Tetris is a foldback transposon that provided the building blocks for an emerging satellite DNA of Drosophila virilis.

PubMed

Dias, Guilherme B; Svartman, Marta; Delprat, Alejandra; Ruiz, Alfredo; Kuhn, Gustavo C S

2014-05-24

Transposable elements (TEs) and satellite DNAs (satDNAs) are abundant components of most eukaryotic genomes studied so far and their impact on evolution has been the focus of several studies. A number of studies linked TEs with satDNAs, but the nature of their evolutionary relationships remains unclear. During in silico analyses of the Drosophila virilis assembled genome, we found a novel DNA transposon we named Tetris based on its modular structure and diversity of rearranged forms. We aimed to characterize Tetris and investigate its role in generating satDNAs. Data mining and sequence analysis showed that Tetris is apparently nonautonomous, with a structure similar to foldback elements, and present in D. virilis and D. americana. Herein, we show that Tetris shares the final portions of its terminal inverted repeats (TIRs) with DAIBAM, a previously described miniature inverted transposable element implicated in the generation of chromosome inversions. Both elements are likely to be mobilized by the same autonomous TE. Tetris TIRs contain approximately 220-bp internal tandem repeats that we have named TIR-220. We also found TIR-220 repeats making up longer (kb-size) satDNA-like arrays. Using bioinformatic, phylogenetic and cytogenomic tools, we demonstrated that Tetris has contributed to shaping the genomes of D. virilis and D. americana, providing internal tandem repeats that served as building blocks for the amplification of satDNA arrays. The β-heterochromatic genomic environment seemed to have favored such amplification. Our results imply for the first time a role for foldback elements in generating satDNAs. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

PubMed

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

2014-01-01

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

Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula

PubMed Central

Grzebelus, Dariusz; Lasota, Slawomir; Gambin, Tomasz; Kucherov, Gregory; Gambin, Anna

2007-01-01

Background Transposable elements constitute a significant fraction of plant genomes. The PIF/Harbinger superfamily includes DNA transposons (class II elements) carrying terminal inverted repeats and producing a 3 bp target site duplication upon insertion. The presence of an ORF coding for the DDE/DDD transposase, required for transposition, is characteristic for the autonomous PIF/Harbinger-like elements. Based on the above features, PIF/Harbinger-like elements were identified in several plant genomes and divided into several evolutionary lineages. Availability of a significant portion of Medicago truncatula genomic sequence allowed for mining PIF/Harbinger-like elements, starting from a single previously described element MtMaster. Results Twenty two putative autonomous, i.e. carrying an ORF coding for TPase and complete terminal inverted repeats, and 67 non-autonomous PIF/Harbinger-like elements were found in the genome of M. truncatula. They were divided into five families, MtPH-A5, MtPH-A6, MtPH-D,MtPH-E, and MtPH-M, corresponding to three previously identified and two new lineages. The largest families, MtPH-A6 and MtPH-M were further divided into four and three subfamilies, respectively. Non-autonomous elements were usually direct deletion derivatives of the putative autonomous element, however other types of rearrangements, including inversions and nested insertions were also observed. An interesting structural characteristic – the presence of 60 bp tandem repeats – was observed in a group of elements of subfamily MtPH-A6-4. Some families could be related to miniature inverted repeat elements (MITEs). The presence of empty loci (RESites), paralogous to those flanking the identified transposable elements, both autonomous and non-autonomous, as well as the presence of transposon insertion related size polymorphisms, confirmed that some of the mined elements were capable for transposition. Conclusion The population of PIF/Harbinger-like elements in the genome of M. truncatula is diverse. A detailed intra-family comparison of the elements' structure proved that they proliferated in the genome generally following the model of abortive gap repair. However, the presence of tandem repeats facilitated more pronounced rearrangements of the element internal regions. The insertion polymorphism of the MtPH elements and related MITE families in different populations of M. truncatula, if further confirmed experimentally, could be used as a source of molecular markers complementary to other marker systems. PMID:17996080

The organization of repeating units in mitochondrial DNA from yeast petite mutants.

PubMed

Bos, J L; Heyting, C; Van der Horst, G; Borst, P

1980-04-01

We have reinvestigated the linkage orientation of repeating units in mtDNAs of yeast ρ(-) petite mutants containing an inverted duplication. All five petite mtDNAs studied contain a continuous segment of wild-type mtDNA, part of which is duplicated and present in inverted form in the repeat. We show by restriction enzyme analysis that the non-duplicated segments between the inverted duplications are present in random orientation in all five petite mtDNAs. There is no segregation of sub-types with unique orientation. We attribute this to the high rate of intramolecular recombination between the inverted duplications. The results provide additional evidence for the high rate of recombination of yeast mtDNA even in haploid ρ(-) petite cells.We conclude that only two types of stable sequence organization exist in petite mtDNA: petites without an inverted duplication have repeats linked in straight head-to-tail arrangement (abcabc); petites with an inverted duplication have repeats in which the non-duplicated segments are present in random orientation.

Identification of novel MITEs (miniature inverted-repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution.

PubMed

Wachter, Shaun; Raghavan, Rahul; Wachter, Jenny; Minnick, Michael F

2018-04-11

Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii's genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature inverted-repeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited. We describe two MITE families discovered during research on small non-coding RNAs (sRNAs) of C. burnetii. Two sRNAs, Cbsr3 and Cbsr13, were found to originate from a novel MITE family, termed QMITE1. Another sRNA, CbsR16, was found to originate from a separate and novel MITE family, termed QMITE2. Members of each family occur ~ 50 times within the strains evaluated. QMITE1 is a typical MITE of 300-400 bp with short (2-3 nt) direct repeats (DRs) of variable sequence and is often found overlapping annotated open reading frames (ORFs). Additionally, QMITE1 elements possess sigma-70 promoters and are transcriptionally active at several loci, potentially influencing expression of nearby genes. QMITE2 is smaller (150-190 bps), but has longer (7-11 nt) DRs of variable sequences and is mainly found in the 3' untranslated region of annotated ORFs and intergenic regions. QMITE2 contains a GTAG repetitive extragenic palindrome (REP) that serves as a target for IS1111 TE insertion. Both QMITE1 and QMITE2 display inter-strain linkage and sequence conservation, suggesting that they are adaptive and existed before divergence of C. burnetii strains. We have discovered two novel MITE families of C. burnetii. Our finding that MITEs serve as a source for sRNAs is novel. QMITE2 has a unique structure and occurs in large or small versions with unique DRs that display linkage and sequence conservation between strains, allowing for tracking of genomic rearrangements. QMITE1 and QMITE2 copies are hypothesized to influence expression of neighboring genes involved in DNA repair and virulence through transcriptional interference and ribonuclease processing.

[Convergent origin of repeats in genes coding for globular proteins. An analysis of the factors determining the presence of inverted and symmetrical repeats].

PubMed

Solov'ev, V V; Kel', A E; Kolchanov, N A

1989-01-01

The factors, determining the presence of inverted and symmetrical repeats in genes coding for globular proteins, have been analysed. An interesting property of genetical code has been revealed in the analysis of symmetrical repeats: the pairs of symmetrical codons corresponded to pairs of amino acids with mostly similar physical-chemical parameters. This property may explain the presence of symmetrical repeats and palindromes only in genes coding for beta-structural proteins-polypeptides, where amino acids with similar physical-chemical properties occupy symmetrical positions. A stochastic model of evolution of polynucleotide sequences has been used for analysis of inverted repeats. The modelling demonstrated that only limiting of sequences (uneven frequencies of used codons) is enough for arising of nonrandom inverted repeats in genes.

Identification of a recently active Prunus-specific non-autonomous Mutator element with considerable genome shaping force.

PubMed

Halász, Júlia; Kodad, Ossama; Hegedűs, Attila

2014-07-01

Miniature inverted-repeat transposable elements (MITEs) are known to contribute to the evolution of plants, but only limited information is available for MITEs in the Prunus genome. We identified a MITE that has been named Falling Stones, FaSt. All structural features (349-bp size, 82-bp terminal inverted repeats and 9-bp target site duplications) are consistent with this MITE being a putative member of the Mutator transposase superfamily. FaSt showed a preferential accumulation in the short AT-rich segments of the euchromatin region of the peach genome. DNA sequencing and pollination experiments have been performed to confirm that the nested insertion of FaSt into the S-haplotype-specific F-box gene of apricot resulted in the breakdown of self-incompatibility (SI). A bioinformatics-based survey of the known Rosaceae and other genomes and a newly designed polymerase chain reaction (PCR) assay verified the Prunoideae-specific occurrence of FaSt elements. Phylogenetic analysis suggested a recent activity of FaSt in the Prunus genome. The occurrence of a nested insertion in the apricot genome further supports the recent activity of FaSt in response to abiotic stress conditions. This study reports on a presumably active non-autonomous Mutator element in Prunus that exhibits a major indirect genome shaping force through inducing loss-of-function mutation in the SI locus. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

Bigfoot. a new family of MITE elements characterized from the Medicago genus.

PubMed

Charrier, B; Foucher, F; Kondorosi, E; d'Aubenton-Carafa, Y; Thermes, C; Kondorosi, A; Ratet, P

1999-05-01

We have characterized from the legume plant Medicago a new family of miniature inverted-repeat transposable elements (MITE), called the Bigfoot transposable elements. Two of these insertion elements are present only in a single allele of two different M. sativa genes. Using a PCR strategy we have isolated 19 other Bigfoot elements from the M. sativa and M. truncatula genomes. They differ from the previously characterized MITEs by their sequence, a target site of 9 bp and a partially clustered genomic distribution. In addition, we show that they exhibit a significantly stable secondary structure. These elements may represent up to 0.1% of the genome of the outcrossing Medicago sativa but are present at a reduced copy number in the genome of the autogamous M. truncatula plant, revealing major differences in the genome organization of these two plants.

Novel MSVPWM to reduce the inductor current ripple for Z-source inverter in electric vehicle applications.

PubMed

Zhang, Qianfan; Dong, Shuai; Xue, Ping; Zhou, Chaowei; Cheng, ShuKang

2014-01-01

A novel modified space vector pulse width modulation (MSVPWM) strategy for Z-Source inverter is presented. By rearranging the position of shoot-through states, the frequency of inductor current ripple is kept constant. Compared with existing MSVPWM strategies, the proposed approach can reduce the maximum inductor current ripple. So the volume of Z-source network inductor can be designed smaller, which brings the beneficial effect on the miniaturization of the electric vehicle controller. Theoretical findings in the novel MSVPWM for Z-Source inverter have been verified by experiment results.

Novel MSVPWM to Reduce the Inductor Current Ripple for Z-Source Inverter in Electric Vehicle Applications

PubMed Central

Zhang, Qianfan; Dong, Shuai; Xue, Ping; Zhou, Chaowei; Cheng, ShuKang

2014-01-01

A novel modified space vector pulse width modulation (MSVPWM) strategy for Z-Source inverter is presented. By rearranging the position of shoot-through states, the frequency of inductor current ripple is kept constant. Compared with existing MSVPWM strategies, the proposed approach can reduce the maximum inductor current ripple. So the volume of Z-source network inductor can be designed smaller, which brings the beneficial effect on the miniaturization of the electric vehicle controller. Theoretical findings in the novel MSVPWM for Z-Source inverter have been verified by experiment results. PMID:24883412

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

PubMed

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

2017-05-01

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

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 interstitial, inverted CNVs pivotal in human health and evolution. PMID:26700858

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

PubMed

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

2015-12-01

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 interstitial, inverted CNVs pivotal in human health and evolution.

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.

Fragile DNA Motifs Trigger Mutagenesis at Distant Chromosomal Loci in Saccharomyces cerevisiae

PubMed Central

Saini, Natalie; Zhang, Yu; Nishida, Yuri; Sheng, Ziwei; Choudhury, Shilpa; Mieczkowski, Piotr; Lobachev, Kirill S.

2013-01-01

DNA sequences capable of adopting non-canonical secondary structures have been associated with gross-chromosomal rearrangements in humans and model organisms. Previously, we have shown that long inverted repeats that form hairpin and cruciform structures and triplex-forming GAA/TTC repeats induce the formation of double-strand breaks which trigger genome instability in yeast. In this study, we demonstrate that breakage at both inverted repeats and GAA/TTC repeats is augmented by defects in DNA replication. Increased fragility is associated with increased mutation levels in the reporter genes located as far as 8 kb from both sides of the repeats. The increase in mutations was dependent on the presence of inverted or GAA/TTC repeats and activity of the translesion polymerase Polζ. Mutagenesis induced by inverted repeats also required Sae2 which opens hairpin-capped breaks and initiates end resection. The amount of breakage at the repeats is an important determinant of mutations as a perfect palindromic sequence with inherently increased fragility was also found to elevate mutation rates even in replication-proficient strains. We hypothesize that the underlying mechanism for mutagenesis induced by fragile motifs involves the formation of long single-stranded regions in the broken chromosome, invasion of the undamaged sister chromatid for repair, and faulty DNA synthesis employing Polζ. These data demonstrate that repeat-mediated breaks pose a dual threat to eukaryotic genome integrity by inducing chromosomal aberrations as well as mutations in flanking genes. PMID:23785298

Self-calibration of a W/Re thermocouple using a miniature Ru-C (1954 °C) eutectic cell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ongrai, O.; University of Surrey, Guildford, Surrey; National Institute of Metrology, Klong 5, Klong Luang, Pathumthani

2013-09-11

Previous successful investigations of miniature cobalt-carbon (Co-C, 1324 °C) and palladium-carbon (Pd-C, 1492 °C) high temperature fixed-point cells for thermocouple self-calibration have been reported [1-2]. In the present work, we describe a series of measurements of a miniature ruthenium-carbon (Ru-C) eutectic cell (melting point 1954 °C) to evaluate the repeatability and stability of a W/Re thermocouple (type C) by means of in-situ calibration. A miniature Ru-C eutectic fixed-point cell with outside diameter 14 mm and length 30 mm was fabricated to be used as a self-calibrating device. The performance of the miniature Ru-C cell and the type C thermocouple ismore » presented, including characterization of the stability, repeatability, thermal environment influence, ITS-90 temperature realization and measurement uncertainty.« less

Within-genome evolution of REPINs: a new family of miniature mobile DNA in bacteria.

PubMed

Bertels, Frederic; Rainey, Paul B

2011-06-01

Repetitive sequences are a conserved feature of many bacterial genomes. While first reported almost thirty years ago, and frequently exploited for genotyping purposes, little is known about their origin, maintenance, or processes affecting the dynamics of within-genome evolution. Here, beginning with analysis of the diversity and abundance of short oligonucleotide sequences in the genome of Pseudomonas fluorescens SBW25, we show that over-represented short sequences define three distinct groups (GI, GII, and GIII) of repetitive extragenic palindromic (REP) sequences. Patterns of REP distribution suggest that closely linked REP sequences form a functional replicative unit: REP doublets are over-represented, randomly distributed in extragenic space, and more highly conserved than singlets. In addition, doublets are organized as inverted repeats, which together with intervening spacer sequences are predicted to form hairpin structures in ssDNA or mRNA. We refer to these newly defined entities as REPINs (REP doublets forming hairpins) and identify short reads from population sequencing that reveal putative transposition intermediates. The proximal relationship between GI, GII, and GIII REPINs and specific REP-associated tyrosine transposases (RAYTs), combined with features of the putative transposition intermediate, suggests a mechanism for within-genome dissemination. Analysis of the distribution of REPs in a range of RAYT-containing bacterial genomes, including Escherichia coli K-12 and Nostoc punctiforme, show that REPINs are a widely distributed, but hitherto unrecognized, family of miniature non-autonomous mobile DNA.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhattacharya, Monolekha; Das, Amit Kumar, E-mail: amitk@hijli.iitkgp.ernet.in

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 notmore » 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.« less

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

PubMed Central

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

2015-01-01

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

Genetic and DNA sequence analysis of the kanamycin resistance transposon Tn903.

PubMed Central

Grindley, N D; Joyce, C M

1980-01-01

The kanamycin resistance transposon Tn903 consists of a unique region of about 1000 base pairs bounded by a pair of 1050-base-pair inverted repeat sequences. Each repeat contains two Pvu II endonuclease cleavage sites separated by 520 base pairs. We have constructed derivatives of Tn903 in which this 520-base-pair fragment is deleted from one or both repeats. Those derivatives that lack both 520-base-pair fragments cannot transpose, whereas those that lack just one remain transposition proficient. One such transposable derivative, Tn903 delta I, has been selected for further study. We have determined the sequence of the intact inverted repeat. The 18 base pairs at each end are identical and inverted relative to one another, a structure characteristic of insertion sequences. Additional experiments indicate that a single inverted repeat from Tn903 can, in fact, transpose; we propose that this element be called IS903. To correlate the DNA sequence with genetic activities, we have created mutations by inserting a 10-base-pair DNA fragment at several sites within the intact repeat of Tn903 delta 1, and we have examined the effect of such insertions on transposability. The results suggest that IS903 encodes a 307-amino-acid polypeptide (a "transposase") that is absolutely required for transposition of IS903 or Tn903. Images PMID:6261245

Inversion and contrast polarity reversal affect both encoding and recognition processes of unfamiliar faces: a repetition study using ERPs.

PubMed

Itier, Roxane J; Taylor, Margot J

2002-02-01

Using ERPs in a face recognition task, we investigated whether inversion and contrast reversal, which seem to disrupt different aspects of face configuration, differentially affected encoding and memory for faces. Upright, inverted, and negative (contrast-reversed) unknown faces were either immediately repeated (0-lag) or repeated after 1 intervening face (1-lag). The encoding condition (new) consisted of the first presentation of items correctly recognized in the two repeated conditions. 0-lag faces were recognized better and faster than 1-lag faces. Inverted and negative pictures elicited longer reaction times, lower hit rates, and higher false alarm rates than upright faces. ERP analyses revealed that negative and inverted faces affected both early (encoding) and late (recognition) stages of face processing. Early components (N170, VPP) were delayed and enhanced by both inversion and contrast reversal which also affected P1 and P2 components. Amplitudes were higher for inverted faces at frontal and parietal sites from 350 to 600 ms. Priming effects were seen at encoding stages, revealed by shorter latencies and smaller amplitudes of N170 for repeated stimuli, which did not differ depending on face type. Repeated faces yielded more positive amplitudes than new faces from 250 to 450 ms frontally and from 400 to 600 ms parietally. However, ERP differences revealed that the magnitude of this repetition effect was smaller for negative and inverted than upright faces at 0-lag but not at 1-lag condition. Thus, face encoding and recognition processes were affected by inversion and contrast-reversal differently.

Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria

PubMed Central

Bertels, Frederic; Rainey, Paul B.

2011-01-01

Repetitive sequences are a conserved feature of many bacterial genomes. While first reported almost thirty years ago, and frequently exploited for genotyping purposes, little is known about their origin, maintenance, or processes affecting the dynamics of within-genome evolution. Here, beginning with analysis of the diversity and abundance of short oligonucleotide sequences in the genome of Pseudomonas fluorescens SBW25, we show that over-represented short sequences define three distinct groups (GI, GII, and GIII) of repetitive extragenic palindromic (REP) sequences. Patterns of REP distribution suggest that closely linked REP sequences form a functional replicative unit: REP doublets are over-represented, randomly distributed in extragenic space, and more highly conserved than singlets. In addition, doublets are organized as inverted repeats, which together with intervening spacer sequences are predicted to form hairpin structures in ssDNA or mRNA. We refer to these newly defined entities as REPINs (REP doublets forming hairpins) and identify short reads from population sequencing that reveal putative transposition intermediates. The proximal relationship between GI, GII, and GIII REPINs and specific REP-associated tyrosine transposases (RAYTs), combined with features of the putative transposition intermediate, suggests a mechanism for within-genome dissemination. Analysis of the distribution of REPs in a range of RAYT–containing bacterial genomes, including Escherichia coli K-12 and Nostoc punctiforme, show that REPINs are a widely distributed, but hitherto unrecognized, family of miniature non-autonomous mobile DNA. PMID:21698139

Single inverted terminal repeats of the Junonia coenia Densovirus promotes somatic chromosomal integration of vector plasmids in insect cells and supports high efficiency expression

USDA-ARS?s Scientific Manuscript database

Plasmids that contain a disrupted genome of the Junonia coenia densovirus (JcDNV) integrate into the chromosomes of the somatic cells of insects. When subcloned individually, both the P9 inverted terminal repeat (P9-ITR) and the P93-ITR promote the chromosomal integration of vector plasmids in insec...

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

PubMed Central

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

2011-01-01

Mobile genetic elements are widespread in Pseudomonas syringae, and often associate with virulence genes. Genome reannotation of the model bean pathogen P. syringae pv. phaseolicola 1448A identified seventeen types of insertion sequences and two miniature inverted-repeat transposable elements (MITEs) with a biased distribution, representing 2.8% of the chromosome, 25.8% of the 132-kb virulence plasmid and 2.7% of the 52-kb plasmid. Employing an entrapment vector containing sacB, we estimated that transposition frequency oscillated between 2.6×10−5 and 1.1×10−6, depending on the clone, although it was stable for each clone after consecutive transfers in culture media. Transposition frequency was similar for bacteria grown in rich or minimal media, and from cells recovered from compatible and incompatible plant hosts, indicating that growth conditions do not influence transposition in strain 1448A. Most of the entrapped insertions contained a full-length IS801 element, with the remaining insertions corresponding to sequences smaller than any transposable element identified in strain 1448A, and collectively identified as miniature sequences. From these, fragments of 229, 360 and 679-nt of the right end of IS801 ended in a consensus tetranucleotide and likely resulted from one-ended transposition of IS801. An average 0.7% of the insertions analyzed consisted of IS801 carrying a fragment of variable size from gene PSPPH_0008/PSPPH_0017, showing that IS801 can mobilize DNA in vivo. Retrospective analysis of complete plasmids and genomes of P. syringae suggests, however, that most fragments of IS801 are likely the result of reorganizations rather than one-ended transpositions, and that this element might preferentially contribute to genome flexibility by generating homologous regions of recombination. A further miniature sequence previously found to affect host range specificity and virulence, designated MITEPsy1 (100-nt), represented an average 2.4% of the total number of insertions entrapped in sacB, demonstrating for the first time the mobilization of a MITE in bacteria. PMID:22016774

Miniature transposable sequences are frequently mobilized in the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola.

PubMed

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

2011-01-01

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

Adeno-associated virus inverted terminal repeats stimulate gene editing.

PubMed

Hirsch, M L

2015-02-01

Advancements in genome editing have relied on technologies to specifically damage DNA which, in turn, stimulates DNA repair including homologous recombination (HR). As off-target concerns complicate the therapeutic translation of site-specific DNA endonucleases, an alternative strategy to stimulate gene editing based on fragile DNA was investigated. To do this, an episomal gene-editing reporter was generated by a disruptive insertion of the adeno-associated virus (AAV) inverted terminal repeat (ITR) into the egfp gene. Compared with a non-structured DNA control sequence, the ITR induced DNA damage as evidenced by increased gamma-H2AX and Mre11 foci formation. As local DNA damage stimulates HR, ITR-mediated gene editing was investigated using DNA oligonucleotides as repair substrates. The AAV ITR stimulated gene editing >1000-fold in a replication-independent manner and was not biased by the polarity of the repair oligonucleotide. Analysis of additional human DNA sequences demonstrated stimulation of gene editing to varying degrees. In particular, inverted yet not direct, Alu repeats induced gene editing, suggesting a role for DNA structure in the repair event. Collectively, the results demonstrate that inverted DNA repeats stimulate gene editing via double-strand break repair in an episomal context and allude to efficient gene editing of the human chromosome using fragile DNA sequences.

Ureaplasma antigenic variation beyond MBA phase variation: DNA inversions generating chimeric structures and switching in expression of the MBA N-terminal paralogue UU172

PubMed Central

Zimmerman, Carl-Ulrich R; Rosengarten, Renate; Spergser, Joachim

2011-01-01

Phase variation of the major ureaplasma surface membrane protein, the multiple-banded antigen (MBA), with its counterpart, the UU376 protein, was recently discussed as a result of DNA inversion occurring at specific inverted repeats. Two similar inverted repeats to the ones within the mba locus were found in the genome of Ureaplasma parvum serovar 3; one within the MBA N-terminal paralogue UU172 and another in the adjacent intergenic spacer region. In this report, we demonstrate on both genomic and protein level that DNA inversion at these inverted repeats leads to alternating expression between UU172 and the neighbouring conserved hypothetical ORF UU171. Sequence analysis of this phase-variable ‘UU172 element’ from both U. parvum and U. urealyticum strains revealed that it is highly conserved among both species and that it also includes the orthologue of UU144. A third inverted repeat region in UU144 is proposed to serve as an additional potential inversion site from which chimeric genes can evolve. Our results indicate that site-specific recombination events in the genome of U. parvum serovar 3 are dynamic and frequent, leading to a broad spectrum of antigenic variation by which the organism may evade host immune responses. PMID:21255110

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

PubMed Central

Silby, Mark W; Cerdeño-Tárraga, Ana M; Vernikos, Georgios S; Giddens, Stephen R; Jackson, Robert W; Preston, Gail M; Zhang, Xue-Xian; Moon, Christina D; Gehrig, Stefanie M; Godfrey, Scott AC; Knight, Christopher G; Malone, Jacob G; Robinson, Zena; Spiers, Andrew J; Harris, Simon; Challis, Gregory L; Yaxley, Alice M; Harris, David; Seeger, Kathy; Murphy, Lee; Rutter, Simon; Squares, Rob; Quail, Michael A; Saunders, Elizabeth; Mavromatis, Konstantinos; Brettin, Thomas S; Bentley, Stephen D; Hothersall, Joanne; Stephens, Elton; Thomas, Christopher M; Parkhill, Julian; Levy, Stuart B; Rainey, Paul B; Thomson, Nicholas R

2009-01-01

Background Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome. PMID:19432983

Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.)

PubMed Central

Benjak, Andrej; Boué, Stéphanie; Forneck, Astrid

2009-01-01

Miniature inverted-repeat transposable elements (MITEs) are a particular type of defective class II transposons present in genomes as highly homogeneous populations of small elements. Their high copy number and close association to genes make their potential impact on gene evolution particularly relevant. Here, we present a detailed analysis of the MITE families directly related to grapevine “cut-and-paste” transposons. Our results show that grapevine MITEs have transduplicated and amplified genomic sequences, including gene sequences and fragments of other mobile elements. Our results also show that although some of the MITE families were already present in the ancestor of the European and American Vitis wild species, they have been amplified and have been actively transposing accompanying grapevine domestication and breeding. We show that MITEs are abundant in grapevine and some of them are frequently inserted within the untranslated regions of grapevine genes. MITE insertions are highly polymorphic among grapevine cultivars, which frequently generate transcript variability. The data presented here show that MITEs have greatly contributed to the grapevine genetic diversity which has been used for grapevine domestication and breeding. PMID:20333179

Loss-of-function of a ubiquitin-related modifier promotes the mobilization of the active MITE mPing.

