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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”

    USDA-ARS?s Scientific Manuscript database

    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. Two new miniature inverted-repeat transposable elements in the genome of the clam Donax trunculus.

    PubMed

    Šatović, Eva; Plohl, Miroslav

    2017-06-26

    Repetitive sequences are important components of eukaryotic genomes that drive their evolution. Among them are different types of mobile elements that share the ability to spread throughout the genome and form interspersed repeats. To broaden the generally scarce knowledge on bivalves at the genome level, in the clam Donax trunculus we described two new non-autonomous DNA transposons, miniature inverted-repeat transposable elements (MITEs), named DTC M1 and DTC M2. Like other MITEs, they are characterized by their small size, their A + T richness, and the presence of terminal inverted repeats (TIRs). DTC M1 and DTC M2 are 261 and 286 bp long, respectively, and in addition to TIRs, both of them contain a long imperfect palindrome sequence in their central parts. These elements are present in complete and truncated versions within the genome of the clam D. trunculus. The two new MITEs share only structural similarity, but lack any nucleotide sequence similarity to each other. In a search for related elements in databases, blast search revealed within the Crassostrea gigas genome a larger element sharing sequence similarity only to DTC M1 in its TIR sequences. The lack of sequence similarity with any previously published mobile elements indicates that DTC M1 and DTC M2 elements may be unique to D. trunculus.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  5. 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

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

    PubMed Central

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

    2013-01-01

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

  7. 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

  8. 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

  9. 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.

  10. Recent amplification of miniature inverted-repeat transposable elements in the vector mosquito Culex pipiens: characterization of the Mimo family.

    PubMed

    Feschotte, C; Mouchès, C

    2000-05-30

    We describe a new family of repetitive elements, named Mimo, from the mosquito Culex pipiens. Structural characteristics of these elements fit well with those of miniature inverted-repeat transposable elements (MITEs), which are ubiquitous and highly abundant in plant genomes. The occurrence of Mimo in C. pipiens provides new evidence that MITEs are not restricted to plant genomes, but may be widespread in arthropods as well. The copy number of Mimo elements in C. pipiens ( approximately 1000 copies in a 540Mb genome) supports the hypothesis that there is a positive correlation between genome size and the magnitude of MITE proliferation. In contrast to most MITE families described so far, members of the Mimo family share a high sequence conservation, which may reflect a recent amplification history in this species. In addition, we found that Mimo elements are a frequent nest for other MITE-like elements, suggesting that multiple and successive MITE transposition events have occurred very recently in the C. pipiens genome. Despite evidence for recent mobility of these MITEs, no element has been found to encode a protein; therefore, we do not know how they have transposed and have spread in the genome. However, some sequence similarities in terminal inverted-repeats suggest a possible filiation of some of these mosquito MITEs with pogo-like DNA transposons.

  11. 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.

  12. Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla).

    PubMed

    Zhou, Mingbing; Tao, Guiyun; Pi, Peiyao; Zhu, Yihang; Bai, Youhuang; Meng, Xianwen

    2016-10-01

    Moso bamboo MITEs were genome-wide identified first time, and data shows that MITEs contribute to the genomic diversity and differentiation of bamboo. Miniature inverted-repeat transposable elements (MITEs) are widespread in animals and plants. There are a large number of transposable elements in moso bamboo (Phyllostachys heterocycla var. pubescens) genome, but the genome-wide information of moso bamboo MITEs is not known yet. Here we identified 362 MITE families with a total of 489,592 MITE-related sequences, accounting for 4.74 % of the moso bamboo genome. The 362 MITE families are clustered into six known and one unknown super-families. Our analysis indicated that moso bamboo MITEs preferred to reside in or near the genes that might be involved in regulation of host gene expression. Of the seven super-families, three might undergo major expansion event twice, respectively, during 8-11 million years ago (mya) ago and 22-28 mya ago; two might experience a long expansion period from 6 to 13 mya. Almost 1/3 small RNAs might be derived from the MITE sequences. Some MITE families generate small RNAs mainly from the terminals, while others predominantly from the central region. Given the high copy number of MITEs, many siRNAs and miRNAs derived from MITE sequences and the preferential insertion of MITE into gene regions, MITEs may contribute to the genomic diversity and differentiation of bamboo.

  13. 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

  14. 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.

  15. 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.

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

    PubMed Central

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

    2014-01-01

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

  17. Miniature Inverted Repeat Transposable Element Insertions Provide a Source of Intron Length Polymorphism Markers in the Carrot (Daucus carota L.)

    PubMed Central

    Stelmach, Katarzyna; Macko-Podgórni, Alicja; Machaj, Gabriela; Grzebelus, Dariusz

    2017-01-01

    The prevalence of non-autonomous class II transposable elements (TEs) in plant genomes may serve as a tool for relatively rapid and low-cost development of gene-associated molecular markers. Miniature inverted-repeat transposable element (MITE) copies inserted within introns can be exploited as potential intron length polymorphism (ILP) markers. ILPs can be detected by PCR with primers anchored in exon sequences flanking the target introns. Here, we designed primers for 209 DcSto (Daucus carota Stowaway-like) MITE insertion sites within introns along the carrot genome and validated them as candidate ILP markers in order to develop a set of markers for genotyping the carrot. As a proof of concept, 90 biallelic DcS-ILP markers were selected and used to assess genetic diversity of 27 accessions comprising wild Daucus carota and cultivated carrot of different root shape. The number of effective alleles was 1.56, mean polymorphism informative content was 0.27, while the average observed and expected heterozygosity was 0.24 and 0.34, respectively. Sixty-seven loci showed positive values of Wright's fixation index. Using Bayesian approach, two clusters comprising four wild and 23 cultivated accessions, respectively, were distinguished. Within the cultivated carrot gene pool, four subclusters representing accessions from Chantenay, Danvers, Imperator, and Paris Market types were revealed. It is the first molecular evidence for root-type associated diversity structure in western cultivated carrot. DcS-ILPs detected substantial genetic diversity among the studied accessions and, showing considerable discrimination power, may be exploited as a tool for germplasm characterization and analysis of genome relationships. The developed set of DcS-ILP markers is an easily accessible molecular marker genotyping system based on TE insertion polymorphism. PMID:28536590

  18. Molecular and evolutionary analysis of two divergent subfamilies of a novel miniature inverted repeat transposable element in the yellow fever mosquito, Aedes aegypti.

    PubMed

    Tu, Z

    2000-09-01

    A novel family of miniature inverted repeat transposable elements (MITEs) named Pony was discovered in the yellow fever mosquito, Aedes aegypti. It has all the characteristics of MITEs, including terminal inverted repeats, no coding potential, A+T richness, small size, and the potential to form stable secondary structures. Past mobility of PONY: was indicated by the identification of two Pony insertions which resulted in the duplication of the TA dinucleotide targets. Two highly divergent subfamilies, A and B, were identified in A. aegypti based on sequence comparison and phylogenetic analysis of 38 elements. These subfamilies showed less than 62% sequence similarity. However, within each subfamily, most elements were highly conserved, and multiple subgroups could be identified, indicating recent amplifications from different source genes. Different scenarios are presented to explain the evolutionary history of these subfamilies. Both subfamilies share conserved terminal inverted repeats similar to those of the Tc2 DNA transposons in Caenorhabditis elegans, indicating that Pony may have been borrowing the transposition machinery from a Tc2-like transposon in mosquitoes. In addition to the terminal inverted repeats, full-length and partial subterminal repeats of a sequence motif TTGATTCAWATTCCGRACA represent the majority of the conservation between the two subfamilies, indicating that they may be important structural and/or functional components of the Pony elements. In contrast to known autonomous DNA transposons, both subfamilies of PONY: are highly reiterated in the A. aegypti genome (8,400 and 9, 900 copies, respectively). Together, they constitute approximately 1. 1% of the entire genome. Pony elements were frequently found near other transposable elements or in the noncoding regions of genes. The relative abundance of MITEs varies in eukaryotic genomes, which may have in part contributed to the different organizations of the genomes and reflect different types

  19. 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

  20. 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.

  1. A novel hAT element in Bombyx mori and Rhodnius prolixus: its relationship with miniature inverted repeat transposable elements (MITEs) and horizontal transfer.

    PubMed

    Zhang, H-H; Shen, Y-H; Xu, H-E; Liang, H-Y; Han, M-J; Zhang, Z

    2013-10-01

    Comparative analysis of transposable elements (TEs) from different species can make it possible to reconstruct their history over evolutionary time. In this study, we identified a novel hAT element in Bombyx mori and Rhodnius prolixus with characteristic GGGCGGCA repeats in its subterminal region. Meanwhile, phylogenetic analysis demonstrated that the elements in these two species might represent a separate cluster of the hAT superfamily. Strikingly, a previously identified miniature inverted repeat transposable element (MITE) shared high identity with this autonomous element across the entire length, supporting the hypothesis that MITEs are derived from the internal deletion of DNA transposons. Interestingly, identity of the consensus sequences of this novel hAT element between B. mori and R. prolixus, which diverged about 370 million years ago, was as high as 96.5% over their full length (about 3.6 kb) at the nucleotide level. The patchy distribution amongst species, coupled with overall lack of intense purifying selection acting on this element, suggest that this novel hAT element might have experienced horizontal transfer between the ancestors of B. mori and R. prolixus. Our results highlight that this novel hAT element could be used as a potential tool for germline transformation of R. prolixus to control the transmission of Trypanosoma cruzi, which causes Chagas disease. © 2013 Royal Entomological Society.

  2. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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, ...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  12. 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.

  13. 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.

  14. Mutagenic inverted repeat assisted genome engineering (MIRAGE)

    PubMed Central

    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. PMID:19050015

  15. The excess of small inverted repeats in prokaryotes.

    PubMed

    Ladoukakis, Emmanuel D; Eyre-Walker, Adam

    2008-09-01

    Recent analyses have shown that there is a large excess of perfect inverted repeats in many prokaryotic genomes but not in eukaryotic ones. This difference could be due to a genuine difference between prokaryotes and eukaryotes or to differences in the methods and types of data analyzed--full genome versus protein coding sequences. We used simulations to show that the method used previously tends to underestimate the expected number of inverted repeats. However, this bias is not large and cannot explain the excess of inverted repeats observed in real data. In contrast, our method is unbiased. When both methods are applied to bacterial protein coding sequences they both detect an excess of inverted repeats, which is much lower than previously reported in whole prokaryotic genomes. This suggests that the reported large excess of inverted repeats is due to repeats found in intergenic regions. These repeats could be due to transcription factor binding sites, or other types of repetitive DNA, on opposite strands of the DNA sequence. In contrast, the smaller, but significant, excess of inverted repeats that we report in protein coding sequences may be due to sequence-directed mutagenesis (SDM). SDM is a process where one copy of a small, imperfect, inverted repeat corrects the other copy via strand misalignment, resulting in a perfect repeat and a series of mutations. We show by simulation that even very low levels of SDM, relative to the rate of point mutation, can generate a substantial excess of inverted repeats.

  16. 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.

  17. DNA Inversions between Short Inverted Repeats in Escherichia Coli

    PubMed Central

    Schofield, M. A.; Agbunag, R.; Miller, J. H.

    1992-01-01

    Using site-specific mutagenesis in vitro, we have constructed Escherichia coli strains that allow the detection of the inversion of an 800-bp segment in the lac region. The invertible segment is bounded by inverted repeats of either 12 or 23 bp. Inversions occurring at these inverted repeats will restore the Lac(+) phenotype. Inversions can be detected at both short homologies at frequencies ranging from 0.5 X 10(-8) to 1 X 10(-7). These events, which have been verified by DNA sequence analysis, are reduced up to 1000-fold in strains deficient for either RecA, RecB or RecC. They are not reduced in strains deficient in the RecF,J pathway. These results show that the RecB,C,D system can mediate rearrangements at short sequence repeats, and probably plays a major role in cellular rearrangements. PMID:1427029

  18. 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.

  19. Structure and Function of Na+-Symporters with Inverted Repeats

    PubMed Central

    Abramson, Jeff; Wright, Ernest M.

    2009-01-01

    Summary Symporters are membrane proteins that couple energy stored in electrochemical potential gradients to drive the cotransport of molecules and ions into cells. Traditionally, proteins are classified into gene families based on sequence homology and functional properties, e.g. the sodium glucose (SLC5 or Sodium Solute Symporter Family, SSS or SSF) and GABA (SLC6 or Neurotransmitter Sodium Symporter Family, NSS or SNF) symporter families [1-4]. Recently, it has been established that four Na+-symporter proteins with unrelated sequences have a common structural core containing an inverted repeat of 5 transmembrane (TM) helices [5-8]. Analysis of these four structures reveals that they reside in different conformations along the transport cycle providing atomic insight into the mechanism of sodium solute cotransport. PMID:19631523

  20. 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

  1. Associations between inverted repeats and the structural evolution of bacterial genomes.

    PubMed Central

    Achaz, Guillaume; Coissac, Eric; Netter, Pierre; Rocha, Eduardo P C

    2003-01-01

    The stability of the structure of bacterial genomes is challenged by recombination events. Since major rearrangements (i.e., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation to the conservation of chromosomal structure. First, we show that there is a strong under-representation of inverted repeats, relative to direct repeats, in most chromosomes, especially among the ones regarded as most stable. Second, we show that the avoidance of repeats is frequently associated with the stability of the genomes. Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats. Third, when using replication strand bias as a proxy for genome stability, we find a significant negative correlation between this strand bias and the abundance of inverted repeats. Fourth, when measuring the recombining potential of inverted repeats and their eventual impact on different features of the chromosomal structure, we observe a tendency of repeats to be located in the chromosome in such a way that rearrangements produce a smaller strand switch and smaller asymmetries than expected by chance. Finally, we discuss the limitations of our analysis and the influence of factors such as the nature of repeats, e.g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats. PMID:12930739

  2. Associations between inverted repeats and the structural evolution of bacterial genomes.

    PubMed

    Achaz, Guillaume; Coissac, Eric; Netter, Pierre; Rocha, Eduardo P C

    2003-08-01

    The stability of the structure of bacterial genomes is challenged by recombination events. Since major rearrangements (i.e., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation to the conservation of chromosomal structure. First, we show that there is a strong under-representation of inverted repeats, relative to direct repeats, in most chromosomes, especially among the ones regarded as most stable. Second, we show that the avoidance of repeats is frequently associated with the stability of the genomes. Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats. Third, when using replication strand bias as a proxy for genome stability, we find a significant negative correlation between this strand bias and the abundance of inverted repeats. Fourth, when measuring the recombining potential of inverted repeats and their eventual impact on different features of the chromosomal structure, we observe a tendency of repeats to be located in the chromosome in such a way that rearrangements produce a smaller strand switch and smaller asymmetries than expected by chance. Finally, we discuss the limitations of our analysis and the influence of factors such as the nature of repeats, e.g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats.

