated results must then be concatenated into a single source, and then presented in an integrated form for human curation. Results We have designed, implemented, and assessed a Perl-based workflow named DAWGPAWS for the generation of computational results for human curation of the genes and transposable elements in plant genomes. The use of DAWGPAWS was found to accelerate annotation of 80–200 kb wheat DNA inserts in bacterial artificial chromosome (BAC) vectors by approximately twenty-fold and to also significantly improve the quality of the annotation in terms of completeness and accuracy. Conclusion The DAWGPAWS genome annotation pipeline fills an important need in the annotation of plant genomes by generating computational evidences in a high throughput manner, translating these results to a common file format, and facilitating the human curation of these computational results. We have verified the value of DAWGPAWS by using this pipeline to annotate the genes and transposable elements in 220 BAC insertions from the hexaploid wheat genome (Triticum aestivum L.). DAWGPAWS can be applied to annotation efforts in other plant genomes with minor modifications of program-specific configuration files, and the modular design of the workflow facilitates integration into existing pipelines. PMID:19545381

  1. 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

  2. Transposable element fragments in protein-coding regions and their contributions to human functional proteins.

    PubMed

    Wu, Ming; Li, Li; Sun, Zhirong

    2007-10-15

    Transposable elements (TEs) and their contributions to protein-coding regions are of particular interest. Here we searched for TE fragments in Homo sapiens at both the transcript and protein levels. We found evidence in support of TE exonization and its association with alternative splicing. Despite recent findings that long evolutionary times are required to incorporate TE into proteins, we found many functional proteins with translated TE cassettes derived from young TEs. Analyses of two Bcl-family proteins and Alu-encoded segments suggest the coding and functional potential of TE sequences.

  3. Method of Lines Transpose an Implicit Vlasov Maxwell Solver for Plasmas

    DTIC Science & Technology

    2015-04-17

    Benjamin Ong , and Lee Van Groningen, Method of lines transpose: An implicit solution to the wave equation, Mathematics of Computation (2014). 9. Matthew F...Lagrangian method for the Vlasov Equation”, Journal of Computational Physics, 229(4), 1130–1149, 2010. 2. A.J. Christlieb, C.B. Macdonald and B. Ong , “Parallel...for load-balanced parallel grid- less DSMC”, Computer Physics Communications, issn 0010-4655, 2010. 4. A.J. Christlieb and B. Ong , “Implicit Parallel

  4. 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

  5. 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.

  6. Miniature Grating for Spectrally-Encoded Endoscopy

    PubMed Central

    Kang, Dongkyun; Martinez, Ramses V.; Whitesides, George M.

    2013-01-01

    Spectrally-encoded endoscopy (SEE) is an ultraminiature endoscopy technology that acquires high-definition images of internal organs through a sub-mm endoscopic probe. In SEE, a grating at the tip of the imaging optics diffracts the broadband light into multiple beams, where each beam with a distinctive wavelength is illuminated on a unique transverse location of the tissue. By encoding one transverse coordinate with the wavelength, SEE can image a line of the tissue at a time without using any beam scanning devices. This feature of the SEE technology allows the SEE probe to be miniaturized to sub-mm dimensions. While previous studies have shown that SEE has the potential to be utilized for various clinical imaging applications, the translation of SEE for medicine has been hampered by challenges in fabricating the miniature grating inherent to SEE probes. This paper describes a new fabrication method for SEE probes. The new method uses a soft lithographic approach to pattern a high-aspect-ratio grating at the tip of the miniature imaging optics. Using this technique, we have constructed a 500-μm-diameter SEE probe. The miniature grating at the tip of the probe had a measured diffraction efficiency of 75%. The new SEE probe was used to image a human finger and formalin fixed mouse embryos, demonstrating the capability of this device to visualize key anatomic features of tissues with high image contrast. In addition to providing high quality imaging SEE optics, the soft lithography method allows cost-effective and reliable fabrication of these miniature endoscopes, which will facilitate the clinical translation of SEE technology. PMID:23503940

  7. 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.

  8. 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

  9. 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).

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

    DOE PAGES

    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

  11. A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes.

    PubMed

    Gupta, Smriti; Gallavotti, Andrea; Stryker, Gabrielle A; Schmidt, Robert J; Lal, Shailesh K

    2005-01-01

    We recently described a maize mutant caused by an insertion of a Helitron type transposable element (Lal, S.K., Giroux, M.J., Brendel, V., Vallejos, E. and Hannah, L.C., 2003, Plant Cell, 15: 381-391). Here we describe another Helitron insertion in the barren stalk1 gene of maize. The termini of a 6525 bp insertion in the proximal promoter region of the mutant reference allele of maize barren stalk1 gene (ba1-ref) shares striking similarity to the Helitron insertion we reported in the Shrunken-2 gene. This insertion is embedded with pseudogenes that differ from the pseudogenes discovered in the mutant Shrunken-2 insertion. Using the common terminal ends of the mutant insertions as a query, we discovered other Helitron insertions in maize BAC clones. Based on the comparison of the insertion site and PCR amplified genomic sequences, these elements inserted between AT dinucleotides. These putative non-autonomous Helitron insertions completely lacked sequences similar to RPA (replication protein A) and DNA Helicases reported in other species. A blastn analysis indicated that both the 5' and 3' termini of Helitrons are repeated in the maize genome. These data provide strong evidence that Helitron type transposable elements are active and may have played an essential role in the evolution and expansion of the maize genome.

  12. 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.

  13. Phase transitions for random states and a semicircle law for the partial transpose

    NASA Astrophysics Data System (ADS)

    Aubrun, Guillaume; Szarek, Stanisław J.; Ye, Deping

    2012-03-01

    For a system of N identical particles in a random pure state, there is a threshold k0=k0(N)˜N/5 such that two subsystems of k particles each typically share entanglement if k>k0, and typically do not share entanglement if ktranspose (PPT) property can be described even more precisely. For example, for N qubits the two subsystems of size k are typically in a PPT state if kk1. Since, for a given state of the entire system, the induced state of a subsystem is given by the partial trace, the above facts can be rephrased as properties of random induced states. An important step in the analysis depends on identifying the asymptotic spectral density of the partial transposes of such random induced states, a result which is interesting in its own right.

  14. Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

    PubMed

    Kijima, T E; Innan, Hideki

    2013-11-01

    A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

  15. Expressing genes do not forget their LINEs: transposable elements and gene expression.

    PubMed

    Kines, Kristine J; Belancio, Victoria P

    2012-01-01

    Historically the accumulated mass of mammalian transposable elements (TEs), particularly those located within gene boundaries, was viewed as a genetic burden potentially detrimental to the genomic landscape. This notion has been strengthened by the discovery that transposable sequences can alter the architecture of the transcriptome, not only through insertion, but also long after the integration process is completed. Insertions previously considered harmless are now known to impact the expression of host genes via modification of the transcript quality or quantity, transcriptional interference, or by the control of pathways that affect the mRNA life-cycle. Conversely, several examples of the evolutionary advantageous impact of TEs on the host gene structure that diversified the cellular transcriptome are reported. TE-induced changes in gene expression can be tissue- or disease-specific, raising the possibility that the impact of TE sequences may vary during development, among normal cell types, and between normal and disease-affected tissues. The understanding of the rules and abundance of TE-interference with gene expression is in its infancy, and its contribution to human disease and/or evolution remains largely unexplored.

  16. 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.

  17. Intrinsic characteristics of neighboring DNA modulate transposable element activity in Drosophila melanogaster.

    PubMed

    Esnault, Caroline; Palavesam, Azhahianambi; Pilitt, Kristina; O'Brochta, David A

    2011-01-01

    Identifying factors influencing transposable element activity is essential for understanding how these elements impact genomes and their evolution as well as for fully exploiting them as functional genomics tools and gene-therapy vectors. Using a genetics-based approach, the influence of genomic position on piggyBac mobility in Drosophila melanogaster was assessed while controlling for element structure, genetic background, and transposase concentration. The mobility of piggyBac elements varied over more than two orders of magnitude solely as a result of their locations within the genome. The influence of genomic position on element activities was independent of factors resulting in position-dependent transgene expression ("position effects"). Elements could be relocated to new genomic locations without altering their activity if ≥ 500 bp of genomic DNA originally flanking the element was also relocated. Local intrinsic factors within the neighboring DNA that determined the activity of piggyBac elements were portable not only within the genome but also when elements were moved to plasmids. The predicted bendability of the first 50 bp flanking the 5' and 3' termini of piggyBac elements could account for 60% of the variance in position-dependent activity observed among elements. These results are significant because positional influences on transposable element activities will impact patterns of accumulation of elements within genomes. Manipulating and controlling the local sequence context of piggyBac elements could be a powerful, novel way of optimizing gene vector activity.

  18. 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

  19. 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.

  20. 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.

  1. SMARBot: a modular miniature mobile robot platform

    NASA Astrophysics Data System (ADS)

    Meng, Yan; Johnson, Kerry; Simms, Brian; Conforth, Matthew

    2008-04-01

    Miniature robots have many advantages over their larger counterparts, such as low cost, low power, and easy to build a large scale team for complex tasks. Heterogeneous multi miniature robots could provide powerful situation awareness capability due to different locomotion capabilities and sensor information. However, it would be expensive and time consuming to develop specific embedded system for different type of robots. In this paper, we propose a generic modular embedded system architecture called SMARbot (Stevens Modular Autonomous Robot), which consists of a set of hardware and software modules that can be configured to construct various types of robot systems. These modules include a high performance microprocessor, a reconfigurable hardware component, wireless communication, and diverse sensor and actuator interfaces. The design of all the modules in electrical subsystem, the selection criteria for module components, and the real-time operating system are described. Some proofs of concept experimental results are also presented.

  2. 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.

  3. 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.

  4. Degenerative myelopathy in an adult miniature poodle.

    PubMed

    Matthews, N S; de Lahunta, A

    1985-06-01

    Degenerative myelopathy was diagnosed at necropsy of an adult Miniature Poodle with a 33-month history of progressive pelvic limb ataxia and proprioceptive deficit. Microscopic examination of the cord revealed diffuse degenerative myelopathy. Degenerative myelopathy is usually seen in adult, large-breed dogs and progresses over a period of months. In this case, the myelopathy progressed slowly and the degree of paralysis became more extensive than usually seen.

  5. 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.

  6. Sub miniaturized laser doppler velocimeter sensor

    NASA Technical Reports Server (NTRS)

    Gharib, Morteza (Inventor); Modaress, Darius (Inventor); Taugwalder, Frederic (Inventor)

    2003-01-01

    A miniaturized laser Doppler velocimeter is formed in a housing that is preferably 3 mm in diameter or less. A laser couples light to a first diffractive optical element that is formed on the fiber end. The light is coupled to a lens that also includes a diffractive optical element. The same lens is also used to collect receive light, and receives includes another diffractive optical element to collect that received light.

  7. 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.

  8. Strain controlled cyclic tests on miniaturized specimens

    NASA Astrophysics Data System (ADS)

    Procházka, R.; Džugan, J.

    2017-02-01

    The paper is dealing with strain controlled cyclic tests using a non-contact strain measurement based on digital image correlation techniques on proportional sizes of conventional specimens. The cyclic behaviour of 34CrNiMo6 high-strength steel was investigated on miniaturized round specimens with diameter of 2mm that were compared with specimens in accordance with ASTM E606 standards. The cycle asymmetry coefficient was R= -1. This application is intended to be used for life time assessment of in service components in future work which enables to carried out a group of mechanical tests from a limited amount of the experimental material. The attention was paid to confirm the suitability of the proposed size miniaturization geometry, testing set up and procedure. The test results obtained enabled to construct Manson-Coffin curves and assess fatigue parameters. The purpose of this study is to present differences between cyclic curves and cyclic parameters which have been evaluated based on conventional and miniaturized specimens.

  9. 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.

  10. Miniature standoff Raman probe for neurosurgical applications

    NASA Astrophysics Data System (ADS)

    Stevens, Oliver A. C.; Hutchings, Joanne; Gray, William; Vincent, Rosa Louise; Day, John C.

    2016-08-01

    Removal of intrinsic brain tumors is a delicate process, where a high degree of specificity is required to remove all of the tumor tissue without damaging healthy brain. The accuracy of this process can be greatly enhanced by intraoperative guidance. Optical biopsies using Raman spectroscopy are a minimally invasive and lower-cost alternative to current guidance methods. A miniature Raman probe for performing optical biopsies of human brain tissue is presented. The probe allows sampling inside a conventional stereotactic brain biopsy system: a needle of length 200 mm and inner diameter of 1.8 mm. By employing a miniature stand-off Raman design, the probe removes the need for any additional components to be inserted into the brain. Additionally, the probe achieves a very low internal silica background while maintaining good collection of Raman signal. To illustrate this, the probe is compared with a Raman probe that uses a pair of optical fibers for collection. The miniature stand-off Raman probe is shown to collect a comparable number of Raman scattered photons, but the Raman signal to background ratio is improved by a factor of five at Raman shifts below ˜500 cm-1. The probe's suitability for use on tissue is demonstrated by discriminating between different types of healthy porcine brain tissue.

  11. 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.

  12. Abundance, distribution and potential impact of transposable elements in the genome of Mycosphaerella fijiensis

    PubMed Central

    2012-01-01

    Background Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed repetitive DNA sequences found in a host genome. These elements have the ability to move from one location to another within the genome, and their insertion can cause a wide spectrum of mutations in their hosts. Some of the deleterious effects of TEs may be due to ectopic recombination among TEs of the same family. In addition, some transposons are physically linked to genes and can control their expression. To prevent possible damage caused by the presence of TEs in the genome, some fungi possess TE-silencing mechanisms, such as RIP (Repeat Induced Point mutation). In this study, the abundance, distribution and potential impact of TEs in the genome of M. fijiensis were investigated. Results A total of 613 LTR-Gypsy and 27 LTR-Copia complete elements of the class I were detected. Among the class II elements, a total of 28 Mariner, five Mutator and one Harbinger complete elements were identified. The results of this study indicate that transposons were and are important ectopic recombination sites. A distribution analysis of a transposable element from each class of the M. fijiensis isolates revealed variable hybridization profiles, indicating the activity of these elements. Several genes encoding proteins involved in important metabolic pathways and with potential correlation to pathogenicity systems were identified upstream and downstream of transposable elements. A comparison of the sequences from different transposon groups suggested the action of the RIP silencing mechanism in the genome of this microorganism. Conclusions The analysis of TEs in M. fijiensis suggests that TEs play an important role in the evolution of this organism because the

  13. 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

  14. 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,…

  15. 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...