PubMed

Tsukiyama, Takuji; Teramoto, Shota; Yasuda, Kanako; Horibata, Akira; Mori, Nanako; Okumoto, Yutaka; Teraishi, Masayoshi; Saito, Hiroki; Onishi, Akiko; Tamura, Kanako; Tanisaka, Takatoshi

2013-05-01

Miniature inverted-repeat transposable elements (MITEs) are widespread in both prokaryotic and eukaryotic genomes, where their copy numbers can attain several thousands. Little is known, however, about the genetic factor(s) affecting their transpositions. Here, we show that disruption of a gene encoding ubiquitin-like protein markedly enhances the transposition activity of a MITE mPing in intact rice plants without any exogenous stresses. We found that the transposition activity of mPing is far higher in the lines harboring a non-functional allele at the Rurm1 (Rice ubiquitin-related modifier-1) locus than in the wild-type line. Although the alteration of cytosine methylation pattern triggers the activation of transposable elements under exogenous stress conditions, the methylation degrees in the whole genome, the mPing-body region, and the mPing-flanking regions of the non-functional Rurm1 line were unchanged. This study provides experimental evidence for one of the models of genome shock theory that genetic accidents within cells enhance the transposition activities of transposable elements.

High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice.

PubMed

Barrera-Figueroa, Blanca E; Gao, Lei; Wu, Zhigang; Zhou, Xuefeng; Zhu, Jianhua; Jin, Hailing; Liu, Renyi; Zhu, Jian-Kang

2012-08-03

MicroRNAs (miRNAs) are small RNA molecules that play important regulatory roles in plant development and stress responses. Identification of stress-regulated miRNAs is crucial for understanding how plants respond to environmental stimuli. Abiotic stresses are one of the major factors that limit crop growth and yield. Whereas abiotic stress-regulated miRNAs have been identified in vegetative tissues in several plants, they are not well studied in reproductive tissues such as inflorescences. We used Illumina deep sequencing technology to sequence four small RNA libraries that were constructed from the inflorescences of rice plants that were grown under control condition and drought, cold, or salt stress. We identified 227 miRNAs that belong to 127 families, including 70 miRNAs that are not present in the miRBase. We validated 62 miRNAs (including 10 novel miRNAs) using published small RNA expression data in DCL1, DCL3, and RDR2 RNAi lines and confirmed 210 targets from 86 miRNAs using published degradome data. By comparing the expression levels of miRNAs, we identified 18, 15, and 10 miRNAs that were regulated by drought, cold and salt stress conditions, respectively. In addition, we identified 80 candidate miRNAs that originated from transposable elements or repeats, especially miniature inverted-repeat elements (MITEs). We discovered novel miRNAs and stress-regulated miRNAs that may play critical roles in stress response in rice inflorescences. Transposable elements or repeats, especially MITEs, are rich sources for miRNA origination.

Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends.

PubMed

Chuzhanova, Nadia; Abeysinghe, Shaun S; Krawczak, Michael; Cooper, David N

2003-09-01

Translocations and gross deletions are responsible for a significant proportion of both cancer and inherited disease. Although such gene rearrangements are nonuniformly distributed in the human genome, the underlying mutational mechanisms remain unclear. We have studied the potential involvement of various types of repetitive sequence elements in the formation of secondary structure intermediates between the single-stranded DNA ends that recombine during rearrangements. Complexity analysis was used to assess the potential of these ends to form secondary structures, the maximum decrease in complexity consequent to a gross rearrangement being used as an indicator of the type of repeat and the specific DNA ends involved. A total of 175 pairs of deletion/translocation breakpoint junction sequences available from the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] were analyzed. Potential secondary structure was noted between the 5' flanking sequence of the first breakpoint and the 3' flanking sequence of the second breakpoint in 49% of rearrangements and between the 5' flanking sequence of the second breakpoint and the 3' flanking sequence of the first breakpoint in 36% of rearrangements. Inverted repeats, inversions of inverted repeats, and symmetric elements were found in association with gross rearrangements at approximately the same frequency. However, inverted repeats and inversions of inverted repeats accounted for the vast majority (83%) of deletions plus small insertions, symmetric elements for one-half of all antigen receptor-mediated translocations, while direct repeats appear only to be involved in mediating simple deletions. These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions. Copyright 2003 Wiley-Liss, Inc.

The Effect of Syllable Repetition Rate on Vocal Characteristics

ERIC Educational Resources Information Center

Topbas, Oya; Orlikoff, Robert F.; St. Louis, Kenneth O.

2012-01-01

This study examined whether mean vocal fundamental frequency ("F"[subscript 0]) or speech sound pressure level (SPL) varies with changes in syllable repetition rate. Twenty-four young adults (12 M and 12 F) repeated the syllables/p[inverted v]/,/p[inverted v]t[schwa]/, and/p[inverted v]t[schwa]k[schwa]/at a modeled "slow" rate of approximately one…

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

Performance characteristics of a low-cost, field-deployable miniature CCD spectrometer

PubMed Central

Coles, Simon; Nimmo, Malcolm; Worsfold, Paul J.

2000-01-01

Miniature spectrometers incorporating array detectors are becoming a viable, low-cost option for field and process deployments. The performance characteristics of one such instrument are reported and compared with those of a conventional benchtop instrument. The parameters investigated were wavelength repeatability, photometric linearity, instrumental noise (photometric precision) and instrumental drift. PMID:18924863

Observations on the elicitation of secondary and inverted primary nystagmus from the cat by unilateral caloric irrigation.

DOT National Transportation Integrated Search

1963-02-01

Vestibular stimulation by repeated unilateral caloric irrigation of cats occasioned the appearance of secondary, tertiary, and inverted primary nystagmus in some animals. These inverse responses were recorded with stimulus temperatures of 5, 23.5, an...

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

PubMed Central

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

2014-01-01

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

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

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

DNA transposons have colonized the genome of the giant virus Pandoravirus salinus.

PubMed

Sun, Cheng; Feschotte, Cédric; Wu, Zhiqiang; Mueller, Rachel Lockridge

2015-06-12

Transposable elements are mobile DNA sequences that are widely distributed in prokaryotic and eukaryotic genomes, where they represent a major force in genome evolution. However, transposable elements have rarely been documented in viruses, and their contribution to viral genome evolution remains largely unexplored. Pandoraviruses are recently described DNA viruses with genome sizes that exceed those of some prokaryotes, rivaling parasitic eukaryotes. These large genomes appear to include substantial noncoding intergenic spaces, which provide potential locations for transposable element insertions. However, no mobile genetic elements have yet been reported in pandoravirus genomes. Here, we report a family of miniature inverted-repeat transposable elements (MITEs) in the Pandoravirus salinus genome, representing the first description of a virus populated with a canonical transposable element family that proliferated by transposition within the viral genome. The MITE family, which we name Submariner, includes 30 copies with all the hallmarks of MITEs: short length, terminal inverted repeats, TA target site duplication, and no coding capacity. Submariner elements show signs of transposition and are undetectable in the genome of Pandoravirus dulcis, the closest known relative Pandoravirus salinus. We identified a DNA transposon related to Submariner in the genome of Acanthamoeba castellanii, a species thought to host pandoraviruses, which contains remnants of coding sequence for a Tc1/mariner transposase. These observations suggest that the Submariner MITEs of P. salinus belong to the widespread Tc1/mariner superfamily and may have been mobilized by an amoebozoan host. Ten of the 30 MITEs in the P. salinus genome are located within coding regions of predicted genes, while others are close to genes, suggesting that these transposons may have contributed to viral genetic novelty. Our discovery highlights the remarkable ability of DNA transposons to colonize and shape genomes from all domains of life, as well as giant viruses. Our findings continue to blur the division between viral and cellular genomes, adhering to the emerging view that the content, dynamics, and evolution of the genomes of giant viruses do not substantially differ from those of cellular organisms.

Transposon diversity in Arabidopsis thaliana

PubMed Central

Le, Quang Hien; Wright, Stephen; Yu, Zhihui; Bureau, Thomas

2000-01-01

Recent availability of extensive genome sequence information offers new opportunities to analyze genome organization, including transposon diversity and accumulation, at a level of resolution that was previously unattainable. In this report, we used sequence similarity search and analysis protocols to perform a fine-scale analysis of a large sample (≈17.2 Mb) of the Arabidopsis thaliana (Columbia) genome for transposons. Consistent with previous studies, we report that the A. thaliana genome harbors diverse representatives of most known superfamilies of transposons. However, our survey reveals a higher density of transposons of which over one-fourth could be classified into a single novel transposon family designated as Basho, which appears unrelated to any previously known superfamily. We have also identified putative transposase-coding ORFs for miniature inverted-repeat transposable elements (MITEs), providing clues into the mechanism of mobility and origins of the most abundant transposons associated with plant genes. In addition, we provide evidence that most mined transposons have a clear distribution preference for A + T-rich sequences and show that structural variation for many mined transposons is partly due to interelement recombination. Taken together, these findings further underscore the complexity of transposons within the compact genome of A. thaliana. PMID:10861007

Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion.

PubMed

Vaschetto, Luis María

2018-04-01

In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular type of transposons referred to as miniature inverted-repeat transposable elements (MITEs) has shown a series of interesting characteristics for designing functional drivers. Here, recent insights into MITE elements and versatile RNA-guided CRISPR/Cas9 genome engineering system are given to understand how to deploy the potential of TEs for control of the host transcriptional activity.

Stoichiometry of the Cre recombinase bound to the lox recombining site.

PubMed Central

Mack, A; Sauer, B; Abremski, K; Hoess, R

1992-01-01

The site-specific recombinase Cre from bacteriophage P1 binds and carries out recombination at a 34 bp lox site. The lox site consists of two 13 bp inverted repeats, separated by an 8 bp spacer region. Both the palindromic nature of the site and the results of footprinting and band shift experiments suggest that a minimum of two Cre molecules bind to a lox site. We report here experiments that demonstrate the absolute stoichiometry of the Cre-lox complex to be one molecule of Cre bound per inverted repeat, or two molecules per lox site. Images PMID:1408747

Design and fabrication of inverted rib waveguide Bragg grating

NASA Astrophysics Data System (ADS)

Huang, Cheng-Sheng; Wang, Wei-Chih

2009-03-01

A polymeric SU8 rib waveguide Bragg grating filterfabricated using reactive ion etching (RIE) and solvent assisted microcontact molding (SAMIM) is presented. SAMIM is one kind of soft lithography. The technique is unique in which that a composite hPDMS/PDMS stamp was used to transfer the grating pattern onto an inverted SU8 rib waveguide system. The composite grating stamp can be used repeatedly several times with degradation. Using this stamp and inverter rib waveguide structure, the Bragg grating filter fabrication can be significantly simplified.

Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

PubMed Central

Niu, Zhi-Tao; Liu, Wei; Xue, Qing-Yun; Ding, Xiao-Yu

2014-01-01

The orchid family Orchidaceae is one of the largest angiosperm families, including many species of important economic value. While chloroplast genomes are very informative for systematics and species identification, there is very limited information available on chloroplast genomes in the Orchidaceae. Here, we report the complete chloroplast genomes of the medicinal plant Dendrobium officinale and the ornamental orchid Cypripedium macranthos, demonstrating their gene content and order and potential RNA editing sites. The chloroplast genomes of the above two species and five known photosynthetic orchids showed similarities in structure as well as gene order and content, but differences in the organization of the inverted repeat/small single-copy junction and ndh genes. The organization of the inverted repeat/small single-copy junctions in the chloroplast genomes of these orchids was classified into four types; we propose that inverted repeats flanking the small single-copy region underwent expansion or contraction among Orchidaceae. The AT-rich regions of the ycf1 gene in orchids could be linked to the recombination of inverted repeat/small single-copy junctions. Relative species in orchids displayed similar patterns of variation in ndh gene contents. Furthermore, fifteen highly divergent protein-coding genes were identified, which are useful for phylogenetic analyses in orchids. To test the efficiency of these genes serving as markers in phylogenetic analyses, coding regions of four genes (accD, ccsA, matK, and ycf1) were used as a case study to construct phylogenetic trees in the subfamily Epidendroideae. High support was obtained for placement of previously unlocated subtribes Collabiinae and Dendrobiinae in the subfamily Epidendroideae. Our findings expand understanding of the diversity of orchid chloroplast genomes and provide a reference for study of the molecular systematics of this family. PMID:24911363

Comparative chloroplast genomes of photosynthetic orchids: insights into evolution of the Orchidaceae and development of molecular markers for phylogenetic applications.

PubMed

Luo, Jing; Hou, Bei-Wei; Niu, Zhi-Tao; Liu, Wei; Xue, Qing-Yun; Ding, Xiao-Yu

2014-01-01

The orchid family Orchidaceae is one of the largest angiosperm families, including many species of important economic value. While chloroplast genomes are very informative for systematics and species identification, there is very limited information available on chloroplast genomes in the Orchidaceae. Here, we report the complete chloroplast genomes of the medicinal plant Dendrobium officinale and the ornamental orchid Cypripedium macranthos, demonstrating their gene content and order and potential RNA editing sites. The chloroplast genomes of the above two species and five known photosynthetic orchids showed similarities in structure as well as gene order and content, but differences in the organization of the inverted repeat/small single-copy junction and ndh genes. The organization of the inverted repeat/small single-copy junctions in the chloroplast genomes of these orchids was classified into four types; we propose that inverted repeats flanking the small single-copy region underwent expansion or contraction among Orchidaceae. The AT-rich regions of the ycf1 gene in orchids could be linked to the recombination of inverted repeat/small single-copy junctions. Relative species in orchids displayed similar patterns of variation in ndh gene contents. Furthermore, fifteen highly divergent protein-coding genes were identified, which are useful for phylogenetic analyses in orchids. To test the efficiency of these genes serving as markers in phylogenetic analyses, coding regions of four genes (accD, ccsA, matK, and ycf1) were used as a case study to construct phylogenetic trees in the subfamily Epidendroideae. High support was obtained for placement of previously unlocated subtribes Collabiinae and Dendrobiinae in the subfamily Epidendroideae. Our findings expand understanding of the diversity of orchid chloroplast genomes and provide a reference for study of the molecular systematics of this family.

SU8 inverted-rib waveguide Bragg grating filter.

PubMed

Huang, Cheng-Sheng; Wang, Wei-Chih

2013-08-01

A polymeric SU8 inverted-rib waveguide Bragg grating filter fabricated using reactive ion etching (RIE) and solvent assisted microcontact molding (SAMIM) is presented. SAMIM is one kind of soft lithography. The technique is unique in that a composite hard-polydimethysiloxane/polydimethysiloxane stamp is used to transfer the grating pattern onto an inverted SU8 rib waveguide system. The composite grating stamp can be used repeatedly several times without degradation. Using this stamp and inverter-rib waveguide structure, the Bragg grating filter fabrication can be significantly simplified. The experiment result shows an attenuation dip in the transmission spectra, with a value of -7 dBm at 1550 nm for a grating with a period of 0.492 μm on an inverted-rib waveguide with 6.6 μm width and 4 μm height.

The complete chloroplast genome sequence of Curcuma flaviflora (Curcuma).

PubMed

Zhang, Yan; Deng, Jiabin; Li, Yangyi; Gao, Gang; Ding, Chunbang; Zhang, Li; Zhou, Yonghong; Yang, Ruiwu

2016-09-01

The complete chloroplast (cp) genome of Curcuma flaviflora, a medicinal plant in Southeast Asia, was sequenced. The genome size was 160 478 bp in length, with 36.3% GC content. A pair of inverted repeats (IRs) of 26 946 bp were separated by a large single copy (LSC) of 88 008 bp and a small single copy (SSC) of 18 578 bp, respectively. The cp genome contained 132 annotated genes, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. And 19 of these genes were duplicated in inverted repeat regions.

Regulation of HFE expression by Poly(ADP-ribose) polymerase-1 (PARP1) through an inverted repeat DNA sequence in the distal promoter

PubMed Central

Rodova, Marianna; Rudolph, Angela; Chipps, Elizabeth; Islam, M. Rafiq

2013-01-01

Hereditary hemochromatosis (HH) is a common autosomal recessive disorder of iron overload among Caucasians of northern European descent. Over 85% of all cases with HH are due to mutations in the hemochromatosis protein (HFE) involved in iron metabolism. Although the importance in iron homeostasis is well recognized, the mechanism of sensing and regulating iron absorption by HFE, especially in the absence of iron response element in its gene, is not fully understood. In this report, we have identified an inverted repeat sequence (ATGGTcttACCTA) within 1700 bp (−1675/+35) of the HFE promoter capable to form cruciform structure that binds PARP1 and strongly represses HFE promoter. Knockdown of PARP1 increases HFE mRNA and protein. Similarly, hemin or FeCl3 treatments resulted in increase in HFE expression by reducing nuclear PARP1 pool via its apoptosis induced cleavage, leading to upregulation of the iron regulatory hormone hepcidin mRNA. Thus, PARP1 binding to the inverted repeat sequence on the HFE promoter may serve as a novel iron sensing mechanism as increased iron level can trigger PARP1 cleavage and relief of HFE transcriptional repression. PMID:24184271

Regulation of HFE expression by poly(ADP-ribose) polymerase-1 (PARP1) through an inverted repeat DNA sequence in the distal promoter.

PubMed

Pelham, Christopher; Jimenez, Tamara; Rodova, Marianna; Rudolph, Angela; Chipps, Elizabeth; Islam, M Rafiq

2013-12-01

Hereditary hemochromatosis (HH) is a common autosomal recessive disorder of iron overload among Caucasians of northern European descent. Over 85% of all cases with HH are due to mutations in the hemochromatosis protein (HFE) involved in iron metabolism. Although the importance in iron homeostasis is well recognized, the mechanism of sensing and regulating iron absorption by HFE, especially in the absence of iron response element in its gene, is not fully understood. In this report, we have identified an inverted repeat sequence (ATGGTcttACCTA) within 1700bp (-1675/+35) of the HFE promoter capable to form cruciform structure that binds PARP1 and strongly represses HFE promoter. Knockdown of PARP1 increases HFE mRNA and protein. Similarly, hemin or FeCl3 treatments resulted in increase in HFE expression by reducing nuclear PARP1 pool via its apoptosis induced cleavage, leading to upregulation of the iron regulatory hormone hepcidin mRNA. Thus, PARP1 binding to the inverted repeat sequence on the HFE promoter may serve as a novel iron sensing mechanism as increased iron level can trigger PARP1 cleavage and relief of HFE transcriptional repression. © 2013.

DNA-directed mutations. Leading and lagging strand specificity

NASA Technical Reports Server (NTRS)

Sinden, R. R.; Hashem, V. I.; Rosche, W. A.

1999-01-01

The fidelity of replication has evolved to reproduce B-form DNA accurately, while allowing a low frequency of mutation. The fidelity of replication can be compromised, however, by defined order sequence DNA (dosDNA) that can adopt unusual or non B-DNA conformations. These alternative DNA conformations, including hairpins, cruciforms, triplex DNAs, and slipped-strand structures, may affect enzyme-template interactions that potentially lead to mutations. To analyze the effect of dosDNA elements on spontaneous mutagenesis, various mutational inserts containing inverted repeats or direct repeats were cloned in a plasmid containing a unidirectional origin of replication and a selectable marker for the mutation. This system allows for analysis of mutational events that are specific for the leading or lagging strands during DNA replication in Escherichia coli. Deletions between direct repeats, involving misalignment stabilized by DNA secondary structure, occurred preferentially on the lagging strand. Intermolecular strand switch events, correcting quasipalindromes to perfect inverted repeats, occurred preferentially during replication of the leading strand.

The complete chloroplast genome sequence of American bird pepper (Capsicum annuum var. glabriusculum).

PubMed

Zeng, Fan-chun; Gao, Cheng-wen; Gao, Li-zhi

2016-01-01

The complete chloroplast genome sequence of American bird pepper (Capsicum annuum var. glabriusculum) is reported and characterized in this study. The genome size is 156,612 bp, containing a pair of inverted repeats (IRs) of 25,776 bp separated by a large single-copy region of 87,213 bp and a small single-copy region of 17,851 bp. The chloroplast genome harbors 130 known genes, including 89 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. A total of 18 of these genes are duplicated in the inverted repeat regions, 16 genes contain 1 intron, and 2 genes and one ycf have 2 introns.

Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera)

PubMed Central

Huang, Ya-Yi; Matzke, Antonius J. M.; Matzke, Marjori

2013-01-01

Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available. PMID:24023703

Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera).

PubMed

Huang, Ya-Yi; Matzke, Antonius J M; Matzke, Marjori

2013-01-01

Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.

The Variation Analysis of DNA Methylation in Wheat Carrying Gametocidal Chromosome 3C from Aegilops triuncialis.

PubMed

Wang, Dan; Zhao, Jieyu; Bai, Yan; Ao, You; Guo, Changhong

2017-08-10

Gametocidal (Gc) chromosomes can ensure their preferential transmission by killing the gametes without themselves through causing chromosome breakage and therefore have been exploited as an effective tool for genetic breeding. However, to date very little is known about the molecular mechanism of Gc action. In this study, we used methylation-sensitive amplified polymorphism (MSAP) technique to assess the extent and pattern of cytosine methylation alterations at the whole genome level between two lines of wheat Gc addition line and their common wheat parent. The results indicated that the overall levels of cytosine methylation of two studied Gc addition lines (CS-3C and CS-3C3C, 48.68% and 48.65%, respectively) were significantly increased when compared to common wheat CS (41.31%) and no matter fully methylated or hemimethylated rates enhanced in Gc addition lines. A set of 30 isolated fragments that showed different DNA methylation or demethylation patterns between the three lines were sequenced and the results indicated that 8 fragments showed significant homology to known sequences, of which three were homologous to MITE transposon (Miniature inverted-repeat transposable elements), LTR-retrotransposon WIS-1p and retrotransposon Gypsy , respectively. Overall, our results showed that DNA methylation could play a role in the Gc action.

Proflavine binding to poly(rC-rA) inverts the CD spectrum but not the helix handedness.

PubMed

Westhof, E; Sundaralingam, M

1984-08-01

The interaction of proflavine hemisulfate with the sodium salt of poly(rC-rA) in solution (unbuffered) yields an inverted (mirror-like) circular dichroism (CD) spectrum to that of the free poly(rC-rA). Simultaneously, an induced negative Cotton effect appears in the proflavine band region with a maximum at 467 nm and a slight shoulder at 420 nm. This observation may be explained as resulting from the formation of a poly(rC-rA).proflavine complex with the polynucleotide existing as a right-handed parallel chain duplex with the proflavine intercalated between the CpA sequence and not the ApC sequence. The intercalation geometry here is expected to be analogous to that found in the crystal structure of the dinucleotide CpA.proflavine complex (Westhof et al. J. Mol. Biol., 1981) which forms a miniature right-handed helix. Although normally an inverted spectra could be attributed to a reversal in the helix handedness, the similarity in the 31P nuclear magnetic resonance spectra between the free and proflavine bound poly(rC-rA) indicates that their handedness is the same. The inverted CD spectrum may be a result of the different stacking orientation between the intercalated proflavine and the A-A base-pair on one hand and the triply hydrogen bonded protonated C-C base-pair on the other.

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

Laser direct marking applied to rasterizing miniature Data Matrix Code on aluminum alloy

NASA Astrophysics Data System (ADS)

Li, Xia-Shuang; He, Wei-Ping; Lei, Lei; Wang, Jian; Guo, Gai-Fang; Zhang, Teng-Yun; Yue, Ting

2016-03-01

Precise miniaturization of 2D Data Matrix (DM) Codes on Aluminum alloy formed by raster mode laser direct part marking is demonstrated. The characteristic edge over-burn effects, which render vector mode laser direct part marking inadequate for producing precise and readable miniature codes, are minimized with raster mode laser marking. To obtain the control mechanism for the contrast and print growth of miniature DM code by raster laser marking process, the temperature field model of long pulse laser interaction with material is established. From the experimental results, laser average power and Q frequency have an important effect on the contrast and print growth of miniature DM code, and the threshold of laser average power and Q frequency for an identifiable miniature DM code are respectively 3.6 W and 110 kHz, which matches the model well within normal operating conditions. In addition, the empirical model of correlation occurring between laser marking parameters and module size is also obtained, and the optimal processing parameter values for an identifiable miniature DM code of different but certain data size are given. It is also found that an increase of the repeat scanning number effectively improves the surface finish of bore, the appearance consistency of modules, which has benefit to reading. The reading quality of miniature DM code is greatly improved using ultrasonic cleaning in water by avoiding the interference of color speckles surrounding modules.

Genome-Wide Stochastic Adaptive DNA Amplification at Direct and Inverted DNA Repeats in the Parasite Leishmania

PubMed Central

Plourde, Marie; Gingras, Hélène; Roy, Gaétan; Lapointe, Andréanne; Leprohon, Philippe; Papadopoulou, Barbara; Corbeil, Jacques; Ouellette, Marc

2014-01-01

Gene amplification of specific loci has been described in all kingdoms of life. In the protozoan parasite Leishmania, the product of amplification is usually part of extrachromosomal circular or linear amplicons that are formed at the level of direct or inverted repeated sequences. A bioinformatics screen revealed that repeated sequences are widely distributed in the Leishmania genome and the repeats are chromosome-specific, conserved among species, and generally present in low copy number. Using sensitive PCR assays, we provide evidence that the Leishmania genome is continuously being rearranged at the level of these repeated sequences, which serve as a functional platform for constitutive and stochastic amplification (and deletion) of genomic segments in the population. This process is adaptive as the copy number of advantageous extrachromosomal circular or linear elements increases upon selective pressure and is reversible when selection is removed. We also provide mechanistic insights on the formation of circular and linear amplicons through RAD51 recombinase-dependent and -independent mechanisms, respectively. The whole genome of Leishmania is thus stochastically rearranged at the level of repeated sequences, and the selection of parasite subpopulations with changes in the copy number of specific loci is used as a strategy to respond to a changing environment. PMID:24844805

Miniaturized material sampling and transfer devices for extraterrestrial exploration

NASA Astrophysics Data System (ADS)

Gorevan, S.; Rafeek, S.; Myrick, T.; Kong, K. Y.; Mahaffey, P.