  3. 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.

  4. Tandem inverted repeats in mitochondrial DNA of petite mutants of Saccharomyces cerevisiae.

    PubMed

    Locker, J; Rabinowitz, M; Getz, G S

    1974-04-01

    Denatured mitochondrial DNA (mtDNA) from a grande (wild-type) yeast strain and a series of derived genetically characterized cytoplasmic petite mutants was examined in the electron microscope as DNA-protein monolayers prepared under conditions that permitted little bimolecular renaturation. In the grande and some petite strains, the mtDNA remained predominantly single-stranded. However, in several petite strains, a large proportion of molecules contained double-stranded segments indicative of unimolecular renaturation due to the presence of inverted repeat sequences. The length of the double-stranded segments of strain E41 was compared to the periodicity seen on denaturation maps. A repeat spacing twice the length of the inverted repeats was observed in the denaturation map. Inverted repeat length was similar to contour length of circular mtDNA molecules in this strain. On the basis of these observations most of the mtDNA from petite strain E41 appeared to consist of polymers of tandem inverted repeats interspersed with a small single-stranded "spacer" sequence between the repeat segments. In contrast, petite strain F13 mtDNA had few or no inverted repeats and showed a regular periodicity of 0.14 mum in the denaturation map, similar in length to the 0.13-mum circles present in the isolated mtDNA.

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Inverted-repeat DNA: a new gene-silencing tool for seed lipid modification.

    PubMed

    Singh, S; Green, A; Stoutjesdijk, P; Liu, Q

    2000-12-01

    Post-transcriptional gene silencing (PTGS) has been successfully used to modify seed lipids in oilseed crops like soybean, canola and sunflower. Conventionally, PTGS has been induced by transforming the plants with either antisense or co-suppression constructs targeted against key seed lipid biosynthesis genes. A major drawback of this approach has been the recovery of only a modest proportion of silenced individuals from large populations of transgenic plants. In this report we show that inverted-repeat DNA constructs containing an intron encoding RNA with a hairpin structure can induce PTGS with very high frequency.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Cryptic satellites rich in inverted repeats comprise 30% of the genome of a hermit crab

    SciTech Connect

    Fowler, R.F.; Skinner, D.M.

    1985-01-25

    One major very highly repeated (VHR) DNA (approx. 7 x 10W copies/genome; repeat unit = 156 base pairs (bp)), a family of three minor VHR DNAs (approx. 2.8 x 10W copies/genome; repeat units = 71-74 bp), and a number of trace components account for almost 30% of the genome of a hermit crab. The repeat units of the three minor variants are defined by identical 14-bp G + C-rich inverted repeats that might form cruciforms. Two copies of the repeat unit (CCTA) of one of two patent satellites of this crab occur at the center of one in seven of the G + C-rich inverted repeats; copies of the other patent satellite are found in main component DNA. The sequences of both the major and minor VHR DNAs are characterized by short tracts of A/sub n/ and/or T/sub n/ (n = 4-7) residues whose presence would permit the formation of perfectly matched stems separated by loops of 8-16 bp. The A/sub n/ and/or T/sub n/ tracts are interspersed with segments of G + C-rich DNA and are arranged differently in the major and minor VHR DNAs. Although the repeat units of the major and the three minor VHR DNAs are arranged in tandem, the composition and sequence of their bases are such that they do not form distinct bands in CsCl gradients; they are cryptic satellites. 42 references, 7 figures, 1 table.

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    1980-06-01

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

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

    PubMed Central

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

    2010-01-01

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

  2. 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.

  3. 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

  4. 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.

  5. 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

  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. 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.

  9. 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

  10. 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

  11. Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes

    PubMed Central

    Chen, Song; Li, Xianchun

    2007-01-01

    Background Transposons, i.e. transposable elements (TEs), are the major internal spontaneous mutation agents for the variability of eukaryotic genomes. To address the general issue of whether transposons mediate genomic changes in environment-adaptation genes, we scanned two alleles per each of the six xenobiotic-metabolizing Helicoverpa zea cytochrome P450 loci, including CYP6B8, CYP6B27, CYP321A1, CYP321A2, CYP9A12v3 and CYP9A14, for the presence of transposon insertions by genome walking and sequence analysis. We also scanned thirteen Drosophila melanogaster P450s genes for TE insertions by in silico mapping and literature search. Results Twelve novel transposons, including LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), MITEs (miniature inverted-repeat transposable elements), one full-length transib-like transposon, and one full-length Tcl-like DNA transpson, are identified from the alleles of the six H. zea P450 genes. The twelve transposons are inserted into the 5'flanking region, 3'flanking region, exon, or intron of the six environment-adaptation P450 genes. In D. melanogaster, seven out of the eight Drosophila P450s (CYP4E2, CYP6A2, CYP6A8, CYP6A9, CYP6G1, CYP6W1, CYP12A4, CYP12D1) implicated in insecticide resistance are associated with a variety of transposons. By contrast, all the five Drosophila P450s (CYP302A1, CYP306A1, CYP307A1, CYP314A1 and CYP315A1) involved in ecdysone biosynthesis and developmental regulation are free of TE insertions. Conclusion These results indicate that TEs are selectively retained within or in close proximity to xenobiotic-metabolizing P450 genes. PMID:17381843

  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. Hot Fusion: An Efficient Method to Clone Multiple DNA Fragments as Well as Inverted Repeats without Ligase

    PubMed Central

    Fu, Changlin; Donovan, William P.; Shikapwashya-Hasser, Olga; Ye, Xudong; Cole, Robert H.

    2014-01-01

    Molecular cloning is utilized in nearly every facet of biological and medical research. We have developed a method, termed Hot Fusion, to efficiently clone one or multiple DNA fragments into plasmid vectors without the use of ligase. The method is directional, produces seamless junctions and is not dependent on the availability of restriction sites for inserts. Fragments are assembled based on shared homology regions of 17–30 bp at the junctions, which greatly simplifies the construct design. Hot Fusion is carried out in a one-step, single tube reaction at 50°C for one hour followed by cooling to room temperature. In addition to its utility for multi-fragment assembly Hot Fusion provides a highly efficient method for cloning DNA fragments containing inverted repeats for applications such as RNAi. The overall cloning efficiency is in the order of 90–95%. PMID:25551825

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. Identification of multiple binding sites for the THAP domain of the Galileo transposase in the long terminal inverted-repeats.

    PubMed

    Marzo, Mar; Liu, Danxu; Ruiz, Alfredo; Chalmers, Ronald

    2013-08-01

    Galileo is a DNA transposon responsible for the generation of several chromosomal inversions in Drosophila. In contrast to other members of the P-element superfamily, it has unusually long terminal inverted-repeats (TIRs) that resemble those of Foldback elements. To investigate the function of the long TIRs we derived consensus and ancestral sequences for the Galileo transposase in three species of Drosophilids. Following gene synthesis, we expressed and purified their constituent THAP domains and tested their binding activity towards the respective Galileo TIRs. DNase I footprinting located the most proximal DNA binding site about 70 bp from the transposon end. Using this sequence we identified further binding sites in the tandem repeats that are found within the long TIRs. This suggests that the synaptic complex between Galileo ends may be a complicated structure containing higher-order multimers of the transposase. We also attempted to reconstitute Galileo transposition in Drosophila embryos but no events were detected. Thus, although the limited numbers of Galileo copies in each genome were sufficient to provide functional consensus sequences for the THAP domains, they do not specify a fully active transposase. Since the THAP recognition sequence is short, and will occur many times in a large genome, it seems likely that the multiple binding sites within the long, internally repetitive, TIRs of Galileo and other Foldback-like elements may provide the transposase with its binding specificity. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  4. 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.

  5. Tm1: A Mutator/Foldback Transposable Element Family in Root-Knot Nematodes

    PubMed Central

    Gross, Stephen M.; Williamson, Valerie M.

    2011-01-01

    Three closely related parthenogenetic species of root-knot nematodes, collectively termed the Meloidogyne incognita-group, are economically significant pathogens of diverse crop species. Remarkably, these asexual root-knot nematodes are capable of acquiring heritable changes in virulence even though they lack sexual reproduction and meiotic recombination. Characterization of a near isogenic pair of M. javanica strains differing in response to tomato with the nematode resistance gene Mi-1 showed that the virulent strain carried a deletion spanning a gene called Cg-1. Herein, we present evidence that the Cg-1 gene lies within a member of a novel transposable element family (Tm1; Transposon in Meloidogyne-1). This element family is defined by composite terminal inverted repeats of variable lengths similar to those of Foldback (FB) transposable elements and by 9 bp target site duplications. In M. incognita, Tm1 elements can be classified into three general groups: 1) histone-hairpin motif elements; 2) MITE-like elements; 3) elements encoding a putative transposase. The predicted transposase shows highest similarity to gene products encoded by aphids and mosquitoes and resembles those of the Phantom subclass of the Mutator transposon superfamily. Interestingly, the meiotic, sexually-reproducing root-knot nematode species M. hapla has Tm1 elements with similar inverted repeat termini, but lacks elements with histone hairpin motifs and contains no elements encoding an intact transposase. These Tm1 elements may have impacts on root-knot nematode genomes and contribute to genetic diversity of the asexual species. PMID:21931741

  6. Tm1: a mutator/foldback transposable element family in root-knot nematodes.

    PubMed

    Gross, Stephen M; Williamson, Valerie M

    2011-01-01

    Three closely related parthenogenetic species of root-knot nematodes, collectively termed the Meloidogyne incognita-group, are economically significant pathogens of diverse crop species. Remarkably, these asexual root-knot nematodes are capable of acquiring heritable changes in virulence even though they lack sexual reproduction and meiotic recombination. Characterization of a near isogenic pair of M. javanica strains differing in response to tomato with the nematode resistance gene Mi-1 showed that the virulent strain carried a deletion spanning a gene called Cg-1. Herein, we present evidence that the Cg-1 gene lies within a member of a novel transposable element family (Tm1; Transposon in Meloidogyne-1). This element family is defined by composite terminal inverted repeats of variable lengths similar to those of Foldback (FB) transposable elements and by 9 bp target site duplications. In M. incognita, Tm1 elements can be classified into three general groups: 1) histone-hairpin motif elements; 2) MITE-like elements; 3) elements encoding a putative transposase. The predicted transposase shows highest similarity to gene products encoded by aphids and mosquitoes and resembles those of the Phantom subclass of the Mutator transposon superfamily. Interestingly, the meiotic, sexually-reproducing root-knot nematode species M. hapla has Tm1 elements with similar inverted repeat termini, but lacks elements with histone hairpin motifs and contains no elements encoding an intact transposase. These Tm1 elements may have impacts on root-knot nematode genomes and contribute to genetic diversity of the asexual species.

  7. Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat.

    PubMed

    Sanderson, Michael J; Copetti, Dario; Búrquez, Alberto; Bustamante, Enriquena; Charboneau, Joseph L M; Eguiarte, Luis E; Kumar, Sudhir; Lee, Hyun Oh; Lee, Junki; McMahon, Michelle; Steele, Kelly; Wing, Rod; Yang, Tae-Jin; Zwickl, Derrick; Wojciechowski, Martin F

    2015-07-01

    • Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.• Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).• The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid ndh genes. This loss supports a statistically strong association across seed plants between the loss of ndh genes and the loss of the IR. Many nonplastid copies of plastid ndh genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear pgr5, which functions in a partially redundant pathway, was intact.• The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid ndh gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR. © 2015 Botanical Society of America, Inc.

  8. The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs

    PubMed Central

    2011-01-01

    Background The piRNA pathway has been shown in model organisms to be involved in silencing of transposons thereby providing genome stability. In D. melanogaster the majority of piRNAs map to these sequences. The medically important mosquito species Aedes aegypti has a large genome size, a high transposon load which includes Miniature Inverted repeat Transposable Elements (MITES) and an expansion of the piRNA biogenesis genes. Studies of transgenic lines of Ae. aegypti have indicated that introduced transposons are poorly remobilized and we sought to explore the basis of this. We wished to analyze the piRNA profile of Ae. aegypti and thereby determine if it is responsible for transposon silencing in this mosquito. Results Estimated piRNA sequence diversity was comparable between Ae. aegypti and D. melanogaster, but surprisingly only 19% of mosquito piRNAs mapped to transposons compared to 51% for D. melanogaster. Ae. aegypti piRNA clusters made up a larger percentage of the total genome than those of D. melanogaster but did not contain significantly higher percentages of transposon derived sequences than other regions of the genome. Ae. aegypti contains a number of protein coding genes that may be sources of piRNA biogenesis with two, traffic jam and maelstrom, implicated in this process in model organisms. Several genes of viral origin were also targeted by piRNAs. Examination of six mosquito libraries that had previously been transformed with transposon derived sequence revealed that new piRNA sequences had been generated to the transformed sequences, suggesting that they may have stimulated a transposon inactivation mechanism. Conclusions Ae. aegypti has a large piRNA complement that maps to transposons but primarily gene sequences, including many viral-derived sequences. This, together the more uniform distribution of piRNA clusters throughout its genome, suggest that some aspects of the piRNA system differ between Ae. aegypti and D. melanogaster. PMID:22171608

  9. The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs.

    PubMed

    Arensburger, Peter; Hice, Robert H; Wright, Jennifer A; Craig, Nancy L; Atkinson, Peter W

    2011-12-15

    The piRNA pathway has been shown in model organisms to be involved in silencing of transposons thereby providing genome stability. In D. melanogaster the majority of piRNAs map to these sequences. The medically important mosquito species Aedes aegypti has a large genome size, a high transposon load which includes Miniature Inverted repeat Transposable Elements (MITES) and an expansion of the piRNA biogenesis genes. Studies of transgenic lines of Ae. aegypti have indicated that introduced transposons are poorly remobilized and we sought to explore the basis of this. We wished to analyze the piRNA profile of Ae. aegypti and thereby determine if it is responsible for transposon silencing in this mosquito. Estimated piRNA sequence diversity was comparable between Ae. aegypti and D. melanogaster, but surprisingly only 19% of mosquito piRNAs mapped to transposons compared to 51% for D. melanogaster. Ae. aegypti piRNA clusters made up a larger percentage of the total genome than those of D. melanogaster but did not contain significantly higher percentages of transposon derived sequences than other regions of the genome. Ae. aegypti contains a number of protein coding genes that may be sources of piRNA biogenesis with two, traffic jam and maelstrom, implicated in this process in model organisms. Several genes of viral origin were also targeted by piRNAs. Examination of six mosquito libraries that had previously been transformed with transposon derived sequence revealed that new piRNA sequences had been generated to the transformed sequences, suggesting that they may have stimulated a transposon inactivation mechanism. Ae. aegypti has a large piRNA complement that maps to transposons but primarily gene sequences, including many viral-derived sequences. This, together the more uniform distribution of piRNA clusters throughout its genome, suggest that some aspects of the piRNA system differ between Ae. aegypti and D. melanogaster.