  16. A transposable class I composite transposon carrying mph (methyl parathion hydrolase) from Pseudomonas sp. strain WBC-3.

    PubMed

    Wei, Min; Zhang, Jun-Jie; Liu, Hong; Wang, Shu-Jun; Fu, He; Zhou, Ning-Yi

    2009-03-01

    Pseudomonas sp. strain WBC-3 utilizes methyl parathion (O,O-dimethyl O-p-nitrophenol phosphorothioate) or para-nitrophenol as the sole source of carbon, nitrogen and energy. A gene encoding methyl parathion hydrolase (MPH) had been characterized previously and found to be located on a typical class I composite transposon that comprised IS6100 (Tnmph). In this study, the transposability of this transposon was confirmed by transposition assays in two distinct mating-out systems. Tnmph was demonstrated to transpose efficiently in a random manner in Pseudomonas putida PaW340 by Southern blot and in Ralstonia sp. U2 by sequence analysis of the Tnmph insertion sites, both exhibiting MPH activity. The linkage of the mph-like gene with IS6100, together with the transposability of Tnmph, as well as its capability to transpose in other phylogenetically divergent bacterial species, suggest that Tnmph may contribute to the wide distribution of mph-like genes and the adaptation of bacteria to organophosphorus compounds.

  17. Gene Marker Loss Induced by the Transposable Element, En, in Maize

    PubMed Central

    Cormack, J.; Peterson, P. A.

    1994-01-01

    The En/Spm transposable element system in maize includes the functional element, En/Spm and the receptor element I/dSpm. An En receptor has been found that shows En-induced breakage. This En-responsive receptor (designated 1836518) is located on the short arm of chromosome 9, proximal to Wx. In the presence of En, markers distal to the receptor show a loss of gene expression. Kernels heterozygous for aleurone and endosperm marker genes have a variegated appearance. The hypothesis is advanced that this variegation represents a physical loss of the chromosome segments carrying the genes distal to the receptor position. It is the first case of an En-controlled breakage event. PMID:8005421

  18. 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.

  19. The First Rule of Plant Transposable Element Silencing: Location, Location, Location

    PubMed Central

    Sigman, Meredith J.; Slotkin, R. Keith

    2016-01-01

    Transposable elements (TEs) are mobile units of DNA that comprise large portions of plant genomes. Besides creating mutations via transposition and contributing to genome size, TEs play key roles in chromosome architecture and gene regulation. TE activity is repressed by overlapping mechanisms of chromatin condensation, epigenetic transcriptional silencing, and targeting by small interfering RNAs. The specific regulation of different TEs, as well as their different roles in chromosome architecture and gene regulation, is specified by where on the chromosome the TE is located: near a gene, within a gene, in a pericentromere/TE island, or at the centromere core. In this Review, we investigate the silencing mechanisms responsible for inhibiting TE activity for each of these chromosomal contexts, emphasizing that chromosomal location is the first rule dictating the specific regulation of each TE. PMID:26869697

  20. Transposable elements and two other molecular markers as typing tools for the genus Paracoccidioides.

    PubMed

    Alves, Fernanda Lourenço; Ribeiro, Mariceli Araújo; Hahn, Rosane Christine; de Melo Teixeira, Marcus; de Camargo, Zoilo Pires; Cisalpino, Patrícia Silva; Marini, Marjorie Mendes

    2015-02-01

    Studies comparing Paracoccidioides brasiliensis and Paracoccidioides lutzii have shown that these fungi have significant genomic differences that may have implications in the clinical manifestation, diagnosis, and treatment of paracoccidioidomycosis caused by them. Thus, molecular typing methods are required that can distinguish between various species of Paracoccidioides. The aim of this study was to explore the potential use as molecular markers of the transposable elements Trem A-H recently identified and characterized in the genus Paracoccidioides as a means of differentiating the species. We take advantage of the abundance and distribution of these transposons in the Paracoccidioides genomes to develop a simple and highly reproducible polymerase chain reaction (PCR)-based technique. Furthermore we compare the performance of this test with two other molecular markers already in use to identify these fungi.

  1. The devil is in the details: Transposable element analysis of the Tasmanian devil genome

    PubMed Central

    Nilsson, Maria A.

    2016-01-01

    ABSTRACT The third marsupial genome was sequenced from the Tasmanian devil (Sarcophilus harrisii), a species that currently is driven to extinction by a rare transmissible cancer. The transposable element (TE) landscape of the Tasmanian devil genome revealed that the main driver of retrotransposition the Long INterspersed Element 1 (LINE1) seem to have become inactivated during the past 12 million years. Strangely, the Short INterspersed Elements (SINE), that normally hijacks the LINE1 retrotransposition system, became inactive prior to LINE1 at around 30 million years ago. The SINE inactivation was in vitro verified in several species. Here I discuss that the apparent LINE1 inactivation might be caused by a genome assembly artifact. The repetitive fraction of any genome is highly complex to assemble and the observed problems are not unique to the Tasmanian devil genome. PMID:27066301

  2. Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification.

    PubMed

    Becker, Kailey E; Thomas, Mary C; Martini, Samer; Shuipys, Tautvydas; Didorchuk, Volodymyr; Shanker, Rachyl M; Laten, Howard M

    2016-10-01

    Transposable elements (TEs) dominate the landscapes of most plant and animal genomes. Once considered junk DNA and genetic parasites, these interspersed, repetitive DNA elements are now known to play major roles in both genetic and epigenetic processes that sponsor genome variation and regulate gene expression. Knowledge of TE consensus sequences from elements in species whose genomes have not been sequenced is limited, and the individual TEs that are encountered in clones or short-reads rarely represent potentially canonical, let alone, functional representatives. In this study, we queried the Repbase database with eight BAC clones from white clover (Trifolium repens), identified a large number of candidate TEs, and used polymerase chain reaction and Sanger sequencing to create consensus sequences for three new TE families. The results show that TE family consensus sequences can be obtained experimentally in species for which just a single, full-length member of a TE family has been sequenced.

  3. Population and clinical genetics of human transposable elements in the (post) genomic era

    PubMed Central

    Rishishwar, Lavanya; Wang, Lu; Clayton, Evan A.; Mariño-Ramírez, Leonardo; McDonald, John F.; Jordan, I. King

    2017-01-01

    ABSTRACT Recent technological developments—in genomics, bioinformatics and high-throughput experimental techniques—are providing opportunities to study ongoing human transposable element (TE) activity at an unprecedented level of detail. It is now possible to characterize genome-wide collections of TE insertion sites for multiple human individuals, within and between populations, and for a variety of tissue types. Comparison of TE insertion site profiles between individuals captures the germline activity of TEs and reveals insertion site variants that segregate as polymorphisms among human populations, whereas comparison among tissue types ascertains somatic TE activity that generates cellular heterogeneity. In this review, we provide an overview of these new technologies and explore their implications for population and clinical genetic studies of human TEs. We cover both recent published results on human TE insertion activity as well as the prospects for future TE studies related to human evolution and health. PMID:28228978

  4. Novel trends in genetics: transposable elements and their application in medicine.

    PubMed

    Vand Rajabpour, Fatemeh; Raoofian, Reza; Habibi, Laleh; Akrami, Seyed Mohammad; Tabrizi, Mina

    2014-10-01

    Forty-five percent of the human genome is composed of Transposable Elements (TEs); therefore, TEs have had an undisputed impact on evolution of the most evolved creature by a very simple mechanism of action.  Scientists have been studying this simple mechanism of action and are currently using it to develop efficient and safe gene delivery systems especially for treatment of diseases. TEs have also been used safely in generating induced Pluripotent Stem Cells (iPSC) for regenerative medicine, which opens the door to a world of possibilities in our approach in trying to wrestle with many challenges in medicine. The PiggyBac (PB) system has yielded more success in generation of induced pluripotent stem cells in regenerative medicine, and the Sleeping Beauty (SB) has been more successful in Gene Therapy. Recent advances are indicative of more good news to come regarding the potential heights of successes achievable by the use of the TE-based systems.

  5. 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

  6. 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.

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

    PubMed

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

    2015-03-25

    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.

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

    PubMed Central

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

    2013-01-01

    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

  9. The devil is in the details: Transposable element analysis of the Tasmanian devil genome.

    PubMed

    Nilsson, Maria A

    2016-01-01

    The third marsupial genome was sequenced from the Tasmanian devil (Sarcophilus harrisii), a species that currently is driven to extinction by a rare transmissible cancer. The transposable element (TE) landscape of the Tasmanian devil genome revealed that the main driver of retrotransposition the Long INterspersed Element 1 (LINE1) seem to have become inactivated during the past 12 million years. Strangely, the Short INterspersed Elements (SINE), that normally hijacks the LINE1 retrotransposition system, became inactive prior to LINE1 at around 30 million years ago. The SINE inactivation was in vitro verified in several species. Here I discuss that the apparent LINE1 inactivation might be caused by a genome assembly artifact. The repetitive fraction of any genome is highly complex to assemble and the observed problems are not unique to the Tasmanian devil genome.

  10. [Chromatin structure, heterochromatin, and transposable genetic elements--are they from one team?].

    PubMed

    Leĭbovich, B A

    2002-01-01

    Gene content proved to be less than expected in completely sequenced eukaryotic genomes. Moreover, gene number differs only three times between such distant organisms as human and Drosophila. Hence it is likely that the essential functional and structural differences between the two species mostly depend on the regulation of gene activity than on the set and quality of genes themselves. New data demonstrate that changes in chromatin structure play a greater role in the fine gene activity regulation than considered before. R.B. Khesin had foresaw many chromatin functions that only recently came to be recognized. Khesin was interested in genome inconstancy over his last years. A higher content of several important chromosomal proteins was recently revealed in chromatin of transposable genetic elements (TGE). The possible role of TGE in chromatin organization in the nucleus is considered.

  11. Mutational Analysis of the Open Reading Frames in the Transposable Element Is1

    PubMed Central

    Jakowec, M.; Prentki, P.; Chandler, M.; Galas, D. J.

    1988-01-01

    IS1 is one of the smallest transposable elements found in bacteria (768 bp). It contains eight overlapping open-reading-frames (ORFs) greater than 50 codons, designated insA to insG and insB'. To determine which of the ORFs actually code for proteins involved in transposition, we have introduced amber codons into each ORF by site-directed mutagenesis which make neutral changes in the overlapping ORFs. Each mutant IS1 was then tested for its ability to mediate cointegrate formation in Su(+) and Su(-) backgrounds. The mutant elements were also tested for trans-complementation in an IS1-free Salmonella background. Our results show that the products of the insA and insB genes are the only ones essential for cointegrate formation. We suggest that other ORFs may, however, encode accessory proteins. PMID:2851480

  12. What makes up plant genomes: The vanishing line between transposable elements and genes.

    PubMed

    Zhao, Dongyan; Ferguson, Ann A; Jiang, Ning

    2016-02-01

    The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes.

  13. Transposable element distribution, abundance and role in genome size variation in the genus Oryza

    PubMed Central

    Zuccolo, Andrea; Sebastian, Aswathy; Talag, Jayson; Yu, Yeisoo; Kim, HyeRan; Collura, Kristi; Kudrna, Dave; Wing, Rod A

    2007-01-01

    Background The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop – rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. Results We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Conclusion Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus. PMID:17727727

  14. Complete Sequence and Evolutionary Genomic Analysis of the Pseudomonas aeruginosa Transposable Bacteriophage D3112

    PubMed Central

    Wang, Pauline W.; Chu, Linda; Guttman, David S.

    2004-01-01

    Bacteriophage D3112 represents one of two distinct groups of transposable phage found in the clinically relevant, opportunistic pathogen Pseudomonas aeruginosa. To further our understanding of transposable phage in P. aeruginosa, we have sequenced the complete genome of D3112. The genome is 37,611 bp, with an overall G+C content of 65%. We have identified 53 potential open reading frames, including three genes (the c repressor gene and early genes A and B) that have been previously characterized and sequenced. The organization of the putative coding regions corresponds to published genetic and transcriptional maps and is very similar to that of enterobacteriophage Mu. In contrast, the International Committee on Taxonomy of Viruses has classified D3112 as a λ-like phage on the basis of its morphology. Similarity-based analyses identified 27 open reading frames with significant matches to proteins in the NCBI databases. Forty-eight percent of these were similar to Mu-like phage and prophage sequences, including proteins responsible for transposition, transcriptional regulation, virion morphogenesis, and capsid formation. The tail proteins were highly similar to prophage sequences in Escherichia coli and phage Phi12 from Staphylococcus aureus, while proteins at the right end were highly similar to proteins in Xylella fastidiosa. We performed phylogenetic analyses to understand the evolutionary relationships of D3112 with respect to Mu-like versus λ-like bacteriophages. Different results were obtained from similarity-based versus phylogenetic analyses in some instances. Overall, our findings reveal a highly mosaic structure and suggest that extensive horizontal exchange of genetic material played an important role in the evolution of D3112. PMID:14702309

  15. Distribution patterns and impact of transposable elements in genes of green algae.

    PubMed

    Philippsen, Gisele S; Avaca-Crusca, Juliana S; Araujo, Ana P U; DeMarco, Ricardo

    2016-12-05

    Transposable elements (TEs) are DNA sequences able to transpose in the host genome, a remarkable feature that enables them to influence evolutive trajectories of species. An investigation about the TE distribution and TE impact in different gene regions of the green algae species Chlamydomonas reinhardtii and Volvox carteri was performed. Our results indicate that TEs are very scarce near introns boundaries, suggesting that insertions in this region are negatively selected. This contrasts with previous results showing enrichment of tandem repeats in introns boundaries and suggests that different evolutionary forces are acting in these different classes of repeats. Despite the relatively low abundance of TEs in the genome of green algae when compared to mammals, the proportion of poly(A) sites derived from TEs found in C. reinhardtii was similar to that described in human and mice. This fact, associated with the enrichment of TEs in gene 5' and 3' flanks of C. reinhardtii, opens up the possibility that TEs may have considerably contributed for gene regulatory sequences evolution in this species. Moreover, it was possible identify several instances of TE exonization for C. reinhardtii, with a particularly interesting case from a gene coding for Condensin II, a protein involved in the maintenance of chromosomal structure, where the addition of a transposomal PHD finger may contribute to binding specificity of this protein. Taken together, our results suggest that the low abundance of TEs in green algae genomes is correlated with a strict negative selection process, combined with the retention of copies that contribute positively with gene structures.