1997-01-01

For early extraterrestrial exploration with a limited payload, miniaturized sampling devices that can be mounted on a rover platform will be crucial in locating areas with high resource concentration for future extraction, storage and utilization. Two such rover friendly sampling devices are the gas Sniffer and the Sample Acquisition and Transfer Mechanism (SATM). The Sniffer is a miniaturized gas sampler that can be utilized for the characterization of atmospheric, surface and subsurface molecular composition as a function of time and site location. The device is embodied in the tip of a non-rotating, drill sleeve just behind the auger and cutting head. SATM is another highly developed miniature sampling device that can repeatedly deliver solid samples (acquired from the surface to depths of 1 meter below surface) to a number of on-board instruments such as microscopes (for cataloging), ovens (for composition analyses) and/or to a hermetically sealed sample return canister for a sample return mission.

The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms.

PubMed

Yi, Xuan; Gao, Lei; Wang, Bo; Su, Ying-Juan; Wang, Ting

2013-01-01

We have determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana. Gene order transformation analyses indicate that when distinct isomers are considered as alternative structures for the ancestral cp genome of cupressophyte and Pinaceae lineages, it is not possible to distinguish between hypotheses favoring retention of the same IR region in cupressophyte and Pinaceae cp genomes from a hypothesis proposing independent loss of IRA and IRB. Furthermore, in cupressophyte cp genomes, the highly reduced IRs are replaced by short repeats that have the potential to mediate homologous recombination, analogous to the situation in Pinaceae. The importance of repeats in the mutational dynamics of cupressophyte cp genomes is also illustrated by the accD reading frame, which has undergone extreme length expansion in cupressophytes. This has been caused by a large insertion comprising multiple repeat sequences. Overall, we find that the distribution of repeats, indels, and substitutions is significantly correlated in Cephalotaxus cp genomes, consistent with a hypothesis that repeats play a role in inducing substitutions and indels in conifer cp genomes.

The whole chloroplast genome of wild rice (Oryza australiensis).

PubMed

Wu, Zhiqiang; Ge, Song

2016-01-01

The whole chloroplast genome of wild rice (Oryza australiensis) is characterized in this study. The genome size is 135,224  bp, exhibiting a typical circular structure including a pair of 25,776  bp inverted repeats (IRa,b) separated by a large single-copy region (LSC) of 82,212  bp and a small single-copy region (SSC) of 12,470  bp. The overall GC content of the genome is 38.95%. 110 unique genes were annotated, including 76 protein-coding genes, 4 ribosomal RNA genes, and 30t RNA genes. Among these, 18 are duplicated in the inverted repeat regions, 13 genes contain one intron, and 2 genes (rps12 and ycf3) have two introns.

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

The complete chloroplast genome of salt cress (Eutrema salsugineum).

PubMed

Guo, Xinyi; Hao, Guoqian; Ma, Tao

2016-07-01

The complete chloroplast (cp) sequence of the salt cress (Eutrema salsugineum), a plant well-adapted to salt stress, was presented in this study. The circular molecule is 153,407 bp in length and exhibit a typical quadripartite structure containing an 83,894 bp large single copy (LSC) region, a 17,607 bp small single copy (SSC) region, and the two 25,953 bp inverted repeats (IRs). The salt cress cp genome contains 135 known genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 40 tRNA genes; 21 of these are located in the inverted repeat region. As expected, phylogenetic analysis support the idea that E. salsugineum is sister to Brassiceae species within the Brassicaceae family.

Tunable microwave bandpass filter integrated power divider based on the high anisotropy electro-optic nematic liquid crystal.

PubMed

Liu, Yupeng; Liu, Yang; Li, Haiyan; Jiang, Di; Cao, Weiping; Chen, Hui; Xia, Lei; Xu, Ruimin

2016-07-01

A novel, compact microwave tunable bandpass filter integrated power divider, based on the high anisotropy electro-optic nematic liquid crystal, is proposed in this letter. Liquid crystal, as the electro-optic material, is placed between top inverted microstrip line and the metal plate. The proposed structure can realize continuous tunable bandpass response and miniaturization. The proposed design concept is validated by the good performance of simulation results and experimental results. The electro-optic material has shown great potential for microwave application.

Alternative Medicine

MedlinePlus

... medications or doctor visits! Yoga and Recreational Body Inversion The long-term effects of repeatedly assuming a ... shoulder and headstands or any other recreational body inversion exercises that result in head-down or inverted ...

The Influence of Primary and Secondary DNA Structure in Deletion and Duplication between Direct Repeats in Escherichia Coli

PubMed Central

Trinh, T. Q.; Sinden, R. R.

1993-01-01

We describe a system to measure the frequency of both deletions and duplications between direct repeats. Short 17- and 18-bp palindromic and nonpalindromic DNA sequences were cloned into the EcoRI site within the chloramphenicol acetyltransferase gene of plasmids pBR325 and pJT7. This creates an insert between direct repeated EcoRI sites and results in a chloramphenicol-sensitive phenotype. Selection for chloramphenicol resistance was utilized to select chloramphenicol resistant revertants that included those with precise deletion of the insert from plasmid pBR325 and duplication of the insert in plasmid pJT7. The frequency of deletion or duplication varied more than 500-fold depending on the sequence of the short sequence inserted into the EcoRI site. For the nonpalindromic inserts, multiple internal direct repeats and the length of the direct repeats appear to influence the frequency of deletion. Certain palindromic DNA sequences with the potential to form DNA hairpin structures that might stabilize the misalignment of direct repeats had a high frequency of deletion. Other DNA sequences with the potential to form structures that might destabilize misalignment of direct repeats had a very low frequency of deletion. Duplication mutations occurred at the highest frequency when the DNA between the direct repeats contained no direct or inverted repeats. The presence of inverted repeats dramatically reduced the frequency of duplications. The results support the slippage-misalignment model, suggesting that misalignment occurring during DNA replication leads to deletion and duplication mutations. The results also support the idea that the formation of DNA secondary structures during DNA replication can facilitate and direct specific mutagenic events. PMID:8325478

Nanoparticle separation with a miniaturized asymmetrical flow field-flow fractionation cartridge

PubMed Central

Müller, David; Cattaneo, Stefano; Meier, Florian; Welz, Roland; de Mello, Andrew J.

2015-01-01

Asymmetrical Flow Field-Flow Fractionation (AF4) is a separation technique applicable to particles over a wide size range. Despite the many advantages of AF4, its adoption in routine particle analysis is somewhat limited by the large footprint of currently available separation cartridges, extended analysis times and significant solvent consumption. To address these issues, we describe the fabrication and characterization of miniaturized AF4 cartridges. Key features of the down-scaled platform include simplified cartridge and reagent handling, reduced analysis costs and higher throughput capacities. The separation performance of the miniaturized cartridge is assessed using certified gold and silver nanoparticle standards. Analysis of gold nanoparticle populations indicates shorter analysis times and increased sensitivity compared to conventional AF4 separation schemes. Moreover, nanoparticulate titanium dioxide populations exhibiting broad size distributions are analyzed in a rapid and efficient manner. Finally, the repeatability and reproducibility of the miniaturized platform are investigated with respect to analysis time and separation efficiency. PMID:26258119

Nanoparticle separation with a miniaturized asymmetrical flow field-flow fractionation cartridge

NASA Astrophysics Data System (ADS)

Müller, David; Cattaneo, Stefano; Meier, Florian; Welz, Roland; deMello, Andrew

2015-07-01

Asymmetrical Flow Field-Flow Fractionation (AF4) is a separation technique applicable to particles over a wide size range. Despite the many advantages of AF4, its adoption in routine particle analysis is somewhat limited by the large footprint of currently available separation cartridges, extended analysis times and significant solvent consumption. To address these issues, we describe the fabrication and characterization of miniaturized AF4 cartridges. Key features of the scale-down platform include simplified cartridge and reagent handling, reduced analysis costs and higher throughput capacities. The separation performance of the miniaturized cartridge is assessed using certified gold and silver nanoparticle standards. Analysis of gold nanoparticle populations indicates shorter analysis times and increased sensitivity compared to conventional AF4 separation schemes. Moreover, nanoparticulate titanium dioxide populations exhibiting broad size distributions are analyzed in a rapid and efficient manner. Finally, the repeatability and reproducibility of the miniaturized platform are investigated with respect to analysis time and separation efficiency.

Miniaturized Planar Room Temperature Ionic Liquid Electrochemical Gas Sensor for Rapid Multiple Gas Pollutants Monitoring.

PubMed

Wan, Hao; Yin, Heyu; Lin, Lu; Zeng, Xiangqun; Mason, Andrew J

2018-02-01

The growing impact of airborne pollutants and explosive gases on human health and occupational safety has escalated the demand of sensors to monitor hazardous gases. This paper presents a new miniaturized planar electrochemical gas sensor for rapid measurement of multiple gaseous hazards. The gas sensor features a porous polytetrafluoroethylene substrate that enables fast gas diffusion and room temperature ionic liquid as the electrolyte. Metal sputtering was utilized for platinum electrodes fabrication to enhance adhesion between the electrodes and the substrate. Together with carefully selected electrochemical methods, the miniaturized gas sensor is capable of measuring multiple gases including oxygen, methane, ozone and sulfur dioxide that are important to human health and safety. Compared to its manually-assembled Clark-cell predecessor, this sensor provides better sensitivity, linearity and repeatability, as validated for oxygen monitoring. With solid performance, fast response and miniaturized size, this sensor is promising for deployment in wearable devices for real-time point-of-exposure gas pollutant monitoring.

Assessing Diversity of DNA Structure-Related Sequence Features in Prokaryotic Genomes

PubMed Central

Huang, Yongjie; Mrázek, Jan

2014-01-01

Prokaryotic genomes are diverse in terms of their nucleotide and oligonucleotide composition as well as presence of various sequence features that can affect physical properties of the DNA molecule. We present a survey of local sequence patterns which have a potential to promote non-canonical DNA conformations (i.e. different from standard B-DNA double helix) and interpret the results in terms of relationships with organisms' habitats, phylogenetic classifications, and other characteristics. Our present work differs from earlier similar surveys not only by investigating a wider range of sequence patterns in a large number of genomes but also by using a more realistic null model to assess significant deviations. Our results show that simple sequence repeats and Z-DNA-promoting patterns are generally suppressed in prokaryotic genomes, whereas palindromes and inverted repeats are over-represented. Representation of patterns that promote Z-DNA and intrinsic DNA curvature increases with increasing optimal growth temperature (OGT), and decreases with increasing oxygen requirement. Additionally, representations of close direct repeats, palindromes and inverted repeats exhibit clear negative trends with increasing OGT. The observed relationships with environmental characteristics, particularly OGT, suggest possible evolutionary scenarios of structural adaptation of DNA to particular environmental niches. PMID:24408877

Realizing Broadband and Invertible Linear-to-circular Polarization Converter with Ultrathin Single-layer Metasurface

PubMed Central

Li, Zhancheng; Liu, Wenwei; Cheng, Hua; Chen, Shuqi; Tian, Jianguo

2015-01-01

The arbitrary control of the polarization states of light has attracted the interest of the scientific community because of the wide range of modern optical applications that such control can afford. However, conventional polarization control setups are bulky and very often operate only within a narrow wavelength range, thereby resisting optical system miniaturization and integration. Here, we present the basic theory, simulated demonstration, and in-depth analysis of a high-performance broadband and invertible linear-to-circular (LTC) polarization converter composed of a single-layer gold nanorod array with a total thickness of ~λ/70 for the near-infrared regime. This setup can transform a circularly polarized wave into a linearly polarized one or a linearly polarized wave with a wavelength-dependent electric field polarization angle into a circularly polarized one in the transmission mode. The broadband and invertible LTC polarization conversion can be attributed to the tailoring of the light interference at the subwavelength scale via the induction of the anisotropic optical resonance mode. This ultrathin single-layer metasurface relaxes the high-precision requirements of the structure parameters in general metasurfaces while retaining the polarization conversion performance. Our findings open up intriguing possibilities towards the realization of novel integrated metasurface-based photonics devices for polarization manipulation, modulation, and phase retardation. PMID:26667360

Recombination Analysis of Herpes Simplex Virus 1 Reveals a Bias toward GC Content and the Inverted Repeat Regions

PubMed Central

Lee, Kyubin; Kolb, Aaron W.; Sverchkov, Yuriy; Cuellar, Jacqueline A.; Craven, Mark

2015-01-01

ABSTRACT Herpes simplex virus 1 (HSV-1) causes recurrent mucocutaneous ulcers and is the leading cause of infectious blindness and sporadic encephalitis in the United States. HSV-1 has been shown to be highly recombinogenic; however, to date, there has been no genome-wide analysis of recombination. To address this, we generated 40 HSV-1 recombinants derived from two parental strains, OD4 and CJ994. The 40 OD4-CJ994 HSV-1 recombinants were sequenced using the Illumina sequencing system, and recombination breakpoints were determined for each of the recombinants using the Bootscan program. Breakpoints occurring in the terminal inverted repeats were excluded from analysis to prevent double counting, resulting in a total of 272 breakpoints in the data set. By placing windows around the 272 breakpoints followed by Monte Carlo analysis comparing actual data to simulated data, we identified a recombination bias toward both high GC content and intergenic regions. A Monte Carlo analysis also suggested that recombination did not appear to be responsible for the generation of the spontaneous nucleotide mutations detected following sequencing. Additionally, kernel density estimation analysis across the genome found that the large, inverted repeats comprise a recombination hot spot. IMPORTANCE Herpes simplex virus 1 (HSV-1) virus is the leading cause of sporadic encephalitis and blinding keratitis in developed countries. HSV-1 has been shown to be highly recombinogenic, and recombination itself appears to be a significant component of genome replication. To date, there has been no genome-wide analysis of recombination. Here we present the findings of the first genome-wide study of recombination performed by generating and sequencing 40 HSV-1 recombinants derived from the OD4 and CJ994 parental strains, followed by bioinformatics analysis. Recombination breakpoints were determined, yielding 272 breakpoints in the full data set. Kernel density analysis determined that the large inverted repeats constitute a recombination hot spot. Additionally, Monte Carlo analyses found biases toward high GC content and intergenic and repetitive regions. PMID:25926637

pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements

PubMed Central

Xiang, Xiaoyu; Huang, Xiaoxing; Wang, Haina; Huang, Li

2015-01-01

Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading. PMID:25686154

pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements.

PubMed

Xiang, Xiaoyu; Huang, Xiaoxing; Wang, Haina; Huang, Li

2015-02-12

Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading.

Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function

PubMed Central

Chillón, Isabel; Pyle, Anna M.

2016-01-01

LincRNA-p21 is a long intergenic non-coding RNA (lincRNA) involved in the p53-mediated stress response. We sequenced the human lincRNA-p21 (hLincRNA-p21) and found that it has a single exon that includes inverted repeat Alu elements (IRAlus). Sense and antisense Alu elements fold independently of one another into a secondary structure that is conserved in lincRNA-p21 among primates. Moreover, the structures formed by IRAlus are involved in the localization of hLincRNA-p21 in the nucleus, where hLincRNA-p21 colocalizes with paraspeckles. Our results underscore the importance of IRAlus structures for the function of hLincRNA-p21 during the stress response. PMID:27378782

Isolation and molecular characterization of dTnp1, a mobile and defective transposable element of Nicotiana plumbaginifolia.

PubMed

Meyer, C; Pouteau, S; Rouzé, P; Caboche, M

1994-01-01

By Northern blot analysis of nitrate reductase-deficient mutants of Nicotiana plumbaginifolia, we identified a mutant (mutant D65), obtained after gamma-ray irradiation of protoplasts, which contained an insertion sequence in the nitrate reductase (NR) mRNA. This insertion sequence was localized by polymerase chain reaction (PCR) in the first exon of NR and was also shown to be present in the NR gene. The mutant gene contained a 565 bp insertion sequence that exhibits the sequence characteristics of a transposable element, which was thus named dTnp1. The dTnp1 element has 14 bp terminal inverted repeats and is flanked by an 8-bp target site duplication generated upon transposition. These inverted repeats have significant sequence homology with those of other transposable elements. Judging by its size and the absence of a long open reading frame, dTnp1 appears to represent a defective, although mobile, transposable element. The octamer motif TTTAGGCC was found several times in direct orientation near the 5' and 3' ends of dTnp1 together with a perfect palindrome located after the 5' inverted repeat. Southern blot analysis using an internal probe of dTnp1 suggested that this element occurs as a single copy in the genome of N. plumbaginifolia. It is also present in N. tabacum, but absent in tomato or petunia. The dTnp1 element is therefore of potential use for gene tagging in Nicotiana species.

Formation of Linear Amplicons with Inverted Duplications in Leishmania Requires the MRE11 Nuclease

PubMed Central

Laffitte, Marie-Claude N.; Genois, Marie-Michelle; Mukherjee, Angana; Légaré, Danielle; Masson, Jean-Yves; Ouellette, Marc

2014-01-01

Extrachromosomal DNA amplification is frequent in the protozoan parasite Leishmania selected for drug resistance. The extrachromosomal amplified DNA is either circular or linear, and is formed at the level of direct or inverted homologous repeated sequences that abound in the Leishmania genome. The RAD51 recombinase plays an important role in circular amplicons formation, but the mechanism by which linear amplicons are formed is unknown. We hypothesized that the Leishmania infantum DNA repair protein MRE11 is required for linear amplicons following rearrangements at the level of inverted repeats. The purified LiMRE11 protein showed both DNA binding and exonuclease activities. Inactivation of the LiMRE11 gene led to parasites with enhanced sensitivity to DNA damaging agents. The MRE11−/− parasites had a reduced capacity to form linear amplicons after drug selection, and the reintroduction of an MRE11 allele led to parasites regaining their capacity to generate linear amplicons, but only when MRE11 had an active nuclease activity. These results highlight a novel MRE11-dependent pathway used by Leishmania to amplify portions of its genome to respond to a changing environment. PMID:25474106

Molecular and bioinformatic analysis of the FB-NOF transposable element.

PubMed

Badal, Martí; Portela, Anna; Xamena, Noel; Cabré, Oriol

2006-04-12

The Drosophila melanogaster transposable element FB-NOF is known to play a role in genome plasticity through the generation of all sort of genomic rearrangements. Moreover, several insertional mutants due to FB mobilizations have been reported. Its structure and sequence, however, have been poorly studied mainly as a consequence of the long, complex and repetitive sequence of FB inverted repeats. This repetitive region is composed of several 154 bp blocks, each with five almost identical repeats. In this paper, we report the sequencing process of 2 kb long FB inverted repeats of a complete FB-NOF element, with high precision and reliability. This achievement has been possible using a new map of the FB repetitive region, which identifies unambiguously each repeat with new features that can be used as landmarks. With this new vision of the element, a list of FB-NOF in the D. melanogaster genomic clones has been done, improving previous works that used only bioinformatic algorithms. The availability of many FB and FB-NOF sequences allowed an analysis of the FB insertion sequences that showed no sequence specificity, but a preference for A/T rich sequences. The position of NOF into FB is also studied, revealing that it is always located after a second repeat in a random block. With the results of this analysis, we propose a model of transposition in which NOF jumps from FB to FB, using an unidentified transposase enzyme that should specifically recognize the second repeat end of the FB blocks.

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. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Analysis of the genome sequence of the pathogenic Muscovy duck parvovirus strain YY reveals a 14-nucleotide-pair deletion in the inverted terminal repeats.

PubMed

Wang, Jianye; Huang, Yu; Zhou, Mingxu; Zhu, Guoqiang

2016-09-01

Genomic information about Muscovy duck parvovirus is still limited. In this study, the genome of the pathogenic MDPV strain YY was sequenced. The full-length genome of YY is 5075 nucleotides (nt) long, 57 nt shorter than that of strain FM. Sequence alignment indicates that the 5' and 3' inverted terminal repeats (ITR) of strain YY contain a 14-nucleotide-pair deletion in the stem of the palindromic hairpin structure in comparison to strain FM and FZ91-30. The deleted region contains one "E-box" site and one repeated motif with the sequence "TTCCGGT" or "ACCGGAA". Phylogenetic trees constructed based the protein coding genes concordantly showed that YY, together with nine other MDPV isolates from various places, clustered in a separate branch, distinct from the branch formed by goose parvovirus (GPV) strains. These results demonstrate that, despite the distinctive deletion, the YY strain still belongs to the classical MDPV group. Moreover, the deletion of ITR may contribute to the genome evolution of MDPV under immunization pressure.

Sarcoptes infestation in two miniature pigs with zoonotic transmission - a case report.

PubMed

Grahofer, Alexander; Bannoehr, Jeanette; Nathues, Heiko; Roosje, Petra

2018-03-13

Scabies is a contagious skin disease rarely described in miniature pigs. To the best of the authors' knowledge, a zoonotic transfer from infected pet pigs to humans has not been reported previously. This case report describes the infestation with Sarcoptes scabiei mites in two miniature pigs presenting with unusual clinical signs, and disease transmission to a child. Two 7-month-old male castrated miniature pig siblings were examined. Both had developed skin lesions, one animal was presented for neurological signs and emaciation. They were housed together in an indoor- and outdoor enclosure. Dermatological examination revealed a dull, greasy coat with generalized hypotrichosis and multifocal erythema. Microscopic examination of skin scrapings, impression smears of affected skin and ear swabs revealed high numbers of Sarcoptes mites in both animals as well as bacterial overgrowth. A subcutaneous injection of ivermectin 0.3 mg/kg was administered to both animals and repeated after 2 weeks. Both miniature pigs received subcutaneous injections with butafosfan and cyanocobalamin, were washed with a 3% chlorhexidine shampoo and were fed on a well-balanced diet. Pig enclosures were cleaned. The infested child was examined by a physician and an antipruritic cream was prescribed. Both miniature pigs and the child went into clinical remission after treatment. Sarcoptic mange is rare or even eradicated in commercial pig farming in many countries but miniature pigs may represent a niche for Sarcoptes scabiei infections. This case report indicates that miniature pigs kept as pets can efficiently transmit zoonotic disease to humans. In addition, these animals may represent a niche for Sarcoptes scabiei infestation in countries where sarcoptic mange in commercial pig farms has been eradicated and could therefore pose, a hazard for specific pathogen free farms.

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.

Flexible DNA binding of the BTB/POZ-domain protein FBI-1.

PubMed

Pessler, Frank; Hernandez, Nouria

2003-08-01

POZ-domain transcription factors are characterized by the presence of a protein-protein interaction domain called the POZ or BTB domain at their N terminus and zinc fingers at their C terminus. Despite the large number of POZ-domain transcription factors that have been identified to date and the significant insights that have been gained into their cellular functions, relatively little is known about their DNA binding properties. FBI-1 is a BTB/POZ-domain protein that has been shown to modulate HIV-1 Tat trans-activation and to repress transcription of some cellular genes. We have used various viral and cellular FBI-1 binding sites to characterize the interaction of a POZ-domain protein with DNA in detail. We find that FBI-1 binds to inverted sequence repeats downstream of the HIV-1 transcription start site. Remarkably, it binds efficiently to probes carrying these repeats in various orientations and spacings with no particular rotational alignment, indicating that its interaction with DNA is highly flexible. Indeed, FBI-1 binding sites in the adenovirus 2 major late promoter, the c-fos gene, and the c-myc P1 and P2 promoters reveal variously spaced direct, inverted, and everted sequence repeats with the consensus sequence G(A/G)GGG(T/C)(C/T)(T/C)(C/T) for each repeat.

Structures of ω repressors bound to direct and inverted DNA repeats explain modulation of transcription

PubMed Central

Weihofen, Wilhelm Andreas; Cicek, Aslan; Pratto, Florencia; Alonso, Juan Carlos; Saenger, Wolfram

2006-01-01

Repressor ω regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. ω belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel β-sheet for DNA major groove binding. Homodimeric ω2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5′-A/TATCACA/T-3′, symbolized by →) in palindromic inverted, converging (→←) or diverging (←→) orientation and also, unique to ω2 and contrasting other RHH2 repressors, to non-palindromic direct (→→) repeats. Here we investigate with crystal structures how ω2 binds specifically to heptads in minimal operators with (→→) and (→←) repeats. Since the pseudo-2-fold axis relating the monomers in ω2 passes the central C–G base pair of each heptad with ∼0.3 Å downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (→→), ∼0.6 Å shorter in (→←) but would be ∼0.6 Å longer in (←→). These variations grade interactions between adjacent ω2 and explain modulations in cooperative binding affinity of ω2 to operators with different heptad orientations. PMID:16528102

Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter.

PubMed

Weyand, Simone; Shimamura, Tatsuro; Yajima, Shunsuke; Suzuki, Shun'ichi; Mirza, Osman; Krusong, Kuakarun; Carpenter, Elisabeth P; Rutherford, Nicholas G; Hadden, Jonathan M; O'Reilly, John; Ma, Pikyee; Saidijam, Massoud; Patching, Simon G; Hope, Ryan J; Norbertczak, Halina T; Roach, Peter C J; Iwata, So; Henderson, Peter J F; Cameron, Alexander D

2008-10-31

The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.

Ribosomal protein S14 transcripts are edited in Oenothera mitochondria.

PubMed Central

Schuster, W; Unseld, M; Wissinger, B; Brennicke, A

1990-01-01

The gene encoding ribosomal protein S14 (rps14) in Oenothera mitochondria is located upstream of the cytochrome b gene (cob). Sequence analysis of independently derived cDNA clones covering the entire rps14 coding region shows two nucleotides edited from the genomic DNA to the mRNA derived sequences by C to U modifications. A third editing event occurs four nucleotides upstream of the AUG initiation codon and improves a potential ribosome binding site. A CGG codon specifying arginine in a position conserved in evolution between chloroplasts and E. coli as a UGG tryptophan codon is not edited in any of the cDNAs analysed. An inverted repeat 3' of an unidentified open reading frame is located upstream of the rps14 gene. The inverted repeat sequence is highly conserved at analogous regions in other Oenothera mitochondrial loci. Images PMID:2326162

Hot Fusion: an efficient method to clone multiple DNA fragments as well as inverted repeats without ligase.

PubMed

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%.

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

Dynamic response characteristics of two transport models tested in the National Transonic Facility

NASA Technical Reports Server (NTRS)

Young, Clarence P., Jr.