  10. 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

    Pistón, Fernando; Gil-Humanes, Javier; Barro, Francisco

    2013-09-17

    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. 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. 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.

  11. 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

  12. 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

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

    PubMed

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

    2016-02-11

    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.

  14. Transposable elements in cancer.

    PubMed

    Burns, Kathleen H

    2017-07-01

    Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1). LINE-1 sequences are self-propagating, protein-coding retrotransposons, and their activity results in somatically acquired insertions in cancer genomes. Altered expression of transposable elements and animation of genomic LINE-1 sequences appear to be hallmarks of cancer, and can be responsible for driving mutations in tumorigenesis.

  15. Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats.

    PubMed

    Wang, Dan; Li, Shuaicheng; Guo, Fei; Ning, Kang; Wang, Lusheng

    2017-03-29

    Genome rearrangement describes gross changes of chromosomal regions, plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. With more and more complete genomes accomplished, lots of genomic comparisons have been conducted in order to find genome rearrangements and the mechanisms which underlie the rearrangement events. In our opinion, genomic comparison of different individuals/strains within the same species (pan-genome) is more helpful to reveal the mechanisms for genome rearrangements since genomes of the same species are much closer to each other. We study the mechanism for inversion events via core-genome scaffold comparison of different strains within the same species. We focus on two kinds of bacteria, Pseudomonas aeruginosa and Escherichia coli, and investigate the inversion events among different strains of the same species. We find an interesting phenomenon that long (larger than 10,000 bp) inversion regions are flanked by a pair of Inverted Repeats (IRs). This mechanism can also explain why the breakpoint reuses for inversion events happen. We study the prevalence of the phenomenon and find that it is a major mechanism for inversions. The other observation is that for different rearrangement events such as transposition and inverted block interchange, the two ends of the swapped regions are also associated with repeats so that after the rearrangement operations the two ends of the swapped regions remain unchanged. To our knowledge, this is the first time such a phenomenon is reported for transposition event. In both Pseudomonas aeruginosa and Escherichia coli strains, IRs were found at the two ends of long sequence inversions. The two ends of the inversion remained unchanged before and after the inversion event. The existence of IRs can explain the breakpoint reuse phenomenon. We also observed that other rearrangement operations such as transposition, inverted transposition, and

  16. Plant transposable elements

    SciTech Connect

    Nelson, O. )

    1988-01-01

    This document presents 27 publications from a symposium on the transposable portions of various plant genomes. Topics include gene regulation, genetic analysis, recombinant technology, mutator functions, gene tagging, extrachromosomal elements, and gene activation in common laboratory plants like tobacco, maize, and alfalfa. Individual papers were processed separately for the data base. (TEM)

  17. Expression of cloned herpesvirus genes. I. Detection of nuclear antigens from herpes simplex virus type 2 inverted repeat regions in transfected mouse cells.

    PubMed Central

    Middleton, M H; Reyes, G R; Ciufo, D M; Buchan, A; Macnab, J C; Hayward, G S

    1982-01-01

    Three different recombinant plasmids containing the entire 15-kilobase L and S inverted repeat sequence of herpes simplex virus type 2 DNA have been introduced into cultured Ltk- or BSC cells by both the calcium and DEAE-dextran transfection procedures. In each case, after 24 h approximately 1% of the cells gave strongly positive nuclear staining when assayed by immunofluorescence with hyperimmune antisera made against early and immediate-early infected-cell polypeptides. The nuclear fluorescence pattern and intensity mimicked that observed within 2 to 3 h after infection of Ltk- cells with either herpes simplex virus type 1 or type 2 wild-type virus. Herpes simplex virus type 1 (KOStsB2)-infected Ltk- cells under nonpermissive conditions did not express these antigens in the nucleus. Therefore, we conclude that either one or both of the 185,000- and 110,000-molecular-weight immediate early proteins, or some other as yet unknown gene product encoded entirely within the inverted repeats, can be transiently expressed in large amounts in transfected cells in the absence of other viral genes or accompanying virion components. Permanent mouse cell lines derived from transfection with these plasmids by using the thymidine kinase coselection procedure did not express sufficient nuclear antigen to be detectable by immunofluorescence. Images PMID:6292452

  18. 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.

  19. 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.

  20. 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.

  1. Transposable elements in Drosophila

    PubMed Central

    McCullers, Tabitha J.; Steiniger, Mindy

    2017-01-01

    ABSTRACT Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster. PMID:28580197

  2. Eukaryotic transposable elements as mutagenic agents

    SciTech Connect

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

    1988-01-01

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

  3. 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

  4. 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

  5. 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.

  6. A transposable element from Halobacterium halobium which inactivates the bacteriorhodopsin gene.

    PubMed Central

    Simsek, M; DasSarma, S; RajBhandary, U L; Khorana, H G

    1982-01-01

    We describe the characterization of a transposable element from an archaebacterium. The bacteriorhodopsin genes from the wild-type and two mutant Halobacterium halobium strains have been cloned as BamHI fragments in pBR322. The cloned DNA fragments from the two mutants both contain a 1.1-kilobase-pair insertion sequence (ISH1) near the NH2 terminus of the bacteriorhodopsin coding sequence. ISH1 is present in the two mutants in an identical palindromic site but in opposite orientations. The complete sequence of ISH1 has been determined; it is 1,118 nucleotides long, it has 8-base-pair interrupted inverted repeats at the ends, and it duplicates an 8-base-pair (A-G-T-T-A-T-T-G) target sequence upon insertion. As for most eukaryotic and some prokaryotic transposable elements, the sequence of the ISH1 begins with T-G and ends in C-A. ISH1 contains an open reading frame 810 nucleotides long and codes for an RNA approximately 900 nucleotides long. The copy number of ISH1 ranges from one to five or more in different H. halobium strains. In at least one of the strains, one copy of ISH1 is present also on a plasmid DNA. Images PMID:6296826

  7. 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.

  8. Mung bean nuclease cleavage of a dA + dT-rich sequence or an inverted repeat sequence in supercoiled PM2 DNA depends on ionic environment.

    PubMed Central

    Sheflin, L G; Kowalski, D

    1984-01-01

    We have determined the nucleotide sequences around two alternative sites cleaved in supercoiled PM2 DNA by single-strand-specific mung bean nuclease in different ionic environments. In 10 mM Tris-HC1 (pH 7.0, 37 degrees C), the major site is a dA+dT-rich sequence which maps with a known early denaturation region at 0.75 map units. About 30 cleavages occurred in a 135 bp region. Cleavages were largely excluded at (dA)n . (dT)n (n = 3-7) sequences. Cleavage patterns of this type have not been previously observed in dA+dT-rich sequences. With the addition of 0.1 M NaC1 the major alternative site occurred in a hyphenated inverted repeat sequence 500 bp away (0.70 map units) and did not map to an early denaturation region. One major and 4 minor cleavages occurred in the region between the repeats, suggesting that a hairpin containing at most a 12 bp stem and 10 base loop is recognized. The basis for nuclease recognition of the dA+dT-rich sequence is not clear. The differences in the sequences and cleavage patterns at the alternative sites indicate that their secondary structures differ. Images PMID:6091054

  9. 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.

  10. 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.

  11. 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

  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. 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

  14. 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

  15. 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

  16. 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.

  17. 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

  18. Transposable elements for insect transformation

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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%),...

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. A correlation between host-mediated expression of parasite genes as tandem inverted repeats and abrogation of development of female Heterodera glycines cyst formation during infection of Glycine max.

    PubMed

    Klink, Vincent P; Kim, Kyung-Hwan; Martins, Veronica; Macdonald, Margaret H; Beard, Hunter S; Alkharouf, Nadim W; Lee, Seong-Kon; Park, Soo-Chul; Matthews, Benjamin F

    2009-06-01

    Host-mediated (hm) expression of parasite genes as tandem inverted repeats was investigated as a means to abrogate the formation of mature Heterodera glycines (soybean cyst nematode) female cysts during its infection of Glycine max (soybean). A Gateway-compatible hm plant transformation system was developed specifically for these experiments in G. max. Three steps then were taken to identify H. glycines candidate genes. First, a pool of 150 highly conserved H. glycines homologs of genes having lethal mutant phenotypes or phenocopies from the free living nematode Caenorhabditis elegans were identified. Second, annotation of those 150 genes on the Affymetrix soybean GeneChip allowed for the identification of a subset of 131 genes whose expression could be monitored during the parasitic phase of the H. glycines life cycle. Third, a microarray analyses identified a core set of 32 genes with induced expression (>2.0-fold, log base 2) during the parasitic stages of infection. H. glycines homologs of small ribosomal protein 3a and 4 (Hg-rps-3a [accession number CB379877] and Hg-rps-4 [accession number CB278739]), synaptobrevin (Hg-snb-1 [accession number BF014436]) and a spliceosomal SR protein (Hg-spk-1 [accession number BI451523.1]) were tested for functionality in hm expression studies. Effects on H. glycines development were observed 8 days after infection. Experiments demonstrated that 81-93% fewer females developed on transgenic roots containing the genes engineered as tandem inverted repeats. The effect resembles RNA interference. The methodology has been used here as an alternative approach to engineer resistance to H. glycines.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Entangled states with strong positive partial transpose

    SciTech Connect

    Ha, Kil-Chan

    2010-06-15

    Chruscinski, Jurkowski, and Kossakowski [Phys. Rev. A 77, 022113 (2008)] studied quantum states with strong positive partial transpose (SPPT) and conjectured that all SPPT states are separable. We construct a two-parameter class of 3 x 3 entangled SPPT states, so the conjecture does not hold true for general SPPT states.

  13. 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

  14. 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)

  15. 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)

  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

    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.

  17. The 2.1-kb inverted repeat DNA sequences flank the mat2,3 silent region in two species of Schizosaccharomyces and are involved in epigenetic silencing in Schizosaccharomyces pombe.

    PubMed Central

    Singh, Gurjeet; Klar, Amar J S

    2002-01-01

    The mat2,3 region of the fission yeast Schizosaccharomyces pombe exhibits a phenomenon of transcriptional silencing. This region is flanked by two identical DNA sequence elements, 2.1 kb in length, present in inverted orientation: IRL on the left and IRR on the right of the silent region. The repeats do not encode any ORF. The inverted repeat DNA region is also present in a newly identified related species, which we named S. kambucha. Interestingly, the left and right repeats share perfect identity within a species, but show approximately 2% bases interspecies variation. Deletion of IRL results in variegated expression of markers inserted in the silent region, while deletion of the IRR causes their derepression. When deletions of these repeats were genetically combined with mutations in different trans-acting genes previously shown to cause a partial defect in silencing, only mutations in clr1 and clr3 showed additive defects in silencing with the deletion of IRL. The rate of mat1 switching is also affected by deletion of repeats. The IRL or IRR deletion did not cause significant derepression of the mat2 or mat3 loci. These results implicate repeats for maintaining full repression of the mat2,3 region, for efficient mat1 switching, and further support the notion that multiple pathways cooperate to silence the mat2,3 domain. PMID:12399374

  18. The 2.1-kb inverted repeat DNA sequences flank the mat2,3 silent region in two species of Schizosaccharomyces and are involved in epigenetic silencing in Schizosaccharomyces pombe.

    PubMed

    Singh, Gurjeet; Klar, Amar J S

    2002-10-01

    The mat2,3 region of the fission yeast Schizosaccharomyces pombe exhibits a phenomenon of transcriptional silencing. This region is flanked by two identical DNA sequence elements, 2.1 kb in length, present in inverted orientation: IRL on the left and IRR on the right of the silent region. The repeats do not encode any ORF. The inverted repeat DNA region is also present in a newly identified related species, which we named S. kambucha. Interestingly, the left and right repeats share perfect identity within a species, but show approximately 2% bases interspecies variation. Deletion of IRL results in variegated expression of markers inserted in the silent region, while deletion of the IRR causes their derepression. When deletions of these repeats were genetically combined with mutations in different trans-acting genes previously shown to cause a partial defect in silencing, only mutations in clr1 and clr3 showed additive defects in silencing with the deletion of IRL. The rate of mat1 switching is also affected by deletion of repeats. The IRL or IRR deletion did not cause significant derepression of the mat2 or mat3 loci. These results implicate repeats for maintaining full repression of the mat2,3 region, for efficient mat1 switching, and further support the notion that multiple pathways cooperate to silence the mat2,3 domain.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Male Germline Control of Transposable Elements1

    PubMed Central

    Bao, Jianqiang; Yan, Wei

    2012-01-01

    ABSTRACT Repetitive sequences, especially transposon-derived interspersed repetitive elements, account for a large fraction of the genome in most eukaryotes. Despite the repetitive nature, these transposable elements display quantitative and qualitative differences even among species of the same lineage. Although transposable elements contribute greatly as a driving force to the biological diversity during evolution, they can induce embryonic lethality and genetic disorders as a result of insertional mutagenesis and genomic rearrangement. Temporary relaxation of the epigenetic control of retrotransposons during early germline development opens a risky window that can allow retrotransposons to escape from host constraints and to propagate abundantly in the host genome. Because germline mutations caused by retrotransposon activation are heritable and thus can be deleterious to the offspring, an adaptive strategy has evolved in host cells, especially in the germline. In this review, we will attempt to summarize general defense mechanisms deployed by the eukaryotic genome, with an emphasis on pathways utilized by the male germline to confer retrotransposon silencing. PMID:22357546

  9. Transposable elements and vertebrate protein diversity.

    PubMed

    Lorenc, Anna; Makałowski, Wojciech

    2003-07-01

    Interspersed repetitive sequences are major components of eukaryotic genomes. Repetitive elements comprise about 50% of the mammalian genome. They interact with the whole genome and influence its evolution. Repetitive elements may serve as recombination hot spots or acquire specific cellular functions such as RNA transcription control or become part of protein coding regions. The latter is a subject of presented analysis. We searched all currently available vertebrate protein sequences, including human proteome complement for the presence of transposable elements. It appears that insertion of TE-cassettes into open reading frames is a general phenomena. They can be found in all vertebrate lineages and originate in all types of transposable elements. It seems that genomes use those cassettes as 'ready to use' motifs in their evolutionary experiments. Most of TE-cassettes are used to create alternative forms of a message and usually the other form, without TE-cassette, is expressed in a cell. Tables listing vertebrate messages with TE-cassettes are available at http://warta.bio.psu.edu/ScrapYard/.