  16. RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

    PubMed Central

    Chen, Jinfeng; Wrightsman, Travis R.; Wessler, Susan R.

    2017-01-01

    Background Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE polymorphisms, particularly transposition events or non-reference insertion sites can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools. Methods We have developed the tool RelocaTE2 for identification of TE insertion sites at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD) of TE insertions allowing it to report TE polymorphism loci with single base pair precision. Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrate high level of sensitivity and specificity, particularly when the sequence coverage is not shallow. In comparison to other tools tested, RelocaTE2 achieves the best balance between sensitivity and specificity. In particular, RelocaTE2 performs best in prediction of TSDs for TE insertions. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE insertion sites and can be incorporated into

  17. Miniature loops in the solar corona

    NASA Astrophysics Data System (ADS)

    Barczynski, K.; Peter, H.; Savage, S. L.

    2017-03-01

    Context. Magnetic loops filled with hot plasma are the main building blocks of the solar corona. Usually they have lengths of the order of the barometric scale height in the corona that is 50 Mm. Aims: Previously it has been suggested that miniature versions of hot loops exist. These would have lengths of only 1 Mm barely protruding from the chromosphere and spanning across just one granule in the photosphere. Such short loops are well established at transition region temperatures (0.1 MK), and we investigate if such miniature loops also exist at coronal temperatures (>1 MK). Methods: We used extreme UV (EUV) imaging observations from the High-resolution Coronal Imager (Hi-C) at an unprecedented spatial resolution of 0.3'' to 0.4''. Together with EUV imaging and magnetogram data from the Solar Dynamics Observatory (SDO) and X-Ray Telescope (XRT) data from Hinode we investigated the spatial, temporal and thermal evolution of small loop-like structures in the solar corona above a plage region close to an active region and compared this to a moss area within the active region. Results: We find that the size, motion and temporal evolution of the loop-like features are consistent with photospheric motions, suggesting a close connection to the photospheric magnetic field. Aligned magnetograms show that one of their endpoints is rooted at a magnetic concentration. Their thermal structure, as revealed together with the X-ray observations, shows significant differences to moss-like features. Conclusions: Considering different scenarios, these features are most probably miniature versions of hot loops rooted at magnetic concentrations at opposite sides of a granule in small emerging magnetic loops (or flux tubes).

  18. 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.

  19. 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.

  20. 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

  1. A miniature tactical Rb frequency standard

    NASA Technical Reports Server (NTRS)

    Kwon, T. M.; Dagle, R.; Debley, W.; Dellamano, H.; Hahn, T.; Horste, J.; Lam, L. K.; Magnuson, R.; Mcclelland, T.

    1984-01-01

    Work on an innovative design for miniature rubidium frequency standards has reached the pre-production demonstration stage at Litton Guidance and Control Systems. Pre-production units were built and tested under contract to the Rome Air Development Center of the U.S. Air Force Systems Command. The units, which are designed for use in tactical military applications, feature fast warm-up, low power consumption, and vibration insensitivity. The output stability under vibration is maintained without the need for external shock-mounts. The design objectives and test results are discussed.

  2. 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.

  3. Endocrine alopecia in a miniature poodle.

    PubMed

    Allan, F J; Jones, B R; Purdie, E C

    1995-06-01

    Hypothyroidism and concurrent sex hormone imbalance associated with alopecia was diagnosed in a 5 year-old entire male Miniature Poodle. The dog had a 3-year history of alopecia, seborrhoea and recurrent superficial pyoderma. Abnormal thyrotropin releasing hormone stimulation test results supported a diagnosis of hypothyroidism. Partial hair regrowth occurred after interstitial cell tumours, which were present in both testicles, were removed by castration. Complete hair regrowth, however, occurred only after thyroid hormone supplementation. This case highlighted difficulties which may be encountered when interpreting serum hormone concentrations and endocrine function tests.

  4. 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.

  5. Miniature ruggedized optical correlator for flight testing

    NASA Astrophysics Data System (ADS)

    Karins, James P.; Mills, Stuart A.; Szegedi, N. J.; Ryan, James R.; Kelly, Louis G., Jr.; Goldstein, Dennis H.; Augustus, Eric P.; Wangler, Richard J.

    1994-03-01

    An electro-optic processor (EOP) incorporating a miniature ruggedized optical correlator (MROC) has been fabricated for use on a remotely piloted vehicle (RPV). The EOP consists of a single-board computer for system control, a MaxVideo 20 card for interfacing to the sensor and performing image processing functions, and an MROC module. The MROC and associated electronics (SLM drive electronics, CCD readout electronics, laser controller, preprocessor, and controller) are configured in a chassis that is placed into an RPV with a visible camera for signal input and a telemetry system for output of the optical processor to the ground.

  6. Surface-micromachined miniature rf switch

    NASA Astrophysics Data System (ADS)

    Guo, Fangmin; Lai, Zongsheng; Zhu, Ziqiang; Fan, Zhong; Long, Yongfu; Yang, Gen Q.; Ge, Xiaohong; Chen, Siqin; Xie, Jianfang

    2001-09-01

    A surface micromachined miniature switch has been made on silicon substrate using an electroplated gold micro-beam as the cantilevered arm, a chromium-to-gold electrical contact, and electrostatic actuation as the switching mechanism. The switch has an electrical isolation of -30dB in the 'off' state and an insertion loss of 4-7dB form 1 to 10 Ghz with a return loss of -15dB in the 'on' state. The high insertion loss has attributed to generation of parasitic current in low resistivity of the silicon substrate.

  7. A plasma-shielded, miniature Rogowski probe

    NASA Astrophysics Data System (ADS)

    Torbert, E.; Furno, I.; Intrator, T.; Hemsing, E.

    2003-12-01

    The design and first results from an electrically isolated and plasma-shielded Rogowski probe, used in the reconnection scaling experiment (RSX), are presented. The probe is designed to withstand extreme thermal shock, plasma corrosion, and be vacuum sanitary, which is accomplished with a machinable boron nitride shell. The novel miniature design, with an inner detecting area of 0.79 cm2, allows accurate position detection of plasma current channels with ≈2 cm radius and to measure local current density profiles. The temporal resolution (<1 μs) is sufficiently high to resolve the dynamic evolution of RSX plasma current channels.

  8. 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.

  9. 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.

  10. A Miniaturized Class IV Flextensional Ultrasonic Transducer

    NASA Astrophysics Data System (ADS)

    Feeney, Andrew; Tweedie, Andrew; Mathieson, Andrew; Lucas, Margaret

    The class V transducer has found popularity in a diverse range of applications such as surgical and underwater projection systems, where high vibration amplitude for relatively low piezoceramic volume is generated. The class IV transducer offers the potential to attain even higher performance per volume than the class V. In this research, a miniaturized class IV power ultrasonic flextensional transducer is proposed. Simulations were performed using PZFlex finite element analysis, and electrical impedance analysis and experimental modal analysis were conducted for validation, where a high correlation between simulation and experiment has been demonstrated.

  11. Miniaturized detection system for handheld PCR assays

    NASA Astrophysics Data System (ADS)

    Richards, James B.; Benett, William J.; Stratton, Paul; Hadley, Dean R.; Nasarabadi, Shanavaz L.; Milanovich, Fred P.

    2000-12-01

    We have developed and delivered a four chamber, battery powered, handheld instrument referred to as the HANAA which monitors the polymerase chain reaction (PCR) process using a TaqMan based fluorescence assay. The detection system differs form standard configurations in two essential ways. First, the size is miniaturized, with a combined cycling and optics plug-in module for a duplex assay begin about the size of a small box of matches. Second, the detection/analysis system is designed to call a positive sample in real time.

  12. 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.

  13. Recent advances in miniaturization of infrared spectrometers

    NASA Astrophysics Data System (ADS)

    Daly, James T.; Johnson, Edward A.; Bodkin, W. Andrew; Stevenson, William A.; White, David A.

    2000-03-01

    In the past ten years, a number of miniature spectrometers covering the visible and near infrared wavelengths out to 2.5 microns wavelength have been developed and are now commercially available. These small but high performance instruments have taken advantage of continuing advances in high sensitivity detectors--both CCD's and diode arrays, improvements in holographic gratings, and the availability of low-loss optical materials both in bulk and fiber form that transmit at these wavelengths and that can readily be formed into monolithic shapes for complex optical structures. More recently, a number of researchers have addressed the more intractable problems of extending these miniaturization innovations to spectrometers capable of operation in the mid-infrared wavelengths from 3 microns to 12 microns and beyond. Key enabling technologies for this effort include the recent development of high D*, uncooled thermopile and micro-bolometer detector arrays, new low- mass, high-efficiency pulsed infrared sources, and the design and fabrication of novel monolithic optical structures and waveguides using high index infrared optical materials. This paper reviews the development of these innovative infrared spectrometers and, in particular, the development of the `wedge' spectrometer by Foster-Miller, Inc. and the MicroSpecTM, a MEMS-based solid state spectrograph, by Ion Optics, Inc.

  14. Miniature bioreactors: current practices and future opportunities.

    PubMed

    Betts, Jonathan I; Baganz, Frank

    2006-05-25

    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.

  15. Modular injection systems for miniature engines

    NASA Astrophysics Data System (ADS)

    Cochran, Mike

    1992-07-01

    Mission requirements for Kinetic Energy Weapons will require miniaturization of current vehicle propulsion systems for future Space Defence Iniative Programs. A modular injection system (MIS) valve is presented which will decrease cost, size and weight of miniaturized storable bipropellant rocket engines and features two poppet-type propellant valve modules pneumatically linked to a pilot solenoid module. A prototype modular injection valve sized for 100lbf thrust was designed and is being tested to show lower costs, fewer moving parts and a reduction in weight and size. Results show that this valve meets objectives of one-half weight, one-half cost and one-fifth the envelopment of current production valves. Studies indicate that a cruciform configuration of four nominal 100lbf thrust engines can be controlled by four modular injection valve systems in a single housing of less than 1.0 m3. Following further development and correlation of results this concept may be scaled to control four higher thrust engines.

  16. 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.

  17. Miniaturization in sample treatment for environmental analysis.

    PubMed

    Ramos, L; Ramos, J J; Brinkman, U A Th

    2005-01-01

    The increasing demand for faster, more cost-effective and environmentally friendly analytical methods is a major incentive to improve the classical procedures used for sample treatment in environmental analysis. In most classical procedures, the use of rapid and powerful instrumental techniques for the final separation and detection of the analytes contrasts with the time-consuming and usually manual methods used for sample preparation, which slows down the total analytical process. The efforts made in this field in the past ten years have led to the adaptation of existing methods and the development of new techniques to save time and chemicals, and improve overall performance. One route has been to develop at-line or on-line and, frequently, automated systems. In these approaches, miniaturization has been a key factor in designing integrated analytical systems to provide higher sample throughput and/or unattended operation. Selected examples of novel developments in the field of miniaturized sample preparation for environmental analysis are used to evaluate the merits of the various techniques on the basis of published data on real-life analyses of trace-level organic pollutants. Perspectives and trends are briefly discussed.

  18. 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.

  19. Miniaturization of Chip-Scale Photonic Circuits

    NASA Astrophysics Data System (ADS)

    Zamek, Steve

    Chip-scale photonic circuits promise to alleviate some fundamental physical barriers encountered in many areas of the life sciences and information technologies. This work investigates routes to miniaturization of chip-scale optical devices. Two new techniques and devices based thereon are introduced for the first time. One technique makes use of integrated metallic mirrors to construct reflectors which are by an order of magnitude smaller than their counterparts. Another technique is based on folding of chip-scale devices to fit long structures into small area on a chip. Although both techniques are demonstrated on some specific examples, the developed toolkit is applicable to a wide range of chip-scale devices including modulators, filters, channel add-drop multiplexers, detectors, and others. The major part of this Thesis focuses on miniaturization of waveguide reflectors and the devices based thereon. Fitting long waveguide Bragg gratings into a small area on a chip is demonstrated based on curved waveguide Bragg gratings; theory and analytical model of such structures is developed. In the second part of the Thesis, integrated metallic mirrors are proposed as reflectors with properties complementary to Bragg gratings - low polarization sensitivity, high reflectivity for different transverse modes, and good manufacturability. The feasibility of the proposed ideas is tested in both simulations and experiments. The demonstrated devices including biochemical sensors, micro-resonators, and inline filters are promising for applications in the life sciences and information technologies.

  20. Miniaturized low-cost digital holographic interferometer

    NASA Astrophysics Data System (ADS)

    Michalkiewicz, Aneta; Kujawinska, Małgorzata; Marc, Paweł; Jaroszewicz, Leszek R.

    2006-04-01

    Digital holography (DH) and digital holographic interferometry (DHI) are very useful, robust, full-field visualization and measurement techniques applied for small objects, especially in the field of bioengineering and microelements system testing. Nowadays CCD/CMOS detectors and microlasers allow to build miniaturized and compact digital holographic head. Various approaches to develop DH/DHI systems including a variety of optical and mechanical solutions have been made. The main recent requirements for holocamera design include compactness, insensitivity to vibrations environmental changes and with good quality of output data. Other requirement is the ability to build a low-cost and robust system for sensing applications. In our paper, we propose a design of miniaturized holo-camera head with fibre optics light delivery system and remote data read-out. The opto-mechanical architecture allows out-of-plane and shape measurements of diffuse and reflective surfaces. The possible data capture schemes and software for enhanced quality numerical reconstruction of complex objects are discussed and the optimized methodology is determined. Also real-time optoelectronic hologram reconstruction is demonstrated on the base of remote data delivery to liquid crystal on silicon spatial light modulator. The performance of the system is tested on the resolution amplitude test and master sphere, while engineering objects in the experiments are static and dynamic microelements.

  1. 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...

  2. 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

  3. Miniature and Molecularly Specific Optical Screening Technologies for Breast Cancer

    DTIC Science & Technology

    2011-10-01

    05-1-0363 TITLE: Miniature and Molecularly Specific Optical Screening Technologies for Breast Cancer PRINCIPAL INVESTIGATOR...and Molecularly Specific Optical Screening Technologies for Breast Cancer Duke University Durham, NC 27705 Nirmala Ramanujam The goal of this...proposal is to harness the power of light to create “miniature and molecularly specific optical technologies” for breast cancer diagnosis and

  4. 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 ...