1993-01-01

This paper documents recent experiences with measuring the dynamic response characteristics of a commercial transport and a military transport model during full scale Reynolds number tests in the National Transonic Facility. Both models were limited in angle of attack while testing at full scale Reynolds number and cruise Mach number due to pitch or stall buffet response. Roll buffet (wing buzz) was observed for both models at certain Mach numbers while testing at high Reynolds number. Roll buffet was more severe and more repeatable for the military transport model at cruise Mach number. Miniature strain-gage type accelerometers were used for the first time for obtaining dynamic data as a part of the continuing development of miniature dynamic measurements instrumentation for cryogenic applications. This paper presents the results of vibration measurements obtained for both the commercial and military transport models and documents the experience gained in the use of miniature strain gage type accelerometers.

Repeat-Associated Fission Yeast-Like Regional Centromeres in the Ascomycetous Budding Yeast Candida tropicalis

PubMed Central

Chatterjee, Gautam; Sankaranarayanan, Sundar Ram; Guin, Krishnendu; Thattikota, Yogitha; Padmanabhan, Sreedevi; Siddharthan, Rahul; Sanyal, Kaustuv

2016-01-01

The centromere, on which kinetochore proteins assemble, ensures precise chromosome segregation. Centromeres are largely specified by the histone H3 variant CENP-A (also known as Cse4 in yeasts). Structurally, centromere DNA sequences are highly diverse in nature. However, the evolutionary consequence of these structural diversities on de novo CENP-A chromatin formation remains elusive. Here, we report the identification of centromeres, as the binding sites of four evolutionarily conserved kinetochore proteins, in the human pathogenic budding yeast Candida tropicalis. Each of the seven centromeres comprises a 2 to 5 kb non-repetitive mid core flanked by 2 to 5 kb inverted repeats. The repeat-associated centromeres of C. tropicalis all share a high degree of sequence conservation with each other and are strikingly diverged from the unique and mostly non-repetitive centromeres of related Candida species—Candida albicans, Candida dubliniensis, and Candida lusitaniae. Using a plasmid-based assay, we further demonstrate that pericentric inverted repeats and the underlying DNA sequence provide a structural determinant in CENP-A recruitment in C. tropicalis, as opposed to epigenetically regulated CENP-A loading at centromeres in C. albicans. Thus, the centromere structure and its influence on de novo CENP-A recruitment has been significantly rewired in closely related Candida species. Strikingly, the centromere structural properties along with role of pericentric repeats in de novo CENP-A loading in C. tropicalis are more reminiscent to those of the distantly related fission yeast Schizosaccharomyces pombe. Taken together, we demonstrate, for the first time, fission yeast-like repeat-associated centromeres in an ascomycetous budding yeast. PMID:26845548

Insights into mutagenesis using Escherichia coli chromosomal lacZ strains that enable detection of a wide spectrum of mutational events.

PubMed

Seier, Tracey; Padgett, Dana R; Zilberberg, Gal; Sutera, Vincent A; Toha, Noor; Lovett, Susan T

2011-06-01

Strand misalignments at DNA repeats during replication are implicated in mutational hotspots. To study these events, we have generated strains carrying mutations in the Escherichia coli chromosomal lacZ gene that revert via deletion of a short duplicated sequence or by template switching within imperfect inverted repeat (quasipalindrome, QP) sequences. Using these strains, we demonstrate that mutation of the distal repeat of a quasipalindrome, with respect to replication fork movement, is about 10-fold higher than the proximal repeat, consistent with more common template switching on the leading strand. The leading strand bias was lost in the absence of exonucleases I and VII, suggesting that it results from more efficient suppression of template switching by 3' exonucleases targeted to the lagging strand. The loss of 3' exonucleases has no effect on strand misalignment at direct repeats to produce deletion. To compare these events to other mutations, we have reengineered reporters (designed by Cupples and Miller 1989) that detect specific base substitutions or frameshifts in lacZ with the reverting lacZ locus on the chromosome rather than an F' element. This set allows rapid screening of potential mutagens, environmental conditions, or genetic loci for effects on a broad set of mutational events. We found that hydroxyurea (HU), which depletes dNTP pools, slightly elevated templated mutations at inverted repeats but had no effect on deletions, simple frameshifts, or base substitutions. Mutations in nucleotide diphosphate kinase, ndk, significantly elevated simple mutations but had little effect on the templated class. Zebularine, a cytosine analog, elevated all classes.

UAVSAR: Airborne L-band Radar for Repeat Pass Interferometry

NASA Technical Reports Server (NTRS)

Moes, Timothy R.

2009-01-01

The primary objectives of the UAVSAR Project were to: a) develop a miniaturized polarimetric L-band synthetic aperture radar (SAR) for use on an unmanned aerial vehicle (UAV) or piloted vehicle. b) develop the associated processing algorithms for repeat-pass differential interferometric measurements using a single antenna. c) conduct measurements of geophysical interest, particularly changes of rapidly deforming surfaces such as volcanoes or earthquakes. Two complete systems were developed. Operational Science Missions began on February 18, 2009 ... concurrent development and testing of the radar system continues.

Floating-Gate Manipulated Graphene-Black Phosphorus Heterojunction for Nonvolatile Ambipolar Schottky Junction Memories, Memory Inverter Circuits, and Logic Rectifiers.

PubMed

Li, Dong; Chen, Mingyuan; Zong, Qijun; Zhang, Zengxing

2017-10-11

The Schottky junction is an important unit in electronics and optoelectronics. However, its properties greatly degrade with device miniaturization. The fast development of circuits has fueled a rapid growth in the study of two-dimensional (2D) crystals, which may lead to breakthroughs in the semiconductor industry. Here we report a floating-gate manipulated nonvolatile ambipolar Schottky junction memory from stacked all-2D layers of graphene-BP/h-BN/graphene (BP, black phosphorus; h-BN, hexagonal boron nitride) in a designed floating-gate field-effect Schottky barrier transistor configuration. By manipulating the voltage pulse applied to the control gate, the device exhibits ambipolar characteristics and can be tuned to act as graphene-p-BP or graphene-n-BP junctions with reverse rectification behavior. Moreover, the junction exhibits good storability properties of more than 10 years and is also programmable. On the basis of these characteristics, we further demonstrate the application of the device to dual-mode nonvolatile Schottky junction memories, memory inverter circuits, and logic rectifiers.

Identification of Genetic Elements Associated with EPSPS Gene Amplification

PubMed Central

Gaines, Todd A.; Wright, Alice A.; Molin, William T.; Lorentz, Lothar; Riggins, Chance W.; Tranel, Patrick J.; Beffa, Roland; Westra, Philip; Powles, Stephen B.

2013-01-01

Weed populations can have high genetic plasticity and rapid responses to environmental selection pressures. For example, 100-fold amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene evolved in the weed species Amaranthus palmeri to confer resistance to glyphosate, the world’s most important herbicide. However, the gene amplification mechanism is unknown. We sequenced the EPSPS gene and genomic regions flanking EPSPS loci in A. palmeri, and searched for mobile genetic elements or repetitive sequences. The EPSPS gene was 10,229 bp, containing 8 exons and 7 introns. The gene amplification likely proceeded through a DNA-mediated mechanism, as introns exist in the amplified gene copies and the entire amplified sequence is at least 30 kb in length. Our data support the presence of two EPSPS loci in susceptible (S) A. palmeri, and that only one of these was amplified in glyphosate-resistant (R) A. palmeri. The EPSPS gene amplification event likely occurred recently, as no sequence polymorphisms were found within introns of amplified EPSPS copies from R individuals. Sequences with homology to miniature inverted-repeat transposable elements (MITEs) were identified next to EPSPS gene copies only in R individuals. Additionally, a putative Activator (Ac) transposase and a repetitive sequence region were associated with amplified EPSPS genes. The mechanism controlling this DNA-mediated amplification remains unknown. Further investigation is necessary to determine if the gene amplification may have proceeded via DNA transposon-mediated replication, and/or unequal recombination between different genomic regions resulting in replication of the EPSPS gene. PMID:23762434

Expression of Wheat High Molecular Weight Glutenin Subunit 1Bx Is Affected by Large Insertions and Deletions Located in the Upstream Flanking Sequences

PubMed Central

Hao, Chenyang; Tang, Saijun; Zhang, Xueyong; Li, Tian

2014-01-01

To better understand the transcriptional regulation of high molecular weight glutenin subunit (HMW-GS) expression, we isolated four Glu-1Bx promoters from six wheat cultivars exhibiting diverse protein expression levels. The activities of the diverse Glu-1Bx promoters were tested and compared with β-glucuronidase (GUS) reporter fusions. Although all the full-length Glu-1Bx promoters showed endosperm-specific activities, the strongest GUS activity was observed with the 1Bx7OE promoter in both transient expression assays and stable transgenic rice lines. A 43 bp insertion in the 1Bx7OE promoter, which is absent in the 1Bx7 promoter, led to enhanced expression. Analysis of promoter deletion constructs confirmed that a 185 bp MITE (miniature inverted-repeat transposable element) in the 1Bx14 promoter had a weak positive effect on Glu-1Bx expression, and a 54 bp deletion in the 1Bx13 promoter reduced endosperm-specific activity. To investigate the effect of the 43 bp insertion in the 1Bx7OE promoter, a functional marker was developed to screen 505 Chinese varieties and 160 European varieties, and only 1Bx7-type varieties harboring the 43 bp insertion in their promoters showed similar overexpression patterns. Hence, the 1Bx7OE promoter should be important tool in crop genetic engineering as well as in molecular assisted breeding. PMID:25133580

Complete Genomic Structure of the Bloom-forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843

PubMed Central

Kaneko, Takakazu; Nakajima, Nobuyoshi; Okamoto, Shinobu; Suzuki, Iwane; Tanabe, Yuuhiko; Tamaoki, Masanori; Nakamura, Yasukazu; Kasai, Fumie; Watanabe, Akiko; Kawashima, Kumiko; Kishida, Yoshie; Ono, Akiko; Shimizu, Yoshimi; Takahashi, Chika; Minami, Chiharu; Fujishiro, Tsunakazu; Kohara, Mitsuyo; Katoh, Midori; Nakazaki, Naomi; Nakayama, Shinobu; Yamada, Manabu; Tabata, Satoshi; Watanabe, Makoto M.

2007-01-01

Abstract The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5 842 795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restriction-modification systems were notable characteristics of the M. aeruginosa genome. PMID:18192279

In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome

PubMed Central

2013-01-01

Background Only a few transposable elements are known to exhibit site-specific insertion patterns, including the well-studied R-element retrotransposons that insert into specific sites within the multigene rDNA. The only known rDNA-specific DNA transposon, Pokey (superfamily: piggyBac) is found in the freshwater microcrustacean, Daphnia pulex. Here, we present a genome-wide analysis of Pokey based on the recently completed whole genome sequencing project for D. pulex. Results Phylogenetic analysis of Pokey elements recovered from the genome sequence revealed the presence of four lineages corresponding to two divergent autonomous families and two related lineages of non-autonomous miniature inverted repeat transposable elements (MITEs). The MITEs are also found at the same 28S rRNA gene insertion site as the Pokey elements, and appear to have arisen as deletion derivatives of autonomous elements. Several copies of the full-length Pokey elements may be capable of producing an active transposase. Surprisingly, both families of Pokey possess a series of 200 bp repeats upstream of the transposase that is derived from the rDNA intergenic spacer (IGS). The IGS sequences within the Pokey elements appear to be evolving in concert with the rDNA units. Finally, analysis of the insertion sites of Pokey elements outside of rDNA showed a target preference for sites similar to the specific sequence that is targeted within rDNA. Conclusions Based on the target site preference of Pokey elements and the concerted evolution of a segment of the element with the rDNA unit, we propose an evolutionary path by which the ancestors of Pokey elements have invaded the rDNA niche. We discuss how specificity for the rDNA unit may have evolved and how this specificity has played a role in the long-term survival of these elements in the subgenus Daphnia. PMID:24059783

A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed in Echinococcus multilocularis Stem Cells

PubMed Central

Koziol, Uriel; Radio, Santiago; Smircich, Pablo; Zarowiecki, Magdalena; Fernández, Cecilia; Brehm, Klaus

2015-01-01

Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we report the discovery of a novel family of small nonautonomous long terminal repeat retrotransposons (also known as terminal-repeat retrotransposons in miniature, TRIMs) which we have named ta-TRIM (taeniid TRIM). ta-TRIMs are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. These elements originated at the base of the taeniid tree and have expanded during taeniid diversification, including after the divergence of closely related species such as Echinococcus multilocularis and Echinococcus granulosus. They are massively expressed in larval stages, from a small proportion of full-length copies and from isolated terminal repeats that show transcriptional read-through into downstream regions, generating novel noncoding RNAs and transcriptional fusions to coding genes. In E. multilocularis, ta-TRIMs are specifically expressed in the germinative cells (the somatic stem cells) during asexual reproduction of metacestode larvae. This would provide a developmental mechanism for insertion of ta-TRIMs into cells that will eventually generate the adult germ line. Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes. PMID:26133390

Miniaturized microscope for high throughput screening of tumor spheroids in microfluidic devices

NASA Astrophysics Data System (ADS)

Uranga, Javier; Rodríguez-Pena, Alejandro; Gahigiro, Desiré; Ortiz-de-Solorzano, Carlos

2018-02-01

High-throughput in vitro screening of highly physiological three-dimensional cell cultures (3D-HTS) is rapidly gaining importance in preclinical studies, to study the effect of the microenvironment in tumor development, and to evaluate the efficacy of new anticancer drugs. Furthermore, it could also be envisioned the use of 3D-HTS systems in personalized anti-cancer treatment planning, based on tumor organoids or spheroids grown from tumor biopsies or isolated tumor circulating cells. Most commercial, multi-well plate based 3D-HTS systems are large, expensive, and are based on the use of multi-well plates that hardly provide a physiological environment and require the use of large amounts of biological material and reagents. In this paper we present a novel, miniaturized inverted microscope (hereinafter miniscospe), made up of low-cost, mass producible parts, that can be used to monitor the growth of living tumor cell spheroids within customized three-dimensional microfluidic platforms. Our 3D-HTS miniscope combines phase contrast imaging based on oblique back illumination technique with traditional widefield epi-fluorescence imaging, implemented using miniaturized electro-optical parts and gradient-index refraction lenses. This small (3x6x2cm), lightweight device can effectively image overtime the growth of (>200) tumor spheroids in a controlled and reproducible environment. Our miniscope can be used to acquire time-lapse images of cellular living spheroids over the course of several hours and captures their growth before and after drug treatment, to evaluate the effectiveness of the drug.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janardhanraj, S.; Jagadeesh, G., E-mail: jaggie@aero.iisc.ernet.in

A novel concept to generate miniature shockwaves in a safe, repeatable, and controllable manner in laboratory confinements using an in situ oxyhydrogen generator has been proposed and demonstrated. This method proves to be more advantageous than existing methods because there is flexibility to vary strength of the shockwave, there is no need for storage of high pressure gases, and there is minimal waste disposal. The required amount of oxyhydrogen mixture is generated using alkaline electrolysis that produces hydrogen and oxygen gases in stoichiometric quantity. The rate of oxyhydrogen mixture production for the newly designed oxyhydrogen generator is found to bemore » around 8 ml/s experimentally. The oxyhydrogen generator is connected to the driver section of a specially designed 10 mm square miniature shock tube assembly. A numerical code that uses CANTERA software package is used to predict the properties of the driver gas in the miniature shock tube. This prediction along with the 1-D shock tube theory is used to calculate the properties of the generated shockwave and matches reasonably well with the experimentally obtained values for oxyhydrogen mixture fill pressures less than 2.5 bars. The miniature shock tube employs a modified tri-clover clamp assembly to facilitate quick changing of diaphragm and replaces the more cumbersome nut and bolt system of fastening components. The versatile nature of oxyhydrogen detonation-driven miniature shock tube opens up new horizons for shockwave-assisted interdisciplinary applications.« less

Miniaturized blood sampling techniques to benefit reduction in mice and refinement in nonhuman primates: applications to bioanalysis in toxicity studies with antibody-drug conjugates.

PubMed

Caron, Alexis; Lelong, Christine; Pascual, Marie-Hélène; Benning, Véronique

2015-03-01

Minimizing the number of animals in regulatory toxicity studies while achieving study objectives to support the development of future medicines contributes to good scientific and ethical practices. Recent advances in technology have enabled the development of miniaturized blood sampling methods (including microsampling and dried blood spots) applicable to toxicokinetic determinations of small-molecule drugs. Implementation of miniaturized blood sampling methods in the context of biotherapeutic drugs is desirable because a limitation to this type of medicine remains the total blood volume needed from a single animal to support toxicokinetic determinations of several analytes (parent drug, metabolites[s], antidrug antibodies, and so forth). We describe here the technical details, applicability, and relevance of new miniaturized blood sampling procedures in mice and nonhuman primates in the context of the toxicologic evaluation of biotherapeutic drugs consisting of antibody-drug conjugates developed for oncology indications. These examples illustrate how these techniques can benefit the reduction of animal usage in mouse toxicity studies by decreasing the number of animals dedicated to toxicokinetic determinations and the refinement of practices in nonhuman primate toxicity studies by decreasing the blood volume repeatedly drawn for toxicokinetic determinations.

Miniaturized Blood Sampling Techniques to Benefit Reduction in Mice and Refinement in Nonhuman Primates: Applications to Bioanalysis in Toxicity Studies with Antibody–Drug Conjugates

PubMed Central

Caron, Alexis; Lelong, Christine; Pascual, Marie-Hélène; Benning, Véronique

2015-01-01

Minimizing the number of animals in regulatory toxicity studies while achieving study objectives to support the development of future medicines contributes to good scientific and ethical practices. Recent advances in technology have enabled the development of miniaturized blood sampling methods (including microsampling and dried blood spots) applicable to toxicokinetic determinations of small-molecule drugs. Implementation of miniaturized blood sampling methods in the context of biotherapeutic drugs is desirable because a limitation to this type of medicine remains the total blood volume needed from a single animal to support toxicokinetic determinations of several analytes (parent drug, metabolites[s], antidrug antibodies, and so forth). We describe here the technical details, applicability, and relevance of new miniaturized blood sampling procedures in mice and nonhuman primates in the context of the toxicologic evaluation of biotherapeutic drugs consisting of antibody–drug conjugates developed for oncology indications. These examples illustrate how these techniques can benefit the reduction of animal usage in mouse toxicity studies by decreasing the number of animals dedicated to toxicokinetic determinations and the refinement of practices in nonhuman primate toxicity studies by decreasing the blood volume repeatedly drawn for toxicokinetic determinations. PMID:25836960

Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms

PubMed Central

Vergara-Jaque, Ariela; Fenollar-Ferrer, Cristina; Kaufmann, Desirée; Forrest, Lucy R.

2015-01-01

Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to one or other side of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (a)symmetry of these systems has been successfully used as a bioinformatic tool, called “repeat-swap modeling” to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that nucleoside transport also occurs via an elevator-like mechanism. PMID:26388773

BAC Modification through Serial or Simultaneous Use of CRE/Lox Technology

PubMed Central

Parrish, Mark; Unruh, Jay; Krumlauf, Robb

2011-01-01

Bacterial Artificial Chromosomes (BACs) are vital tools in mouse genomic analyses because of their ability to propagate large inserts. The size of these constructs, however, prevents the use of conventional molecular biology techniques for modification and manipulation. Techniques such as recombineering and Cre/Lox methodologies have thus become heavily relied upon for such purposes. In this work, we investigate the applicability of Lox variant sites for serial and/or simultaneous manipulations of BACs. We show that Lox spacer mutants are very specific, and inverted repeat variants reduce Lox reaction rates through reducing the affinity of Cre for the site, while retaining some functionality. Employing these methods, we produced serial modifications encompassing four independent changes which generated a mouse HoxB BAC with fluorescent reporter proteins inserted into four adjacent Hox genes. We also generated specific, simultaneous deletions using combinations of spacer variants and inverted repeat variants. These techniques will facilitate BAC manipulations and open a new repertoire of methods for BAC and genome manipulation. PMID:21197414

Strand invasion structures in the inverted repeat of Candida albicans mitochondrial DNA reveal a role for homologous recombination in replication.

PubMed

Gerhold, Joachim M; Aun, Anu; Sedman, Tiina; Jõers, Priit; Sedman, Juhan

2010-09-24

Molecular recombination and transcription are proposed mechanisms to initiate mitochondrial DNA (mtDNA) replication in yeast. We conducted a comprehensive analysis of mtDNA from the yeast Candida albicans. Two-dimensional agarose gel electrophoresis of mtDNA intermediates reveals no bubble structures diagnostic of specific replication origins, but rather supports recombination-driven replication initiation of mtDNA in yeast. Specific species of Y structures together with DNA copy number analyses of a C. albicans mutant strain provide evidence that a region in a mainly noncoding inverted repeat is predominantly involved in replication initiation via homologous recombination. Our further findings show that the C. albicans mtDNA forms a complex branched network that does not contain detectable amounts of circular molecules. We provide topological evidence for recombination-driven mtDNA replication initiation and introduce C. albicans as a suitable model organism to study wild-type mtDNA maintenance in yeast. Copyright © 2010 Elsevier Inc. All rights reserved.

Inverted Nipple Correction with Selective Dissection of Lactiferous Ducts Using an Operative Microscope and a Traction Technique.

PubMed

Sowa, Yoshihiro; Itsukage, Sizu; Morita, Daiki; Numajiri, Toshiaki

2017-10-01

An inverted nipple is a common congenital condition in young women that may cause breastfeeding difficulty, psychological distress, repeated inflammation, and loss of sensation. Various surgical techniques have been reported for correction of inverted nipples, and all have advantages and disadvantages. Here, we report a new technique for correction of an inverted nipple using an operative microscope and traction that results in low recurrence and preserves lactation function and sensation. Between January 2010 and January 2013, we treated eight inverted nipples in seven patients with selective lactiferous duct dissection using an operative microscope. An opposite Z-plasty was added at the junction of the nipple and areola. Postoperatively, traction was applied through an apparatus made from a rubber gasket attached to a sterile syringe. Patients were followed up for 15-48 months. Adequate projection was achieved in all patients, and there was no wound dehiscence or complications such as infection. Three patients had successful pregnancies and subsequent breastfeeding that was not adversely affected by the treatment. There was no loss of sensation in any patient during the postoperative period. Our technique for treating an inverted nipple is effective and preserves lactation function and nipple sensation. The method maintains traction for a longer period, which we believe increases the success rate of the surgery for correction of severely inverted nipples. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

An L-band SAR for repeat pass deformation measurements on a UAV platform

NASA Technical Reports Server (NTRS)

Wheeler, Kevin; Hensley, Scott; Lou, Yunling

2004-01-01

We are proposing to develop a miniaturized polarimetric L-band synthetic aperture radar (SAR) for repeatpass differential interferometric measurements of deformation for rapidly deforming surfaces of geophysical interest such as volcanoes or earthquakes that is to be flown on a unmanned aerial vehicle (UAV or minimally piloted vehicle (MPV).

Inverted drop testing and neck injury potential.

PubMed

Forrest, Stephen; Herbst, Brian; Meyer, Steve; Sances, Anthony; Kumaresan, Srirangam

2003-01-01

Inverted drop testing of vehicles is a methodology that has long been used by the automotive industry and researchers to test roof integrity and is currently being considered by the National Highway Traffic Safety Administration as a roof strength test. In 1990 a study was reported which involved 8 dolly rollover tests and 5 inverted drop tests. These studies were conducted with restrained Hybrid III instrumented Anthropometric Test Devices (ATD) in production and rollcaged vehicles to investigate the relationship between roof strength and occupant injury potential. The 5 inverted drop tests included in the study provided a methodology producing "repeatable roof impacts" exposing the ATDs to the similar impact environment as those seen in the dolly rollover tests. Authors have conducted two inverted drop test sets as part of an investigation of two real world rollover accidents. Hybrid-III ATD's were used in each test with instrumented head and necks. Both test sets confirm that reduction of roof intrusion and increased headroom can significantly enhance occupant protection. In both test pairs, the neck force of the dummy in the vehicle with less crush and more survival space was significantly lower. Reduced roof crush and dynamic preservation of the occupant survival space resulted in only minor occupant contact and minimal occupant loading, establishing a clear causal relationship between roof crush and neck injuries.

Collaborated measurement of three-dimensional position and orientation errors of assembled miniature devices with two vision systems

NASA Astrophysics Data System (ADS)

Wang, Xiaodong; Zhang, Wei; Luo, Yi; Yang, Weimin; Chen, Liang

2013-01-01

In assembly of miniature devices, the position and orientation of the parts to be assembled should be guaranteed during or after assembly. In some cases, the relative position or orientation errors among the parts can not be measured from only one direction using visual method, because of visual occlusion or for the features of parts located in a three-dimensional way. An automatic assembly system for precise miniature devices is introduced. In the modular assembly system, two machine vision systems were employed for measurement of the three-dimensionally distributed assembly errors. High resolution CCD cameras and high position repeatability precision stages were integrated to realize high precision measurement in large work space. The two cameras worked in collaboration in measurement procedure to eliminate the influence of movement errors of the rotational or translational stages. A set of templates were designed for calibration of the vision systems and evaluation of the system's measurement accuracy.

Integrated circuits and logic operations based on single-layer MoS2.

PubMed

Radisavljevic, Branimir; Whitwick, Michael Brian; Kis, Andras

2011-12-27

Logic circuits and the ability to amplify electrical signals form the functional backbone of electronics along with the possibility to integrate multiple elements on the same chip. The miniaturization of electronic circuits is expected to reach fundamental limits in the near future. Two-dimensional materials such as single-layer MoS(2) represent the ultimate limit of miniaturization in the vertical dimension, are interesting as building blocks of low-power nanoelectronic devices, and are suitable for integration due to their planar geometry. Because they are less than 1 nm thin, 2D materials in transistors could also lead to reduced short channel effects and result in fabrication of smaller and more power-efficient transistors. Here, we report on the first integrated circuit based on a two-dimensional semiconductor MoS(2). Our integrated circuits are capable of operating as inverters, converting logical "1" into logical "0", with room-temperature voltage gain higher than 1, making them suitable for incorporation into digital circuits. We also show that electrical circuits composed of single-layer MoS(2) transistors are capable of performing the NOR logic operation, the basis from which all logical operations and full digital functionality can be deduced.

Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.