  10. Transposable elements in the Anopheles funestus transcriptome.

    PubMed

    Fernández-Medina, Rita D; Carareto, Claudia M A; Struchiner, Cláudio J; Ribeiro, José M C

    2017-06-01

    Transposable elements (TEs) are present in most of the eukaryotic genomes and their impact on genome evolution is increasingly recognized. Although there is extensive information on the TEs present in several eukaryotic genomes, less is known about the expression of these elements at the transcriptome level. Here we present a detailed analysis regarding the expression of TEs in Anopheles funestus, the second most important vector of human malaria in Africa. Several transcriptionally active TE families belonging both to Class I and II were identified and characterized. Interestingly, we have identified a full-length putative active element (including the presence of full length TIRs in the genomic sequence) belonging to the hAT superfamily, which presents active members in other insect genomes. This work contributes to a comprehensive understanding of the landscape of transposable elements in A. funestus transcriptome. Our results reveal that TEs are abundant and diverse in the mosquito and that most of the TE families found in the genome are represented in the mosquito transcriptome, a fact that could indicate activity of these elements.The vast diversity of TEs expressed in A. funestus suggests that there is ongoing amplification of several families in this organism.

  11. 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. © 2013 Wiley Periodicals, Inc.

  12. Miniature Radioisotope Power Source

    NASA Technical Reports Server (NTRS)

    Chmielewski, Artur B.

    1995-01-01

    Proposed miniature power source generates electricity for years from heat developed in small radioisotope unit without addition of fuel or dependence on sunlight. Called powerstick, is relatively inexpensive, lightweight, and rugged. Supplies power to small vehicles or scientific instruments in remote locations on Earth or in outer space. Envisioned uses include Mars miniature rovers and monitoring equipment for toxic or nuclear storage sites.

  13. 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…

  14. 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…

  15. Genetic and epigenetic variation of transposable elements in Arabidopsis.

    PubMed

    Underwood, Charles J; Henderson, Ian R; Martienssen, Robert A

    2017-04-01

    Transposable elements are mobile genetic elements that are prevalent in plant genomes and are silenced by epigenetic modification. Different epigenetic modification pathways play distinct roles in the control of transposable element transcription, replication and recombination. The Arabidopsis genome contains families of all of the major transposable element classes, which are differentially enriched in particular genomic regions. Whole genome sequencing and DNA methylation profiling of hundreds of natural Arabidopsis accessions has revealed that transposable elements exhibit significant intraspecific genetic and epigenetic variation, and that genetic variation often underlies epigenetic variation. Together, epigenetic modification and the forces of selection define the scope within which transposable elements can contribute to, and control, genome evolution. Copyright © 2017. Published by Elsevier Ltd.

  16. 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.

  17. Miniature TV Camera

    NASA Technical Reports Server (NTRS)

    2004-01-01

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

  18. Miniature oxygen resuscitator

    NASA Technical Reports Server (NTRS)

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

    1969-01-01

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

  19. 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.

  20. Silencing transposable elements in the Drosophila germline.

    PubMed

    Yang, Fu; Xi, Rongwen

    2017-02-01

    Transposable elements or transposons are DNA pieces that can move around within the genome and are, therefore, potential threat to genome stability and faithful transmission of the genetic information in the germline. Accordingly, self-defense mechanisms have evolved in the metazoan germline to silence transposons, and the primary mechanism requires the germline-specific non-coding small RNAs, named Piwi-interacting RNA (piRNAs), which are in complex with Argonaute family of PIWI proteins (the piRNA-RISC complexes), to silence transposons. piRNA-mediated transposon silencing occurs at both transcriptional and post-transcriptional levels. With the advantages of genetic manipulation and advances of sequencing technology, much progress has been made on the molecular mechanisms of piRNA-mediated transposon silencing in Drosophila melanogaster, which will be the focus of this review. Because piRNA-mediated transposon silencing is evolutionarily conserved in metazoan, model organisms, such as Drosophila, will continue to be served as pioneer systems towards the complete understanding of transposon silencing in the metazoan germline.

  1. 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

  2. Reading transposed text: effects of transposed letter distance and consonant-vowel status on eye movements.

    PubMed

    Blythe, Hazel I; Johnson, Rebecca L; Liversedge, Simon P; Rayner, Keith

    2014-11-01

    Two experiments were conducted to investigate the flexibility of letter-position encoding in word identification during reading. In both experiments, two tasks were used. First, participants' eye movements were measured as they read sentences containing transposed letter (TL) strings. Second, participants were presented with the TL strings in isolation and were asked to discriminate them from nonwords. In Experiment 1, we manipulated the distance between transposed letters (ligament vs. liagment vs. limagent vs. lieamgnt). Reading/response times increased with the distance between TLs. In Experiment 2, we manipulated whether the TLs were consonants, vowels, or one of each (ssytem vs. faeture vs. fromat). Reading/response times showed that CV transpositions were the most disruptive. In both experiments, response accuracy was particularly poor for words presented in isolation when there was an intervening letter between TLs. These data show that processing across multiple fixations, and the presence of a meaningful sentence context, are important for flexible letter position encoding in lexical identification.

  3. 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

  4. Response of transposable elements to environmental stressors.

    PubMed

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

    2015-01-01

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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Miniature multichannel biotelemeter system

    NASA Technical Reports Server (NTRS)

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

    1974-01-01

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

  16. 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.

  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. Entangled states with positive partial transposes arising from indecomposable positive linear maps

    NASA Astrophysics Data System (ADS)

    Ha, Kil-Chan; Kye, Seung-Hyeok; Park, Young Sung

    2003-06-01

    We construct entangled states with positive partial transposes using indecomposable positive linear maps between matrix algebras. We also exhibit concrete examples of entangled states with positive partial transposes arising in this way, and show that they generate extreme rays in the cone of all positive semi-definite matrices with positive partial transposes. They also have Schmidt numbers two.

  19. 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

  20. 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.

  1. 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…

  2. [Vascular dialysis access with transposed superficial femoral vein].

    PubMed

    Buček, J; Staffa, R; Kříž, Z; Vlachovský, R

    2015-11-01

    The authors describe the case report of a 63 years old female patient with chronic renal failure in systemic lupus erythematosus. Vascular dialysis access in upper limbs could no more be used. The condition was approached by constructing an arteriovenous (AV) fistula in the thigh with transposed superficial femoral vein as the first procedure in the Czech Republic.

  3. 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…

  4. Equipment for drilling miniature holes

    SciTech Connect

    Gillespie, L K

    1981-04-01

    Miniature holes are produced on 16 different types of mechanical drilling equipment. Each equipment type has significant advantages for a specific type of part. The basic capabilities vary greatly between equipment types. Some produce very precise holes and others produce very high volumes of commercial tolerance holes. At the present time machines are available for mechanicaly drilling up to 100,000 miniature holes per hour. Lasers currently are drilling as many as 15,000,000 ultra-miniature holes per hour.

  5. 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.

  6. 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).

  7. 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).

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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

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

    PubMed

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

    2014-01-01

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

  15. Transposed-Letter Priming Across Inflectional Morpheme Boundaries.

    PubMed

    Zargar, Ehsan Shafiee; Witzel, Naoko

    2017-02-01

    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 structure, i.e., inflectionally complex words, using masked priming. Experiment 1 tested TL priming with nonword primes and inflected targets (FOCUSING). Nonword primes were formed by transposing letters either within the root morpheme (fcousing) or across two morphemes (focuisng). Experiment 2 used the same nonword primes, but had the root words as targets (FOCUS). Both experiments showed similar TL priming effects for within-morpheme and across-boundary positions, indicating that morphological decomposition takes place only after letter positions in a word have been assigned. This finding provides additional evidence to previous research testing derived and compound words showing TL priming regardless of the position of transposition.

  16. Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis.

    PubMed

    Cox, D G; Canzian, F

    2001-08-01

    The purpose of this work is to provide the modern molecular geneticist with tools to perform more efficient and more accurate analysis of the genotype data they produce. By using Microsoft Excel macros written in Visual Basic, we can translate genotype data into a form readable by the versatile software 'Arlequin', read the Arlequin output, calculate statistics of linkage disequilibrium, and put the results in a format for viewing with the software 'GOLD'. The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype&_Transposer/. Arlequin is available at: http://lgb.unige.ch/arlequin/. GOLD is available at: http://www.well.ox.ac.uk/asthma/GOLD/.

  17. Partial transpose of random quantum states: Exact formulas and meanders

    SciTech Connect

    Fukuda, Motohisa; Sniady, Piotr

    2013-04-15

    We investigate the asymptotic behavior of the empirical eigenvalues distribution of the partial transpose of a random quantum state. The limiting distribution was previously investigated via Wishart random matrices indirectly (by approximating the matrix of trace 1 by the Wishart matrix of random trace) and shown to be the semicircular distribution or the free difference of two free Poisson distributions, depending on how dimensions of the concerned spaces grow. Our use of Wishart matrices gives exact combinatorial formulas for the moments of the partial transpose of the random state. We find three natural asymptotic regimes in terms of geodesics on the permutation groups. Two of them correspond to the above two cases; the third one turns out to be a new matrix model for the meander polynomials. Moreover, we prove the convergence to the semicircular distribution together with its extreme eigenvalues under weaker assumptions, and show large deviation bound for the latter.

  18. 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.

  19. Unwrapping ADMM: Efficient Distributed Computing via Transpose Reduction

    DTIC Science & Technology

    2016-05-11

    convergence rates of the proposed schemes and demonstrate the efficiency of this approach by fitting linear classifiers and sparse linear models to...unwrapped ADMM for this problem requires the formation of DiDTi on each server, rather than DTi Di. 5 Applications: Linear Classifiers and Sparsity...In addition to penalized regression problems, transpose re- duction can train linear classifiers . If D ∈ Rm×n contains feature vectors and l ∈ Rm

  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. 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.

  2. 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.

  3. 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.

  4. Miniature Heat Pipes

    NASA Technical Reports Server (NTRS)

    1997-01-01

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

  5. 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.

  6. 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.

  7. 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.

  8. Gene expression variation in Drosophila melanogaster due to rare transposable element insertion alleles of large effect.

    PubMed

    Cridland, Julie M; Thornton, Kevin R; Long, Anthony D

    2015-01-01

    Transposable elements are a common source of genetic variation that may play a substantial role in contributing to gene expression variation. However, the contribution of transposable elements to expression variation thus far consists of a handful of examples. We used previously published gene expression data from 37 inbred Drosophila melanogaster lines from the Drosophila Genetic Reference Panel to perform a genome-wide assessment of the effects of transposable elements on gene expression. We found thousands of transcripts with transposable element insertions in or near the transcript and that the presence of a transposable element in or near a transcript is significantly associated with reductions in expression. We estimate that within this example population, ∼2.2% of transcripts have a transposable element insertion, which significantly reduces expression in the line containing the transposable element. We also find that transcripts with insertions within 500 bp of the transcript show on average a 0.67 standard deviation decrease in expression level. These large decreases in expression level are most pronounced for transposable element insertions close to transcripts and the effect diminishes for more distant insertions. This work represents the first genome-wide analysis of gene expression variation due to transposable elements and suggests that transposable elements are an important class of mutation underlying expression variation in Drosophila and likely in other systems, given the ubiquity of these mobile elements in eukaryotic genomes. Copyright © 2015 by the Genetics Society of America.

  9. The Whole new world of miniature technology

    SciTech Connect

    Gillespie, L.K.

    1980-07-01

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

  10. 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.

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

    PubMed

    Majumdar, Sharmistha; Rio, Donald C

    2015-04-01

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

  12. P transposable elements in Drosophila and other eukaryotic organisms

    PubMed Central

    Majumdar, Sharmistha; Rio, Donald C.

    2015-01-01

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

  13. Complications following Staged Hypospadias Repair Using Transposed Preputial Skin Flaps.

    PubMed

    Stanasel, Irina; Le, Hoang-Kim; Bilgutay, Aylin; Roth, David R; Gonzales, Edmond T; Janzen, Nicolette; Koh, Chester J; Gargollo, Patricio; Seth, Abhishek

    2015-08-01

    Proximal hypospadias repair using a staged approach is a complex reconstructive operation with the potential for significant complications requiring repeat surgery. We report outcomes of staged hypospadias repair using transposed preputial skin flaps and factors predictive of postoperative complications. We retrospectively analyzed patients who underwent staged proximal hypospadias repair using transposed preputial skin flaps between 2002 and 2013. Patient demographics, operative details, complications, reoperations and factors predictive of complications were reviewed. A total of 56 patients were identified with a mean age of 14.1 months (median 14.3) at first stage. Mean followup was 38.6 months (median 34.1). Complications requiring additional unplanned operation(s) were observed in 38 patients (68%), including fistulas in 32 (57%), diverticula in 8 (14%), meatal stenosis in 5 (9%), urethral stricture in 8 (14%) and glans dehiscence in 3 (5%). In addition, redo first stage repair was performed in 4 patients (7%). Since some patients had more than 1 complication, the total number of complications is greater than the number of patients undergoing a redo operation. On univariate analyses the use of small intestinal submucosa was significantly associated with an increased risk of fistula (91% vs 49%, p = 0.02) and urethral diverticulum (64% vs 24%, p = 0.04). Incision of the tunica albuginea of the corpora was associated with an increased likelihood of fistula (77% vs 44%, p = 0.03). Finally, patients with glans dehiscence were significantly younger at first stage (5.8 vs 14.8 months, p = 0.01). The reoperation rate for complications in children undergoing staged hypospadias repair using transposed preputial skin flaps is higher than previously reported. Copyright © 2015 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  14. 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

  15. 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.

  16. 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.

  17. Mobilizing diversity: transposable element insertions in genetic variation and disease

    PubMed Central

    2010-01-01

    Transposable elements (TEs) comprise a large fraction of mammalian genomes. A number of these elements are actively jumping in our genomes today. As a consequence, these insertions provide a source of genetic variation and, in rare cases, these events cause mutations that lead to disease. Yet, the extent to which these elements impact their host genomes is not completely understood. This review will summarize our current understanding of the mechanisms underlying transposon regulation and the contribution of TE insertions to genetic diversity in the germline and in somatic cells. Finally, traditional methods and emerging technologies for identifying transposon insertions will be considered. PMID:20813032

  18. Miniature Intelligent Sensor Module

    NASA Technical Reports Server (NTRS)

    Beech, Russell S.