  5. A miniaturized artificial mastoid using a skull simulator.

    PubMed

    Stenfelt, S P; Håkansson, B E

    1998-01-01

    A miniaturized artificial mastoid of size and weight that allow calibration and measurement of bone conduction hearing aids in a conventional audiometric soundproof box has been developed. Its level of mechanical impedance corresponds to the standard IEC 373 (1990) within the frequency range 250 Hz to 8 kHz. The miniaturized artificial mastoid consists of three parts: coupler, skull simulator (TU-1000), and an external electrical correction filter. The coupler is a highly damped mass-spring system designed to give the miniaturized artificial mastoid mechanical impedance in accordance with the standard IEC 373 (1990). It was found that the miniaturized artificial mastoid yielded results that are in correspondence with results obtained with the Brüel & Kjaer type 4930 artificial mastoid for frequencies above 450 Hz. Thus, at these frequencies, the miniaturized artificial mastoid can be used for audiometer calibration as well as measurement of bone conduction hearing aids.

  6. The role of the transposable element hobo in the origin of endemic inversions in wild populations of Drosophila melanogaster.

    PubMed

    Lyttle, T W; Haymer, D S

    1992-01-01

    Evidence from in situ hybridizations of DNA from the transposable element hobo to polytene salivary gland chromosome squashes reveals that hobo occupies both cytological breakpoints of three of four endemic inversions sampled from natural populations of Drosophila melanogaster in the Hawaiian islands. The fourth endemic inversion has a single hobo insert at one breakpoint. Cosmopolitan inversions on the same chromosomes do not show this association. Frequencies of both endemic and cosmopolitan inversions in Hawaiian populations fall in ranges typical for natural populations of D. melanogaster sampled worldwide, suggesting that these results may be typical of other regions besides Hawaii. This appears to be the first direct demonstration that transposable elements are responsible for causing specific rearrangements found in nature; consequently, it is also the first direct demonstration that chromosome rearrangements can arise in nature in a manner predicted by results of hybrid dysgenic crosses in the laboratory. Possible population genetic and evolutionary consequences are discussed.

  7. Assessing the influence of letter position in reading normal and transposed texts using a letter detection task.

    PubMed

    Guérard, Katherine; Saint-Aubin, Jean; Poirier, Marie; Demetriou, Constantina

    2012-12-01

    During word recognition, some letters appear to play a more important role than others. Although some studies have suggested that the first and last letters of a word have a privileged status, there is no consensus with regards to the importance of the different letter positions when reading connected text. In the current experiments, we used a simple letter search task to examine the impact of letter position on word identification in connected text using a classic paper and pencil procedure (Experiment 1) and an eye movement monitoring procedure (Experiment 2). In Experiments 3 and 4, a condition with transposed letters was included. Our results show that the first letter of a word is detected more easily than the other letters, and transposing letters in a word revealed the importance of the final letter. It is concluded that both the initial and final letters play a special role in word identification during reading but that the underlying processes might differ.

  8. Spec Rekindled-A Simple Torque Correction Mechanics for Transposed Teeth in Conjunction with Pre-adjusted Edgewise Appliance System

    PubMed Central

    Singh, Harpreet; Thakkar, Surbhi

    2016-01-01

    Complete transposition of teeth is a rather rare phenomenon. After correction of transposed and malaligned lateral incisor and canine, attainment of appropriate individual antagonistic tooth torque is indispensable, which many orthodontists consider to be a herculean task. Here, a novel method is proposed which demonstrates the use of Spec reverse torquing auxillary as an effective adjunctive aid in conjunction with pre-adjusted edgewise brackets. PMID:28209017

  9. Spec Rekindled-A Simple Torque Correction Mechanics for Transposed Teeth in Conjunction with Pre-adjusted Edgewise Appliance System.

    PubMed

    Singh, Harpreet; Maurya, Raj Kumar; Thakkar, Surbhi

    2016-12-01

    Complete transposition of teeth is a rather rare phenomenon. After correction of transposed and malaligned lateral incisor and canine, attainment of appropriate individual antagonistic tooth torque is indispensable, which many orthodontists consider to be a herculean task. Here, a novel method is proposed which demonstrates the use of Spec reverse torquing auxillary as an effective adjunctive aid in conjunction with pre-adjusted edgewise brackets.

  10. 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.

  11. 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.

  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. Portable, miniaturized, fibre delivered, multimodal CARS exoscope.

    PubMed

    Smith, Brett; Naji, Majid; Murugkar, Sangeeta; Alarcon, Emilio; Brideau, Craig; Stys, Peter; Anis, Hanan

    2013-07-15

    We demonstrate for the first time, a portable multimodal coherent anti-Stokes Raman scattering microscope (exoscope) for minimally invasive in-vivo imaging of tissues. This device is based around a micro-electromechanical system scanning mirror and miniaturized optics with light delivery accomplished by a photonic crystal fibre. A single Ti:sapphire femtosecond pulsed laser is used as the light source to produce CARS, two photon excitation fluorescence and second harmonic generation images. The high resolution and distortion-free images obtained from various resolution and bio-samples, particularly in backward direction (epi) successfully demonstrate proof of concept, and pave the path towards future non or minimally-invasive in vivo imaging.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Miniature aerosol lidar for automated airborne application

    NASA Astrophysics Data System (ADS)

    Matthey, Renaud; Mitev, Valentin; Mileti, Gaetano; Makarov, Vladislav S.; Turin, Alexander V.; Morandi, Marco; Santacesaria, Vincenzo

    2000-09-01

    The Russian Mjasishchev 55 (M-55) <> high altitude aircraft is dedicated to atmospheric science research. It carries onboard a set of mutually complementary instruments for in- situ and remote sensing. The Green Miniature Aerosol Lidar (GMAL) has been developed to operate automatically on this platform. It is a short-range, zenith-looking, depolarization elastic-backscatter lidar based on a 532 nm micro-chip Nd-YAG laser. Compact, low-power consuming, it stands in a 27-litre isolating and warmed hermetic box. The device participated successfully to an extended test campaign in Italy during December 1998 and January 1999, and to the APE/THESEO campaign in the Indian Ocean during February-March 1999. It also showed capabilities for unattended measurement of the low troposphere from the ground. Description of the instrument and preliminary results are presented.

  4. 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.

  5. A highly miniaturized NDIR methane sensor

    NASA Astrophysics Data System (ADS)

    Ayerden, N. P.; de Graaf, Ger; Enoksson, Peter; Wolffenbuttel, Reinoud F.

    2016-04-01

    The increasing demand for handheld systems for absorption spectroscopy has triggered the development of microspectrometers at various wavelength ranges. Several MEMS implementations of the light source, interferometer/optical filter, and detector have already been reported in the literature. However, the size of microspectrometers is still limited by the required absorption path length in the sample gas cell. This paper presents a compact MEMS linear-variable optical filter (LVOF) where the resonator cavity of the filter is also used as a sample gas cell to measure the absorption of methane at 3392nm wavelength. The physical resonator cavity length is elongated 62.2-fold, using multiple reflections from highly reflective Bragg mirrors to achieve a sufficiently long effective optical absorption path. Although the LVOF would in principle enable operation as a robust portable microspectrometer, here it is used in a miniaturized NDIR methane sensor for wavelength selection and calibration.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Assessment of transposed ovarian movement: how much of a safety margin should be added during pelvic radiotherapy?

    PubMed

    Soda, Itaru; Ishiyama, Hiromichi; Ono, Shigemitsu; Takenaka, Kouji; Arai, Masahide; Arai, Tsutomu; Iwase, Haruko; Sekiguchi, Akane; Kawakami, Shogo; Komori, Shouko; Onda, Takashi; Hayakawa, Kazushige

    2015-03-01

    The purpose of this study was to analyze transposed ovarian movement. Data from 27 patients who underwent ovarian transposition after surgical treatment for uterine cancer were retrospectively analyzed. Computed tomography (CT) images including transposed ovaries were superimposed on other CT images acquired at different times, and were matched on bony structures. Differences in ovarian position between the CT images were measured. The planning organ at risk volume (PRV) margins were calculated from the formula of the 90% reference intervals (RIs) and the 95% RI, which were defined as mean ± 1.65 standard deviation (SD) and mean ± 1.96 SD, respectively. The 90% RI in the cranial, caudal, anterior, posterior, left and right directions were 1.5, 1.5, 1.4, 1.0, 1.7 and 0.9 cm, respectively. The 95% RI in the corresponding directions were 1.5, 2.0, 1.7, 1.2, 1.9 and 1.2 cm, respectively. These data suggest that bilateral ovaries need a PRV margin of ∼2 cm in all directions. The present study suggests that a transposed ovary needs the same PRV margin as a normal ovary (∼2 cm). Even after transposition, ovaries should be kept away from the radiation field to take into consideration the degree of ovarian movement.

  11. An active hAT transposable element causing bud mutation of carnation by insertion into the flavonoid 3'-hydroxylase gene.

    PubMed

    Momose, Masaki; Nakayama, Masayoshi; Itoh, Yoshio; Umemoto, Naoyuki; Toguri, Toshihiro; Ozeki, Yoshihiro

    2013-04-01

    The molecular mechanisms underlying spontaneous bud mutations, which provide an important breeding tool in carnation, are poorly understood. Here we describe a new active hAT type transposable element, designated Tdic101, the movement of which caused a bud mutation in carnation that led to a change of flower color from purple to deep pink. The color change was attributed to Tdic101 insertion into the second intron of F3'H, the gene for flavonoid 3'-hydroxylase responsible for purple pigment production. Regions on the deep pink flowers of the mutant can revert to purple, a visible phenotype of, as we show, excision of the transposable element. Sequence analysis revealed that Tdic101 has the characteristics of an autonomous element encoding a transposase. A related, but non-autonomous element dTdic102 was found to move in the genome of the bud mutant as well. Its mobilization might be the result of transposase activities provided by other elements such as Tdic101. In carnation, therefore, the movement of transposable elements plays an important role in the emergence of a bud mutation.

  12. Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes

    PubMed Central

    Puterova, Janka; Razumova, Olga; Martinek, Tomas; Alexandrov, Oleg; Divashuk, Mikhail; Kubat, Zdenek; Hobza, Roman; Karlov, Gennady

    2017-01-01

    Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites but most satellites were found on autosomes. Transposable elements were located mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes. PMID:28057732

  13. Substituted-letter and transposed-letter effects in a masked priming paradigm with French developing readers and dyslexics.

    PubMed

    Lété, 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 primes were used in a masked priming paradigm with third graders, fifth graders, adults, and phonological dyslexics matched on reading level with the third graders. No priming effect was found in third graders. In adults, only a transposed-letter priming effect was found; there was no substituted-letter priming effect. Finally, fifth graders and dyslexics showed both substituted-letter and transposed-letter priming effects. Priming effects between the two groups were of the same magnitude after response time (RT) z-score transformation. Taken together, our results show that the pattern of priming effects found by Castles and colleagues in English normal readers emerges later in French normal readers. In other words, language orthographies seem to constrain the tuning of the orthographic system, with an opaque orthography producing faster tuning of orthographic processing than more transparent orthographies because of the high level of reliance on phonological decoding while learning to read.

  14. Enhancer/Suppressor mutator (En/Spm)-like transposable elements of cassava (Manihot esculenta) are transcriptionally inactive.

    PubMed

    Gbadegesin, M A; Beeching, J R

    2010-04-13

    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.

  15. Cloning of inversion breakpoints in the Anopheles gambiae complex traces a transposable element at the inversion junction.

    PubMed

    Mathiopoulos, K D; della Torre, A; Predazzi, V; Petrarca, V; Coluzzi, M

    1998-10-13

    Anopheles arabiensis, one of the two most potent malaria vectors of the gambiae complex, is characterized by the presence of chromosomal paracentric inversions. Elucidation of the nature and the dynamics of these inversions is of paramount importance for the understanding of the population genetics and evolutionary biology of this mosquito and of the impact on malaria epidemiology. We report here the cloning of the breakpoints of the naturally occurring polymorphic inversion 2Rd' of A. arabiensis. A cDNA clone that cytologically mapped on the proximal breakpoint was the starting material for the isolation of a cosmid clone that spanned the breakpoint. Analysis of the surrounding sequences demonstrated that adjacent to the distal breakpoint lies a repetitive element that exhibits distinct distribution in different A. arabiensis strains. Sequencing analysis of that area revealed elements characteristic of transposable element terminal repeats. We called this presumed transposable element Odysseus. The presence of Odysseus at the junction of the naturally occuring inversion 2Rd' suggests that the inversion may be the result of the transposable element's activity. Characteristics of Odysseus' terminal region as well as its cytological distribution in different strains may indicate a relatively recent activity of Odysseus.

  16. The genomic proliferation of transposable elements in colonizing populations: Schistosoma mansoni in the new world.

    PubMed

    Wijayawardena, Bhagya K; DeWoody, J Andrew; Minchella, Dennis J

    2015-06-01

    Transposable elements (TEs) are mobile genes with an inherent ability to move within and among genomes. Theory predicts that TEs proliferate extensively during physiological stress due to the breakdown of TE repression systems. We tested this hypothesis in Schistosoma mansoni, a widespread trematode parasite that causes the human disease schistosomiasis. According to phylogenetic analysis, S. mansoni invaded the new world during the last 500 years. We hypothesized that new world strains of S. mansoni would have more copies of TEs than old world strains due to the physiological stress associated with invasion of the new world. We quantified the copy number of six TEs (Saci-1, Saci-2 and Saci-3, Perere-1, Merlin-sm1, and SmTRC1) in the genome and the transcriptome of old world and new world strains of S. mansoni, using qPCR relative quantification. As predicted, the genomes of new world parasites contain significantly more copies of class I and class II TEs in both laboratory and field strains. However, such differences are not observed in the transcriptome suggesting that either TE silencing mechanisms have reactivated to control the expression of these elements or the presence of inactive truncated copies of TEs.