PubMed

Tajaddod, Mansoureh; Tanzer, Andrea; Licht, Konstantin; Wolfinger, Michael T; Badelt, Stefan; Huber, Florian; Pusch, Oliver; Schopoff, Sandy; Janisiw, Michael; Hofacker, Ivo; Jantsch, Michael F

2016-10-25

Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution. Moreover, Alu elements within mRNAs have also been reported to control gene expression at different levels. Here, we undertake a genome-wide analysis of insertion patterns of human Alus within transcribed portions of the genome. Multiple, nearby insertions of SINEs within one transcript are more abundant in tandem orientation than in inverted orientation. Indeed, analysis of transcriptome-wide expression levels of 15 ENCODE cell lines suggests a cis-repressive effect of inverted Alu elements on gene expression. Using reporter assays, we show that the negative effect of inverted SINEs on gene expression is independent of known sensors of double-stranded RNAs. Instead, transcriptional elongation seems impaired, leading to reduced mRNA levels. Our study suggests that there is a bias against multiple SINE insertions that can promote intramolecular base pairing within a transcript. Moreover, at a genome-wide level, mRNAs harboring inverted SINEs are less expressed than mRNAs harboring single or tandemly arranged SINEs. Finally, we demonstrate a novel mechanism by which inverted SINEs can impact on gene expression by interfering with RNA polymerase II.

A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed in Echinococcus multilocularis Stem Cells.

PubMed

Koziol, Uriel; Radio, Santiago; Smircich, Pablo; Zarowiecki, Magdalena; Fernández, Cecilia; Brehm, Klaus

2015-07-01

Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we report the discovery of a novel family of small nonautonomous long terminal repeat retrotransposons (also known as terminal-repeat retrotransposons in miniature, TRIMs) which we have named ta-TRIM (taeniid TRIM). ta-TRIMs are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. These elements originated at the base of the taeniid tree and have expanded during taeniid diversification, including after the divergence of closely related species such as Echinococcus multilocularis and Echinococcus granulosus. They are massively expressed in larval stages, from a small proportion of full-length copies and from isolated terminal repeats that show transcriptional read-through into downstream regions, generating novel noncoding RNAs and transcriptional fusions to coding genes. In E. multilocularis, ta-TRIMs are specifically expressed in the germinative cells (the somatic stem cells) during asexual reproduction of metacestode larvae. This would provide a developmental mechanism for insertion of ta-TRIMs into cells that will eventually generate the adult germ line. Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Single-breath analysis using a novel simple sampler and capillary electrophoresis with contactless conductometric detection.

PubMed

Greguš, Michal; Foret, František; Kubáň, Petr

2015-02-01

The analysis of ionic content of exhaled breath condensate (EBC) from one single breath by CE with C(4) D is demonstrated for the first time. A miniature sampler made from a 2-mL syringe and an aluminum cooling cylinder for collection of EBC was developed. Various parameters of the sampler that influence its collection efficiency, repeatability, and effect of respiratory patterns were studied in detail. Efficient procedures for the cleanup of the miniature sampler were also developed and resulted in significant improvement of sampling repeatability. Analysis of EBC was performed by CE-C(4) D in a 60 mM MES/l-histidine BGE with 30 μM CTAB and 2 mM 18-crown-6 at pH 6 and excellent repeatability of migration times (RSD < 1.3% (n = 7)) and peak areas (RSD < 7% (n = 7)) of 12 inorganic anions, cations, and organic acids was obtained. It has been shown that the breathing pattern has a significant impact on the concentration of the analytes in the collected EBC. As the ventilatory pattern can be easily controlled during single exhalation, the developed collection system and method provides a highly reproducible and fast way of collecting EBC with applicability in point-of-care diagnostics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Asymmetry of inverted-topology repeats in the AE1 anion exchanger suggests an elevator-like mechanism

PubMed Central

Faraldo-Gómez, José D.

2017-01-01

The membrane transporter anion exchanger 1 (AE1), or band 3, is a key component in the processes of carbon-dioxide transport in the blood and urinary acidification in the renal collecting duct. In both erythrocytes and the basolateral membrane of the collecting-duct α-intercalated cells, the role of AE1 is to catalyze a one-for-one exchange of chloride for bicarbonate. After decades of biochemical and functional studies, the structure of the transmembrane region of AE1, which catalyzes the anion-exchange reaction, has finally been determined. Each protomer of the AE1 dimer comprises two repeats with inverted transmembrane topologies, but the structures of these repeats differ. This asymmetry causes the putative substrate-binding site to be exposed only to the extracellular space, consistent with the expectation that anion exchange occurs via an alternating-access mechanism. Here, we hypothesize that the unknown, inward-facing conformation results from inversion of this asymmetry, and we propose a model of this state constructed using repeat-swap homology modeling. By comparing this inward-facing model with the outward-facing experimental structure, we predict that the mechanism of AE1 involves an elevator-like motion of the substrate-binding domain relative to the nearly stationary dimerization domain and to the membrane plane. This hypothesis is in qualitative agreement with a wide range of biochemical and functional data, which we review in detail, and suggests new avenues of experimentation. PMID:29167180

Target Site Recognition by a Diversity-Generating Retroelement

PubMed Central

Guo, Huatao; Tse, Longping V.; Nieh, Angela W.; Czornyj, Elizabeth; Williams, Steven; Oukil, Sabrina; Liu, Vincent B.; Miller, Jeff F.

2011-01-01

Diversity-generating retroelements (DGRs) are in vivo sequence diversification machines that are widely distributed in bacterial, phage, and plasmid genomes. They function to introduce vast amounts of targeted diversity into protein-encoding DNA sequences via mutagenic homing. Adenine residues are converted to random nucleotides in a retrotransposition process from a donor template repeat (TR) to a recipient variable repeat (VR). Using the Bordetella bacteriophage BPP-1 element as a prototype, we have characterized requirements for DGR target site function. Although sequences upstream of VR are dispensable, a 24 bp sequence immediately downstream of VR, which contains short inverted repeats, is required for efficient retrohoming. The inverted repeats form a hairpin or cruciform structure and mutational analysis demonstrated that, while the structure of the stem is important, its sequence can vary. In contrast, the loop has a sequence-dependent function. Structure-specific nuclease digestion confirmed the existence of a DNA hairpin/cruciform, and marker coconversion assays demonstrated that it influences the efficiency, but not the site of cDNA integration. Comparisons with other phage DGRs suggested that similar structures are a conserved feature of target sequences. Using a kanamycin resistance determinant as a reporter, we found that transplantation of the IMH and hairpin/cruciform-forming region was sufficient to target the DGR diversification machinery to a heterologous gene. In addition to furthering our understanding of DGR retrohoming, our results suggest that DGRs may provide unique tools for directed protein evolution via in vivo DNA diversification. PMID:22194701

Molecular epidemiology of infectious laryngotracheitis: a review

USDA-ARS?s Scientific Manuscript database

Falconid herpesvirus type 1 (FHV-1) is the causative agent of falcon inclusion body disease, an acute, highly contagious disease of raptors. The complete nucleotide sequence of the genome of FHV-1 has been determined. The genome is arranged as a D-type genome with large inverted repeats flanking a ...

The rolling-circle melting-pot model for porcine circovirus DNA replication

USDA-ARS?s Scientific Manuscript database

A stem-loop structure, formed by a pair of inverted repeats during DNA replication, is a conserved feature at the origin of DNA replication (Ori) among plant and animal viruses, bacteriophages and plasmids that replicate their genomes via the rolling-circle replication (RCR) mechanism. Porcine circo...

Dual-Band Dual-Mode Button Antenna for On-Body and Off-Body Communications.

PubMed

Zhang, Xiu Yin; Wong, Hang; Mo, Te; Cao, Yun Fei

2017-08-01

A dual-band dual-mode button antenna for body centric communications is presented. At the lower band, a spiral inverted-F antenna is designed with omnidirectional radiation pattern for on-body communication. At the upper band, the high-order mode of the inverted-F antenna is utilized together with a metal reflector to realize broadside radiation for off-body communication. For demonstration, a prototype is implemented. The measured peak gains on the phantom at the lower and upper bands are -0.6 and 4.3 dBi, respectively. The antenna operating on the phantom has measured efficiencies of 46.3% at the lower band and 69.3% at the upper band. The issue of specific absorption rate (SAR) is studied. The maximum transmitted power under the SAR regulation of 1.6 W/kg is found to be 26.4 dB·m, which is high enough for body centric communications. In addition, the transmission performance between two proposed antennas mounted on the body is investigated by measuring the transmission loss. With an overall miniaturized size, the robust button antenna could be integrated in clothes and be a potential candidate for wireless body area network applications.

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. Molecular dating analyses suggest that Ranunculaceae and Berberidaceae diverged between 90 and 84 mya, which is congruent with the fossil records and with recent estimates of the divergence time of these two taxa. © 2013.

An open source, wireless capable miniature microscope system

NASA Astrophysics Data System (ADS)

Liberti, William A., III; Perkins, L. Nathan; Leman, Daniel P.; Gardner, Timothy J.

2017-08-01

Objective. Fluorescence imaging through head-mounted microscopes in freely behaving animals is becoming a standard method to study neural circuit function. Flexible, open-source designs are needed to spur evolution of the method. Approach. We describe a miniature microscope for single-photon fluorescence imaging in freely behaving animals. The device is made from 3D printed parts and off-the-shelf components. These microscopes weigh less than 1.8 g, can be configured to image a variety of fluorophores, and can be used wirelessly or in conjunction with active commutators. Microscope control software, based in Swift for macOS, provides low-latency image processing capabilities for closed-loop, or BMI, experiments. Main results. Miniature microscopes were deployed in the songbird premotor region HVC (used as a proper name), in singing zebra finches. Individual neurons yield temporally precise patterns of calcium activity that are consistent over repeated renditions of song. Several cells were tracked over timescales of weeks and months, providing an opportunity to study learning related changes in HVC. Significance. 3D printed miniature microscopes, composed completely of consumer grade components, are a cost-effective, modular option for head-mounting imaging. These easily constructed and customizable tools provide access to cell-type specific neural ensembles over timescales of weeks.

Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction.

PubMed

Wu, Chen; Twort, Victoria G; Crowhurst, Ross N; Newcomb, Richard D; Buckley, Thomas R

2017-11-16

Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri genome size yet are surprisingly absent from the T. cristinae genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick insects.

Inverted ILM flap, free ILM flap and conventional ILM peeling for large macular holes.

PubMed

Velez-Montoya, Raul; Ramirez-Estudillo, J Abel; Sjoholm-Gomez de Liano, Carl; Bejar-Cornejo, Francisco; Sanchez-Ramos, Jorge; Guerrero-Naranjo, Jose Luis; Morales-Canton, Virgilio; Hernandez-Da Mota, Sergio E

2018-01-01

To assess closure rate after a single surgery of large macular holes and their visual recovery in the short term with three different surgical techniques. Prospective multicenter randomized controlled trial. We included treatment-naïve patients with diagnosis of large macular hole (minimum diameter of > 400 µm). All patients underwent a comprehensive ophthalmological examination. Before surgery, the patients were randomized into three groups: group A: conventional internal limiting membrane peeling, group B: inverted-flap technique and group C: free-flap technique. All study measurements were repeated within the period of 1 and 3 months after surgery. Continuous variables were assessed with a Kruskal-Wallis test, change in visual acuity was assessed with analysis of variance for repeated measurements with a Bonferroni correction for statistical significance. Thirty-eight patients were enrolled (group A: 12, group B: 12, group C: 14). The closure rate was in group A and B: 91.6%; 95% CI 61.52-99.79%. In group C: 85.71%; 95% CI 57.19-98.22%. There were no differences in the macular hole closure rate between groups ( p  = 0.85). All groups improved ≈ 0.2 logMAR, but only group B reached statistical significance ( p  < 0.007). Despite all techniques displayed a trend toward visual improvement, the inverted-flap technique seems to induce a faster and more significant recovery in the short term.

Examining impulse-variability in overarm throwing.

PubMed

Urbin, M A; Stodden, David; Boros, Rhonda; Shannon, David

2012-01-01

The purpose of this study was to examine variability in overarm throwing velocity and spatial output error at various percentages of maximum to test the prediction of an inverted-U function as predicted by impulse-variability theory and a speed-accuracy trade-off as predicted by Fitts' Law Thirty subjects (16 skilled, 14 unskilled) were instructed to throw a tennis ball at seven percentages of their maximum velocity (40-100%) in random order (9 trials per condition) at a target 30 feet away. Throwing velocity was measured with a radar gun and interpreted as an index of overall systemic power output. Within-subject throwing velocity variability was examined using within-subjects repeated-measures ANOVAs (7 repeated conditions) with built-in polynomial contrasts. Spatial error was analyzed using mixed model regression. Results indicated a quadratic fit with variability in throwing velocity increasing from 40% up to 60%, where it peaked, and then decreasing at each subsequent interval to maximum (p < .001, η2 = .555). There was no linear relationship between speed and accuracy. Overall, these data support the notion of an inverted-U function in overarm throwing velocity variability as both skilled and unskilled subjects approach maximum effort. However, these data do not support the notion of a speed-accuracy trade-off. The consistent demonstration of an inverted-U function associated with systemic power output variability indicates an enhanced capability to regulate aspects of force production and relative timing between segments as individuals approach maximum effort, even in a complex ballistic skill.

Identification of Novel Inverted Terminal Repeat (ITR) Deletions of Human Adenovirus (AD) From Infected Host: Virulent Ads Containing Mixed Populations of Genomic Sequences

DTIC Science & Technology

2006-11-01

terminal repetition of adenvirus type 4 DNA. Gene 18:329-334. 20. Van der Veen , J., and J. H. Dijkman . 1962. Association of type 21 adenovirus with acute respiratory illness in military recruits. Am J Hyg 76:149-159.

Molecular characterization of the complete genome of falconid herpesvirus strain S-18

USDA-ARS?s Scientific Manuscript database

Falconid herpesvirus type 1 (FHV-1) is the causative agent of falcon inclusion body disease, an acute, highly contagious disease of raptors. The complete nucleotide sequence of the genome of FHV-1 has been determined. The genome is arranged as a D-type genome with large inverted repeats flanking a ...

Large diversity of the piggyBac-like elements in the genome of Tribolium castaneum

PubMed Central

Wang, Jianjun; Du, Yuzhou; Wang, Suzhi; Brown, Sue; Park, Yoonseong

2011-01-01

The piggyBac transposable element, originally discovered in the cabbage looper, Trichoplusia ni, has been widely used in insect transgenesis including the red flour beetle Tribolium castaneum. We surveyed piggyBac-like (PLE) sequences in the genome of Tribolium castaneum by homology searches using as queries the diverse PLE sequences that have been described previously. The search yielded a total of 32 piggyBac-like elements (TcPLEs) which were classified into 14 distinct groups. Most of the TcPLEs contain defective functional motifs in that they are lacking inverted terminal repeats or have disrupted open reading frames. Only one single copy of TcPLE1 appears to be intact with imperfect 16 bp inverted terminal repeats flanking an open reading frame encoding a transposase of 571 amino acid residues. Many copies of TcPLEs were found to be inserted into or close to other transposon-like sequences. This large diversity of TcPLEs with generally low copy numbers suggests multiple invasions of the TcPLEs over a long evolutionary time without extensive multiplications or occurrence of rapid loss of TcPLEs copies. PMID:18342253

A fast processing route of aspheric polydimethylsiloxane lenses array (APLA) and optical characterization for smartphone microscopy

NASA Astrophysics Data System (ADS)

Fuh, Yiin-Kuen; Lai, Zheng-Hong

2017-02-01

A fast processing route of aspheric polydimethylsiloxane (PDMS) lenses array (APLA) is proposed via the combined effect of inverted gravitational and heat-assisted forces. The fabrication time can be dramatically reduced to 30 s, compared favorably to the traditional duration of 2 hours of repeated cycles of addition-curing processes. In this paper, a low-cost flexible lens can be fabricated by repeatedly depositing, inverting, curing a hanging transparent PDMS elastomer droplet on a previously deposited curved structure. Complex structures with aspheric curve features and various focal lengths can be successfully produced and the fabricated 4 types of APLA have various focal lengths in the range of 7.03 mm, 6.00 mm, 5.33 mm, and 4.43 mm, respectively. Empirically, a direct relationship between the PDMS volume and focal lengths of the lenses can be experimentally deducted. Using these fabricated APLA, an ordinary commercial smartphone camera can be easily transformed to a low-cost, portable digital microscopy (50×magnification) such that point of care diagnostic can be implemented pervasively.

Fabrication and Characterization of Flexible and Miniaturized Humidity Sensors Using Screen-Printed TiO2 Nanoparticles as Sensitive Layer

PubMed Central

Dubourg, Georges; Segkos, Apostolos; Katona, Jaroslav; Radović, Marko; Savić, Slavica; Crnojević-Bengin, Vesna

2017-01-01

This paper describes the fabrication and the characterization of an original example of a miniaturized resistive-type humidity sensor, printed on flexible substrate in a large-scale manner. The fabrication process involves laser ablation for the design of interdigitated electrodes on PET (Poly-Ethylene Terephthalate) substrate and a screen-printing process for the deposition of the sensitive material, which is based on TiO2 nanoparticles. The laser ablation process was carefully optimized to obtain micro-scale and well-resolved electrodes on PET substrate. A functional paste based on cellulose was prepared in order to allow the precise screen-printing of the TiO2 nanoparticles as sensing material on the top of the electrodes. The current against voltage (I–V) characteristic of the sensor showed good linearity and potential for low-power operation. The results of a humidity-sensing investigation and mechanical testing showed that the fabricated miniaturized sensors have excellent mechanical stability, sensing characteristics, good repeatability, and relatively fast response/recovery times operating at room temperature. PMID:28800063

Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices

PubMed Central

Zanoli, Laura Maria; Spoto, Giuseppe

2012-01-01

Diagnostic tools for biomolecular detection need to fulfill specific requirements in terms of sensitivity, selectivity and high-throughput in order to widen their applicability and to minimize the cost of the assay. The nucleic acid amplification is a key step in DNA detection assays. It contributes to improving the assay sensitivity by enabling the detection of a limited number of target molecules. The use of microfluidic devices to miniaturize amplification protocols reduces the required sample volume and the analysis times and offers new possibilities for the process automation and integration in one single device. The vast majority of miniaturized systems for nucleic acid analysis exploit the polymerase chain reaction (PCR) amplification method, which requires repeated cycles of three or two temperature-dependent steps during the amplification of the nucleic acid target sequence. In contrast, low temperature isothermal amplification methods have no need for thermal cycling thus requiring simplified microfluidic device features. Here, the use of miniaturized analysis systems using isothermal amplification reactions for the nucleic acid amplification will be discussed. PMID:25587397

Development of a miniature solid propellant rocket motor for use in plume simulation studies

NASA Technical Reports Server (NTRS)

Baran, W. J.

1974-01-01

A miniature solid propellant rocket motor has been developed to be used in a program to determine those parameters which must be duplicated in a cold gas flow to produce aerodynamic effects on an experimental model similar to those produced by hot, particle-laden exhaust plumes. Phenomena encountered during the testing of the miniature solid propellant motors included erosive propellant burning caused by high flow velocities parallel to the propellant surface, regressive propellant burning as a result of exposed propellant edges, the deposition of aluminum oxide on the nozzle surfaces sufficient to cause aerodynamic nozzle throat geometry changes, and thermal erosion of the nozzle throat at high chamber pressures. A series of tests was conducted to establish the stability of the rocket chamber pressure and the repeatibility of test conditions. Data are presented which define the tests selected to represent the final test matrix. Qualitative observations are also presented concerning the phenomena experienced based on the results of a large number or rocket tests not directly applicable to the final test matrix.

Fabrication of Miniature Thermoelectric Generators Using Bulk Materials

NASA Astrophysics Data System (ADS)

Joo, Sung-Jae; Ryu, Byungki; Min, Bok-Ki; Lee, Ji-Eun; Kim, Bong-Seo; Park, Su-Dong; Lee, Hee-Woong

2016-07-01

Miniature thermoelectric modules (TEMs) are required for micro power generation as well as local cooling, and they should have small size and high performance. However, conventional bulk TEMs generally have in-plane dimensions of a few centimeters, and empty space between the legs for electrical isolation makes efficient miniaturization difficult. In this study, a miniature TEM with footprint of about 0.35 cm2 and leg height of 0.97 mm was fabricated by reducing the dimensions of the legs and attaching them together to form a closely packed assembly, without using microelectromechanical processes. First, Bi0.4Sb1.6Te3 (BST) and Bi2Te2.7Se0.3 (BTS) ingots were made by ball milling and spark plasma sintering, and the ingots were cut into thin plates. These BST and BTS plates were then attached alternately using polyimide tapes, and the attached plates were sliced vertically to produce thin sheets. This process was repeated once again to make chessboard-like assemblies having 20 p- n pairs in an area of 0.35 cm2, and electrical contacts were formed by Ni sputtering and Ag paste coating. Finally, thermally conductive silicone pads (~500 μm) were attached on both sides of the assembly using electrically insulating interface thermal tapes (˜180 μm). The maximum output power ( P max) from the miniature module was about 28 μW and 2.0 mW for temperature difference (Δ T) of 5.6°C and 50.5°C, respectively. Reducing the contact resistance was considered to be the key to increase the output power.

Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion.

PubMed

Ni, ZhouXian; Ye, YouJu; Bai, Tiandao; Xu, Meng; Xu, Li-An

2017-09-11

The chloroplast genome (CPG) of Pinus massoniana belonging to the genus Pinus (Pinaceae), which is a primary source of turpentine, was sequenced and analyzed in terms of gene rearrangements, ndh genes loss, and the contraction and expansion of short inverted repeats (IRs). P. massoniana CPG has a typical quadripartite structure that includes large single copy (LSC) (65,563 bp), small single copy (SSC) (53,230 bp) and two IRs (IRa and IRb, 485 bp). The 108 unique genes were identified, including 73 protein-coding genes, 31 tRNAs, and 4 rRNAs. Most of the 81 simple sequence repeats (SSRs) identified in CPG were mononucleotides motifs of A/T types and located in non-coding regions. Comparisons with related species revealed an inversion (21,556 bp) in the LSC region; P. massoniana CPG lacks all 11 intact ndh genes (four ndh genes lost completely; the five remained truncated as pseudogenes; and the other two ndh genes remain as pseudogenes because of short insertions or deletions). A pair of short IRs was found instead of large IRs, and size variations among pine species were observed, which resulted from short insertions or deletions and non-synchronized variations between "IRa" and "IRb". The results of phylogenetic analyses based on whole CPG sequences of 16 conifers indicated that the whole CPG sequences could be used as a powerful tool in phylogenetic analyses.

Topology mapping to characterize cyanobacterial bicarbonate transporters: BicA (SulP/SLC26 family) and SbtA.

PubMed

Price, G Dean; Howitt, Susan M

2014-09-01

This mini-review addresses advances in understanding the transmembrane topologies of two unrelated, single-subunit bicarbonate transporters from cyanobacteria, namely BicA and SbtA. BicA is a Na(+)-dependent bicarbonate transporter that belongs to the SulP/SLC26 family that is widespread in both eukaryotes and prokaryotes. Topology mapping of BicA via the phoA/lacZ fusion reporter method identified 12 transmembrane helices with an unresolved hydrophobic region just beyond helix 8. Re-interpreting this data in the light of a recent topology study on rat prestin leads to a consensus topology of 14 transmembrane domains with a 7+7 inverted repeat structure. SbtA is also a Na(+)-dependent bicarbonate transporter, but of considerably higher affinity (Km 2-5 μM versus >100 μM for BicA). Whilst SbtA is widespread in cyanobacteria and a few bacteria, it appears to be absent from eukaryotes. Topology mapping of SbtA via the phoA/lacZ fusion reporter method identified 10 transmembrane helices. The topology consists of a 5+5 inverted repeat, with the two repeats separated by a large intracellular loop. The unusual location of the N and C-termini outside the cell raises the possibility that SbtA forms a novel fold, not so far identified by structural and topological studies on transport proteins.

Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes.

PubMed

Sabir, Jamal; Schwarz, Erika; Ellison, Nicholas; Zhang, Jin; Baeshen, Nabih A; Mutwakil, Muhammed; Jansen, Robert; Ruhlman, Tracey

2014-08-01

Land plant plastid genomes (plastomes) provide a tractable model for evolutionary study in that they are relatively compact and gene dense. Among the groups that display an appropriate level of variation for structural features, the inverted-repeat-lacking clade (IRLC) of papilionoid legumes presents the potential to advance general understanding of the mechanisms of genomic evolution. Here, are presented six complete plastome sequences from economically important species of the IRLC, a lineage previously represented by only five completed plastomes. A number of characters are compared across the IRLC including gene retention and divergence, synteny, repeat structure and functional gene transfer to the nucleus. The loss of clpP intron 2 was identified in one newly sequenced member of IRLC, Glycyrrhiza glabra. Using deeply sequenced nuclear transcriptomes from two species helped clarify the nature of the functional transfer of accD to the nucleus in Trifolium, which likely occurred in the lineage leading to subgenus Trifolium. Legumes are second only to cereal crops in agricultural importance based on area harvested and total production. Genetic improvement via plastid transformation of IRLC crop species is an appealing proposition. Comparative analyses of intergenic spacer regions emphasize the need for complete genome sequences for developing transformation vectors for plastid genetic engineering of legume crops. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Interaction of the putative tyrosine recombinases RipX (UU145), XerC (UU222), and CodV (UU529) of Ureaplasma parvum serovar 3 with specific DNA

PubMed Central

Zimmerman, Carl-Ulrich R; Rosengarten, Renate; Spergser, Joachim

2013-01-01

Phase variation of two loci (‘mba locus’ and ‘UU172 phase-variable element’) in Ureaplasma parvum serovar 3 has been suggested as result of site-specific DNA inversion occurring at short inverted repeats. Three potential tyrosine recombinases (RipX, XerC, and CodV encoded by the genes UU145, UU222, and UU529) have been annotated in the genome of U. parvum serovar 3, which could be mediators in the proposed recombination event. We document that only orthologs of the gene xerC are present in all strains that show phase variation in the two loci. We demonstrate in vitro binding of recombinant maltose-binding protein fusions of XerC to the inverted repeats of the phase-variable loci, of RipX to a direct repeat that flanks a 20-kbp region, which has been proposed as putative pathogenicity island, and of CodV to a putative dif site. Co-transformation of the model organism Mycoplasma pneumoniae M129 with both the ‘mba locus’ and the recombinase gene xerC behind an active promoter region resulted in DNA inversion in the ‘mba locus’. Results suggest that XerC of U. parvum serovar 3 is a mediator in the proposed DNA inversion event of the two phase-variable loci. PMID:23305333

Inverter Load Rejection Over-Voltage Testing: SolarCity CRADA Task 1a Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, A.; Hoke, A.; Chakraborty, S.