    2007-01-01

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

  19. The plant MITE mPing is mobilized in anther culture.

    PubMed

    Kikuchi, Kazuhiro; Terauchi, Kazuki; Wada, Masamitsu; Hirano, Hiro-Yuki

    2003-01-09

    Transposable elements constitute a large portion of eukaryotic genomes and contribute to their evolution and diversification. Miniature inverted-repeat transposable elements (MITEs) constitute one of the main groups of transposable elements and are distributed ubiquitously in the genomes of plants and animals such as maize, rice, Arabidopsis, human, insect and nematode. Because active MITEs have not been identified, the transposition mechanism of MITEs and their accumulation in eukaryotic genomes remain poorly understood. Here we describe a new class of MITE, called miniature Ping (mPing), in the genome of Oryza sativa (rice). mPing elements are activated in cells derived from anther culture, where they are excised efficiently from original sites and reinserted into new loci. An mPing-associated Ping element, which has a putative PIF family transposase, is implicated in the recent proliferation of this MITE family in a subspecies of rice.

  20. 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.

  1. 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.

  2. LINE dancing in the human genome: transposable elements and disease

    PubMed Central

    2009-01-01

    Transposable elements (TEs) have been consistently underestimated in their contribution to genetic instability and human disease. TEs can cause human disease by creating insertional mutations in genes, and also contributing to genetic instability through non-allelic homologous recombination and introduction of sequences that evolve into various cis-acting signals that alter gene expression. Other outcomes of TE activity, such as their potential to cause DNA double-strand breaks or to modulate the epigenetic state of chromosomes, are less fully characterized. The currently active human transposable elements are members of the non-LTR retroelement families, LINE-1, Alu (SINE), and SVA. The impact of germline insertional mutagenesis by TEs is well established, whereas the rate of post-insertional TE-mediated germline mutations and all forms of somatic mutations remain less well quantified. The number of human diseases discovered to be associated with non-allelic homologous recombination between TEs, and particularly between Alu elements, is growing at an unprecedented rate. Improvement in the technology for detection of such events, as well as the mounting interest in the research and medical communities in resolving the underlying causes of the human diseases with unknown etiology, explain this increase. Here, we focus on the most recent advances in understanding of the impact of the active human TEs on the stability of the human genome and its relevance to human disease. PMID:19863772

  3. 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.

  4. Conceptual and empirical challenges of ascribing functions to transposable elements.

    PubMed

    Elliott, Tyler A; Linquist, Stefan; Gregory, T Ryan

    2014-07-01

    Media attention and the subsequent scientific backlash engendered by the claim by spokespeople for the Encyclopedia of DNA Elements (ENCODE) project that 80% of the human genome has a biochemical function highlight the need for a clearer understanding of function concepts in biology. This article provides an overview of two major function concepts that have been developed in the philosophy of science--the causal role concept and the selected effects concept--and their relevance to ENCODE. Unlike in some previous critiques, the ENCODE project is not considered problematic here because it employed a causal role definition of function (which is relatively common in genetics) but because of how this concept was misused. In addition, several unique challenges that arise when dealing with transposable elements (TEs) but that were ignored by ENCODE are highlighted. These include issues surrounding TE-level versus organism-level selection, the origins versus the persistence of elements, and accidental versus functional organism-level benefits. Finally, some key questions are presented that should be addressed in any study aiming to ascribe functions to major portions of large eukaryotic genomes, the majorities of which are made up of transposable elements.

  5. Serial mechanism in transposed letters effects: A developmental study.

    PubMed

    Colombo, Lucia; Sulpizio, Simone; Peressotti, Francesca

    2017-09-01

    The study describes the developmental trend of transposed letters (TL) effects in a lexical decision task. The TL effect refers to the fact that nonwords derived from words by transposing two middle letters (e.g., talbe from table) are responded to more slowly than control nonwords in which two letters are replaced (RL [replaced letters]; e.g., tafde). We measured this effect in three groups of children (second, third, and fifth graders) and a group of adults. Length was manipulated with short letter strings (four or five letters) and long letter strings (seven or eight letters). In long letter strings, position of letter transposition/replacement was also manipulated; half of the stimuli contained the TL/RL toward the beginning of the string and half toward the end of the string. The results showed that the size of the TL effect increased with age and that this developmental pattern was more marked for transpositions involving the final part of the word. The results suggest that with the increase in reading ability, the reading system relies more strongly on a coarse orthographic representation in which letter position is not precisely coded. Furthermore, the effect of position suggests that a serial mechanism is used to scan the letter string. This determines the extent to which nonwords activate the base words, modulating the influence of lexical effects in nonword decisions. The nature of this effect is discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. 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

  7. 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.

  8. [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.

  9. 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…

  10. 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.

  11. 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.

  12. 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.

  13. Transpose Algorithms and Visualization in Computational Plasma Physics

    NASA Astrophysics Data System (ADS)

    von Nessi, G.; Candy, J.

    2000-10-01

    We present a systematic study of ``transpose'' algorithms required for parallel data distribution. The need for an algorithm of this type arises naturally when applying operator-splitting methods to multidimensional PDEs. Specifically, we are interested in the solution of the gyrokinetic-Maxwell equations using a fixed Eulerian grid. We discuss strategies to determine optimal stride length and data grouping scheme for given grid dimensions. We also explore the problems of data I/O, visualization, and image rendering. One aspect in particular we hope to explore is the feasibility of using multiple processors to analyze and render data generated by plasma simulation code. In addition to this, the implementation of the MDSplus data format to store simulation data is investigated. The goal is to achieve as much as possible using open source software such as Visualization Toolkit (VTK) in order to minimize the fusion community's reliance on expensive commerical software such as Interactive Data Language (IDL).

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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. © 2016. Published by The Company of Biologists Ltd.

  1. Biology, dynamics, and applications of transposable elements in basidiomycete fungi.

    PubMed

    Castanera, Raúl; Borgognone, Alessandra; Pisabarro, Antonio G; Ramírez, Lucía

    2017-02-01

    The phylum Basidiomycota includes filamentous fungi and yeast species with different ecological and genomic characteristics. Transposable elements (TEs) are abundant components of most eukaryotic genomes, and their transition from being genomic parasites to key drivers of genomic architecture, functionality, and evolution is a subject receiving much attention. In light of the abundant genomic information released during the last decade, the aims of this mini-review are to discuss the dynamics and impact of TEs in basidiomycete fungi. To do this, we surveyed and explored data from 75 genomes, which encompass the phylogenetic diversity of the phylum Basidiomycota. We describe annotation approaches and analyze TE distribution in the context of species phylogeny and genome size. Further, we review the most relevant literature about the role of TEs in species lifestyle, their impact on genome architecture and functionality, and the defense mechanisms evolved to control their proliferation. Finally, we discuss potential applications of TEs that can drive future innovations in fungal research.

  2. 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.

  3. 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

  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 in Human Cancer: Causes and Consequences of Deregulation

    PubMed Central

    Anwar, Sumadi Lukman; Wulaningsih, Wahyu; Lehmann, Ulrich

    2017-01-01

    Transposable elements (TEs) comprise nearly half of the human genome and play an essential role in the maintenance of genomic stability, chromosomal architecture, and transcriptional regulation. TEs are repetitive sequences consisting of RNA transposons, DNA transposons, and endogenous retroviruses that can invade the human genome with a substantial contribution in human evolution and genomic diversity. TEs are therefore firmly regulated from early embryonic development and during the entire course of human life by epigenetic mechanisms, in particular DNA methylation and histone modifications. The deregulation of TEs has been reported in some developmental diseases, as well as for different types of human cancers. To date, the role of TEs, the mechanisms underlying TE reactivation, and the interplay with DNA methylation in human cancers remain largely unexplained. We reviewed the loss of epigenetic regulation and subsequent genomic instability, chromosomal aberrations, transcriptional deregulation, oncogenic activation, and aberrations of non-coding RNAs as the potential mechanisms underlying TE deregulation in human cancers. PMID:28471386

  6. Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres.

    PubMed

    Arkhipova, Irina R; Yushenova, Irina A; Rodriguez, Fernando

    2017-09-01

    Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here, we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3'-end of the RNA template immediately adjacent to a hammerhead ribozyme motif. Terminon units, which can exceed 40 kb in length, display an unusually complex and diverse structure, and can form very long chains, with host genes often captured between units. As the principal polymerizing component, Terminons contain Athena reverse transcriptases previously described in bdelloid rotifers and belonging to the enigmatic group of Penelope-like elements, but can additionally accumulate multiple cooriented ORFs, including DEDDy 3'-exonucleases, GDSL esterases/lipases, GIY-YIG-like endonucleases, rolling-circle replication initiator (Rep) proteins, and putatively structural ORFs with coiled-coil motifs and transmembrane domains. The extraordinary length and complexity of Terminons and the high degree of interfamily variability in their ORF content challenge the current views on the structural organization of eukaryotic retroelements, and highlight their possible connections with the viral world and the implications for the elevated frequency of gene transfer. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. Nucleosides with Transposed Base or 4'-Hydroxymethyl Moieties and Their Corresponding Oligonucleotides.

    PubMed

    Toti, Kiran; Renders, Marleen; Groaz, Elisabetta; Herdewijn, Piet; Van Calenbergh, Serge

    2015-12-23

    This review focuses on 4'-hydroxymethyl- or nucleobase-transposed nucleosides, nucleotides, and nucleoside phosphonates, their stereoisomers, and their close analogues. The biological activities of all known 4'-hydroxymethyl- or nucleobase-transposed nucleosides, nucleotides, and nucleoside phosphonates as potential antiviral or anticancer agents are compiled. The routes that have been taken for the chemical synthesis of such nucleoside derivatives are described, with special attention to the innovative strategies. The enzymatic synthesis, base-pairing properties, structure, and stability of oligonucleotides containing nucleobase- or 4'-hydroxymethyl-transposed nucleotides are discussed. The use of oligonucleotides containing nucleobase- or 4'-hydroxymethyl-transposed nucleotides as small oligonucleotide (e.g., human immunodeficiency virus integrase) inhibitors, in applications such as antisense therapy, silencing RNA (siRNA), or aptamer selections, is detailed.

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

    PubMed Central

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

    2009-01-01

    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. PMID:19577616

  16. 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.

  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. MnTEdb, a collective resource for mulberry transposable elements

    PubMed Central

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

    2015-01-01

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

  19. 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

  20. No Accumulation of Transposable Elements in Asexual Arthropods

    PubMed Central

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

    2016-01-01

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

  1. 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

  2. Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

    PubMed Central

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

    2014-01-01

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

  3. Transposable element insertions have strongly affected human evolution.

    PubMed

    Britten, Roy J

    2010-11-16

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

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

    PubMed

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

    2016-04-01

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

  5. 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.

  6. Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

    SciTech Connect

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

    2014-06-12

    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. We used methods developed to interrogate both assembled and unassembled sequences, and 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.

  7. Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

    DOE PAGES

    Hess, Jaqueline; Skrede, Inger; Wolfe, Benjamin E.; ...

    2014-06-12

    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) Amanitamore » fungi. We used methods developed to interrogate both assembled and unassembled sequences, and 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.« less

  8. Transposable elements and their potential role in complex lung disorder.

    PubMed

    Sargurupremraj, Muralidharan; Wjst, Matthias

    2013-10-05

    Transposable elements (TEs) are a class of mobile genetic elements (MGEs) that were long regarded as junk DNA, which make up approximately 45% of the genome. Although most of these elements are rendered inactive by mutations and other gene silencing mechanisms, TEs such as long interspersed nuclear elements (LINEs) are still active and translocate within the genome. During transposition, they may create lesions in the genome, thereby acting as epigenetic modifiers. Approximately 65 disease-causing LINE insertion events have been reported thus far; however, any possible role of TEs in complex disorders is not well established. Chronic obstructive pulmonary disease (COPD) is one such complex disease that is primarily caused by cigarette smoking. Although the exact molecular mechanism underlying COPD remains unclear, oxidative stress is thought to be the main factor in the pathogenesis of COPD. In this review, we explore the potential role of oxidative stress in epigenetic activation of TEs such as LINEs and the subsequent cascade of molecular damage. Recent advancements in sequencing and computation have eased the identification of mobile elements. Therefore, a comparative study on the activity of these elements and markers for genome instability would give more insight on the relationship between MGEs and complex disorder such as COPD.

  9. 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

  10. Considering Transposable Element Diversification in De Novo Annotation Approaches

    PubMed Central

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

    2011-01-01

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

  11. Gypsy, RTE and Mariner transposable elements populate Eyprepocnemis plorans genome.

    PubMed

    Montiel, Eugenia E; Cabrero, Josefa; Camacho, Juan Pedro M; López-León, M Dolores

    2012-09-01

    We analyze here the presence and abundance of three types of transposable elements (TEs), i.e. Gypsy, RTE and Mariner, in the genome of the grasshopper Eyprepocnemis plorans. PCR experiments allowed amplification, cloning and sequencing of these elements (EploGypI, EploRTE5, EploMar20) from the E. plorans genome. Fluorescent in situ hybridization (FISH) showed that all three elements are restricted to euchromatic regions, thus being absent from the pericentromeric region of all A chromosomes, which contain a satellite DNA (satDNA) and ribosomal DNA (rDNA), and being very scarce in B chromosomes mostly made up of these two types of repetitive DNA. FISH suggested that EploGypI is the most abundant and EploMar20 is the least abundant, with EploRTE5 showing intermediate abundance. An estimation of copy number, by means of quantitative PCR, showed that EploGypI is, by far, the most abundant element, followed by EploRTE5 and EploMar20, in consistency with FISH results. RNA isolation and PCR experiments on complementary DNA (cDNA) showed the presence of transcripts for the three TE elements. The implications of the preferential location of these TE elements into euchromatin, the significance of TE abundance in the giant genome of this species, and a possible relationship between TEs and B chromosome mutability, are discussed.

  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 elements in reptilian and avian (sauropsida) genomes.

    PubMed

    Kordis, D

    2009-01-01

    Transposable elements (TEs) have profound effects on the structure, function and evolution of their host genomes. Our knowledge about these agents of genomic change in sauropsids, a sister group of mammals that includes all extant reptiles and birds, is still very limited. Invaluable information concerning the diversity, activity and repetitive landscapes in sauropsids has recently emerged from analyses of the draft genomes of chicken and Anolis and other preliminary reptilian genome sequencing projects. Avian and reptilian genomes differ significantly in the classes of TEs present, their fractional representation in the genome and by the level of TE activity. While lepidosaurian genomes contain many young, active TE families, the extant avian genomes have very few active TE lineages. Most reptilian genomes possess quite rich TE repertoires that differ considerably from those of birds and mammals, being more similar in diversity to that of lower vertebrates. The large amount of recently accumulated genome-wide data on TEs in diverse lineages of sauropsids has provided a remarkable opportunity to review current knowledge about TEs of sauropsids in their genomic context. Copyright 2010 S. Karger AG, Basel.