  17. 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

  18. Transposable elements: insertion pattern and impact on gene expression evolution in hominids.

    PubMed

    Warnefors, Maria; Pereira, Vini; Eyre-Walker, Adam

    2010-08-01

    Transposable elements (TEs) can affect the regulation of nearby genes through several mechanisms. Here, we examine to what extent recent TE insertions have contributed to the evolution of gene expression in hominids. We compare expression levels of human and chimpanzee orthologs and detect a weak increase in expression divergence (ED) for genes with species-specific TE insertions compared with unaffected genes. However, we show that genes with TE insertions predating the human-chimpanzee split also exhibit a similar increase in ED and therefore conclude that the increase is not due to the transcriptional influence of the TEs. These results are further confirmed by lineage-specific analysis of ED, using rhesus macaque as an outgroup: Human-chimpanzee ortholog pairs, where one ortholog has suffered TE insertion but not the other, do not show increased ED along the lineage where the insertion occurred, relative to the other lineage. We also show that genes with recent TE insertions tend to produce more alternative transcripts but find no evidence that the TEs themselves promote transcript diversity. Finally, we observe that TEs are enriched upstream relative to downstream of genes and show that this is due to insertional bias, rather than selection, because this bias is only observed in genes expressed in the germ line. This provides an alternative neutral explanation for the accumulation of TEs in upstream sequences.

  19. 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.

  20. Transposed letter priming with horizontal and vertical text in Japanese and English readers.

    PubMed

    Witzel, Naoko; Qiao, Xiaomei; Forster, Kenneth

    2011-06-01

    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 been proposed in which special bigram detectors for frequently occurring nonadjacent letter combinations are developed as a product of perceptual learning. In order to examine this perceptual learning hypothesis, we asked whether bigram detectors are defined in terms of visuospatial coordinates. Japanese-English bilinguals who were equally familiar with horizontal and vertical text in Japanese demonstrated strong TL priming in both orientations when reading Japanese words, but, when reading English words, the evidence for vertical TL priming was not as strong. However, native English speakers showed a clear TL priming effect with vertically presented English words despite minimal exposure to vertical text, which is not consistent with a perceptual learning account. It is proposed instead that the initial letter array is transformed into an abstract ordinal code (first to last) regardless of orientation and that the speed with which this transformation is carried out depends on the familiarity of the script.

  1. 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

  2. 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.

  3. 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

  4. Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element.

    PubMed

    Benson, Meredith A; Ohneck, Elizabeth A; Ryan, Chanelle; Alonzo, Francis; Smith, Hannah; Narechania, Apurva; Kolokotronis, Sergios-Orestis; Satola, Sarah W; Uhlemann, Anne-Catrin; Sebra, Robert; Deikus, Gintaras; Shopsin, Bo; Planet, Paul J; Torres, Victor J

    2014-08-01

    Staphylococcus aureus has evolved as a pathogen that causes a range of diseases in humans. There are two dominant modes of evolution thought to explain most of the virulence differences between strains. First, virulence genes may be acquired from other organisms. Second, mutations may cause changes in the regulation and expression of genes. Here we describe an evolutionary event in which transposition of an IS element has a direct impact on virulence gene regulation resulting in hypervirulence. Whole-genome analysis of a methicillin-resistant S. aureus (MRSA) strain USA500 revealed acquisition of a transposable element (IS256) that is absent from close relatives of this strain. Of the multiple copies of IS256 found in the USA500 genome, one was inserted in the promoter sequence of repressor of toxins (Rot), a master transcriptional regulator responsible for the expression of virulence factors in S. aureus. We show that insertion into the rot promoter by IS256 results in the derepression of cytotoxin expression and increased virulence. Taken together, this work provides new insight into evolutionary strategies by which S. aureus is able to modify its virulence properties and demonstrates a novel mechanism by which horizontal gene transfer directly impacts virulence through altering toxin regulation.

  5. Germline transformation of the diamondback moth, Plutella xylostella L., using the piggyBac transposable element.

    PubMed

    Martins, S; Naish, N; Walker, A S; Morrison, N I; Scaife, S; Fu, G; Dafa'alla, T; Alphey, L

    2012-08-01

    The diamondback moth, Plutella xylostella, is one of the most economically important agricultural pests. The larvae of this moth cause damage by feeding on the foliage of cruciferous vegetables such as cabbage, broccoli, cauliflower and rapeseed. Control generally comprises chemical treatment; however, the diamondback moth is renowned for rapid development of resistance to pesticides. Other methods, such as biological control, have not been able to provide adequate protection. Germline transformation of pest insects has become available in recent years as an enabling technology for new genetics-based control methods, such as the Release of Insects carrying a Dominant Lethal (RIDL(®) ). In the present study, we report the first transformation of the diamondback moth, using the piggyBac transposable element, by embryo microinjection. In generating transgenic strains using four different constructs, the function of three regulatory sequences in this moth was demonstrated in driving expression of fluorescent proteins. The transformation rates achieved, 0.48-0.68%, are relatively low compared with those described in other Lepidoptera, but not prohibitive, and are likely to increase with experience. We anticipate that germline transformation of the diamondback moth will permit the development of RIDL strains for use against this pest and facilitate the wider use of this species as a model organism for basic studies.

  6. 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

  7. Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements.

    PubMed

    Wang, Lu; Rishishwar, Lavanya; Mariño-Ramírez, Leonardo; Jordan, I King

    2016-12-19

    Transposable element (TE) derived sequences are known to contribute to the regulation of the human genome. The majority of known TE-derived regulatory sequences correspond to relatively ancient insertions, which are fixed across human populations. The extent to which human genetic variation caused by recent TE activity leads to regulatory polymorphisms among populations has yet to be thoroughly explored. In this study, we searched for associations between polymorphic TE (polyTE) loci and human gene expression levels using an expression quantitative trait loci (eQTL) approach. We compared locus-specific polyTE insertion genotypes to B cell gene expression levels among 445 individuals from 5 human populations. Numerous human polyTE loci correspond to both cis and trans eQTL, and their regulatory effects are directly related to cell type-specific function in the immune system. PolyTE loci are associated with differences in expression between European and African population groups, and a single polyTE loci is indirectly associated with the expression of numerous genes via the regulation of the B cell-specific transcription factor PAX5 The polyTE-gene expression associations we found indicate that human TE genetic variation can have important phenotypic consequences. Our results reveal that TE-eQTL are involved in population-specific gene regulation as well as transcriptional network modification.

  8. International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories.

    PubMed

    Ainouche, Abdelkader; Bétermier, Mireille; Chandler, Mick; Cordaux, Richard; Cristofari, Gaël; Deragon, Jean-Marc; Lesage, Pascale; Panaud, Olivier; Quesneville, Hadi; Vaury, Chantal; Vieira, Cristina; Vitte, Clémentine

    2012-10-30

    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.

  9. Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

    PubMed Central

    Stuart, Tim; Eichten, Steven R; Cahn, Jonathan; Karpievitch, Yuliya V; Borevitz, Justin O; Lister, Ryan

    2016-01-01

    Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity. Many common TE variants were associated with significantly altered expression of nearby genes, and a major fraction of inter-accession DNA methylation differences were associated with nearby TE insertions. Overall, this demonstrates that TE variants are a rich source of genetic diversity that likely plays an important role in facilitating epigenomic and transcriptional differences between individuals, and indicates a strong genetic basis for epigenetic variation. DOI: http://dx.doi.org/10.7554/eLife.20777.001 PMID:27911260

  10. The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human

    PubMed Central

    Qin, Sheng; Jin, Ping; Zhou, Xue; Chen, Liming; Ma, Fei

    2015-01-01

    MicroRNAs (miRNAs) are crucial regulators of gene expression at the post-transcriptional level in eukaryotes via targeting gene 3'-untranslated regions. Transposable elements (TEs) are considered as natural origins of some miRNAs. However, what miRNAs are and how these miRNAs originate and evolve from TEs remain unclear. We identified 409 TE-derived miRNAs (386 overlapped with TEs and 23 un-overlapped with TEs) which are derived from TEs in human. This indicates that the TEs play important roles in origin of miRNAs in human. In addition, we found that the proportions of miRNAs derived from TEs (MDTEs) in human are more than other vertebrates especially non-mammal vertebrates. Furthermore, we classified MDTEs into three types and found that TE head or tail sequences along with adjacent genomic sequences contribute to generation of human miRNAs. Our current study will improve the understanding of origin and evolution of human miRNAs. PMID:26115450

  11. Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies.

    PubMed

    Platt, Roy N; Blanco-Berdugo, Laura; Ray, David A

    2016-01-21

    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.

  12. The epigenetic regulation of transposable elements by PIWI-interacting RNAs in Drosophila.

    PubMed

    Saito, Kuniaki

    2013-01-01

    A mechanism is required to repress the expression and transposition of transposable elements (TEs) to ensure the stable inheritance of genomic information. Accumulating evidence indicates that small non-coding RNAs are important regulators of TEs. Among small non-coding RNAs, PIWI-interacting RNAs (piRNAs) serve as guide molecules for recognizing and silencing numerous TEs and work in collaboration with PIWI subfamily proteins in gonadal cells. Disruption of the piRNA pathway correlates with loss of proper genomic organization, gene expression control and fertility. Moreover, recent studies on the molecular mechanisms of piRNA biogenesis and on piRNA function have shown that piRNAs act as maternally inherited genic elements, transferring information about repressed TEs to progeny. These findings enable a molecular explanation of mysterious epigenetic phenomena, such as hybrid dysgenesis and TE adaptation with age. Here, I review our current knowledge of piRNAs derived from biochemical and genetic studies and discuss how small RNAs are utilized to maintain genome organization and to provide non-DNA genetic information. I mainly focus on Drosophila but also discuss comparisons with other species.

  13. 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

  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. Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts.

    PubMed

    Lisch, Damon; Slotkin, R Keith

    2011-01-01

    Over the past several years, there has been an explosion in our understanding of the mechanisms by which plant transposable elements (TEs) are epigenetically silenced and maintained in an inactive state over long periods of time. This highly efficient process results in vast numbers of inactive TEs; indeed, the majority of many plant genomes are composed of these quiescent elements. This observation has led to the rather static view that TEs represent an essentially inert portion of plant genomes. However, recent work has demonstrated that TE silencing is a highly dynamic process that often involves transcription of TEs at particular times and places during plant development. Plants appear to use transcripts from silenced TEs as an ongoing source of information concerning the mobile portion of the genome. In contrast to our understanding of silencing pathways, we know relatively little about the ways in which TEs evade silencing. However, vast differences in TE content between even closely related plant species suggest that they are often wildly successful at doing so. Here, we discuss TE activity in plants as the result of a constantly shifting balance between host strategies for TE silencing and TE strategies for escape and amplification.

  16. Spatio-temporal requirements for transposable element piRNA-mediated silencing during Drosophila oogenesis

    PubMed Central

    Dufourt, Jérémy; Dennis, Cynthia; Boivin, Antoine; Gueguen, Nathalie; Théron, Emmanuelle; Goriaux, Coline; Pouchin, Pierre; Ronsseray, Stéphane; Brasset, Emilie; Vaury, Chantal

    2014-01-01

    During Drosophila oogenesis, transposable element (TE) repression involves the Piwi-interacting RNA (piRNA) pathway which ensures genome integrity for the next generation. We developed a transgenic model to study repression of the Idefix retrotransposon in the germline. Using a candidate gene KD-approach, we identified differences in the spatio-temporal requirements of the piRNA pathway components for piRNA-mediated silencing. Some of them (Aub, Vasa, Spn-E) are necessary in very early stages of oogenesis within the germarium and appear to be less important for efficient TE silencing thereafter. Others (Piwi, Ago3, Mael) are required at all stages of oogenesis. Moreover, during early oogenesis, in the dividing cysts within the germarium, Idefix anti-sense transgenes escape host control, and this is associated with very low piwi expression. Silencing of P-element-based transgenes is also strongly weakened in these cysts. This region, termed the ‘Piwiless pocket’ or Pilp, may ensure that new TE insertions occur and are transmitted to the next generation, thereby contributing to genome dynamics. In contrast, piRNA-mediated silencing is strong in germline stem cells in which TE mobilization is tightly repressed ensuring the continued production of viable germline cysts. PMID:24288375

  17. Spatio-temporal requirements for transposable element piRNA-mediated silencing during Drosophila oogenesis.

    PubMed

    Dufourt, Jérémy; Dennis, Cynthia; Boivin, Antoine; Gueguen, Nathalie; Théron, Emmanuelle; Goriaux, Coline; Pouchin, Pierre; Ronsseray, Stéphane; Brasset, Emilie; Vaury, Chantal

    2014-02-01

    During Drosophila oogenesis, transposable element (TE) repression involves the Piwi-interacting RNA (piRNA) pathway which ensures genome integrity for the next generation. We developed a transgenic model to study repression of the Idefix retrotransposon in the germline. Using a candidate gene KD-approach, we identified differences in the spatio-temporal requirements of the piRNA pathway components for piRNA-mediated silencing. Some of them (Aub, Vasa, Spn-E) are necessary in very early stages of oogenesis within the germarium and appear to be less important for efficient TE silencing thereafter. Others (Piwi, Ago3, Mael) are required at all stages of oogenesis. Moreover, during early oogenesis, in the dividing cysts within the germarium, Idefix anti-sense transgenes escape host control, and this is associated with very low piwi expression. Silencing of P-element-based transgenes is also strongly weakened in these cysts. This region, termed the 'Piwiless pocket' or Pilp, may ensure that new TE insertions occur and are transmitted to the next generation, thereby contributing to genome dynamics. In contrast, piRNA-mediated silencing is strong in germline stem cells in which TE mobilization is tightly repressed ensuring the continued production of viable germline cysts.

  18. 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.

  19. BmTEdb: a collective database of transposable elements in the silkworm genome.

    PubMed

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

    2013-01-01

    The silkworm, Bombyx mori, is one of the major insect model organisms, and its draft and fine genome sequences became available in 2004 and 2008, respectively. Transposable elements (TEs) constitute ~40% of the silkworm genome. To better understand the roles of TEs in organization, structure and evolution of the silkworm genome, we used a combination of de novo, structure-based and homology-based approaches for identification of the silkworm TEs and identified 1308 silkworm TE families. These TE families and their classification information were organized into a comprehensive and easy-to-use web-based database, BmTEdb. Users are entitled to browse, search and download the sequences in the database. Sequence analyses such as BLAST, HMMER and EMBOSS GetORF were also provided in BmTEdb. This database will facilitate studies for the silkworm genomics, the TE functions in the silkworm and the comparative analysis of the insect TEs. Database URL: http://gene.cqu.edu.cn/BmTEdb/.