Various interconnection challenges exist when connecting distributed PV into the electrical distribution grid in terms of safety, reliability, and stability of electric power systems. One of the urgent areas for additional research - as identified by inverter manufacturers, installers, and utilities - is the potential for transient over-voltage from PV inverters. In one stage of a cooperative tests were repeated a total of seven times. The maximum over-voltage measured in any test did not exceed 200% of nominal, and typical over-voltage levels were significantly lower. The total voltage duration and the maximum continuous time above each threshold are presented here,more » as well as the time to disconnect for each test. Finally, we present a brief investigation into the effect of DC input voltage as well as a series of no-load tests. This report describes testing conducted at NREL to determine the duration and magnitude of transient over-voltages created by several commercial PV inverters during load-rejection conditions. For this work, a test plan that is currently under development by the Forum on Inverter Grid Integration Issues (FIGII) has been implemented in a custom test setup at NREL. Through a cooperative research and development agreement, NREL is working with SolarCity to address two specific types of transient overvoltage: load rejection overvoltage (LRO) and ground fault overvoltage (GFO). Additional partners in this effort include the Hawaiian Electric Companies, Northern Plains Power Technologies, and the Electric Power Research Institute.« less

Direct and inverted reciprocal chromosome insertions between chromosomes 7 and 14 in a woman with recurrent miscarriages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ying-Tai Wang; Zhao-Cai Wang; Bajalica, S.

We present the first case of direct and inverted reciprocal chromosome insertions between human chromosomes 7 and 14, ascertained because of repeated spontaneous abortions. Prometaphase GTG banding analysis showed the karyotype to be 46, XX, inv ins (7;14)(7pter {yields} 7q11.23::14q32.2 {yields} 14q22::7q21.2 {yields} 7qter), dir ins(14;7)(14pter {yields} 14q22::7q11.23 {yields} 7q21.2::14q32.2 {yields} 14qter). Origins of the insertion have been confirmed by chromosome painting with libraries specific for chromosomes 7 and 14 using fluorescence in situ hybridization. 5 refs., 3 figs.

Linking actions and objects: Context-specific learning of novel weight priors.

PubMed

Trewartha, Kevin M; Flanagan, J Randall

2017-06-01

Distinct explicit and implicit memory processes support weight predictions used when lifting objects and making perceptual judgments about weight, respectively. The first time that an object is encountered weight is predicted on the basis of learned associations, or priors, linking size and material to weight. A fundamental question is whether the brain maintains a single, global representation of priors, or multiple representations that can be updated in a context specific way. A second key question is whether the updating of priors, or the ability to scale lifting forces when repeatedly lifting unusually weighted objects requires focused attention. To investigate these questions we compared the adaptability of weight predictions used when lifting objects and judging their weights in different groups of participants who experienced size-weight inverted objects passively (with the objects placed on the hands) or actively (where participants lift the objects) under full or divided attention. To assess weight judgments we measured the size-weight illusion after every 20 trials of experience with the inverted objects both passively and actively. The attenuation of the illusion that arises when lifting inverted object was found to be context-specific such that the attenuation was larger when the mode of interaction with the inverted objects matched the method of assessment of the illusion. Dividing attention during interaction with the inverted objects had no effect on attenuation of the illusion, but did slow the rate at which lifting forces were scaled to the weight inverted objects. These findings suggest that the brain stores multiple representations of priors that are context specific, and that focused attention is important for scaling lifting forces, but not for updating weight predictions used when judging object weight. Copyright © 2017 Elsevier B.V. All rights reserved.

Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice

PubMed Central

Ou-Yang, Fangqian; Luo, Qing-Jun; Zhang, Yue; Richardson, Casey R.; Jiang, Yingwen; Rock, Christopher D.

2013-01-01

microRNAs (miRNAs) are a class of small RNAs (sRNAs) of ~21 nucleotides (nt) in length processed from foldback hairpins by DICER-LIKE1 (DCL1) or DCL4. They regulate the expression of target mRNAs by base pairing through RNA-Induced Silencing Complex (RISC). In the RISC, ARGONAUTE1 (AGO1) is the key protein that cleaves miRNA targets at position ten of a miRNA:target duplex. The authenticity of many annotated rice miRNA hairpins is under debate because of their homology to repeat sequences. Some of them, like miR1884b, have been removed from the current release of miRBase based on incomplete information. In this study, we investigated the association of transposable element (TE)-derived miRNAs with typical miRNA pathways (DCL1/4- and AGO1-dependent) using publicly available deep sequencing datasets. Seven miRNA hairpins with 13 unique sRNAs were specifically enriched in AGO1 immunoprecipitation samples and relatively reduced in DCL1/4 knockdown genotypes. Interestingly, these species are ~21-nt long, instead of 24-nt as annotated in miRBase and the literature. Their expression profiles meet current criteria for functional annotation of miRNAs. In addition, diagnostic cleavage tags were found in degradome datasets for predicted target mRNAs. Most of these miRNA hairpins share significant homology with miniature inverted-repeat transposable elements (MITEs), one type of abundant DNA transposons in rice. Finally, the root-specific production of a 24 nt miRNA-like sRNA was confirmed by RNA blot for a novel EST that maps to the 3'-UTR of a candidate pseudogene showing extensive sequence homology to miR1884b hairpin. Our data are consistent with the hypothesis that TEs can serve as a driving force for the evolution of some MIRNAs, where co-opting of DICER-LIKE1/4 processing and integration into AGO1 could exapt transcribed TE-associated hairpins into typical miRNA pathways. PMID:23420033

In-Class Robot Flyby of an Endoplanet

NASA Astrophysics Data System (ADS)

Chadwick, A. J.; Capaldi, T.; Aurnou, J. M.

2013-12-01

For our Introduction to Computing class, we have developed a miniature robotic spacecraft mission that performs a flyby of an in-class 'endoplanet.' Our constructed endoplanet contains an internal dipole magnet, tilted with a dip angle that is unknown a priori. The spacecraft analog is a remotely controlled LEGO MINDSTORMS robot programmed using LabVIEW. Students acquire magnetic field data via a first spacecraft flyby past the endoplanet. This dataset is then imported into MATLAB, and is inverted to create a model of the magnet's orientation and dipole moment. Students use their models to predict the magnetic field profile along a different flyby path. They then test the accuracy of their models, comparing their predictions against the data acquired from this secondary flyby. We will be demonstrating this device at our poster in the Moscone Center.

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.

PubMed

Cer, Regina Z; Donohue, Duncan E; Mudunuri, Uma S; Temiz, Nuri A; Loss, Michael A; Starner, Nathan J; Halusa, Goran N; Volfovsky, Natalia; Yi, Ming; Luke, Brian T; Bacolla, Albino; Collins, Jack R; Stephens, Robert M

2013-01-01

The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance.

Clustering of mutations within the inverted repeat regions of a serially-passaged attenuated gallid herpesvirus type 2 strain.

USDA-ARS?s Scientific Manuscript database

Marek’s disease (MD) is the leading cause of losses in chicken production in the world. Over the past 40 years significant progress has been made in the control of MD through the use of vaccines which reduce or delay tumor formation in vaccinated flocks. However, these vaccines fail to induce an imm...

Characterization of the complete chloroplast genome of Platycarya strobilacea (Juglandaceae)

Treesearch

Jing Yan; Kai Han; Shuyun Zeng; Peng Zhao; Keith Woeste; Jianfang Li; Zhan-Lin Liu

2017-01-01

The whole chloroplast genome (cp genome) sequence of Platycarya strobilacea was characterized from Illumina pair-end sequencing data. The complete cp genome was 160,994 bp in length and contained a large single copy region (LSC) of 90,225 bp and a small single copy region (SSC) of 18,371 bp, which were separated by a pair of inverted repeat regions...

Human Xq28 Inversion Polymorphism: From Sex Linkage to Genomics--A Genetic Mother Lode

ERIC Educational Resources Information Center

Kirby, Cait S.; Kolber, Natalie; Salih Almohaidi, Asmaa M.; Bierwert, Lou Ann; Saunders, Lori; Williams, Steven; Merritt, Robert

2016-01-01

An inversion polymorphism of the filamin and emerin genes at the tip of the long arm of the human X-chromosome serves as the basis of an investigative laboratory in which students learn something new about their own genomes. Long, nearly identical inverted repeats flanking the filamin and emerin genes illustrate how repetitive elements can lead to…

Nucleotide sequence of soybean chloroplast DNA regions which contain the psb A and trn H genes and cover the ends of the large single copy region and one end of the inverted repeats.

PubMed

Spielmann, A; Stutz, E

1983-10-25

The soybean chloroplast psb A gene (photosystem II thylakoid membrane protein of Mr 32 000, lysine-free) and the trn H gene (tRNAHisGUG), which both map in the large single copy region adjacent to one of the inverted repeat structures (IR1), have been sequenced including flanking regions. The psb A gene shows in its structural part 92% sequence homology with the corresponding genes of spinach and N. debneyi and contains also an open reading frame for 353 aminoacids. The aminoacid sequence of a potential primary translation product (calculated Mr, 38 904, no lysine) diverges from that of spinach and N. debneyi in only two positions in the C-terminal part. The trn H gene has the same polarity as the psb A gene and the coding region is located at the very end of the large single copy region. The deduced sequence of the soybean chloroplast tRNAHisGUG is identical with that of Zea mays chloroplasts. Both ends of the large single copy region were sequenced including a small segment of the adjacent IR1 and IR2.

DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations

PubMed Central

Rusling, David A.; Laurens, Niels; Pernstich, Christian; Wuite, Gijs J. L.; Halford, Stephen E.

2012-01-01

Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180° bend, while that with repeated sites has a convoluted 360° turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology. PMID:22362745

S Elements: A Family of Tc1-like Transposons in the Genome of Drosophila Melanogaster

PubMed Central

Merriman, P. J.; Grimes, C. D.; Ambroziak, J.; Hackett, D. A.; Skinner, P.; Simmons, M. J.

1995-01-01

The S elements form a diverse family of long-inverted-repeat transposons within the genome of Drosophila melanogaster. These elements vary in size and sequence, the longest consisting of 1736 bp with 234-bp inverted terminal repeats. The longest open reading frame in an intact S element could encode a 345-amino acid polypeptide. This polypeptide is homologous to the transposases of the mariner-Tc1 superfamily of transposable elements. S elements are ubiquitous in D. melanogaster populations and also appear to be present in the genomes of two sibling species; however, they seem to be absent from 17 other Drosophila species that were examined. Within D. melanogaster strains, there are, on average, 37.4 cytologically detectable S elements per diploid genome. These elements are scattered throughout the chromosomes, but several sites in both the euchromatin and β heterochromatin are consistently occupied. The discovery of an S-element-insertion mutation and a reversion of this mutation indicates that S elements are at least occasionally mobile in the D. melanogaster genome. These elements seem to insert at an AT dinucleotide within a short palindrome and apparently duplicate that dinucleotide upon insertion. PMID:8601484

Genomic organization of the canine herpesvirus US region.

PubMed

Haanes, E J; Tomlinson, C C

1998-02-01

Canine herpesvirus (CHV) is an alpha-herpesvirus of limited pathogenicity in healthy adult dogs and infectivity of the virus appears to be largely limited to cells of canine origin. CHV's low virulence and species specificity make it an attractive candidate for a recombinant vaccine vector to protect dogs against a variety of pathogens. As part of the analysis of the CHV genome, the authors determined the complete nucleotide sequence of the CHV US region as well as portions of the flanking inverted repeats. Seven full open reading frames (ORFs) encoding proteins larger than 100 amino acids were identified within, or partially within the CHV US: cUS2, cUS3, cUS4, cUS6, cUS7, cUS8 and cUS9; which are homologs of the herpes simplex virus type-1 US2; protein kinase; gG, gD, gI, gE; and US9 genes, respectively. An eighth ORF was identified in the inverted repeat region, cIR6, a homolog of the equine herpesvirus type-1 IR6 gene. The authors identified and mapped most of the major transcripts for the predicted CHV US ORFs by Northern analysis.

Evolutionary dynamics of hAT DNA transposon families in Saccharomycetaceae.

PubMed

Sarilar, Véronique; Bleykasten-Grosshans, Claudine; Neuvéglise, Cécile

2014-12-21

Transposable elements (TEs) are widespread in eukaryotes but uncommon in yeasts of the Saccharomycotina subphylum, in terms of both host species and genome fraction. The class II elements are especially scarce, but the hAT element Rover is a noteworthy exception that deserves further investigation. Here, we conducted a genome-wide analysis of hAT elements in 40 ascomycota. A novel family, Roamer, was found in three species, whereas Rover was detected in 15 preduplicated species from Kluyveromyces, Eremothecium, and Lachancea genera, with up to 41 copies per genome. Rover acquisition seems to have occurred by horizontal transfer in a common ancestor of these genera. The detection of remote Rover copies in Naumovozyma dairenensis and in the sole Saccharomyces cerevisiae strain AWRI1631, without synteny, suggests that two additional independent horizontal transfers took place toward these genomes. Such patchy distribution of elements prevents any anticipation of TE presence in incoming sequenced genomes, even closely related ones. The presence of both putative autonomous and defective Rover copies, as well as their diversification into five families, indicate particular dynamics of Rover elements in the Lachancea genus. Especially, we discovered the first miniature inverted-repeat transposable elements (MITEs) to be described in yeasts, together with their parental autonomous copies. Evidence of MITE insertion polymorphism among Lachancea waltii strains suggests their recent activity. Moreover, 40% of Rover copies appeared to be involved in chromosome rearrangements, showing the large structural impact of TEs on yeast genome and opening the door to further investigations to understand their functional and evolutionary consequences. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Insertion sequence diversity in archaea.

PubMed

Filée, J; Siguier, P; Chandler, M

2007-03-01

Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.

The Nitrogen-Fixation Island Insertion Site Is Conserved in Diazotrophic Pseudomonas stutzeri and Pseudomonas sp. Isolated from Distal and Close Geographical Regions

PubMed Central

Venieraki, Anastasia; Dimou, Maria; Vezyri, Eleni; Vamvakas, Alexandros; Katinaki, Pagona-Artemis; Chatzipavlidis, Iordanis; Tampakaki, Anastasia; Katinakis, Panagiotis

2014-01-01

The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution. PMID:25251496

The nitrogen-fixation island insertion site is conserved in diazotrophic Pseudomonas stutzeri and Pseudomonas sp. isolated from distal and close geographical regions.

PubMed

Venieraki, Anastasia; Dimou, Maria; Vezyri, Eleni; Vamvakas, Alexandros; Katinaki, Pagona-Artemis; Chatzipavlidis, Iordanis; Tampakaki, Anastasia; Katinakis, Panagiotis

2014-01-01

The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution.

Chloroplast genome of Aconitum barbatum var. puberulum (Ranunculaceae) derived from CCS reads using the PacBio RS platform.

PubMed

Chen, Xiaochen; Li, Qiushi; Li, Ying; Qian, Jun; Han, Jianping

2015-01-01

The chloroplast genome (cp genome) of Aconitum barbatum var. puberulum was sequenced using the third-generation sequencing platform based on the single-molecule real-time (SMRT) sequencing approach. To our knowledge, this is the first reported complete cp genome of Aconitum, and we anticipate that it will have great value for phylogenetic studies of the Ranunculaceae family. In total, 23,498 CCS reads and 20,685,462 base pairs were generated, the mean read length was 880 bp, and the longest read was 2,261 bp. Genome coverage of 100% was achieved with a mean coverage of 132× and no gaps. The accuracy of the assembled genome is 99.973%; the assembly was validated using Sanger sequencing of six selected genes from the cp genome. The complete cp genome of A. barbatum var. puberulum is 156,749 bp in length, including a large single-copy region of 87,630 bp and a small single-copy region of 16,941 bp separated by two inverted repeats of 26,089 bp. The cp genome contains 130 genes, including 84 protein-coding genes, 34 tRNA genes and eight rRNA genes. Four forward, five inverted and eight tandem repeats were identified. According to the SSR analysis, the longest poly structure is a 20-T repeat. Our results presented in this paper will facilitate the phylogenetic studies and molecular authentication on Aconitum.

RNA editing of non-coding RNA and its role in gene regulation.

PubMed

Daniel, Chammiran; Lagergren, Jens; Öhman, Marie

2015-10-01

It has for a long time been known that repetitive elements, particularly Alu sequences in human, are edited by the adenosine deaminases acting on RNA, ADAR, family. The functional interpretation of these events has been even more difficult than that of editing events in coding sequences, but today there is an emerging understanding of their downstream effects. A surprisingly large fraction of the human transcriptome contains inverted Alu repeats, often forming long double stranded structures in RNA transcripts, typically occurring in introns and UTRs of protein coding genes. Alu repeats are also common in other primates, and similar inverted repeats can frequently be found in non-primates, although the latter are less prone to duplex formation. In human, as many as 700,000 Alu elements have been identified as substrates for RNA editing, of which many are edited at several sites. In fact, recent advancements in transcriptome sequencing techniques and bioinformatics have revealed that the human editome comprises at least a hundred million adenosine to inosine (A-to-I) editing sites in Alu sequences. Although substantial additional efforts are required in order to map the editome, already present knowledge provides an excellent starting point for studying cis-regulation of editing. In this review, we will focus on editing of long stem loop structures in the human transcriptome and how it can effect gene expression. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Chloroplast genome of Aconitum barbatum var. puberulum (Ranunculaceae) derived from CCS reads using the PacBio RS platform

PubMed Central

Chen, Xiaochen; Li, Qiushi; Li, Ying; Qian, Jun; Han, Jianping

2015-01-01

The chloroplast genome (cp genome) of Aconitum barbatum var. puberulum was sequenced using the third-generation sequencing platform based on the single-molecule real-time (SMRT) sequencing approach. To our knowledge, this is the first reported complete cp genome of Aconitum, and we anticipate that it will have great value for phylogenetic studies of the Ranunculaceae family. In total, 23,498 CCS reads and 20,685,462 base pairs were generated, the mean read length was 880 bp, and the longest read was 2,261 bp. Genome coverage of 100% was achieved with a mean coverage of 132× and no gaps. The accuracy of the assembled genome is 99.973%; the assembly was validated using Sanger sequencing of six selected genes from the cp genome. The complete cp genome of A. barbatum var. puberulum is 156,749 bp in length, including a large single-copy region of 87,630 bp and a small single-copy region of 16,941 bp separated by two inverted repeats of 26,089 bp. The cp genome contains 130 genes, including 84 protein-coding genes, 34 tRNA genes and eight rRNA genes. Four forward, five inverted and eight tandem repeats were identified. According to the SSR analysis, the longest poly structure is a 20-T repeat. Our results presented in this paper will facilitate the phylogenetic studies and molecular authentication on Aconitum. PMID:25705213

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.

Modeling the Volcanic Source at Long Valley, CA, Using a Genetic Algorithm Technique

NASA Technical Reports Server (NTRS)

Tiampo, Kristy F.

1999-01-01

In this project, we attempted to model the deformation pattern due to the magmatic source at Long Valley caldera using a real-value coded genetic algorithm (GA) inversion similar to that found in Michalewicz, 1992. The project has been both successful and rewarding. The genetic algorithm, coded in the C programming language, performs stable inversions over repeated trials, with varying initial and boundary conditions. The original model used a GA in which the geophysical information was coded into the fitness function through the computation of surface displacements for a Mogi point source in an elastic half-space. The program was designed to invert for a spherical magmatic source - its depth, horizontal location and volume - using the known surface deformations. It also included the capability of inverting for multiple sources.

On the functional design of the DTU10 MW wind turbine scale model of LIFES50+ project

NASA Astrophysics Data System (ADS)

Bayati, I.; Belloli, M.; Bernini, L.; Fiore, E.; Giberti, H.; Zasso, A.

2016-09-01

This paper illustrates the mechatronic design of the wind tunnel scale model of the DTU 10MW reference wind turbine, for the LIFES50+ H2020 European project. This model was designed with the final goal of controlling the angle of attack of each blade by means of miniaturized servomotors, for implementing advanced individual pitch control (IPC) laws on a Floating Offshore Wind Turbine (FOWT) 1/75 scale model. Many design constraints were to be respected: among others, the rotor-nacelle overall mass due to aero-elastic scaling, the limited space of the nacelle, where to put three miniaturized servomotors and the main shaft one, with their own inverters/controllers, the slip rings for electrical rotary contacts, the highest stiffness as possible for the nacelle support and the blade-rotor connections, for ensuring the proper kinematic constraint, considering the first flapwise blade natural frequency, the performance of the servomotors to guarantee the wide frequency band due to frequency scale factors, etc. The design and technical solutions are herein presented and discussed, along with an overview of the building and verification process. Also a discussion about the goals achieved and constraints respected for the rigid wind turbine scale model (LIFES50+ deliverable D.3.1) and the further possible improvements for the IPC-aero-elastic scale model, which is being finalized at the time of this paper.

Inverted electro-mechanical behaviour induced by the irreversible domain configuration transformation in (K,Na)NbO3-based ceramics

PubMed Central

Huan, Yu; Wang, Xiaohui; Koruza, Jurij; Wang, Ke; Webber, Kyle G.; Hao, Yanan; Li, Longtu

2016-01-01

Miniaturization of domains to the nanometer scale has been previously reported in many piezoelectrics with two-phase coexistence. Despite the observation of nanoscale domain configuration near the polymorphic phase transition (PPT) regionin virgin (K0.5Na0.5)NbO3 (KNN) based ceramics, it remains unclear how this domain state responds to external loads and influences the macroscopic electro-mechanical properties. To this end, the electric-field-induced and stress-induced strain curves of KNN-based ceramics over a wide compositional range across PPT were characterized. It was found that the coercive field of the virgin samples was highest in PPT region, which was related to the inhibited domain wall motion due to the presence of nanodomains. However, the coercive field was found to be the lowest in the PPT region after electrical poling. This was related to the irreversible transformation of the nanodomains into micron-sized domains during the poling process. With the similar micron-sized domain configuration for all poled ceramics, the domains in the PPT region move more easily due to the additional polarization vectors. The results demonstrate that the poling process can give rise to the irreversible domain configuration transformation and then account for the inverted macroscopic piezoelectricity in the PPT region of KNN-based ceramics. PMID:26915972

The effects of spatially displaced visual feedback on remote manipulator performance

NASA Technical Reports Server (NTRS)

Smith, Randy L.; Stuart, Mark A.

1989-01-01

The effects of spatially displaced visual feedback on the operation of a camera viewed remote manipulation task are analyzed. A remote manipulation task is performed by operators exposed to the following different viewing conditions: direct view of the work site; normal camera view; reversed camera view; inverted/reversed camera view; and inverted camera view. The task completion performance times are statistically analyzed with a repeated measures analysis of variance, and a Newman-Keuls pairwise comparison test is administered to the data. The reversed camera view is ranked third out of four camera viewing conditions, while the normal viewing condition is found significantly slower than the direct viewing condition. It is shown that generalization to remote manipulation applications based upon the results of direct manipulation studies are quite useful, but they should be made cautiously.

[Correlation of codon biases and potential secondary structures with mRNA translation efficiency in unicellular organisms].

PubMed

Vladimirov, N V; Likhoshvaĭ, V A; Matushkin, Iu G

2007-01-01

Gene expression is known to correlate with degree of codon bias in many unicellular organisms. However, such correlation is absent in some organisms. Recently we demonstrated that inverted complementary repeats within coding DNA sequence must be considered for proper estimation of translation efficiency, since they may form secondary structures that obstruct ribosome movement. We have developed a program for estimation of potential coding DNA sequence expression in defined unicellular organism using its genome sequence. The program computes elongation efficiency index. Computation is based on estimation of coding DNA sequence elongation efficiency, taking into account three key factors: codon bias, average number of inverted complementary repeats, and free energy of potential stem-loop structures formed by the repeats. The influence of these factors on translation is numerically estimated. An optimal proportion of these factors is computed for each organism individually. Quantitative translational characteristics of 384 unicellular organisms (351 bacteria, 28 archaea, 5 eukaryota) have been computed using their annotated genomes from NCBI GenBank. Five potential evolutionary strategies of translational optimization have been determined among studied organisms. A considerable difference of preferred translational strategies between Bacteria and Archaea has been revealed. Significant correlations between elongation efficiency index and gene expression levels have been shown for two organisms (S. cerevisiae and H. pylori) using available microarray data. The proposed method allows to estimate numerically the coding DNA sequence translation efficiency and to optimize nucleotide composition of heterologous genes in unicellular organisms. http://www.mgs.bionet.nsc.ru/mgs/programs/eei-calculator/.

Alu elements shape the primate transcriptome by cis-regulation of RNA editing

PubMed Central

2014-01-01

Background RNA editing by adenosine to inosine deamination is a widespread phenomenon, particularly frequent in the human transcriptome, largely due to the presence of inverted Alu repeats and their ability to form double-stranded structures – a requisite for ADAR editing. While several hundred thousand editing sites have been identified within these primate-specific repeats, the function of Alu-editing has yet to be elucidated. Results We show that inverted Alu repeats, expressed in the primate brain, can induce site-selective editing in cis on sites located several hundred nucleotides from the Alu elements. Furthermore, a computational analysis, based on available RNA-seq data, finds that site-selective editing occurs significantly closer to edited Alu elements than expected. These targets are poorly edited upon deletion of the editing inducers, as well as in homologous transcripts from organisms lacking Alus. Sequences surrounding sites near edited Alus in UTRs, have been subjected to a lesser extent of evolutionary selection than those far from edited Alus, indicating that their editing generally depends on cis-acting Alus. Interestingly, we find an enrichment of primate-specific editing within encoded sequence or the UTRs of zinc finger-containing transcription factors. Conclusions We propose a model whereby primate-specific editing is induced by adjacent Alu elements that function as recruitment elements for the ADAR editing enzymes. The enrichment of site-selective editing with potentially functional consequences on the expression of transcription factors indicates that editing contributes more profoundly to the transcriptomic regulation and repertoire in primates than previously thought. PMID:24485196

The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis.

PubMed

Yao, Xiaohong; Tang, Ping; Li, Zuozhou; Li, Dawei; Liu, Yifei; Huang, Hongwen

2015-01-01

Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.

Molecular cloning and sequence analysis of the gene coding for the 57kDa soluble antigen of the salmonid fish pathogen Renibacterium salmoninarum

USGS Publications Warehouse

Chien, Maw-Sheng; Gilbert , Teresa L.; Huang, Chienjin; Landolt, Marsha L.; O'Hara, Patrick J.; Winton, James R.