  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. Microbattery technologies for miniaturized implantable medical devices.

    PubMed

    Nathan, Menachem

    2010-06-01

    Implanted medical devices (IMDs), in particular neuro-stimulators, drug delivery chips and cochlear implants are undergoing miniaturization. Some of these miniaturized IMDs are "active" in the sense that they require a power source for operation. In most cases, the ideal power source needs to be an implanted battery of dimensions similar to that of the device. The state-of-the-art of battery miniaturization is reviewed with emphasis on novel Li and Li-ion two- and three-dimensional thin-film microbatteries. It is shown that three-dimensional thin-film batteries may provide a solution to the power requirements of miniaturized IMDs.

  16. 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

  17. 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.

  18. Personal miniature electrophysiological tape recorder

    NASA Technical Reports Server (NTRS)

    Green, H.

    1981-01-01

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

  19. 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.

  20. 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.

  1. 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

  2. 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. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. 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.

  4. Transposable elements in disease-associated cryptic exons.

    PubMed

    Vorechovsky, Igor

    2010-02-01

    Transposable elements (TEs) make up a half of the human genome, but the extent of their contribution to cryptic exon activation that results in genetic disease is unknown. Here, a comprehensive survey of 78 mutation-induced cryptic exons previously identified in 51 disease genes revealed the presence of TEs in 40 cases (51%). Most TE-containing exons were derived from short interspersed nuclear elements (SINEs), with Alus and mammalian interspersed repeats (MIRs) covering >18 and >16% of the exonized sequences, respectively. The majority of SINE-derived cryptic exons had splice sites at the same positions of the Alu/MIR consensus as existing SINE exons and their inclusion in the mRNA was facilitated by phylogenetically conserved changes that improved both traditional and auxiliary splicing signals, thus marking intronic TEs amenable for pathogenic exonization. The overrepresentation of MIRs among TE exons is likely to result from their high average exon inclusion levels, which reflect their strong splice sites, a lack of splicing silencers and a high density of enhancers, particularly (G)AA(G) motifs. These elements were markedly depleted in antisense Alu exons, had the most prominent position on the exon-intron gradient scale and are proposed to promote exon definition through enhanced tertiary RNA interactions involving unpaired (di)adenosines. The identification of common mechanisms by which the most dynamic parts of the genome contribute both to new exon creation and genetic disease will facilitate detection of intronic mutations and the development of computational tools that predict TE hot-spots of cryptic exon activation.

  5. 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).

  6. 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. © 2014 by The Mycological Society of America.

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. Miniature multimode monolithic flextensional transducers.

    PubMed

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

    2007-10-01

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

  13. Miniature Telerobots in Space Applications

    NASA Technical Reports Server (NTRS)

    Venema, S. C.; Hannaford, B.

    1995-01-01

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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Miniaturized high-performance MEMS accelerometer detector

    NASA Astrophysics Data System (ADS)

    Gonseth, Stephan; Rudolf, Felix; Eichenberger, Christoph; Durrant, Dick; Airey, Phil

    2015-06-01

    In the framework of the demonstration of European capabilities for future space exploration mission, a high-performance miniaturized MEMS accelerometer detector is developed by Colibrys for incorporation into a compact inertial measurement unit (IMU). The envisaged missions where a miniaturized IMU is under development by SEA should cover: Aerobraking;

  19. 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.

  20. 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

  1. Do transposed-letter similarity effects occur at a prelexical phonological level?

    PubMed

    Perea, Manuel; Carreiras, Manuel

    2006-09-01

    Nonwords created by transposing two letters (e.g., RELOVUTION) are very effective at activating the lexical representation of their base words (Perea & Lupker, 2004). In the present study, we examined whether the nature of transposed-letter (TL) similarity effects was purely orthographic or whether it could also have a phonological component. Specifically, we examined transposed-letter similarity effects for nonwords created by transposing two nonadjacent letters (e.g., relovución-REVOLUCION) in a masked form priming experiment using the lexical decision task (Experiment 1). The controls were (a) a pseudohomophone of the transposed-letter prime (relobución-REVOLUCION; note that B and V are pronounced as /b/ in Spanish) or (b) an orthographic control (relodución-REVOLUCION). Results showed a similar advantage of the TL nonword condition over the phonological and the orthographic control conditions. Experiment 2 showed a masked phonological priming effect when the letter positions in the prime were in the right order. In a third experiment, using a single-presentation lexical decision task, TL nonwords produced longer latencies than the orthographic and phonological controls, whereas there was only a small phonological effect restricted to the error data. These results suggest that TL similarity effects are orthographic--rather than phonological--in nature.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Miniature mechanical transfer optical coupler

    SciTech Connect

    Abel, Philip; Watterson, Carl

    2011-02-15

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

  16. 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.

  17. 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.

  18. 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.

  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. Convex set of quantum states with positive partial transpose analysed by hit and run algorithm

    NASA Astrophysics Data System (ADS)

    Szymański, Konrad; Collins, Benot; Szarek, Tomasz; Życzkowski, Karol

    2017-06-01

    The convex set of quantum states of a composite K × K system with positive partial transpose is analysed. A version of the hit and run algorithm is used to generate a sequence of random points covering this set uniformly and an estimation for the convergence speed of the algorithm is derived. For K≥slant 3 this algorithm works faster than sampling over the entire set of states and verifying whether the partial transpose is positive. The level density of the PPT states is shown to differ from the Marchenko-Pastur distribution, supported in [0, 4] and corresponding asymptotically to the entire set of quantum states. Based on the shifted semi-circle law, describing asymptotic level density of partially transposed states, and on the level density for the Gaussian unitary ensemble with constraints for the spectrum we find an explicit form of the probability distribution supported in [0, 3], which describes well the level density obtained numerically for PPT states.

  1. 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.

  2. ERP correlates of transposed-letter similarity effects: are consonants processed differently from vowels?

    PubMed

    Carreiras, Manuel; Vergara, Marta; Perea, Manuel

    2007-06-04

    Recent research has shown that pseudowords created by transposing letters are very effective for activating the lexical representation of their base words (e.g., relovution activates REVOLUTION). Furthermore, pseudoword transpositions of consonants are more similar to their corresponding base words than the transposition of vowels. We report one experiment using pseudowords created by the transposition of two consonants, two vowels, and their corresponding control conditions (i.e., the replacement of two consonants or two vowels) in a lexical decision task while Event Related Potentials (ERPs) were recorded. The results showed a modulation of the amplitude of the N400 component as a function of the type of pseudoword (transposed-letter versus replacement letter pseudowords), and this modulation was different for transposed consonants and vowels. These results suggest that consonants and vowels play a different role during word processing.

  3. ERP correlates of transposed-letter priming effects: the role of vowels versus consonants.

    PubMed

    Carreiras, Manuel; Vergara, Marta; Perea, Manuel

    2009-01-01

    One key issue for any computational model of visual-word recognition is the choice of an input coding scheme for assigning letter position. Recent research has shown that pseudowords created by transposing two letters are very effective at activating the lexical representation of their base words (e.g., relovution activates REVOLUTION). We report a masked priming lexical decision experiment in which the pseudoword primes were created by transposing/replacing two consonants or two vowels while event-related potentials were recorded. The results showed a modulation of the amplitude at an early window (150-250 ms) and at the N400 component for vowels but not for consonant transpositions. In addition, the peak latencies were faster for transposed than replaced consonants. These results suggest that consonants and vowels play a different role during the process of visual word recognition. We examine the implications for the choice of an input coding scheme in models of visual-word recognition.

  4. A novel multimodal CARS miniaturized microscope

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

    We demonstrate the operation of a novel portable, fibre delivery miniaturized multimodal microscope (exoscope) for coherent anti-Stokes Raman scattering and two-photon excitation fluorescence imaging using a single Ti:sapphire femtosecond pulsed laser. This microscope features a large mode area photonic crystal fibre for light delivery, as well as biaxial scanning microelectromechanical system mirrors and custom miniaturized optics corrected for chromatic aberration. We demonstrate imaging of polystyrene beads, two photon excitation fluorescence beads in both forward and backward (epi) directions. This miniaturized exoscope will enable in-vivo imaging of rat spinal cord.

  5. Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods.

    PubMed

    Kamoun, Choumouss; Payen, Thibaut; Hua-Van, Aurélie; Filée, Jonathan

    2013-10-11

    Insertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and MITEs are relatively simple and basic genetic elements, their detection remains a difficult task due to their remarkable sequence diversity. With the advent of high-throughput genome and metagenome sequencing technologies, the development of fast, reliable and sensitive methods of ISs and MITEs detection become an important challenge. So far, almost all studies dealing with prokaryotic transposons have used classical BLAST-based detection methods against reference libraries. Here we introduce alternative methods of detection either taking advantages of the structural properties of the elements (de novo methods) or using an additional library-based method using profile HMM searches. In this study, we have developed three different work flows dedicated to ISs and MITEs detection: the first two use de novo methods detecting either repeated sequences or presence of Inverted Repeats; the third one use 28 in-house transposase alignment profiles with HMM search methods. We have compared the respective performances of each method using a reference dataset of 30 archaeal and 30 bacterial genomes in addition to simulated and real metagenomes. Compared to a BLAST-based method using ISFinder as library, de novo methods significantly improve ISs and MITEs detection. For example, in the 30 archaeal genomes, we discovered 30 new elements (+20%) in addition to the 141 multi-copies elements already detected by the BLAST approach. Many of the new elements correspond to ISs belonging to unknown or highly divergent families. The total number of MITEs has even doubled with the discovery of elements displaying very limited sequence similarities with their respective autonomous partners (mainly in the Inverted Repeats of the elements). Concerning metagenomes, with the exception of

  6. 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.

  7. 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

  8. 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)

  9. 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.

  10. 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.

  11. 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.

  12. 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)

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Conceptual learning by miniature brains

    PubMed Central

    Avarguès-Weber, Aurore; Giurfa, Martin

    2013-01-01

    Concepts act as a cornerstone of human cognition. Humans and non-human primates learn conceptual relationships such as ‘same’, ‘different’, ‘larger than’, ‘better than’, among others. In all cases, the relationships have to be encoded by the brain independently of the physical nature of objects linked by the relation. Consequently, concepts are associated with high levels of cognitive sophistication and are not expected in an insect brain. Yet, various works have shown that the miniature brain of honeybees rapidly learns conceptual relationships involving visual stimuli. Concepts such as ‘same’, ‘different’, ‘above/below of’ or ‘left/right are well mastered by bees. We review here evidence about concept learning in honeybees and discuss both its potential adaptive advantage and its possible neural substrates. The results reviewed here challenge the traditional view attributing supremacy to larger brains when it comes to the elaboration of concepts and have wide implications for understanding how brains can form conceptual relations. PMID:24107530

  1. 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.

  2. 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.

  3. 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…

  4. 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…

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    ERIC Educational Resources Information Center

    Yang, Jinmian

    2013-01-01

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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  8. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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. 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…

  11. 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…

  12. 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…

  13. 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…

  14. 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…

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

    NASA Astrophysics Data System (ADS)

    Ha, Kil-Chan; Kye, Seung-Hyeok

    2016-03-01

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

  16. 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…

  17. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Miniature EVA Software Defined Radio

    NASA Technical Reports Server (NTRS)

    Pozhidaev, Aleksey

    2012-01-01

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

  7. Trade-offs in miniature quadrupole designs.

    PubMed

    Boumsellek, S; Ferran, R J

    2001-06-01

    Pressing needs for miniature mass spectrometers became apparent during the last decade in process monitoring and control, space exploration, and environmental screening. Besides the small footprint, common requirements include low cost, low power consumption, field portability, reliability, autonomy, and ease-of-use. Design concepts and construction technologies of miniaturized quadrupole sensors were guided by cost reduction requirements without sacrifice of performance. The first miniature and complete quadrupole mass spectrometer system was introduced as the Micropole sensor. The concept featured a novel technique to assemble and operate multiple miniature quadrupoles in parallel. The short analyzer length offers a significant advantage by enabling direct mass filtering at pressures up in the 10(-2) torr range. High voltages at higher frequencies (10-20 MHz) are required for acceptable mass resolving powers. Additional trade-offs were uncovered in miniature sensors leading to designs optimized for each class of applications. Real time ray tracing of ions injected and filtered in the quadrupole field is used early in the design stage to predict the performance and reliability of the device.

  8. Advances in miniature spectrometer and sensor development

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  9. A Laser Interferometric Miniature Sensor

    SciTech Connect

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

    2011-09-12

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

  10. 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.

  11. 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.

  12. 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.

  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. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. Miniature rotating transmissive optical drum scanner

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

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

  3. Continuous flow nitration in miniaturized devices

    PubMed Central

    2014-01-01

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

  4. 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.

  5. 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.

  6. Miniature biotelemeter gives multichannel wideband biomedical data

    NASA Technical Reports Server (NTRS)

    Carraway, J. B.

    1972-01-01

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

  7. 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.

  8. A miniaturized counting technique for anaerobic bacteria.

    PubMed

    Sharpe, A N; Pettipher, G L; Lloyd, G R

    1976-12-01

    A miniaturized counting technique gave results as good as the pour-plate and Most Probable Number (MPN) techniques for enumeration of clostridia spp. and anaerobic isolates from the gut. Highest counts were obtained when ascorbic acid (1%) and dithiothreitol (0.015%) were added to the reinforced clostridial medium used for counting. This minimized the effect of exposure to air before incubation. The miniature technique allowed up to 40 samples to be plated and incubated in one McIntosh-Filde's-type anaerobic jar, compared with 3 or 4 by the normal pour plate.