  20. 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

  1. 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

  2. Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions.

    PubMed

    Muramoto, Hiroki; Yagi, Shintaro; Hirabayashi, Keiji; Sato, Shinya; Ohgane, Jun; Tanaka, Satoshi; Shiota, Kunio

    2010-08-01

    Embryonic stem cells (ESCs) have a distinctive epigenome, which includes their genome-wide DNA methylation modification status, as represented by the ESC-specific hypomethylation of tissue-dependent and differentially methylated regions (T-DMRs) of Pou5f1 and Nanog. Here, we conducted a genome-wide investigation of sequence characteristics associated with T-DMRs that were differentially methylated between ESCs and somatic cells, by focusing on transposable elements including short interspersed elements (SINEs), long interspersed elements (LINEs) and long terminal repeats (LTRs). We found that hypomethylated T-DMRs were predominantly present in SINE-rich/LINE-poor genomic loci. The enrichment for SINEs spread over 300 kb in cis and there existed SINE-rich genomic domains spreading continuously over 1 Mb, which contained multiple hypomethylated T-DMRs. The characterization of sequence information showed that the enriched SINEs were relatively CpG rich and belonged to specific subfamilies. A subset of the enriched SINEs were hypomethylated T-DMRs in ESCs at Dppa3 gene locus, although SINEs are overall methylated in both ESCs and the liver. In conclusion, we propose that SINE enrichment is the genomic property of regions harboring hypomethylated T-DMRs in ESCs, which is a novel aspect of the ESC-specific epigenomic information.

  3. 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

  4. Patterns of Repeat-Induced Point Mutation in Transposable Elements of Basidiomycete Fungi

    PubMed Central

    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

  5. Chromosomal Replication Dynamics and Interaction with the β Sliding Clamp Determine Orientation of Bacterial Transposable Elements

    PubMed Central

    Gómez, Manuel J.; Díaz-Maldonado, Héctor; González-Tortuero, Enrique; López de Saro, Francisco J.

    2014-01-01

    Insertion sequences (ISs) are small transposable elements widespread in bacterial genomes, where they play an essential role in chromosome evolution by stimulating recombination and genetic flow. Despite their ubiquity, it is unclear how ISs interact with the host. Here, we report a survey of the orientation patterns of ISs in bacterial chromosomes with the objective of gaining insight into the interplay between ISs and host chromosomal functions. We find that a significant fraction of IS families present a consistent and family-specific orientation bias with respect to chromosomal DNA replication, especially in Firmicutes. Additionally, we find that the transposases of up to nine different IS families with different transposition pathways interact with the β sliding clamp, an essential replication factor, suggesting that this is a widespread mechanism of interaction with the host. Although we find evidence that the interaction with the β sliding clamp is common to all bacterial phyla, it also could explain the observed strong orientation bias found in Firmicutes, because in this group β is asymmetrically distributed during synthesis of the leading or lagging strands. Besides the interaction with the β sliding clamp, other asymmetries also play a role in the biased orientation of some IS families. The utilization of the highly conserved replication sliding clamps suggests a mechanism for host regulation of IS proliferation and also a universal platform for IS dispersal and transmission within bacterial populations and among phylogenetically distant species. PMID:24614824

  6. 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.

  7. Miniaturization of a SWIR hyperspectral imager

    NASA Astrophysics Data System (ADS)

    Warren, Christopher P.; Pfister, William; Even, Detlev; Velasco, Arleen; Yee, Selwyn; Breitwieser, David; Naungayan, Joseph

    2011-05-01

    A new approach for the design and fabrication of a miniaturized SWIR Hyperspectral imager is described. Previously, good results were obtained with a VNIR Hyperspectral imager, by use of light propagation within bonded solid blocks of fused silica. These designs use the Offner design form, providing excellent, low distortion imaging. The same idea is applied to the SWIR Hyperspectral imager here, resulting in a microHSITM SWIR Hyperspectral sensor, capable of operating in the 850-1700 nm wavelength range. The microHSI spectrometer weighs 910 g from slit input to camera output. This spectrometer can accommodate custom foreoptics to adapt to a wide range of fields-of-view (FOV). The current application calls for a 15 degree FOV, and utilizes an InGaAs image sensor with a spatial format of 640 x 25 micron pixels. This results in a slit length of 16 mm, and a foreoptics focal length of 61 mm, operating at F# = 2.8. The resulting IFOV is 417 μrad for this application, and a spectral dispersion of 4.17 nm/pixel. A prototype SWIR microHSI was fabricated, and the blazed diffraction grating was embedded within the optical blocks, resulting in a 72% diffraction efficiency at the wavelength of 1020 nm. This spectrometer design is capable of accommodating slit lengths of up to 25.6 mm, which opens up a wide variety of applications. The microHSI concepts can be extended to other wavelength regions, and a miniaturized LWIR microHSI sensor is in the conceptual design stage.

  8. Miniaturized radioisotope solid state power sources

    NASA Astrophysics Data System (ADS)

    Fleurial, J.-P.; Snyder, G. J.; Patel, J.; Herman, J. A.; Caillat, T.; Nesmith, B.; Kolawa, E. A.

    2000-01-01

    Electrical power requirements for the next generation of deep space missions cover a wide range from the kilowatt to the milliwatt. Several of these missions call for the development of compact, low weight, long life, rugged power sources capable of delivering a few milliwatts up to a couple of watts while operating in harsh environments. Advanced solid state thermoelectric microdevices combined with radioisotope heat sources and energy storage devices such as capacitors are ideally suited for these applications. By making use of macroscopic film technology, microgenrators operating across relatively small temperature differences can be conceptualized for a variety of high heat flux or low heat flux heat source configurations. Moreover, by shrinking the size of the thermoelements and increasing their number to several thousands in a single structure, these devices can generate high voltages even at low power outputs that are more compatible with electronic components. Because the miniaturization of state-of-the-art thermoelectric module technology based on Bi2Te3 alloys is limited due to mechanical and manufacturing constraints, we are developing novel microdevices using integrated-circuit type fabrication processes, electrochemical deposition techniques and high thermal conductivity substrate materials. One power source concept is based on several thermoelectric microgenerator modules that are tightly integrated with a 1.1W Radioisotope Heater Unit. Such a system could deliver up to 50mW of electrical power in a small lightweight package of approximately 50 to 60g and 30cm3. An even higher degree of miniaturization and high specific power values (mW/mm3) can be obtained when considering the potential use of radioisotope materials for an alpha-voltaic or a hybrid thermoelectric/alpha-voltaic power source. Some of the technical challenges associated with these concepts are discussed in this paper. .

  9. 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.

  10. Reestablishment of radiographic kidney size in Miniature Schnauzer dogs

    PubMed Central

    SOHN, Jungmin; YUN, Sookyung; LEE, Jeosoon; CHANG, Dongwoo; CHOI, Mincheol; YOON, Junghee

    2016-01-01

    Kidney size may be altered in renal diseases, and the detection of kidney size alteration has diagnostic and prognostic values. We hypothesized that radiographic kidney size, the kidney length to the second lumbar vertebra (L2) length ratio, in normal Miniature Schnauzer dogs may be overestimated due to their shorter vertebral length. This study was conducted to evaluate radiographic and ultrasonographic kidney size and L2 length in clinically normal Miniature Schnauzers and other dog breeds to evaluate the effect of vertebral length on radiographic kidney size and to reestablish radiographic kidney size in normal Miniature Schnauzers. Abdominal radiographs and ultrasonograms from 49 Miniature Schnauzers and 54 other breeds without clinical evidence of renal disease and lumbar vertebral abnormality were retrospectively evaluated. Radiographic kidney size, in the Miniature Schnauzer (3.31 ± 0.26) was significantly larger than that in other breeds (2.94 ± 0.27). Relative L2 length, the L2 length to width ratio, in the Miniature Schnauzer (1.11 ± 0.06) was significantly shorter than that in other breeds (1.21 ± 0.09). However, ultrasonographic kidney sizes, kidney length to aorta diameter ratios, were within or very close to normal range both in the Miniature Schnauzer (6.75 ± 0.67) and other breeds (7.16 ± 1.01). Thus, Miniature Schnauzer dogs have breed-specific short vertebrae and consequently a larger radiographic kidney size, which was greater than standard reference in normal adult dogs. Care should be taken when evaluating radiographic kidney size in Miniature Schnauzers to prevent falsely diagnosed renomegaly. PMID:27594274

  11. Diversity of Slovenian maize (Zea mays) populations by Hbr (MITE) markers and morphological traits.

    PubMed

    Kavar, T; Meglic, V; Rozman, L

    2007-09-01

    Hbr markers are based on location presence/absence of the Heartbreaker family of miniature inverted repeat transposable elements (MITEs). Together with the cost-effective technique--Hbr display were developed in 2000. We chose 15 populations from the Slovenian maize germplasm bank and described ten individual samples per each population by 268 Hbr markers and 35 morphological traits (IPGRI descriptors). Samples from the same population had highly similar DNA fingerprints, while the between populations differences were very high. Therefore, only a minor part of the total genetic variance existed within populations (23.3%), and the major part among populations (76.7%). Beli zob (the only dent type population) and stajerski dvanajsterec were the most divergent populations, others were closely related. They shared the majority of bands in the way that each band was shared by different set of populations. This is suggesting the origin from the common gene pool and the high extent of migrations.

  12. Dominant short repeated sequences in bacterial genomes.

    PubMed

    Avershina, Ekaterina; Rudi, Knut

    2015-03-01

    We use a novel multidimensional searching approach to present the first exhaustive search for all possible repeated sequences in 166 genomes selected to cover the bacterial domain. We found an overrepresentation of repeated sequences in all but one of the genomes. The most prevalent repeats by far were related to interspaced short palindromic repeats (CRISPRs)—conferring bacterial adaptive immunity. We identified a deep branching clade of thermophilic Firmicutes containing the highest number of CRISPR repeats. We also identified a high prevalence of tandem repeated heptamers. In addition, we identified GC-rich repeats that could potentially be involved in recombination events. Finally, we identified repeats in a 16322 amino acid mega protein (involved in biofilm formation) and inverted repeats flanking miniature transposable elements (MITEs). In conclusion, the exhaustive search for repeated sequences identified new elements and distribution of these, which has implications for understanding both the ecology and evolution of bacteria.

  13. Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction.

    PubMed

    Wang, Xia; Xu, Yuantao; Zhang, Siqi; Cao, Li; Huang, Yue; Cheng, Junfeng; Wu, Guizhi; Tian, Shilin; Chen, Chunli; Liu, Yan; Yu, Huiwen; Yang, Xiaoming; Lan, Hong; Wang, Nan; Wang, Lun; Xu, Jidi; Jiang, Xiaolin; Xie, Zongzhou; Tan, Meilian; Larkin, Robert M; Chen, Ling-Ling; Ma, Bin-Guang; Ruan, Yijun; Deng, Xiuxin; Xu, Qiang

    2017-04-10

    The emergence of apomixis-the transition from sexual to asexual reproduction-is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.

  14. Distribution of Unlinked Receptor Sites for Transposed Ac Elements from the Bz-M2(ac) Allele in Maize

    PubMed Central

    Dooner, H. K.; Belachew, A.; Burgess, D.; Harding, S.; Ralston, M.; Ralston, E.

    1994-01-01

    We have shown before that the Ac element from the maize bz-m2(Ac) allele, located in the short arm of chromosome 9 (9S), transposes preferentially to sites that are linked to the bz donor locus. Yet, about half of the Ac transpositions recovered from bz-m2(Ac) are in receptor sites not linked to the donor locus. In this study, we have analyzed the distribution of those unlinked receptor sites. Thirty-seven transposed Ac (trAc) elements that recombined independently of the bz locus were mapped using a set of wx reciprocal translocations. We found that the distribution of unlinked receptor sites for trAs was not random. Ten trAcs mapped to 9L, i.e., Ac had transposed to sites physically, if not genetically, linked to the donor site. Among chromosomes other than 9, the Ac element of bz-m2(Ac) appeared to have transposed preferentially to certain chromosomes, such as 5 and 7, but infrequently to others, such as 1, the longest chromosome in the maize genome. The seven trAc elements in chromosome 5 were mapped relative to markers in 5S and 5L and localized to both arms of 5. We also investigated the transposition of Ac to the homolog of the donor chromosome. We found that Ac rarely transposes from bz-m2(Ac) to the homologous chromosome 9. The clustering of Ac receptor sites around the donor locus has been taken to mean that a physical association between the donor site and nearby receptor sites occurs during transposition. The preferential occurrence of 9L among chromosomes harboring unlinked receptor sites would be expected according to this model, since sites in 9L would tend to be physically closer to 9S than sites in other chromosomes. The nonrandom pattern seen among the remaining chromosomes could reflect an underlying nuclear architecture, i.e., an ordering of the chromosomes in the interphase nucleus, as suggested from previous cytological observations. PMID:8138163

  15. 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.

  16. Miniature in vivo robotics and novel robotic surgical platforms.

    PubMed

    Shah, Bhavin C; Buettner, Shelby L; Lehman, Amy C; Farritor, Shane M; Oleynikov, Dmitry

    2009-05-01

    Robotic surgical systems, such as the da Vinci Surgical System (Intuitive Surgical, Inc., Sunnyvale, California), have revolutionized laparoscopic surgery but are limited by large size, increased costs, and limitations in imaging. Miniature in vivo robots are being developed that are inserted entirely into the peritoneal cavity for laparoscopic and natural orifice transluminal endoscopic surgical (NOTES) procedures. In the future, miniature camera robots and microrobots should be able to provide a mobile viewing platform. This article discusses the current state of miniature robotics and novel robotic surgical platforms and the development of future robotic technology for general surgery and urology.

  17. A new miniaturized fiber positioning node for LAMOST

    NASA Astrophysics Data System (ADS)

    Guo, Liang; Gu, Yonggang; Shen, Yuran; Zhai, Chao

    2016-07-01

    To distribute more fiber positioning nodes on the LAMOST focal plate, two steps are proposed to miniaturize the fiber positioning node in this paper. The first step is to miniaturize the mechanical device of the fiber positioning node. The second step is to redesign the entire wireless driving board using smaller and performance-higher devices. As a result, the size of the new miniaturized fiber positioning node has to be reduced by above 40% and the dense of fiber positioning nodes on focal plate increases by 20% at least.