1992-01-01

The complete sequence coding for the 57-kDa major soluble antigen of the salmonid fish pathogen, Renibacterium salmoninarum, was determined. The gene contained an opening reading frame of 1671 nucleotides coding for a protein of 557 amino acids with a calculated Mr value of 57190. The first 26 amino acids constituted a signal peptide. The deduced sequence for amino acid residues 27–61 was in agreement with the 35 N-terminal amino acid residues determined by microsequencing, suggesting the protein in synthesized as a 557-amino acid precursor and processed to produce a mature protein of Mr 54505. Two regions of the protein contained imperfect direct repeats. The first region contained two copies of an 81-residue repeat, the second contained five copies of an unrelated 25-residue repeat. Also, a perfect inverted repeat (including three in-frame UAA stop codons) was observed at the carboxyl-terminus of the gene.

Direct repeat sequences are essential for function of the cis-acting locus of transfer (clt) of Streptomyces phaeochromogenes plasmid pJV1.

PubMed

Franco, Bernardo; González-Cerón, Gabriela; Servín-González, Luis

2003-11-01

The functionality of direct and inverted repeat sequences inside the cis acting locus of transfer (clt) of the Streptomyces plasmid pJV1 was determined by testing the effect of different deletions on plasmid transfer. The results show that the single most important element for pJV1 clt function is a series of evenly spaced 9 bp long direct repeats which match the consensus CCGCACA(C/G)(C/G), since their deletion caused a dramatic reduction in plasmid transfer. The presence of these repeats in the absence of any other clt sequences allowed plasmid transfer to occur at a frequency that was at least two orders of magnitude higher than that obtained in the complete absence of clt. A database search revealed regions with a similar organization, and in the same position, in Streptomyces plasmids pSN22 and pSLS, which have transfer proteins homologous to those of pJV1.

Electrophoresis and spectrometric analyses of adaptation-related proteins in thermally stressed Chromobacterium violaceum.

PubMed

Cordeiro, I B; Castro, D P; Nogueira, P P O; Angelo, P C S; Nogueira, P A; Gonçalves, J F C; Pereira, A M R F; Garcia, J S; Souza, G H M F; Arruda, M A Z; Eberlin, M N; Astolfi-Filho, S; Andrade, E V; López-Lozano, J L

2013-10-29

Chromobacterium violaceum is a Gram-negative proteobacteria found in water and soil; it is widely distributed in tropical and subtropical regions, such as the Amazon rainforest. We examined protein expression changes that occur in C. violaceum at different growth temperatures using electrophoresis and mass spectrometry. The total number of spots detected was 1985; the number ranged from 99 to 380 in each assay. The proteins that were identified spectrometrically were categorized as chaperones, proteins expressed exclusively under heat stress, enzymes involved in the respiratory and fermentation cycles, ribosomal proteins, and proteins related to transport and secretion. Controlling inverted repeat of chaperone expression and inverted repeat DNA binding sequences, as well as regions recognized by sigma factor 32, elements involved in the genetic regulation of the bacterial stress response, were identified in the promoter regions of several of the genes coding proteins, involved in the C. violaceum stress response. We found that 30 °C is the optimal growth temperature for C. violaceum, whereas 25, 35, and 40 °C are stressful temperatures that trigger the expression of chaperones, superoxide dismutase, a probable small heat shock protein, a probable phasing, ferrichrome-iron receptor protein, elongation factor P, and an ornithine carbamoyltransferase catabolite. This information improves our comprehension of the mechanisms involved in stress adaptation by C. violaceum.

Nucleotide sequence of soybean chloroplast DNA regions which contain the psb A and trn H genes and cover the ends of the large single copy region and one end of the inverted repeats.

PubMed Central

Spielmann, A; Stutz, E

1983-01-01

The soybean chloroplast psb A gene (photosystem II thylakoid membrane protein of Mr 32 000, lysine-free) and the trn H gene (tRNAHisGUG), which both map in the large single copy region adjacent to one of the inverted repeat structures (IR1), have been sequenced including flanking regions. The psb A gene shows in its structural part 92% sequence homology with the corresponding genes of spinach and N. debneyi and contains also an open reading frame for 353 aminoacids. The aminoacid sequence of a potential primary translation product (calculated Mr, 38 904, no lysine) diverges from that of spinach and N. debneyi in only two positions in the C-terminal part. The trn H gene has the same polarity as the psb A gene and the coding region is located at the very end of the large single copy region. The deduced sequence of the soybean chloroplast tRNAHisGUG is identical with that of Zea mays chloroplasts. Both ends of the large single copy region were sequenced including a small segment of the adjacent IR1 and IR2. PMID:6314279

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

Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae.

PubMed

Turmel, Monique; Otis, Christian; Lemieux, Claude

2017-04-20

The chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential elimination of genes from the IR copies might lead to IR loss. To gain deeper insights into the evolutionary history of the chloroplast genome in the Ulvophyceae, we analyzed the genomes of Ignatius tetrasporus and Pseudocharacium americanum (Ignatiales, an order not previously sampled), Dangemannia microcystis (Oltmannsiellopsidales), Pseudoneochloris marina (Ulvales) and also Chamaetrichon capsulatum and Trichosarcina mucosa (Ulotrichales). Our comparison of these six chloroplast genomes with those previously reported for nine ulvophyceans revealed unsuspected variability. All newly examined genomes feature an IR, but remarkably, the copies of the IR present in the Ignatiales, Pseudoneochloris, and Chamaetrichon diverge in sequence, with the tRNA genes from the rRNA operon missing in one IR copy. The implications of this unprecedented finding for the mechanism of IR loss and flip-flop recombination are discussed.

The Diversity of Prokaryotic DDE Transposases of the Mutator Superfamily, Insertion Specificity, and Association with Conjugation Machineries

PubMed Central

Guérillot, Romain; Siguier, Patricia; Gourbeyre, Edith; Chandler, Michael; Glaser, Philippe

2014-01-01

Transposable elements (TEs) are major components of both prokaryotic and eukaryotic genomes and play a significant role in their evolution. In this study, we have identified new prokaryotic DDE transposase families related to the eukaryotic Mutator-like transposases. These genes were retrieved by cascade PSI-Blast using as initial query the transposase of the streptococcal integrative and conjugative element (ICE) TnGBS2. By combining secondary structure predictions and protein sequence alignments, we predicted the DDE catalytic triad and the DNA-binding domain recognizing the terminal inverted repeats. Furthermore, we systematically characterized the organization and the insertion specificity of the TEs relying on these prokaryotic Mutator-like transposases (p-MULT) for their mobility. Strikingly, two distant TE families target their integration upstream σA dependent promoters. This allowed us to identify a transposase sequence signature associated with this unique insertion specificity and to show that the dissymmetry between the two inverted repeats is responsible for the orientation of the insertion. Surprisingly, while DDE transposases are generally associated with small and simple transposons such as insertion sequences (ISs), p-MULT encoding TEs show an unprecedented diversity with several families of IS, transposons, and ICEs ranging in size from 1.1 to 52 kb. PMID:24418649

The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae)

PubMed Central

Gu, Cuihua; Tembrock, Luke R.; Johnson, Nels G.; Simmons, Mark P.; Wu, Zhiqiang

2016-01-01

Lagerstroemia (crape myrtle) is an important plant genus used in ornamental horticulture in temperate regions worldwide. As such, numerous hybrids have been developed. However, DNA sequence resources and genome information for Lagerstroemia are limited, hindering evolutionary inferences regarding interspecific relationships. We report the complete plastid genome of Lagerstroemia fauriei. To our knowledge, this is the first reported whole plastid genome within Lythraceae. This genome is 152,440 bp in length with 38% GC content and consists of two single-copy regions separated by a pair of 25,793 bp inverted repeats. The large single copy and the small single copy regions span 83,921 bp and 16,933 bp, respectively. The genome contains 129 genes, including 17 located in each inverted repeat. Phylogenetic analysis of genera sampled from Geraniaceae, Myrtaceae, and Onagraceae corroborated the sister relationship between Lythraceae and Onagraceae. The plastid genomes of L. fauriei and several other Lythraceae species lack the rpl2 intron, which indicating an early loss of this intron within the Lythraceae lineage. The plastid genome of L. fauriei provides a much needed genetic resource for further phylogenetic research in Lagerstroemia and Lythraceae. Highly variable markers were identified for application in phylogenetic, barcoding and conservation genetic applications. PMID:26950701

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut.

PubMed

Power, Imana L; Dang, Phat M; Sobolev, Victor S; Orner, Valerie A; Powell, Joseph L; Lamb, Marshall C; Arias, Renee S

2017-04-01

Aflatoxin contamination is a major constraint in food production worldwide. In peanut (Arachis hypogaea L.), these toxic and carcinogenic aflatoxins are mainly produced by Aspergillus flavus Link and A. parasiticus Speare. The use of RNA interference (RNAi) is a promising method to reduce or prevent the accumulation of aflatoxin in peanut seed. In this study, we performed high-throughput sequencing of small RNA populations in a control line and in two transformed peanut lines that expressed an inverted repeat targeting five genes involved in the aflatoxin-biosynthesis pathway and that showed up to 100% less aflatoxin B 1 than the controls. The objective was to determine the putative involvement of the small RNA populations in aflatoxin reduction. In total, 41 known microRNA (miRNA) families and many novel miRNAs were identified. Among those, 89 known and 10 novel miRNAs were differentially expressed in the transformed lines. We furthermore found two small interfering RNAs derived from the inverted repeat, and 39 sRNAs that mapped without mismatches to the genome of A. flavus and were present only in the transformed lines. This information will increase our understanding of the effectiveness of RNAi and enable the possible improvement of the RNAi technology for the control of aflatoxins. Copyright © 2017 Elsevier B.V. All rights reserved.

Human Xq28 inversion polymorphism: From sex linkage to Genomics--A genetic mother lode.

PubMed

Kirby, Cait S; Kolber, Natalie; Salih Almohaidi, Asmaa M; Bierwert, Lou Ann; Saunders, Lori; Williams, Steven; Merritt, Robert

2016-01-01

An inversion polymorphism of the filamin and emerin genes at the tip of the long arm of the human X-chromosome serves as the basis of an investigative laboratory in which students learn something new about their own genomes. Long, nearly identical inverted repeats flanking the filamin and emerin genes illustrate how repetitive elements can lead to alterations in genome structure (inversions) through nonallelic homologous recombination. The near identity of the inverted repeats is an example of concerted evolution through gene conversion. While the laboratory in its entirety is designed for college level genetics courses, portions of the laboratory are appropriate for courses at other levels. Because the polymorphism is on the X-chromosome, the laboratory can be used in introductory biology courses to enhance understanding of sex-linkage and to test for Hardy-Weinberg equilibrium in females. More advanced topics, such as chromosome interference, the molecular model for recombination, and inversion heterozygosity suppression of recombination can be explored in upper-level genetics and evolution courses. DNA isolation, restriction digests, ligation, long PCR, and iPCR provide experience with techniques in molecular biology. This investigative laboratory weaves together topics stretching from molecular genetics to cytogenetics and sex-linkage, population genetics and evolutionary genetics. © 2016 The International Union of Biochemistry and Molecular Biology.

Fast determination of sugars in Coke and Diet Coke by miniaturized capillary electrophoresis with amperometric detection.

PubMed

Chu, Qingcui; Fu, Liang; Guan, Yueqing; Ye, Jiannong

2005-02-01

The fast separation capability of a novel miniaturized capillary electrophoresis with amperometric detection (CE-AD) system was demonstrated by determining sugar contents in Coke and diet Coke with an estimated separation efficiency of 60,000 TP/m. Factors influencing the separation and detection processes were examined and optimized. The end-capillary 300 microm Cu wire amperometric detector offers favorable signal-to-noise characteristics at a relatively low potential (+0.50 V vs. Ag/AgCl) for detecting sugars. Three sugars (sucrose, glucose, and fructose) have been separated within 330 s in a 8.5 cm length capillary at a separation voltage of 1000 V using a 50 mM NaOH running buffer (pH 12.7). Highly linear response is obtained for the above compounds over the range of 5.0 to 2.0 x 10(2) microg/mL with low detection limit, down to 0.8 microg/mL for glucose (S/N = 3). The injection-to-injection repeatability for analytes in peak current (RSD < 3.6%) and for migration times (RSD < 1.4%) was excellent. The new miniaturized CE-AD system should find a wide range of analytical applications involving assays of carbohydrates as an alternative to conventional CE and micro-CE.

Three dimensional two-photon brain imaging in freely moving mice using a miniature fiber coupled microscope with active axial-scanning.

PubMed

Ozbay, Baris N; Futia, Gregory L; Ma, Ming; Bright, Victor M; Gopinath, Juliet T; Hughes, Ethan G; Restrepo, Diego; Gibson, Emily A

2018-05-25

We present a miniature head mounted two-photon fiber-coupled microscope (2P-FCM) for neuronal imaging with active axial focusing enabled using a miniature electrowetting lens. We show three-dimensional two-photon imaging of neuronal structure and record neuronal activity from GCaMP6s fluorescence from multiple focal planes in a freely-moving mouse. Two-color simultaneous imaging of GFP and tdTomato fluorescence is also demonstrated. Additionally, dynamic control of the axial scanning of the electrowetting lens allows tilting of the focal plane enabling neurons in multiple depths to be imaged in a single plane. Two-photon imaging allows increased penetration depth in tissue yielding a working distance of 450 μm with an additional 180 μm of active axial focusing. The objective NA is 0.45 with a lateral resolution of 1.8 μm, an axial resolution of 10 μm, and a field-of-view of 240 μm diameter. The 2P-FCM has a weight of only ~2.5 g and is capable of repeatable and stable head-attachment. The 2P-FCM with dynamic axial scanning provides a new capability to record from functionally distinct neuronal layers, opening new opportunities in neuroscience research.

The Melting Point of Palladium Using Miniature Fixed Points of Different Ceramic Materials: Part II—Analysis of Melting Curves and Long-Term Investigation

NASA Astrophysics Data System (ADS)

Edler, F.; Huang, K.

2016-12-01

Fifteen miniature fixed-point cells made of three different ceramic crucible materials (Al2O3, ZrO2, and Al2O3(86 %)+ZrO2(14 %)) were filled with pure palladium and used to calibrate type B thermocouples (Pt30 %Rh/Pt6 %Rh). A critical point by using miniature fixed points with small amounts of fixed-point material is the analysis of the melting curves, which are characterized by significant slopes during the melting process compared to flat melting plateaus obtainable using conventional fixed-point cells. The method of the extrapolated starting point temperature using straight line approximation of the melting plateau was applied to analyze the melting curves. This method allowed an unambiguous determination of an electromotive force (emf) assignable as melting temperature. The strict consideration of two constraints resulted in a unique, repeatable and objective method to determine the emf at the melting temperature within an uncertainty of about 0.1 μ V. The lifetime and long-term stability of the miniature fixed points was investigated by performing more than 100 melt/freeze cycles for each crucible of the different ceramic materials. No failure of the crucibles occurred indicating an excellent mechanical stability of the investigated miniature cells. The consequent limitation of heating rates to values below {± }3.5 K min^{-1} above 1100° C and the carefully and completely filled crucibles (the liquid palladium occupies the whole volume of the crucible) are the reasons for successfully preventing the crucibles from breaking. The thermal stability of the melting temperature of palladium was excellent when using the crucibles made of Al2O3(86 %)+ZrO2(14 %) and ZrO2. Emf drifts over the total duration of the long-term investigation were below a temperature equivalent of about 0.1 K-0.2 K.

Starbugs: focal plane fiber positioning technology

NASA Astrophysics Data System (ADS)

Goodwin, Michael; Heijmans, Jeroen; Saunders, Ian; Brzeski, Jurek; Saunders, Will; Muller, Rolf; Haynes, Roger; Gilbert, James

2010-07-01

We report on the technological achievements of our latest Starbug prototypes and their implications for smart focal plane fiber positioning applications for wide-field astronomy. The Starbugs are innovative self-motile miniature robotic devices that can simultaneously and independently position fibers or payloads over a field plate located at the telescope's focal plane. The Starbugs concept overcomes many of the limitations associated with the traditional 'pick and place' positioners where a robot places fixed buttons onto the field plate. The new Starbug prototypes use piezoelectric actuators and have the following features: (i) new 'lift-and-step' method (discrete step) for accurate positioning over different surfaces; and (ii) operate in an inverted hanging position underneath a transparent field plate, removing the need for fibercable retractors. In this paper, we present aspects of the Starbug prototypes, including the theoretical model, mechanical design, experimental setup, algorithms, performance and applications for astronomical instrumentation.

The heterogeneous integration of single-walled carbon nanotubes onto complementary metal oxide semiconductor circuitry for sensing applications.

PubMed

Chen, Chia-Ling; Agarwal, Vinay; Sonkusale, Sameer; Dokmeci, Mehmet R

2009-06-03

A simple methodology for integrating single-walled carbon nanotubes (SWNTs) onto complementary metal oxide semiconductor (CMOS) circuitry is presented. The SWNTs were incorporated onto the CMOS chip as the feedback resistor of a two-stage Miller compensated operational amplifier utilizing dielectrophoretic assembly. The measured electrical properties from the integrated SWNTs yield ohmic behavior with a two-terminal resistance of approximately 37.5 kOmega and the measured small signal ac gain (-2) from the inverting amplifier confirmed successful integration of carbon nanotubes onto the CMOS circuitry. Furthermore, the temperature response of the SWNTs integrated onto CMOS circuitry has been measured and had a thermal coefficient of resistance (TCR) of -0.4% degrees C(-1). This methodology, demonstrated for the integration of SWNTs onto CMOS technology, is versatile, high yield and paves the way for the realization of novel miniature carbon-nanotube-based sensor systems.

Novel instrumentation for multifield time-lapse cinemicrography.

PubMed

Kallman, R F; Blevins, N; Coyne, M A; Prionas, S D

1990-04-01

The most significant feature of the system that is described is its ability to image essentially simultaneously the growth of up to 99 single cells into macroscopic colonies, each in its own microscope field. Operationally, fields are first defined and programmed by a trained observer. All subsequent steps are automatic and under computer control. Salient features of the hardware are stepper motor-controlled movement of the stage and fine adjustment of an inverted microscope, a high-quality 16-mm cine camera with light meter and controls, and a miniature incubator in which cells may be grown under defined conditions directly on the microscope stage. This system, termed MUTLAS, necessitates reordering of the primary images by rephotographing them on fresh film. Software developed for the analysis of cell and colony growth requires frame-by-frame examination of the secondary film and the use of a mouse-driven cursor to trace microscopically visible (4X objective magnification) events.

Variable presence of the inverted repeat and plastome stability in Erodium

PubMed Central

Blazier, John C.; Jansen, Robert K.; Mower, Jeffrey P.; Govindu, Madhu; Zhang, Jin; Weng, Mao-Lun; Ruhlman, Tracey A.

2016-01-01

Background and Aims Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes. We compared the degree of genomic rearrangement in plastomes of Erodium that differ in the presence and absence of the IR. Methods We sequenced 17 new Erodium plastomes. Using 454, Illumina, PacBio and Sanger sequences, 16 genomes were assembled and categorized along with one incomplete and two previously published Erodium plastomes. We conducted phylogenetic analyses among these species using a dataset of 19 protein-coding genes and determined if significantly higher evolutionary rates had caused the long branch seen previously in phylogenetic reconstructions within the genus. Bioinformatic comparisons were also performed to evaluate plastome evolution across the genus. Key Results Erodium plastomes fell into four types (Type 1–4) that differ in their substitution rates, short dispersed repeat content and degree of genomic rearrangement, gene and intron content and GC content. Type 4 plastomes had significantly higher rates of synonymous substitutions (dS) for all genes and for 14 of the 19 genes non-synonymous substitutions (dN) were significantly accelerated. We evaluated the evidence for a single IR loss in Erodium and in doing so discovered that Type 4 plastomes contain a novel IR. Conclusions The presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts. PMID:27192713

Variable presence of the inverted repeat and plastome stability in Erodium.

PubMed

Blazier, John C; Jansen, Robert K; Mower, Jeffrey P; Govindu, Madhu; Zhang, Jin; Weng, Mao-Lun; Ruhlman, Tracey A

2016-06-01

Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes. We compared the degree of genomic rearrangement in plastomes of Erodium that differ in the presence and absence of the IR. We sequenced 17 new Erodium plastomes. Using 454, Illumina, PacBio and Sanger sequences, 16 genomes were assembled and categorized along with one incomplete and two previously published Erodium plastomes. We conducted phylogenetic analyses among these species using a dataset of 19 protein-coding genes and determined if significantly higher evolutionary rates had caused the long branch seen previously in phylogenetic reconstructions within the genus. Bioinformatic comparisons were also performed to evaluate plastome evolution across the genus. Erodium plastomes fell into four types (Type 1-4) that differ in their substitution rates, short dispersed repeat content and degree of genomic rearrangement, gene and intron content and GC content. Type 4 plastomes had significantly higher rates of synonymous substitutions (dS) for all genes and for 14 of the 19 genes non-synonymous substitutions (dN) were significantly accelerated. We evaluated the evidence for a single IR loss in Erodium and in doing so discovered that Type 4 plastomes contain a novel IR. The presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences.

PubMed

Kapila, R; Das, S; Srivastava, P S; Lakshmikumaran, M

1996-08-01

DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5'-TTTAGGG-3'. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31 digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature.

Generalized Grover's Algorithm for Multiple Phase Inversion States

NASA Astrophysics Data System (ADS)

Byrnes, Tim; Forster, Gary; Tessler, Louis

2018-02-01

Grover's algorithm is a quantum search algorithm that proceeds by repeated applications of the Grover operator and the Oracle until the state evolves to one of the target states. In the standard version of the algorithm, the Grover operator inverts the sign on only one state. Here we provide an exact solution to the problem of performing Grover's search where the Grover operator inverts the sign on N states. We show the underlying structure in terms of the eigenspectrum of the generalized Hamiltonian, and derive an appropriate initial state to perform the Grover evolution. This allows us to use the quantum phase estimation algorithm to solve the search problem in this generalized case, completely bypassing the Grover algorithm altogether. We obtain a time complexity of this case of √{D /Mα }, where D is the search space dimension, M is the number of target states, and α ≈1 , which is close to the optimal scaling.

Development of a passive micromixer based on repeated fluid twisting and flattening, and its application to DNA purification.

PubMed

Lee, Nae Yoon; Yamada, Masumi; Seki, Minoru

2005-11-01

We have developed a three-dimensional passive micromixer based on new mixing principles, fluid twisting and flattening. This micromixer is constructed by repeating two microchannel segments, a "main channel" and a "flattened channel", which are very different in size and are arranged perpendicularly. At the intersection of these segments the fluid inside the micromixer is twisted and then, in the flattened channel, the diffusion length is greatly reduced, achieving high mixing efficiency. Several types of micromixer were fabricated and the effect of microchannel geometry on mixing performance was evaluated. We also integrated this micromixer with a miniaturized DNA purification device, in which the concentration of the buffer solution could be rapidly changed, to perform DNA purification based on solid-phase extraction.

Characterization of a Mobile clpL Gene from Lactobacillus rhamnosus

PubMed Central

Suokko, Aki; Savijoki, Kirsi; Malinen, Erja; Palva, Airi; Varmanen, Pekka

2005-01-01

Two genes encoding ClpL ATPase proteins were identified in a probiotic Lactobacillus rhamnosus strain, E-97800. Sequence analyses revealed that the genes, designated clpL1 and clpL2, share 80% identity. The clpL2 gene showed the highest degree of identity (98.5%) to a clpL gene from Lactobacillus plantarum WCFSI, while it was not detected in three other L. rhamnosus strains studied. According to Northern analyses, the expression of clpL1 and the clpL2 were induced during heat shock by >20- and 3-fold, respectively. The functional promoter regions were determined by primer extension analyses, and the clpL1 promoter was found to be overlapped by an inverted repeat structure identical to the conserved CIRCE element, indicating that clpL1 belongs to the HrcA regulon in L. rhamnosus. No consensus binding sites for HrcA or CtsR could be identified in the clpL2 promoter region. Interestingly, the clpL2 gene was found to be surrounded by truncated transposase genes and flanked by inverted repeat structures nearly identical to the terminal repeats of the ISLpl1 from L. plantarum HN38. Furthermore, clpL2 was shown to be mobilized during prolonged cultivation at elevated temperature. The presence of a gene almost identical to clpL2 in L. plantarum and its absence in other L. rhamnosus strains suggest that the L. rhamnosus E-97800 has acquired the clpL2 gene via horizontal transfer. No change in the stress tolerance of the ClpL2-deficient derivative of E-97800 compared to the parental strain was observed. PMID:15812039

The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza.

PubMed

Qian, Jun; Song, Jingyuan; Gao, Huanhuan; Zhu, Yingjie; Xu, Jiang; Pang, Xiaohui; Yao, Hui; Sun, Chao; Li, Xian'en; Li, Chuyuan; Liu, Juyan; Xu, Haibin; Chen, Shilin

2013-01-01

Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,539 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Four forward, three inverted and seven tandem repeats were detected in the Salvia miltiorrhiza cp genome. Simple sequence repeat (SSR) analysis among the 30 asterid cp genomes revealed that most SSRs are AT-rich, which contribute to the overall AT richness of these cp genomes. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the cp genomes. Entire cp genome comparison of Salvia miltiorrhiza and three other Lamiales cp genomes showed a high degree of sequence similarity and a relatively high divergence of intergenic spacers. Sequence divergence analysis discovered the ten most divergent and ten most conserved genes as well as their length variation, which will be helpful for phylogenetic studies in asterids. Our analysis also supports that both regional and functional constraints affect gene sequence evolution. Further, phylogenetic analysis demonstrated a sister relationship between Salvia miltiorrhiza and Sesamum indicum. The complete cp genome sequence of Salvia miltiorrhiza reported in this paper will facilitate population, phylogenetic and cp genetic engineering studies of this medicinal plant.

Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata

PubMed Central

Kazakoff, Stephen H.; Imelfort, Michael; Edwards, David; Koehorst, Jasper; Biswas, Bandana; Batley, Jacqueline; Scott, Paul T.; Gresshoff, Peter M.