  9. 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

  10. 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

  11. Targeting heterochromatin formation to transposable elements in Drosophila: potential roles of the piRNA system.

    PubMed

    Sentmanat, M; Wang, S H; Elgin, S C R

    2013-06-01

    Successful heterochromatin formation is critical for genome stability in eukaryotes, both to maintain structures needed for mitosis and meiosis and to silence potentially harmful transposable elements. Conversely, inappropriate heterochromatin assembly can lead to inappropriate silencing and other deleterious effects. Hence targeting heterochromatin assembly to appropriate regions of the genome is of utmost importance. Here we focus on heterochromatin assembly in Drosophila melanogaster, the model organism in which variegation, or cell-to-cell variable gene expression resulting from heterochromatin formation, was first described. In particular, we review the potential role of transposable elements as genetic determinants of the chromatin state and examine how small RNA pathways may participate in the process of targeted heterochromatin formation.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

    McNulty, Daniel; Tatham, Richard; Mišta, Ladislav

    2014-03-01

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

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

    PubMed

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

    2015-10-01

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

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

    SciTech Connect

    Mozrzymas, Marek; Horodecki, Michał; Studziński, Michał

    2014-03-15

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

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

    SciTech Connect

    Nagata, Koji

    2007-08-15

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

  18. 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.

  19. 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.

  20. Tn4556, a 6.8-kilobase-pair transposable element of Streptomyces fradiae.

    PubMed Central

    Chung, S T

    1987-01-01

    A 6.8-kilobase-pair (kbp) transposable element (Tn4556) was found in a neomycin-producing strain of Streptomyces fradiae. This element was first observed in two 30.3-kbp plasmids (pUC1123 and pUC1124) which arose when a thiostrepton resistance gene (1 kbp) was ligated with the BclI-2 fragment (22.5 kbp) that contains the origin of replication of phage SF1. The Tn4556 segment was deleted when these plasmids were transduced into another S. fradiae host with phage SF1. These deletion plasmids (pUC1210 and pUC1211) had copy numbers of less than 1 per chromosome and were unstable. In contrast, pUC1123 and pUC1124, with copy numbers of 12 to 15 per chromosome, respectively, were relatively stable. When pUC1210 and pUC1211 were reintroduced into S. fradiae by protoplast transformation, the Tn4556 element transposed again to the plasmids at numerous new locations in either of two orientations. A copy of Tn4556 was found in the S. fradiae chromosome by hybridization studies. It appears that Tn4556 originated from the chromosome, transposed into unstable pUC1210 and pUC1211, and made stable plasmids. A temperature-sensitive hybrid plasmid carrying a viomycin resistance derivative of Tn4556 (pMT660::Tn4556::vph) was constructed. When Streptomyces lividans UC8390 containing the hybrid plasmid was grown at 39 degrees C, Tn4556::vph (Tn4560) transposed to random positions in the host chromosome. Images PMID:2820925

  1. 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

  2. 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.

  3. 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.

  4. Letter-transposition effects are not universal: The impact of transposing letters in Hebrew

    PubMed Central

    Velan, Hadas; Frost, Ram

    2009-01-01

    We examined the effects of letter transposition in Hebrew in three masked-priming experiments. Hebrew, like English has an alphabetic orthography where sequential and contiguous letter strings represent phonemes. However, being a Semitic language it has a non-concatenated morphology that is based on root derivations. Experiment 1 showed that transposed-letter (TL) root primes inhibited responses to targets derived from the non-transposed root letters, and that this inhibition was unrelated to relative root frequency. Experiment 2 replicated this result and showed that if the transposed letters of the root created a nonsense-root that had no lexical representation, then no inhibition and no facilitation were obtained. Finally, Experiment 3 demonstrated that in contrast to English, French, or Spanish, TL nonword primes did not facilitate recognition of targets, and when the root letters embedded in them consisted of a legal root morpheme, they produced inhibition. These results suggest that lexical space in alphabetic orthographies may be structured very differently in different languages if their morphological structure diverges qualitatively. In Hebrew, lexical space is organized according to root families rather than simple orthographic structure, so that all words derived from the same root are interconnected or clustered together, independent of overall orthographic similarity. PMID:20161017

  5. 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

  6. Indistinguishability of bipartite states by positive-partial-transpose operations in the many-copy scenario

    NASA Astrophysics Data System (ADS)

    Li, Yinan; Wang, Xin; Duan, Runyao

    2017-05-01

    A bipartite subspace S is called strongly positive-partial-transpose (PPT) unextendible if for every positive integer k , there is no PPT operator supporting on the orthogonal complement of S⊗k. We show that a subspace is strongly PPT unextendible if it contains a PPT-definite operator (a positive semidefinite operator whose partial transpose is positive definite). Based on these, we are able to propose a simple criterion for verifying whether a set of bipartite orthogonal quantum states is indistinguishable by PPT operations in the many-copy scenario. Utilizing this criterion, we further point out that any entangled pure state and its orthogonal complement cannot be distinguished by PPT operations in the many-copy scenario. On the other hand, we investigate that the minimum dimension of strongly PPT-unextendible subspaces in an m ⊗n system is m +n -1 , which involves a generalization of the result that non-positive-partial-transpose subspaces can be as large as any entangled subspace [N. Johnston, Phys. Rev. A 87, 064302 (2013), 10.1103/PhysRevA.87.064302].

  7. Transposable element insertion location bias and the dynamics of gene drive in mosquito populations.

    PubMed

    Rasgon, J L; Gould, F

    2005-10-01

    Some vector-borne disease control strategies using transgenic mosquitoes require transgene spread to high frequency in populations. Transposable elements (TEs) are DNA sequences that replicate and transpose within the genomes of other organisms and may therefore be represented in the next generation in higher frequencies than predicted by Mendelian segregation. This over-representation has allowed some TEs to spread through natural populations. Transgenes incorporated within a TE sequence are expected to be driven into populations as long as there is a positive balance between fitness costs and over-representation. Models have been used to examine parameters that affect this balance but did not take into account biased insertion of TEs to linked sites in the genome. A simulation model was created to examine the impact of insertion bias on TE spread in mosquito populations. TEs that induce no fitness costs are predicted to increase in frequency over a wide range of parameter values but spread is slower for lower levels of transposition and non-local movement. If TEs are costly, high proportions of local movement can slow or halt spread. To function as a robust transgene drive mechanism a TE should replicate and transpose > 10%/insert/generation, induce < 1% fitness cost/insert, and move preferentially to unlinked sites in the genome.

  8. 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

  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. 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...

  11. 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...

  12. 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)

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

    ERIC Educational Resources Information Center

    Macaulay, Sara Grove

    2001-01-01

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

  14. Miniature fluorescence detection system for protein chips

    NASA Astrophysics Data System (ADS)

    Kim, Hoseong; Choi, Jaeho; Lee, Kook-Nyung; Kim, Yongkwon

    2005-01-01

    We report the development of miniature fluorescence detection systems that employ miniature prism, mirrors and low cost CCD camera to detect the fluorescence emitted from 40 fluorescently-labeled protein patterns without scanner. This kind of miniature fluorescence detection systems can be used in point of care. We introduce two systems, one uses prism + mirror block and the other uses prism and two mirrors. A large NA microscope eyepiece and low cost CCD camera are used. We fabricated protein chip containing multi-pattern BSA labeled with Cy5, using MEMS technology and modified the surface chemically to clean and to immobilize proteins. The measurements show that the combination of prism and mirrors can homogenize elliptical excitation light over the sample with higher optical efficiency, and increase the separation between excitation and fluorescence light at the CCD to give higher signal intensity and higher signal to noise ratio. The measurements also show that protein concentrations ranging from 10 ng/ml to 1000 ng/ml can be assayed with very small error. We believe that the proposed fluorescence detection system can be refined to build a commercially valuable hand-held or miniature detection device.

  15. 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…

  16. 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…

  17. Teaching ANOVA Models via Miniature Numerical Samples

    ERIC Educational Resources Information Center

    Bolton, Brian

    1975-01-01

    On the premise that the more formal algebraic presentation of statistics must be placed in a concrete context to facilitate student understanding, the author presents a pedagogical device involving the construction of miniature numerical examples that illustrate how the statistical model imposes structure on empirical data. (JT)

  18. 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.

  19. 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.

  20. Handheld miniature ion trap mass spectrometers.

    PubMed

    Ouyang, Zheng; Noll, Robert J; Cooks, R Graham

    2009-04-01

    For field applications, "miniature" and "rapid" have become almost synonymous, yet these small mass spectrometers are not useful if performance is too severely compromised. (To listen to a podcast about this feature, please go to the Analytical Chemistry website at pubs.acs.org/journal/ancham .).

  1. 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…

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Extending the transposable payload limit of Sleeping Beauty (SB) using the Herpes Simplex Virus (HSV)/SB amplicon vector platform

    PubMed Central

    de Silva, Suresh; Mastrangelo, Michael A.; Lotta, Louis T.; Burris, Clark A.; Federoff, Howard J.; Bowers, William J.

    2009-01-01

    The ability of a viral vector to safely deliver and stably integrate large transgene units (transgenons), which not only include one or several therapeutic genes but also requisite native transcriptional regulatory elements, would be of significant benefit for diseases presently refractory to available technologies. The herpes simplex virus type-1 (HSV-1) amplicon vector has the largest known payload capacity of approximately 130 kb, but its episomal maintenance within the transduced cell nucleus and induction of host cell silencing mechanisms limits the duration of the delivered therapeutic gene(s). Our laboratory developed an integration-competent version of the HSV-1 amplicon by adaptation of the Sleeping Beauty (SB) transposon system, which significantly extends transgene expression in vivo. The maximum size limit of the amplicon-vectored transposable element remains unknown, but previously published plasmid-centric studies have established that DNA segments larger than 6-kb are inefficiently transposed. Herein, we compared the transposition efficiency of SB transposase in the context of both the HSV amplicon vector as well as the HSV amplicon plasmid harboring 7-kb and 12-kb transposable reporter transgene units. Our results indicate that the transposition efficiency of the 12-kb transposable unit via SB transposase was significantly reduced compared to the 7-kb transposable unit when the plasmid version of the HSV amplicon was used. However, the packaged HSV amplicon vector form provided a more amenable platform from which the 12-kb transposable unit was mobilized at a similar efficiency to that of the 7-kb transposable unit via the SB transposase. Overall, our results indicate that SB is competent in stably integrating transgenon units of at least 12 kb in size within the human genome upon delivery of the platform via HSV amplicons. PMID:19865178

  7. 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

  8. 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

  9. A miniature, infrared pressure telemetry system

    NASA Technical Reports Server (NTRS)

    Tcheng, Ping; Schott, Timothy D.; Bryant, Emmett L.

    1988-01-01

    A miniature, single-channel, infrared telemetry system designed for making base pressure measurements on a wind tunnel model has been developed for the 13-inch magnetic suspension and balance system (MSBS) at Langley Research Center. The system consists of a transmitter installed in the wind tunnel model and a receiver station located outside of the test section. The onboard transmitter package includes a miniature pressure transducer, a signal conditioning circuit, and IR LED and a hearing-aid battery package. The IR LED, which is mounted flush with the model's surface, serves as the transmitter. The system is automatically activated in a magnetic field and has low power requirements. The system has been successfully employed to make low speed base pressure measurements at the 13-inch MSBS. The battery powered telemetry transmitter has a demonstrated one-hour operating life and an overall precision of better than 1/2 percent full scale.

  10. 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.

  11. 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.

  12. Miniature synthetic-aperture radar system

    NASA Astrophysics Data System (ADS)

    Stockton, Wayne; Stromfors, Richard D.

    1990-11-01

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

  13. Miniaturization of holographic Fourier-transform spectrometers.

    PubMed

    Agladze, Nikolay I; Sievers, Albert J

    2004-12-20

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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Development of a Miniature Snapshot Multispectral Imager

    DTIC Science & Technology

    2010-09-01

    Martins, J. S.; Wolffenbuttel, R. F.; Correia, J. H. An Array of Fabry – Perot Optical – Channels for Biological Fluids Analysis. Sensors and...applications. The system is low weight and portable with a miniature platform, and requires low power. The imager uses a 4×4 Fabry - Perot filter array...shadow mask technique to fabricate a Fabry - Perot etalon with multilayer dielectric mirrors. The filter array subsystem is installed in a commercial

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. Miniaturized LEDs for flat-panel displays

    NASA Astrophysics Data System (ADS)

    Radauscher, Erich J.; Meitl, Matthew; Prevatte, Carl; Bonafede, Salvatore; Rotzoll, Robert; Gomez, David; Moore, Tanya; Raymond, Brook; Cok, Ronald; Fecioru, Alin; Trindade, António Jose; Fisher, Brent; Goodwin, Scott; Hines, Paul; Melnik, George; Barnhill, Sam; Bower, Christopher A.

    2017-02-01

    Inorganic light emitting diodes (LEDs) serve as bright pixel-level emitters in displays, from indoor/outdoor video walls with pixel sizes ranging from one to thirty millimeters to micro displays with more than one thousand pixels per inch. Pixel sizes that fall between those ranges, roughly 50 to 500 microns, are some of the most commercially significant ones, including flat panel displays used in smart phones, tablets, and televisions. Flat panel displays that use inorganic LEDs as pixel level emitters (μILED displays) can offer levels of brightness, transparency, and functionality that are difficult to achieve with other flat panel technologies. Cost-effective production of μILED displays requires techniques for precisely arranging sparse arrays of extremely miniaturized devices on a panel substrate, such as transfer printing with an elastomer stamp. Here we present lab-scale demonstrations of transfer printed μILED displays and the processes used to make them. Demonstrations include passive matrix μILED displays that use conventional off-the shelf drive ASICs and active matrix μILED displays that use miniaturized pixel-level control circuits from CMOS wafers. We present a discussion of key considerations in the design and fabrication of highly miniaturized emitters for μILED displays.

  5. 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; hide

    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.

  6. 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.

  7. 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.

  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. 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.

  10. RetroSeq: transposable element discovery from next-generation sequencing data

    PubMed Central

    Keane, Thomas M.; Wong, Kim; Adams, David J.

    2013-01-01

    Summary: A significant proportion of eukaryote genomes consist of transposable element (TE)-derived sequence. These elements are known to have the capacity to modulate gene function and genome evolution. We have developed RetroSeq for detecting non-reference TE insertions from Illumina paired-end whole-genome sequencing data. We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls. Availabilty: RetroSeq is open-source and available from https://github.com/tk2/RetroSeq. Contact: tk2@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23233656

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

    PubMed Central

    Burlet, Nelly

    2016-01-01

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

  12. Burst expansion, distribution and diversification of MITEs in the silkworm genome

    PubMed Central

    2010-01-01

    Background Miniature inverted-repeat transposable elements (MITEs) are widespread in plants and animals. Although silkworm (Bombyx mori) has a large amount of and a variety of transposable elements, the genome-wide information of the silkworm MITEs is unknown. Results We used structure-based and homology approaches to search for MITEs in the silkworm genome. We identified 17 MITE families with a total of 5785 members, accounting for ~0.4% of the genome. 7 of 17 MITE families are completely novel based on the nucleotide composition of target site duplication (TSD) and/or terminal inverted repeats (TIR). Silkworm MITEs were widely and nonrandom distributed in the genome. One family named BmMITE-2 might experience a recent burst expansion. Network and diversity analyses for each family revealed different diversification patterns of the silkworm MITEs, reflecting the signatures of genome-shocks that silkworm experienced. Most silkworm MITEs preferentially inserted into or near genes and BmMITE-11 that encodes a germline-restricted small RNA might silence its the closest genes in silkworm ovary through a small RNA pathway. Conclusions Silkworm harbors 17 MITE families. The silkworm MITEs preferred to reside in or near genes and one MITE might be involved in gene silence. Our results emphasize the exceptional role of MITEs in transcriptional regulation of genes and have general implications to understand interaction between MITEs and their host genome. PMID:20875122

  13. 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.