  18. 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

  19. 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

  20. 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

  1. Holliday Junctions Are Associated with Transposable Element Sequences in the Human Genome.

    PubMed

    Ladias, Paris; Markopoulos, Georgios; Lazaros, Leandros; Markoula, Sofia; Tzavaras, Theodore; Georgiou, Ioannis

    2016-02-13

    Holliday junctions (HJs) constitute important intermediate structures for many cell functions such as DNA recombination and DNA repair. They derive from a 10-nt degenerate sequence, with a 3-nt core motif. In this study, we explored the human genome whether the HJ degenerate sequence associates with transposable elements (TEs) and mainly with those of the active and inactive ALU, LINE, SVA and HERV families. We identified six different forms of the HJ sequence motif, and we located the genomic coordinates of sequences containing both HJs and TEs. From 2982 total HJs, a significant number of 1319 TE-associated HJs were found, with a median distribution of 1 per 2.4 Mb. The HJs with higher GC content were observed more frequently at the genome. A high percentage of HJs were associated with all main TE families, with specificity for particular active or inactive elements: DNA elements and the retroelements ALUs, LINEs and HERVs up to 41.94%, 72.72%, 42.94% and 84.5%, respectively. Phylogenetic analysis revealed that HJs occur in both active and inactive TEs. Furthermore, the TE-associated HJs were almost exclusively found within a distance less than 1 Mb from human genes, while only 23 were not associated with any genes. This is the first report associating human HJs, with mobile elements. Our data pinpoint that particular HJ forms show preference for specific active retrotransposon families of ALUs and LINEs, suggesting that retrotransposon-incorporated HJs may relocate or replicate in the genome through retrotransposition, contributing to recombination, genome plasticity and DNA repair.

  2. Rice transposable elements are characterized by various methylation environments in the genome

    PubMed Central

    Takata, Miwako; Kiyohara, Akihiro; Takasu, Atsuko; Kishima, Yuji; Ohtsubo, Hisako; Sano, Yoshio

    2007-01-01

    Background Recent studies using high-throughput methods have revealed that transposable elements (TEs) are a comprehensive target for DNA methylation. However, the relationship between TEs and their genomic environment regarding methylation still remains unclear. The rice genome contains representatives of all known TE families with different characteristics of chromosomal distribution, structure, transposition, size, and copy number. Here we studied the DNA methylation state around 12 TEs in nine genomic DNAs from cultivated rice strains and their closely related wild strains. Results We employed a transposon display (TD) method to analyze the methylation environments in the genomes. The 12 TE families, consisting of four class I elements, seven class II elements, and one element of a different class, were differentially distributed in the rice chromosomes: some elements were concentrated in the centromeric or pericentromeric regions, but others were located in euchromatic regions. The TD analyses revealed that the TE families were embedded in flanking sequences with different methylation degrees. Each TE had flanking sequences with similar degrees of methylation among the nine rice strains. The class I elements tended to be present in highly methylated regions, while those of the class II elements showed widely varying degrees of methylation. In some TE families, the degrees of methylation were markedly lower than the average methylation state of the genome. In two families, dramatic changes of the methylation state occurred depending on the distance from the TE. Conclusion Our results demonstrate that the TE families in the rice genomes can be characterized by the methylation states of their surroundings. The copy number and degree of conservation of the TE family are not likely to be correlated with the degree of methylation. We discuss possible relationships between the methylation state of TEs and their surroundings. This is the first report demonstrating

  3. 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

  4. Transposable element derived DNaseI-hypersensitive sites in the human genome

    PubMed Central

    Mariño-Ramírez, Leonardo; Jordan, I King

    2006-01-01

    Background Transposable elements (TEs) are abundant genomic sequences that have been found to contribute to genome evolution in unexpected ways. Here, we characterize the evolutionary and functional characteristics of TE-derived human genome regulatory sequences uncovered by the high throughput mapping of DNaseI-hypersensitive (HS) sites. Results Human genome TEs were found to contribute substantially to HS regulatory sequences characterized in CD4+ T cells: 23% of HS sites contain TE-derived sequences. While HS sites are far more evolutionarily conserved than non HS sites in the human genome, consistent with their functional importance, TE-derived HS sites are highly divergent. Nevertheless, TE-derived HS sites were shown to be functionally relevant in terms of driving gene expression in CD4+ T cells. Genes involved in immune response are statistically over-represented among genes with TE-derived HS sites. A number of genes with both TE-derived HS sites and immune tissue related expression patterns were found to encode proteins involved in immune response such as T cell specific receptor antigens and secreted cytokines as well as proteins with clinical relevance to HIV and cancer. Genes with TE-derived HS sites have higher average levels of sequence and expression divergence between human and mouse orthologs compared to genes with non TE-derived HS sites. Conclusion The results reported here support the notion that TEs provide a specific genome-wide mechanism for generating functionally relevant gene regulatory divergence between evolutionary lineages. Reviewers This article was reviewed by Wolfgang J. Miller (nominated by Jerzy Jurka), Itai Yanai and Mikhail S.Gelfand. PMID:16857058

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. The genomic landscape shaped by selection on transposable elements across 18 mouse strains

    PubMed Central

    2012-01-01

    Background Transposable element (TE)-derived sequence dominates the landscape of mammalian genomes and can modulate gene function by dysregulating transcription and translation. Our current knowledge of TEs in laboratory mouse strains is limited primarily to those present in the C57BL/6J reference genome, with most mouse TEs being drawn from three distinct classes, namely short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs) and the endogenous retrovirus (ERV) superfamily. Despite their high prevalence, the different genomic and gene properties controlling whether TEs are preferentially purged from, or are retained by, genetic drift or positive selection in mammalian genomes remain poorly defined. Results Using whole genome sequencing data from 13 classical laboratory and 4 wild-derived mouse inbred strains, we developed a comprehensive catalogue of 103,798 polymorphic TE variants. We employ this extensive data set to characterize TE variants across the Mus lineage, and to infer neutral and selective processes that have acted over 2 million years. Our results indicate that the majority of TE variants are introduced though the male germline and that only a minority of TE variants exert detectable changes in gene expression. However, among genes with differential expression across the strains there are twice as many TE variants identified as being putative causal variants as expected. Conclusions Most TE variants that cause gene expression changes appear to be purged rapidly by purifying selection. Our findings demonstrate that past TE insertions have often been highly deleterious, and help to prioritize TE variants according to their likely contribution to gene expression or phenotype variation. PMID:22703977

  11. 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

  12. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates.

    PubMed

    Chalopin, Domitille; Naville, Magali; Plard, Floriane; Galiana, Delphine; Volff, Jean-Nicolas

    2015-01-09

    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.

  13. 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

  14. Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence.

    PubMed

    Oppold, Ann-Marie; Schmidt, Hanno; Rose, Marcel; Hellmann, Sören Lukas; Dolze, Florian; Ripp, Fabian; Weich, Bettina; Schmidt-Ott, Urs; Schmidt, Erwin; Kofler, Robert; Hankeln, Thomas; Pfenninger, Markus

    2017-03-18

    Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), thus contributing to the evolution of endogenous genetic barriers and eventually cause population divergence. We investigated differential TE abundance among conspecific populations of the non-biting midge Chironomus riparius and evaluated their potential role in causing endogenous genetic incompatibilities between these populations. We focussed on a Chironomus-specific TE, the minisatellite-like Cla-element, whose activity is associated with speciation in the genus. Using a newly generated and annotated draft genome for a genomic study with five natural C. riparius populations, we found highly population-specific TE insertion patterns with many private insertions. A significant correlation of the pairwise FST estimated from genome-wide single nucleotide polymorphisms (SNPs) and the FST estimated from TEs, is consistent with drift as the major force driving TE population differentiation. However, the significantly higher Cla-element FST level due to a high proportion of differentially fixed Cla-element insertions also indicates selection against segregating (i.e. heterozygous) insertions. With reciprocal crossing experiments and fluorescent in-situ hybridisation of Cla-elements to polytene chromosomes, we documented phenotypic effects on female fertility and chromosomal mispairings. We propose that the inferred negative selection on heterozygous Cla-element insertions may cause endogenous genetic barriers and therefore acts as DMI among C. riparius populations. The intrinsic genomic turnover exerted by TEs may thus have a direct impact on population divergence that is operationally different from drift and local adaptation. This article is protected by copyright. All rights reserved.

  15. 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

  16. Vibrio cholerae conjugative plasmid pSJ15 contains transposable prophage dVcA1.

    PubMed Central

    Johnson, S R; Romig, W R

    1981-01-01

    Evidence is presented that defective prophage dVcA1 in Vibrio cholerae strain 162 was transposed to the hybrid P::Tn1 plasmid pSJ5. Properties of the resulting conjugative plasmid, pSJ15, indicated that bacteriophage VcA1, like coliphage Mu, can insert at many sites. By analogy with other Hfr-like donors, the high-frequency, polarized chromosomal transfer mediated by plasmid pSJ15 in strain 162 appeared to depend on plasmid integration through the homologous dVcA1 sequences in both replicons. When strain 162(pSJ15) donors were mated to the nonlysogenic El Tor strain RJ1, many potential ampicillin-resistant transconjugants were zygotically induced. However, surviving transconjugants (i) were immune to phage VcA1, (ii) cotransferred immunity and ampicillin resistance to nonlysogenic recipients, and (iii) did not preferentially transfer any chromosomal markers. Recombinant plasmids that transferred wild-type VcA1 prophages were readily isolated from strain RJ1 (VcA1+) lysogens that contained plasmid pSJ15. Physical measurements revealed that plasmid pSJ15 and the recombinant plasmids were about one VcA1 genome (22 to 24 megadaltons) larger than the 51-megadalton pSJ5 plasmid. Similar Hfr-like donors were constructed by introducing plasmid pSJ15 into different strain RJ1 (VcA1+) lysogens. Transfer properties of these donors indicated that the VcA1 prophage was integrated at several sites in the strain RJ1 chromosome. Images PMID:6260754

  17. Effects of Transposable Elements on the Expression of the Forked Gene of Drosophila Melanogaster

    PubMed Central

    Hoover, K. K.; Chien, A. J.; Corces, V. G.

    1993-01-01

    The products of the forked gene are involved in the formation and/or maintenance of a temporary fibrillar structure within the developing bristle rudiment of Drosophila melanogaster. Mutations in the forked locus alter this structure and result in aberrant development of macrochaetae, microchaetae and trichomes. The locus has been characterized at the molecular level by walking, mutant characterization and transcript analysis. Expression of the six forked transcripts is temporally restricted to midlate pupal development. At this time, RNAs of 6.4, 5.6, 5.4, 2.5, 1.9 and 1.1 kilobases (kb) are detected by Northern analysis. The coding region of these RNAs has been found to be within a 21-kb stretch of genomic DNA. The amino terminus of the proteins encoded by the 5.4- and 5.6-kb forked transcripts contain tandem copies of ankyrin-like repeats that may play an important role in the function of forked-encoded products. The profile of forked RNA expression is altered in seven spontaneous mutations characterized during this study. Three forked mutations induced by the insertion of the gypsy retrotransposon contain a copy of this element inserted into an intron of the gene. In these mutants, the 5.6-, 5.4- and 2.5-kb forked mRNAs are truncated via recognition of the polyadenylation site in the 5' long terminal repeat of the gypsy retrotransposon. These results help explain the role of the forked gene in fly development and further our understanding of the role of transposable elements in mutagenesis. PMID:8244011

  18. 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.

  19. 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.

  20. 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)

  1. 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)

  2. Optimum contact conditions for miniaturized surface acoustic wave linear motor

    PubMed

    Takasaki; Kurosawa; Higuchi

    2000-03-01

    This paper reports the successful operation of a 70 MHz driving surface acoustic wave (SAW) linear motor with a miniaturized stator transducer. This paper also deals with an investigation into an optimized slider design for the miniaturized SAW linear motor. The performance of three silicon type sliders, with different projection size, was compared. Output forces of the three sliders were measured with change of pre-load. It was found that the slider with smaller projection tended to produce greater output force.

  3. Computer-Aided High Precision Verification Of Miniature Spring Structure

    NASA Astrophysics Data System (ADS)

    Bow, Sing T.; Wang, Da-hao; Chen, Tsung-sheng; Newell, Darrell E.

    1990-01-01

    A system is proposed for the high precision on-line verification of the minia-ture spring structure, including overall height, diameters of various coils as well as pitches between neighboring coils of the miniature conical springs. High preci-sion measurements without physical contact and short processing time are achieved. Deformations of any kind on the conical springs can be identified even from the worst viewing direction.

  4. 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.

  5. Development of a Prototype Miniature Silicon Microgyroscope

    PubMed Central

    Xia, Dunzhu; Chen, Shuling; Wang, Shourong

    2009-01-01

    A miniature vacuum-packaged silicon microgyroscope (SMG) with symmetrical and decoupled structure was designed to prevent unintended coupling between drive and sense modes. To ensure high resonant stability and strong disturbance resisting capacity, a self-oscillating closed-loop circuit including an automatic gain control (AGC) loop based on electrostatic force feedback is adopted in drive mode, while, dual-channel decomposition and reconstruction closed loops are applied in sense mode. Moreover, the temperature effect on its zero bias was characterized experimentally and a practical compensation method is given. The testing results demonstrate that the useful signal and quadrature signal will not interact with each other because their phases are decoupled. Under a scale factor condition of 9.6 mV/°/s, in full measurement range of ± 300 deg/s, the zero bias stability reaches 15°/h with worse-case nonlinearity of 400 ppm, and the temperature variation trend of the SMG bias is thus largely eliminated, so that the maximum bias value is reduced to one tenth of the original after compensation from -40 °C to 80 °C. PMID:22408543

  6. Miniaturized Amperometric Solid Electrolyte Carbon Dioxide Sensors

    NASA Technical Reports Server (NTRS)

    Hunter, G. W.; Xu, J. C.; Liu, C. C.; Hammond, J. W.; Ward, B.; Lukco, D.; Lampard, P.; Artale, M.; Androjna, D.

    2006-01-01

    A miniaturized electrochemical carbon dioxide (CO2) sensor using Na3Z r2Si2PO12 (NASICON) as a solid electrolyte has been fabricated and de monstrated. Microfabrication techniques were used for sensor fabricat ion to yield a sensing area around 1.0 mm x 1.1 mm. The NASICON solid electrolyte and the Na2CO3/BaCO3 (1:1.7 molar ratio) auxiliary elect rolyte were deposited by sputtering in between and on top of the inte rdigitated finger-shaped platinum electrodes. This structure maximize s the length of the three-phase boundary (electrode, solid electrolyt e, and auxiliary electrolyte), which is critical for gas sensing. The robust CO2 sensor operated up to 600 C in an amperometric mode and a ttempts were made to optimize sensor operating parameters. Concentrat ions of CO2 between 0.02% and 4% were detected and the overall sensor performance was evaluated. Linear response of sensor current output to ln[CO2 concentration] ranging from 0.02% to 1% was achieved.

  7. Miniaturized technology for DNA typing: cassette PCR.

    PubMed

    Manage, Dammika P; Pilarski, Linda M

    2015-01-01

    With the smaller size, low cost, and rapid testing capabilities, miniaturized lab-on-a-chip devices can change the way medical diagnostics are currently performed in the health-care system. We have demonstrated such a device that is self-contained, simple, disposable, and inexpensive. It is capable of performing DNA amplification on an inexpensive instrument suitable for near point of care settings. This technology will enable on the spot evaluation of patients in the clinic for faster medical decision-making and more informed therapeutic choices. Our device, a gel capillary cassette, termed cassette PCR, contains capillary reaction units each holding a defined primer set, with arrays of capillary reaction units for simultaneously detecting multiple targets. With the exception of the sample to be tested, each capillary reaction unit holds all the reagents needed for PCR in a desiccated form that can be stored at room temperature for up to 3 months and even longer in colder conditions. It relies on capillary forces for sample delivery of microliter volumes through capillaries, hence avoiding the need for pumps or valves. In the assembled cassette, the wax architecture supporting the capillaries melts during the PCR and acts as a vapor barrier as well as segregating capillaries with different primer sets. No other chip sealing techniques are required. Cassette PCR accepts raw samples such as urine, genital swabs, and blood. The cassette is made with off-the-shelf components and contains integrated positive and negative controls.

  8. Antenna Miniaturization Using Koch Snowflake Fractal Geometry

    NASA Astrophysics Data System (ADS)

    Minal, Dhama, Nitin

    2010-11-01

    The Wireless Industry is witnessing an volatile emergence today in present era. Also requires the performance over several frequency bands or are reconfigurable as the demands on the system changes. This Paper Presents Rectangular, Koch Fractal Patch Antennas on Single and Multilayer Substrate With and Without Air-Gap using Advanced Design System Simulator (ADS). Fractal Antenna provides Miniaturization over conventional microstrip Antennas. The Antennas Have Been Designed on FR4 substrate with ∈ = 4.2, h = 1.53 and the initial Dimension of the simple Rectangular Patch is 36.08 * 29.6 mm. The experimental Resonant Frequencies of the Fractal Patch with 1st, 2nd & 3rd are observed 2.22, 2.14 & 2.02 GHz Respectively in comparison to Rectangular Patch with 2.43 GHz. The reduced Impedance bandwidth of the Fractal Patch has been improved by designing the patch over multilayer substrate with varying Air-gap between two Substrate. As we increase the air- gap between the two substrate layer further enhancement in impedance bandwidth of Fractal antenna has been Obtained. The Radiation pattern of Koch Fractal antenna is as similar to rectangular patch antenna but with better H-plane Cross Polarization for fractal patch. The all simulated Results are in close Agreement with experimental Results.

  9. Miniaturized Technologies for Enhancement of Motor Plasticity

    PubMed Central

    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

  10. Computational investigation of miniature trailing edge effectors

    NASA Astrophysics Data System (ADS)

    Lee, Hak-Tae

    Miniature trailing edge effectors (MiTEs) are small flaps (typically 1% to 5% chord) actuated with deflection angles of up to 90 degrees. The small size, combined with little required power and good control authority, enables the device to be used for high bandwidth control as well as conventional attitude control. However, some of the aerodynamic characteristics of these devices are complex and poorly understood. This research investigated the aerodynamics of MiTEs using incompressible Navier-Stokes flow solvers, INS2D and INS3D. To understand the flow structure and establish a parametric database, two dimensional steady-state computations were performed for MiTEs with various geometries and flow conditions. Time accurate computations were used to resolve the unsteady characteristics including transient response and vortex shedding phenomena. The frequency response was studied to fully identify the dynamics of MiTEs. Three dimensional computations show the change in control effectiveness with respect to the spanwise length of MiTEs as well as the spanwise lift distribution induced by these devices. Based on the CFD results, an approximate vortex panel model was developed for design purposes that reproduces the key characteristics of MiTEs. Two application areas for MiTEs were explored. Flutter suppression was demonstrated by combining a finite element structural model with the vortex panel model. The application of MiTEs to augment maximum lift and improve the post stall behavior of an airfoil was also investigated.

  11. Miniaturization and globalization of clinical laboratory activities.

    PubMed

    Melo, Murilo R; Clark, Samantha; Barrio, Daniel

    2011-04-01

    Clinical laboratories provide an invaluable service to millions of people around the world in the form of quality diagnostic care. Within the clinical laboratory industry the impetus for change has come from technological development (miniaturization, nanotechnology, and their collective effect on point-of-care testing; POCT) and the increasingly global nature of laboratory services. Potential technological gains in POCT include: the development of bio-sensors, microarrays, genetics and proteomics testing, and enhanced web connectivity. In globalization, prospective opportunities lie in: medical tourism, the migration of healthcare workers, cross-border delivery of testing, and the establishment of accredited laboratories in previously unexplored markets. Accompanying these impressive opportunities are equally imposing challenges. Difficulty transitioning from research to clinical use, poor infrastructure in developing countries, cultural differences and national barriers to global trade are only a few examples. Dealing with the issues presented by globalization and the impact of developing technology on POCT, and on the clinical laboratory services industry in general, will be a daunting task. Despite such concerns, with appropriate countermeasures it will be possible to address the challenges posed. Future laboratory success will be largely dependent on one's ability to adapt in this perpetually shifting landscape.

  12. A locust-inspired miniature jumping robot.

    PubMed

    Zaitsev, Valentin; Gvirsman, Omer; Ben Hanan, Uri; Weiss, Avi; Ayali, Amir; Kosa, Gabor

    2015-11-25

    Unmanned ground vehicles are mostly wheeled, tracked, or legged. These locomotion mechanisms have a limited ability to traverse rough terrain and obstacles that are higher than the robot's center of mass. In order to improve the mobility of small robots it is necessary to expand the variety of their motion gaits. Jumping is one of nature's solutions to the challenge of mobility in difficult terrain. The desert locust is the model for the presented bio-inspired design of a jumping mechanism for a small mobile robot. The basic mechanism is similar to that of the semilunar process in the hind legs of the locust, and is based on the cocking of a torsional spring by wrapping a tendon-like wire around the shaft of a miniature motor. In this study we present the jumping mechanism design, and the manufacturing and performance analysis of two demonstrator prototypes. The most advanced jumping robot demonstrator is power autonomous, weighs 23 gr, and is capable of jumping to a height of 3.35 m, covering a distance of 1.37 m.

  13. A new miniaturized atomic magnetic gradiometer

    NASA Astrophysics Data System (ADS)

    Sheng, Dong; Perry, Abigail; Krzyzewski, Sean; Geller, Shawn; Knappe, Svenja; Kitching, John

    2016-05-01

    We report the development of a new miniaturized magnetic gradiometer using alkali atoms. The gradiometer, with the length of 5 cm and cross section diameter of 11 mm, is made of two chip-scale atomic magnetometers placed on a printed optical bench with a defined separation. Both magnetometers work in the spin-exchange relaxation free regime, share the same beam for pumping and probing to reduce the common mode noises from the lasers, and atom temperature is independently controlled by heating beams at telecom wavelength. With 2 cm baseline, 1 mW pumping beam power, and less than 400 mW input heating beam power, we measure a noise level of 15 fT/ Hz1/2 from the subtraction of two magnetometer outputs, which corresponds to a gradient field sensitivity of 7.5 fT/ Hz1/2/cm. The maximum common mode magnetic field noise rejection is up to 1000 within the gradiometer bandwidth. This device is useful in many fields that require both sensitive gradient field information and high common mode noise cancellation. We are also developing a new hybrid system based on this device to improve its dynamical range.

  14. 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.

  15. Miniature thermo-electric cooled cryogenic pump

    DOEpatents

    Keville, R.F.

    1997-11-18

    A miniature thermo-electric cooled cryogenic pump is described for removing residual water molecules from an inlet sample prior to sample analysis in a mass spectroscopy system, such as ion cyclotron resonance (ICR) mass spectroscopy. The cryogenic pump is a battery operated, low power (<1.6 watts) pump with a {Delta}T=100 C characteristic. The pump operates under vacuum pressures of 5{times}10{sup {minus}4} Torr to ultra high vacuum (UHV) conditions in the range of 1{times}10{sup {minus}7} to 3{times}10{sup {minus}9} Torr and will typically remove partial pressure, 2{times}10{sup {minus}7} Torr, residual water vapor. The cryogenic pump basically consists of an inlet flange piece, a copper heat sink with a square internal bore, four two tier Peltier (TEC) chips, a copper low temperature square cross sectional tubulation, an electronic receptacle, and an exit flange piece, with the low temperature tubulation being retained in the heat sink at a bias angle of 5{degree}, and with the TECs being positioned in parallel to each other with a positive potential being applied to the top tier thereof. 2 figs.

  16. Miniature thermo-electric cooled cryogenic pump

    DOEpatents

    Keville, Robert F.

    1997-01-01

    A miniature thermo-electric cooled cryogenic pump for removing residual water molecules from an inlet sample prior to sample analysis in a mass spectroscopy system, such as ion cyclotron resonance (ICR) mass spectroscopy. The cryogenic pump is a battery operated, low power (<1.6 watts) pump with a .DELTA.T=100.degree. C. characteristic. The pump operates under vacuum pressures of 5.times.10.sup.-4 Torr to ultra high vacuum (UHV) conditions in the range of 1.times.10.sup.-7 to 3.times.10.sup.-9 Torr and will typically remove partial pressure, 2.times.10.sup.-7 Torr, residual water vapor. The cryogenic pump basically consists of an inlet flange piece, a copper heat sink with a square internal bore, four two tier Peltier (TEC) chips, a copper low temperature square cross sectional tubulation, an electronic receptacle, and an exit flange piece, with the low temperature tubulation being retained in the heat sink at a bias angle of 5.degree., and with the TECs being positioned in parallel to each other with a positive potential being applied to the top tier thereof.

  17. Miniature Videoprobe Hockey Stick Delivery System

    SciTech Connect

    Hale, Lester R.; McMurry, Kyle M.

    1998-06-18

    The present invention is a miniature videoprobe system having a probe termination box, a strong back, and a videoprobe housing. The videoprobe system is able to obtain images from a restricted space at least as small as 0.125 inches while producing a high quality image. The strong back has a hockey stick shape with the probe termination box connecting to the top of the handle-like portion of the hockey stick and the videoprobe housing attaching to the opposite end or nose of the hockey stick shape. The videoprobe housing has a roughly arrowhead shape with two thin steel plates sandwiching the internal components there between. The internal components are connected in series to allow for a minor dimension of the videoprobe housing of 0.110 inches. The internal components include an optics train, a CCD chip, and an electronics package. An electrical signal is transmitted from the electronics package through wiring within an internal channel of the strong back to the probe termination box. The strong back has milled into it multiple internal channels for facilitating the transfer of information, items, or devices between the probe termination box and the videoprobe housing.

  18. Low cost miniature data collection platform

    NASA Technical Reports Server (NTRS)

    1977-01-01

    The development of the RF elements of a telecommunications package involved detailed study and analysis of concepts and techniques followed by laboratory testing and evaluation of designs. The design goals for a complete telecommunications package excluding antenna were a total weight of 300 grams, in a total volume of 400 cu cm with a capability of unattended operation for a period of six months. Of utmost importance is extremely low cost when produced in lots of 10,000. Early in the program it became apparent that a single Miniature Data Collection Platform would not satisfy all users. A single high efficiency system would not satisfy a user who had available a large battery capacity but required a low cost system. Conversely, the low cost system would not satisfy the end user who had a very limited battery capacity. A system design to satisfy these varied requirements was implemented by designing several versions of the system building blocks and then constructing three systems from these building blocks.

  19. Oxygen Transfer Characteristics of Miniaturized Bioreactor Systems

    PubMed Central

    Kirk, Timothy V; Szita, Nicolas

    2013-01-01

    Since their introduction in 2001 miniaturized bioreactor systems have made great advances in function and performance. In this article the dissolved oxygen (DO) transfer performance of submilliliter microbioreactors, and 1–10 mL minibioreactors was examined. Microbioreactors have reached kLa values of 460 h-1, and are offering instrumentation and some functionality comparable to production systems, but at high throughput screening volumes. Minibioreactors, aside from one 1,440 h-1 kLa system, have not offered as high rates of DO transfer, but have demonstrated superior integration with automated fluid handling systems. Microbioreactors have been typically limited to studies with E. coli, while minibioreactors have offered greater versatility in this regard. Further, mathematical relationships confirming the applicability of kLa measurements across all scales have been derived, and alternatives to fluorescence lifetime DO sensors have been evaluated. Finally, the influence on reactor performance of oxygen uptake rate (OUR), and the possibility of its real-time measurement have been explored. Biotechnol. Bioeng. 2013; 110: 1005–1019. © 2012 Wiley Periodicals, Inc. PMID:23280578

  20. Design considerations for miniaturized optical neural probes

    NASA Astrophysics Data System (ADS)

    Rudmann, Linda; Ordonez, Juan S.; Stieglitz, Thomas

    2016-03-01

    Neural probes are designed to selectively record from or stimulate nerve cells. In optogenetics it is desirable to build miniaturized and long-term stable optical neural probes, in which the light sources can be directly and chronically implanted into the animals to allow free movement and behavior. Because of the size and the beam shape of the available light sources, it is difficult to target single cells as well as spatially localized networks. We therefore investigated design considerations for packages, which encapsulate the light source hermetically and have integrated hemispherical lens structures that enable to focus the light onto the desired region, by optical simulations. Integration of a biconvex lens into the package lid (diameter = 300 μm, material: silicon carbide) increased the averaged absolute irradiance ηA by 298 % compared to a system without a lens and had a spot size of around 120 μm. Solely integrating a plano-convex lens (same diameter and material) results in an ηA of up to 227 %.