  14. A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

    PubMed Central

    Biémont, Christian

    2010-01-01

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

  15. The Mu Transposable Elements of Maize: Evidence for Transposition and Copy Number Regulation during Development

    PubMed Central

    Alleman, Mary; Freeling, Michael

    1986-01-01

    The Mu transposon of maize exists in a highly mutagenic strain called Robertson's Mutator. Plants of this strain contain 10–50 copies of the Mu element, whereas most maize strains and other plants have none. When Mutator plants are crossed to plants of the inbred line 1S2P, which does not have copies of Mu, the progeny plants have approximately the same number of Mu sequences as did their Mutator parent. Approximately one-half of these copies have segregated from their parent and one-half have arisen by transposition and are integrated into new positions in the genome. This maintenance of copy number can be accounted for by an extremely high rate of transposition of the Mu elements (10–15 transpositions per gamete per generation). When Mutator plants are self-pollinated, the progeny double their Mu copy number in the first generation, but maintain a constant number of Mu sequences with subsequent self-pollinations. Transposition of Mu and the events that lead to copy number maintenance occur very late in the development of the germ cells but before fertilization. A larger version of the Mu element transposes but is not necessary for transposition of the Mu sequences. The progeny of crosses with a Mutator plant occasionally lack Mutator activity; these strains retain copies of the Mu element, but these elements no longer transpose. PMID:3002907

  16. 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.

  17. Centromere Remodeling in Hoolock leuconedys (Hylobatidae) by a New Transposable Element Unique to the Gibbons

    PubMed Central

    Carbone, Lucia; Harris, R. Alan; Mootnick, Alan R.; Milosavljevic, Aleksandar; Martin, David I. K.; Rocchi, Mariano; Capozzi, Oronzo; Archidiacono, Nicoletta; Konkel, Miriam K.; Walker, Jerilyn A.; Batzer, Mark A.; de Jong, Pieter J.

    2012-01-01

    Gibbons (Hylobatidae) shared a common ancestor with the other hominoids only 15–18 million years ago. Nevertheless, gibbons show very distinctive features that include heavily rearranged chromosomes. Previous observations indicate that this phenomenon may be linked to the attenuated epigenetic repression of transposable elements (TEs) in gibbon species. Here we describe the massive expansion of a repeat in almost all the centromeres of the eastern hoolock gibbon (Hoolock leuconedys). We discovered that this repeat is a new composite TE originating from the combination of portions of three other elements (L1ME5, AluSz6, and SVA_A) and thus named it LAVA. We determined that this repeat is found in all the gibbons but does not occur in other hominoids. Detailed investigation of 46 different LAVA elements revealed that the majority of them have target site duplications (TSDs) and a poly-A tail, suggesting that they have been retrotransposing in the gibbon genome. Although we did not find a direct correlation between the emergence of LAVA elements and human–gibbon synteny breakpoints, this new composite transposable element is another mark of the great plasticity of the gibbon genome. Moreover, the centromeric expansion of LAVA insertions in the hoolock closely resembles the massive centromeric expansion of the KERV-1 retroelement reported for wallaby (marsupial) interspecific hybrids. The similarity between the two phenomena is consistent with the hypothesis that evolution of the gibbons is characterized by defects in epigenetic repression of TEs, perhaps triggered by interspecific hybridization. PMID:22593550

  18. Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons.

    PubMed

    Carbone, Lucia; Harris, R Alan; Mootnick, Alan R; Milosavljevic, Aleksandar; Martin, David I K; Rocchi, Mariano; Capozzi, Oronzo; Archidiacono, Nicoletta; Konkel, Miriam K; Walker, Jerilyn A; Batzer, Mark A; de Jong, Pieter J

    2012-01-01

    Gibbons (Hylobatidae) shared a common ancestor with the other hominoids only 15-18 million years ago. Nevertheless, gibbons show very distinctive features that include heavily rearranged chromosomes. Previous observations indicate that this phenomenon may be linked to the attenuated epigenetic repression of transposable elements (TEs) in gibbon species. Here we describe the massive expansion of a repeat in almost all the centromeres of the eastern hoolock gibbon (Hoolock leuconedys). We discovered that this repeat is a new composite TE originating from the combination of portions of three other elements (L1ME5, AluSz6, and SVA_A) and thus named it LAVA. We determined that this repeat is found in all the gibbons but does not occur in other hominoids. Detailed investigation of 46 different LAVA elements revealed that the majority of them have target site duplications (TSDs) and a poly-A tail, suggesting that they have been retrotransposing in the gibbon genome. Although we did not find a direct correlation between the emergence of LAVA elements and human-gibbon synteny breakpoints, this new composite transposable element is another mark of the great plasticity of the gibbon genome. Moreover, the centromeric expansion of LAVA insertions in the hoolock closely resembles the massive centromeric expansion of the KERV-1 retroelement reported for wallaby (marsupial) interspecific hybrids. The similarity between the two phenomena is consistent with the hypothesis that evolution of the gibbons is characterized by defects in epigenetic repression of TEs, perhaps triggered by interspecific hybridization.

  19. 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.

  20. Intrinsic Characteristics of Neighboring DNA Modulate Transposable Element Activity in Drosophila melanogaster

    PubMed Central

    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. PMID:20944016

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Lyakh, Dmitry I.

    2015-04-01

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

  3. 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.

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

    DOE PAGES

    Castanera, Raul; Lopez-Varas, Leticia; Borgognone, Alessandra; ...

    2016-06-13

    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 Classmore » 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.« less

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

    PubMed Central

    Masserang, Kathleen M.; Pollatsek, Alexander

    2012-01-01

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

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

    PubMed

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

    2013-11-06

    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.

  7. 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.

  8. 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).

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

    PubMed Central

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

    2016-01-01

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

  10. Genome-Wide Distribution of Transposed Dissociation Elements in Maize[W][OA

    PubMed Central

    Vollbrecht, Erik; Duvick, Jon; Schares, Justin P.; Ahern, Kevin R.; Deewatthanawong, Prasit; Xu, Ling; Conrad, Liza J.; Kikuchi, Kazuhiro; Kubinec, Tammy A.; Hall, Bradford D.; Weeks, Rebecca; Unger-Wallace, Erica; Muszynski, Michael; Brendel, Volker P.; Brutnell, Thomas P.

    2010-01-01

    The maize (Zea mays) transposable element Dissociation (Ds) was mobilized for large-scale genome mutagenesis and to study its endogenous biology. Starting from a single donor locus on chromosome 10, over 1500 elements were distributed throughout the genome and positioned on the maize physical map. Genetic strategies to enrich for both local and unlinked insertions were used to distribute Ds insertions. Global, regional, and local insertion site trends were examined. We show that Ds transposed to both linked and unlinked sites and displayed a nonuniform distribution on the genetic map around the donor r1-sc:m3 locus. Comparison of Ds and Mutator insertions reveals distinct target preferences, which provide functional complementarity of the two elements for gene tagging in maize. In particular, Ds displays a stronger preference for insertions within exons and introns, whereas Mutator insertions are more enriched in promoters and 5′-untranslated regions. Ds has no strong target site consensus sequence, but we identified properties of the DNA molecule inherent to its local structure that may influence Ds target site selection. We discuss the utility of Ds for forward and reverse genetics in maize and provide evidence that genes within a 2- to 3-centimorgan region flanking Ds insertions will serve as optimal targets for regional mutagenesis. PMID:20581308

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

    PubMed Central

    Kines, Kristine J.; Belancio, Victoria P.

    2012-01-01

    1. ABSTRACT 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. PMID:22201807

  12. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.

    PubMed

    Greally, John M

    2002-01-08

    To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature indicates that the sequence characteristics of currently imprinted regions existed before the mammalian radiation. Transitions from imprinted to nonimprinted genomic regions in cis are characterized by a sharp inflection in SINE content, demonstrating that this genomic characteristic can help predict the presence and extent of regions undergoing imprinting. During primate evolution, SINE accumulation in imprinted regions occurred at a decreased rate compared with control loci. The constraint on SINE accumulation in imprinted regions may be mediated by an active selection process. This selection could be because of SINEs attracting and spreading methylation, as has been found at other loci. Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival.

  13. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome

    PubMed Central

    Greally, John M.

    2002-01-01

    To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature indicates that the sequence characteristics of currently imprinted regions existed before the mammalian radiation. Transitions from imprinted to nonimprinted genomic regions in cis are characterized by a sharp inflection in SINE content, demonstrating that this genomic characteristic can help predict the presence and extent of regions undergoing imprinting. During primate evolution, SINE accumulation in imprinted regions occurred at a decreased rate compared with control loci. The constraint on SINE accumulation in imprinted regions may be mediated by an active selection process. This selection could be because of SINEs attracting and spreading methylation, as has been found at other loci. Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival. PMID:11756672

  14. 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

  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. 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.

  17. Development of Californium-252 Miniature Source Assemblies

    SciTech Connect

    Notspecified, N. A.

    2007-06-26

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

  18. 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).

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Miniature Ground Penetrating Radar, CRUX GPR

    NASA Technical Reports Server (NTRS)

    Kim, Soon Sam; Carnes, Steven R.; Haldemann, Albert F.; Ulmer, Christopher T.; Ng, Eddie; Arcone, Steven A.

    2006-01-01

    Under NASA instrument development programs (PIDDP 2000-2002, MIPD 2003-2005, ESR and T, 2005) we have been developing miniature ground penetrating radars (GPR) for use in mapping subsurface stratigraphy from planetary rovers for Mars and lunar applications. The Mars GPR is for deeper penetration (up to 50 m depth) into the Martian subsurface at moderate resolution (0.5 m) for a geological characterization. As a part of the CRUX (Construction and Resource Utilization Explorer) instrument suite, the CRUX GPR is optimized for a lunar prospecting application. It will have shallower penetration (5 m depth) with higher resolution (10 cm) for construction operations including ISRU (in-situ resource utilization).

  14. Collaborating miniature drones for surveillance and reconnaissance

    NASA Astrophysics Data System (ADS)

    Bürkle, Axel

    2009-09-01

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

  15. Miniaturizing optical antennas using hyperbolic metamaterial wires

    NASA Astrophysics Data System (ADS)

    Smaali, Rafik; Omeis, Fatima; Moreau, Antoine; Centeno, Emmanuel; Taliercio, Thierry

    2017-04-01

    We propose the concept of hyperbolic wires that overcome the actual limitation of metal-insulator-metal (MIM) patch antennas in terms of electromagnetic confinement and efficiency. The use of hyperbolic metamaterials allows one to realize miniaturized resonators sustaining bulk plasmon polaritons squeezed to only one-hundredth of the wavelength. Beyond this tenfold size reduction compared to MIM antennas, we propose a model allowing one to scale the resonant frequencies of hyperbolic wires over a broad spectral range by controlling the filling ratio in metals and dielectrics.

  16. A miniaturized kit for ozone biomonitoring

    SciTech Connect

    Lorenzini, G.

    1994-07-01

    A new miniaturized kit based on very young supersensitive tobacco Bel-W3 plantlets, which can be easily used to detect phytotoxic levels of ozone in ambient air in large scale surveys, is described. It has been developed in laboratory as well as field studies. The optimal sampling time is 5-7 d. The advantages of the kit are its user-friendliness, low cost, and reliability. The kit may be integrated by a passive sampling tube set and may be also proposed for educational programs. 6 refs., 2 figs.

  17. Comparison of the efficacy of upper arm transposed arteriovenous fistulae and upper arm prosthetic grafts.

    PubMed

    Woo, Karen; Doros, Gheorghe; Ng, Tina; Farber, Alik

    2009-12-01

    Direct comparison of transposed arteriovenous fistulas (tAVF) and arteriovenous grafts (AVG) has been hampered by inherent differences in patient characteristics between tAVF and AVG groups. In this study, using matching to control patient variables, we evaluated our outcomes with upper arm tAVF and upper arm prosthetic AVG. A retrospective review of all newly created upper arm tAVF and AVG was performed. One hundred ninety upper arm tAVF were group matched for age, gender, race, diabetes, and history of previous failed access with 168 AVG chosen from a pool of 476 concurrently performed AVG procedures. Complication, patency, and intervention rates were compared using multivariate analysis. Mean follow up for our cohort was 29.1 months. Transposed fistulae consisted of 119 basilic vein and 71 cephalic vein transpositions, which were found to have similar demographic parameters, complication rates, and patency rates. There were no differences in 30 day mortality, 24 hour thrombosis, bleeding requiring exploration, or ischemic steal requiring intervention between the tAVF and AVG groups. More AVG developed infection requiring operative exploration than tAVF (7.9% vs 1.6%, respectively. P = .004). Primary patency for tAVF was higher than for AVG: 48% vs 14% at five years (P < .0001). Secondary patency rate for tAVF was also higher than for AVG: 57% vs 19% at five years (P < .0001). Nine percent of tAVF compared with 53% of AVG required one or more surgical and/or percutaneous revisions to maintain secondary patency (P < .0001). Multivariate analysis revealed that utilization of a tAVF was associated with a reduced risk of primary (Hazard Ratio [HR] 0.47, 95% Confidence Interval [CI] 0.35-0.64, P < .0001) and secondary failure (HR 0.59, 95% CI 0.42-0.81, P = .0001). Transposed arteriovenous fistulas have significantly higher primary and secondary patency rates, require fewer revisions, and are less likely to develop a significant infection than AVG. This study supports

  18. 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

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

    PubMed

    Santana, Mateus F; Silva, José C F; Batista, Aline D; Ribeiro, Lílian E; da Silva, Gilvan F; de Araújo, Elza F; de Queiroz, Marisa V

    2012-12-22

    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. 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. The analysis of TEs in M. fijiensis suggests that TEs play an important role in the evolution of this organism because the activity of these elements, as well

  20. 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