2012-01-01

Pongamia pinnata (syn. Millettia pinnata) is a novel, fast-growing arboreal legume that bears prolific quantities of oil-rich seeds suitable for the production of biodiesel and aviation biofuel. Here, we have used Illumina® ‘Second Generation DNA Sequencing (2GS)’ and a new short-read de novo assembler, SaSSY, to assemble and annotate the Pongamia chloroplast (152,968 bp; cpDNA) and mitochondrial (425,718 bp; mtDNA) genomes. We also show that SaSSY can be used to accurately assemble 2GS data, by re-assembling the Lotus japonicus cpDNA and in the process assemble its mtDNA (380,861 bp). The Pongamia cpDNA contains 77 unique protein-coding genes and is almost 60% gene-dense. It contains a 50 kb inversion common to other legumes, as well as a novel 6.5 kb inversion that is responsible for the non-disruptive, re-orientation of five protein-coding genes. Additionally, two copies of an inverted repeat firmly place the species outside the subclade of the Fabaceae lacking the inverted repeat. The Pongamia and L. japonicus mtDNA contain just 33 and 31 unique protein-coding genes, respectively, and like other angiosperm mtDNA, have expanded intergenic and multiple repeat regions. Through comparative analysis with Vigna radiata we measured the average synonymous and non-synonymous divergence of all three legume mitochondrial (1.59% and 2.40%, respectively) and chloroplast (8.37% and 8.99%, respectively) protein-coding genes. Finally, we explored the relatedness of Pongamia within the Fabaceae and showed the utility of the organellar genome sequences by mapping transcriptomic data to identify up- and down-regulated stress-responsive gene candidates and confirm in silico predicted RNA editing sites. PMID:23272141

Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata.

PubMed

Kazakoff, Stephen H; Imelfort, Michael; Edwards, David; Koehorst, Jasper; Biswas, Bandana; Batley, Jacqueline; Scott, Paul T; Gresshoff, Peter M

2012-01-01

Pongamia pinnata (syn. Millettia pinnata) is a novel, fast-growing arboreal legume that bears prolific quantities of oil-rich seeds suitable for the production of biodiesel and aviation biofuel. Here, we have used Illumina® 'Second Generation DNA Sequencing (2GS)' and a new short-read de novo assembler, SaSSY, to assemble and annotate the Pongamia chloroplast (152,968 bp; cpDNA) and mitochondrial (425,718 bp; mtDNA) genomes. We also show that SaSSY can be used to accurately assemble 2GS data, by re-assembling the Lotus japonicus cpDNA and in the process assemble its mtDNA (380,861 bp). The Pongamia cpDNA contains 77 unique protein-coding genes and is almost 60% gene-dense. It contains a 50 kb inversion common to other legumes, as well as a novel 6.5 kb inversion that is responsible for the non-disruptive, re-orientation of five protein-coding genes. Additionally, two copies of an inverted repeat firmly place the species outside the subclade of the Fabaceae lacking the inverted repeat. The Pongamia and L. japonicus mtDNA contain just 33 and 31 unique protein-coding genes, respectively, and like other angiosperm mtDNA, have expanded intergenic and multiple repeat regions. Through comparative analysis with Vigna radiata we measured the average synonymous and non-synonymous divergence of all three legume mitochondrial (1.59% and 2.40%, respectively) and chloroplast (8.37% and 8.99%, respectively) protein-coding genes. Finally, we explored the relatedness of Pongamia within the Fabaceae and showed the utility of the organellar genome sequences by mapping transcriptomic data to identify up- and down-regulated stress-responsive gene candidates and confirm in silico predicted RNA editing sites.

A miniature Marine Aerosol Reference Tank (miniMART) as a compact breaking wave analogue

NASA Astrophysics Data System (ADS)

Stokes, M. Dale; Deane, Grant; Collins, Douglas B.; Cappa, Christopher; Bertram, Timothy; Dommer, Abigail; Schill, Steven; Forestieri, Sara; Survilo, Mathew

2016-09-01

In order to understand the processes governing the production of marine aerosols, repeatable, controlled methods for their generation are required. A new system, the miniature Marine Aerosol Reference Tank (miniMART), has been designed after the success of the original MART system, to approximate a small oceanic spilling breaker by producing an evolving bubble plume and surface foam patch. The smaller tank utilizes an intermittently plunging jet of water produced by a rotating water wheel, into an approximately 6 L reservoir to simulate bubble plume and foam formation and generate aerosols. This system produces bubble plumes characteristic of small whitecaps without the large external pump inherent in the original MART design. Without the pump it is possible to easily culture delicate planktonic and microbial communities in the bulk water during experiments while continuously producing aerosols for study. However, due to the reduced volume and smaller plunging jet, the absolute numbers of particles generated are approximately an order of magnitude less than in the original MART design.

Prevalence of porcine endogenous retroviruses in domestic, minature, and genetically modified pigs in Japan.

PubMed

Fujimura, T; Miyagawa, S; Takahagi, Y; Shigehisa, T; Murakami, H

2008-03-01

The present study examined the prevalence of porcine endogenous retroviruses (PERV) in pigs available in Japan using polymerase chain reaction (PCR) with primers specific for PERV-A, PERV-B, and PERV-C and for the full-length 5' to 3' long terminal repeat and using PCR-Southern blotting with env A-, env B-, env C-, and pol/pro-specific probes. All 376 pigs tested--Berkshire (B), Landrace (L), Duroc (D), Large White (W), miniature, and genetically modified triple-cross breed (LWD)--harbored both PERV-A and PERV-B genes. However, the prevalence of PERV-C differed among pigs: LWD, miniature, B, D, W, and L pigs were 100% (36/36), 83% (5/6), 68% (129/191), 52% (26/50), 21% (9/43), and 16% (8/50), respectively. These results show that W and L pigs may be preferable as xenotransplantation donors, because they may not produce human-tropic replication-competent hybrids of PERV-A and PERV-C.

Gene Conversion Violates the Stepwise Mutation Model for Microsatellites in Y-Chromosomal Palindromic Repeats

PubMed Central

Balaresque, Patricia; King, Turi E; Parkin, Emma J; Heyer, Evelyne; Carvalho-Silva, Denise; Kraaijenbrink, Thirsa; de Knijff, Peter; Tyler-Smith, Chris; Jobling, Mark A

2014-01-01

The male-specific region of the human Y chromosome (MSY) contains eight large inverted repeats (palindromes), in which high-sequence similarity between repeat arms is maintained by gene conversion. These palindromes also harbor microsatellites, considered to evolve via a stepwise mutation model (SMM). Here, we ask whether gene conversion between palindrome microsatellites contributes to their mutational dynamics. First, we study the duplicated tetranucleotide microsatellite DYS385a,b lying in palindrome P4. We show, by comparing observed data with simulated data under a SMM within haplogroups, that observed heteroallelic combinations in which the modal repeat number difference between copies was large, can give rise to homoallelic combinations with zero-repeats difference, equivalent to many single-step mutations. These are unlikely to be generated under a strict SMM, suggesting the action of gene conversion. Second, we show that the intercopy repeat number difference for a large set of duplicated microsatellites in all palindromes in the MSY reference sequence is significantly reduced compared with that for nonpalindrome-duplicated microsatellites, suggesting that the former are characterized by unusual evolutionary dynamics. These observations indicate that gene conversion violates the SMM for microsatellites in palindromes, homogenizing copies within individual Y chromosomes, but increasing overall haplotype diversity among chromosomes within related groups. PMID:24610746

What Is a Hill? An Analysis of the Meanings of Generic Topographic Terms

DTIC Science & Technology

1985-08-01

to describe the di,.ferent characters of forms. FLAT: An area or surface with gantle, non-varying slope, that is highly platykurtic but not...Slo;e Change Index value of zero. ROLLING: A surface without elevated or Inverted forms, with platykurtic slo a Slope Ctange Index value of zero and...and contour planes of similar extent. POCKMARKEC (pitted): A surface that has within its contour repeated, small, circular or elliptical platykurtic

Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans

PubMed Central

Tan, Benedict G.; Vijgenboom, Erik; Worrall, Jonathan A. R.

2014-01-01

Metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. The copper sensitive operon repressor (CsoR) family is widely distributed in bacteria and controls the expression of copper efflux systems. CsoR operator sites consist of G-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. Here, we use a structurally characterized CsoR from Streptomyces lividans (CsoRSl) together with three specific operator targets to reveal the salient features pertaining to the mechanism of DNA binding. We reveal that CsoRSl binds to its operator site through a 2-fold axis of symmetry centred on a conserved 5′-TAC/GTA-3′ inverted repeat. Operator recognition is stringently dependent not only on electropositive residues but also on a conserved polar glutamine residue. Thermodynamic and circular dichroic signatures of the CsoRSl–DNA interaction suggest selectivity towards the A-DNA-like topology of the G-tracts at the operator site. Such properties are enhanced on protein binding thus enabling the symmetrical binding of two CsoRSl tetramers. Finally, differential binding modes may exist in operator sites having more than one 5′-TAC/GTA-3′ inverted repeat with implications in vivo for a mechanism of modular control. PMID:24121681

SAV742, a Novel AraC-Family Regulator from Streptomyces avermitilis, Controls Avermectin Biosynthesis, Cell Growth and Development.

PubMed

Sun, Di; Zhu, Jianya; Chen, Zhi; Li, Jilun; Wen, Ying

2016-11-14

Avermectins are useful anthelmintic antibiotics produced by Streptomyces avermitilis. We demonstrated that a novel AraC-family transcriptional regulator in this species, SAV742, is a global regulator that negatively controls avermectin biosynthesis and cell growth, but positively controls morphological differentiation. Deletion of its gene, sav_742, increased avermectin production and dry cell weight, but caused delayed formation of aerial hyphae and spores. SAV742 directly inhibited avermectin production by repressing transcription of ave structural genes, and also directly regulated its own gene (sav_742) and adjacent gene sig8 (sav_741). The precise SAV742-binding site on its own promoter region was determined by DNase I footprinting assay coupled with site-directed DNA mutagenesis, and 5-nt inverted repeats (GCCGA-n 10 /n 12 -TCGGC) were found to be essential for SAV742 binding. Similar 5-nt inverted repeats separated by 3, 10 or 15 nt were found in the promoter regions of target ave genes and sig8. The SAV742 regulon was predicted based on bioinformatic analysis. Twenty-six new SAV742 targets were identified and experimentally confirmed, including genes involved in primary metabolism, secondary metabolism and development. Our findings indicate that SAV742 plays crucial roles in not only avermectin biosynthesis but also coordination of complex physiological processes in S. avermitilis.

Asymmetric Preorganization of Inverted Pair Residues in the Sodium-Calcium Exchanger

PubMed Central

Giladi, Moshe; Almagor, Lior; van Dijk, Liat; Hiller, Reuben; Man, Petr; Forest, Eric; Khananshvili, Daniel

2016-01-01

In analogy with many other proteins, Na+/Ca2+ exchangers (NCX) adapt an inverted twofold symmetry of repeated structural elements, while exhibiting a functional asymmetry by stabilizing an outward-facing conformation. Here, structure-based mutant analyses of the Methanococcus jannaschii Na+/Ca2+ exchanger (NCX_Mj) were performed in conjunction with HDX-MS (hydrogen/deuterium exchange mass spectrometry) to identify the structure-dynamic determinants of functional asymmetry. HDX-MS identified hallmark differences in backbone dynamics at ion-coordinating residues of apo-NCX_Mj, whereas Na+or Ca2+ binding to the respective sites induced relatively small, but specific, changes in backbone dynamics. Mutant analysis identified ion-coordinating residues affecting the catalytic capacity (kcat/Km), but not the stability of the outward-facing conformation. In contrast, distinct “noncatalytic” residues (adjacent to the ion-coordinating residues) control the stability of the outward-facing conformation, but not the catalytic capacity. The helix-breaking signature sequences (GTSLPE) on the α1 and α2 repeats (at the ion-binding core) differ in their folding/unfolding dynamics, while providing asymmetric contributions to transport activities. The present data strongly support the idea that asymmetric preorganization of the ligand-free ion-pocket predefines catalytic reorganization of ion-bound residues, where secondary interactions with adjacent residues couple the alternating access. These findings provide a structure-dynamic basis for ion-coupled alternating access in NCX and similar proteins. PMID:26876271

Graft-transmissible movement of inverted-repeat-induced siRNA signals into flowers.

PubMed

Zhang, Wenna; Kollwig, Gregor; Stecyk, Ewelina; Apelt, Federico; Dirks, Rob; Kragler, Friedrich

2014-10-01

In plants, small interfering RNAs (siRNA) and microRNAs move to distant tissues where they control numerous developmental and physiological processes such as morphogenesis and stress responses. Grafting techniques and transient expression systems have been employed to show that sequence-specific siRNAs with a size of 21-24 nucleotides traffic to distant organs. We used inverted-repeat constructs producing siRNA targeting the meiosis factor DISRUPTED MEIOTIC cDNA 1 (DMC1) and GFP to test whether silencing signals move into meiotically active tissues. In grafted Nicotiana tabacum, a transgenic DMC1 siRNA signal made in source tissues preferably entered the anthers formed in the first flowers. Here, the DMC1 siRNA interfered with meiotic progression and, consequently, the flowers were at least partially sterile. In agro-infiltrated N. benthamiana plants, a GFP siRNA signal produced in leaves was allocated and active in most flower tissues including anthers. In hypocotyl-grafted Arabidopsis thaliana plants, the DMC1 silencing signal consistently appeared in leaves, petioles, and stem, and only a small number of plants displayed DMC1 siRNA signals in flowers. In all three tested plant species the systemic silencing signal penetrated male sporogenic tissues suggesting that plants harbour an endogenous long-distance small RNA transport pathway facilitating siRNA signalling into meiotically active cells. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

The mitochondrial genome of Hydra oligactis (Cnidaria, Hydrozoa) sheds new light on animal mtDNA evolution and cnidarian phylogeny.

PubMed

Kayal, Ehsan; Lavrov, Dennis V

2008-02-29

The 16,314-nuceotide sequence of the linear mitochondrial DNA (mtDNA) molecule of Hydra oligactis (Cnidaria, Hydrozoa)--the first from the class Hydrozoa--has been determined. This sequence contains genes for 13 energy pathway proteins, small and large subunit rRNAs, and methionine and tryptophan tRNAs, as is typical for cnidarians. All genes have the same transcriptional orientation and their arrangement in the genome is similar to that of the jellyfish Aurelia aurita. In addition, a partial copy of cox1 is present at one end of the molecule in a transcriptional orientation opposite to the rest of the genes, forming a part of inverted terminal repeat characteristic of linear mtDNA and linear mitochondrial plasmids. The sequence close to at least one end of the molecule contains several homonucleotide runs as well as small inverted repeats that are able to form strong secondary structures and may be involved in mtDNA maintenance and expression. Phylogenetic analysis of mitochondrial genes of H. oligactis and other cnidarians supports the Medusozoa hypothesis but also suggests that Anthozoa may be paraphyletic, with octocorallians more closely related to the Medusozoa than to the Hexacorallia. The latter inference implies that Anthozoa is paraphyletic and that the polyp (rather than a medusa) is the ancestral body type in Cnidaria.

Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome.

PubMed

Weaver, David; Karoonuthaisiri, Nitsara; Tsai, Hsiu-Hwei; Huang, Chih-Hung; Ho, Mai-Lan; Gai, Shuning; Patel, Kedar G; Huang, Jianqiang; Cohen, Stanley N; Hopwood, David A; Chen, Carton W; Kao, Camilla M

2004-03-01

The chromosomes of several widely used laboratory derivatives of Streptomyces coelicolor A3(2) were found to have 1.06 Mb inverted repeat sequences at their termini (i.e. long-terminal inverted repeats; L-TIRs), which are 50 times the length of the 22 kb TIRs of the sequenced S. coelicolor strain M145. The L-TIRs include 1005 annotated genes and increase the overall chromosome size to 9.7 Mb. The 1.06 Mb L-TIRs are the longest reported thus far for an actinomycete, and are proposed to represent the chromosomal state of the original soil isolate of S. coelicolor A3(2). S. coelicolor A3(2), M600 and J1501 possess L-TIRs, whereas approximately half the examined early mutants of A3(2) generated by ultraviolet (UV) or X-ray mutagenesis have truncated their TIRs to the 22 kb length. UV radiation was found to stimulate L-TIR truncation. Two copies of a transposase gene (SCO0020) flank 1.04 Mb of DNA in the right L-TIR, and recombination between them appears to generate strains containing short TIRs. This TIR reduction mechanism may represent a general strategy by which transposable elements can modulate the structure of chromosome ends. The presence of L-TIRs in certain S. coelicolor strains represents a major chromosomal alteration in strains previously thought to be genetically similar.

Transformation of Chloroplast Ribosomal RNA Genes in Chlamydomonas: Molecular and Genetic Characterization of Integration Events

PubMed Central

Newman, S. M.; Boynton, J. E.; Gillham, N. W.; Randolph-Anderson, B. L.; Johnson, A. M.; Harris, E. H.

1990-01-01

Transformation of chloroplast ribosomal RNA (rRNA) genes in Chlamydomonas has been achieved by the biolistic process using cloned chloroplast DNA fragments carrying mutations that confer antibiotic resistance. The sites of exchange employed during the integration of the donor DNA into the recipient genome have been localized using a combination of antibiotic resistance mutations in the 16S and 23S rRNA genes and restriction fragment length polymorphisms that flank these genes. Complete or nearly complete replacement of a region of the chloroplast genome in the recipient cell by the corresponding sequence from the donor plasmid was the most common integration event. Exchange events between the homologous donor and recipient sequences occurred preferentially near the vector:insert junctions. Insertion of the donor rRNA genes and flanking sequences into one inverted repeat of the recipient genome was followed by intramolecular copy correction so that both copies of the inverted repeat acquired identical sequences. Increased frequencies of rRNA gene transformants were achieved by reducing the copy number of the chloroplast genome in the recipient cells and by decreasing the heterology between donor and recipient DNA sequences flanking the selectable markers. In addition to producing bona fide chloroplast rRNA transformants, the biolistic process induced mutants resistant to low levels of streptomycin, typical of nuclear mutations in Chlamydomonas. PMID:1981764

The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes

PubMed Central

Malmstrøm, Martin; Britz, Ralf; Matschiner, Michael; Tørresen, Ole K; Hadiaty, Renny Kurnia; Yaakob, Norsham; Tan, Heok Hui; Jakobsen, Kjetill Sigurd; Salzburger, Walter; Rüber, Lukas

2018-01-01

Abstract The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development. PMID:29684203

Comparison of isometric exercises for activating latissimus dorsi against the upper body weight.

PubMed

Park, Se-yeon; Yoo, Won-gyu; An, Duk-hyun; Oh, Jae-seop; Lee, Jung-hoon; Choi, Bo-ram

2015-02-01

Because there is little agreement as to which exercise is the most effective for activating the latissimus dorsi, and its intramuscular components are rarely compared, we investigated the intramuscular components of the latissimus dorsi during both trunk and shoulder exercises. Sixteen male subjects performed four isometric exercises: inverted row, body lifting, trunk extension, and trunk lateral bending. Surface electromyography (sEMG) was used to collect data from the medial and lateral components of the latissimus dorsi, lower trapezius, and the erector spinae at the 12th thoracic level during the isometric exercises. Two-way repeated analysis of variance with two within-subject factors (muscles and exercise conditions) was used to determine the significance of differences between the muscles and differences between exercise variations. The inverted row showed the highest values for the medial latissimus dorsi, which were significantly higher than those of the body lifting or trunk extension exercises. For the lateral latissimus dorsi, lateral bending showed significantly higher muscle activity than the inverted row or trunk extension. During body lifting, the % maximum voluntary isometric contraction (MVIC) of the erector spinae showed the lowest value, significantly lower than those of the other isometric exercises. The inverted row exercise was effective for activating the medial latissimus dorsi versus the shoulder depression and trunk exertion exercises. The lateral bending and body lifting exercises were favorable for activating the lateral component of the latissimus dorsi. Evaluating trunk lateral bending is essential for examining the function of the latissimus dorsi. Copyright © 2014 Elsevier Ltd. All rights reserved.

PMS2 inactivation by a complex rearrangement involving an HERV retroelement and the inverted 100-kb duplicon on 7p22.1.

PubMed

Vogt, Julia; Wernstedt, Annekatrin; Ripperger, Tim; Pabst, Brigitte; Zschocke, Johannes; Kratz, Christian; Wimmer, Katharina

2016-11-01

Biallelic PMS2 mutations are responsible for more than half of all cases of constitutional mismatch repair deficiency (CMMRD), a recessively inherited childhood cancer predisposition syndrome. The mismatch repair gene PMS2 is partly embedded within one copy of an inverted 100-kb low-copy repeat (LCR) on 7p22.1. In an individual with CMMRD syndrome, PMS2 was found to be homozygously inactivated by a complex chromosomal rearrangement, which separates the 5'-part from the 3'-part of the gene. The rearrangement involves sequences of the inverted 100-kb LCR and a human endogenous retrovirus element and may be associated with an inversion that is indistinguishable from the known inversion polymorphism affecting the ~0.7-Mb sequence intervening the LCR. Its formation is best explained by a replication-based mechanism (RBM) such as fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR). This finding supports the hypothesis that the inverted LCR can not only facilitate the formation of the non-allelic homologous recombination-mediated inversion polymorphism but it also promotes the occurrence of more complex rearrangements that can be associated with a large inversion, as well, but are mediated by a RBM. This further suggests that among the inversion polymorphism on 7p22.1, more complex rearrangements might be hidden. Furthermore, as the locus is embedded in a common fragile site (CFS) region, this rearrangement also supports the recently raised hypothesis that CFS sequence motifs may facilitate replication-based rearrangement mechanisms.

PMS2 inactivation by a complex rearrangement involving an HERV retroelement and the inverted 100-kb duplicon on 7p22.1

PubMed Central

Vogt, Julia; Wernstedt, Annekatrin; Ripperger, Tim; Pabst, Brigitte; Zschocke, Johannes; Kratz, Christian; Wimmer, Katharina

2016-01-01

Biallelic PMS2 mutations are responsible for more than half of all cases of constitutional mismatch repair deficiency (CMMRD), a recessively inherited childhood cancer predisposition syndrome. The mismatch repair gene PMS2 is partly embedded within one copy of an inverted 100-kb low-copy repeat (LCR) on 7p22.1. In an individual with CMMRD syndrome, PMS2 was found to be homozygously inactivated by a complex chromosomal rearrangement, which separates the 5′-part from the 3′-part of the gene. The rearrangement involves sequences of the inverted 100-kb LCR and a human endogenous retrovirus element and may be associated with an inversion that is indistinguishable from the known inversion polymorphism affecting the ~0.7-Mb sequence intervening the LCR. Its formation is best explained by a replication-based mechanism (RBM) such as fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR). This finding supports the hypothesis that the inverted LCR can not only facilitate the formation of the non-allelic homologous recombination-mediated inversion polymorphism but it also promotes the occurrence of more complex rearrangements that can be associated with a large inversion, as well, but are mediated by a RBM. This further suggests that among the inversion polymorphism on 7p22.1, more complex rearrangements might be hidden. Furthermore, as the locus is embedded in a common fragile site (CFS) region, this rearrangement also supports the recently raised hypothesis that CFS sequence motifs may facilitate replication-based rearrangement mechanisms. PMID:27329736

[Mechanical properties of nickel-titanium files following multiple heat sterilizations].

PubMed

Testarelli, L; Gallottini, L; Gambarini, G

2003-04-01

The effect of cycles of sterilization procedures on nickel-titanium (NiTi) endodontic instruments is a serious concern for practitioners. There is no agreement in the literature whether these procedures could adversely affect the mechanical properties of endodontic files, and, consequently, increase the risk of intracanal failure. The purpose of this study was to evaluate the mechanichal resistance of Hero (MicroMega, Besancon, France) instruments, before and after sterilization procedures. Thirty 02, 04, 06 tapered Hero size 30 new instruments were chosen and divided into 3 groups. Group A (control) were tested according to ANSI/ADA Spec.no 28 for torsional resistance, angle of torque and angle at breakage (45 inverted exclamation mark ). Group B files were first sterilized with chemiclave for 10 cycles of 20 minutes at 124 inverted exclamation mark C and then tested as described above. Group C files were first sterilized with glass beads for 10 cycles of 20 sec. at 250 inverted exclamation mark C and then tested as described above. Data were collected and statistically analyzed (t-paired test). Differences among the 3 groups were statistically not significant for both tests. All data were well within Spec.no 28 standard values. From the results of the present study, we may conclude that repeated sterilization procedures do not adversely affect the mechanichal resistance of Hero files.

Three-Dimensional Flexible Complementary Metal-Oxide-Semiconductor Logic Circuits Based On Two-Layer Stacks of Single-Walled Carbon Nanotube Networks.

PubMed

Zhao, Yudan; Li, Qunqing; Xiao, Xiaoyang; Li, Guanhong; Jin, Yuanhao; Jiang, Kaili; Wang, Jiaping; Fan, Shoushan

2016-02-23

We have proposed and fabricated stable and repeatable, flexible, single-walled carbon nanotube (SWCNT) thin film transistor (TFT) complementary metal-oxide-semiconductor (CMOS) integrated circuits based on a three-dimensional (3D) structure. Two layers of SWCNT-TFT devices were stacked, where one layer served as n-type devices and the other one served as p-type devices. On the basis of this method, it is able to save at least half of the area required to construct an inverter and make large-scale and high-density integrated CMOS circuits easier to design and manufacture. The 3D flexible CMOS inverter gain can be as high as 40, and the total noise margin is more than 95%. Moreover, the input and output voltage of the inverter are exactly matched for cascading. 3D flexible CMOS NOR, NAND logic gates, and 15-stage ring oscillators were fabricated on PI substrates with high performance as well. Stable electrical properties of these circuits can be obtained with bending radii as small as 3.16 mm, which shows that such a 3D structure is a reliable architecture and suitable for carbon nanotube electrical applications in complex flexible and wearable electronic devices.

Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

PubMed

Ruhlman, Tracey A; Zhang, Jin; Blazier, John C; Sabir, Jamal S M; Jansen, Robert K

2017-04-01

There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats. © 2017 Botanical Society of America.

Isolation of an insertion sequence (IS1051) from Xanthomonas campestris pv. dieffenbachiae with potential use for strain identification and characterization.

PubMed Central

Berthier, Y; Thierry, D; Lemattre, M; Guesdon, J L

1994-01-01

A new insertion sequence was isolated from Xanthomonas campestris pv. dieffenbachiae. Sequence analysis showed that this element is 1,158 bp long and has 15-bp inverted repeat ends containing two mismatches. Comparison of this sequence with sequences in data bases revealed significant homology with Escherichia coli IS5. IS1051, which detected multiple restriction fragment length polymorphisms, was used as a probe to characterize strains from the pathovar dieffenbachiae. Images PMID:7906933

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

Controlled assembly of organic whispering-gallery-mode microlasers as highly sensitive chemical vapor sensors.

PubMed

Gao, Miaomiao; Wei, Cong; Lin, Xianqing; Liu, Yuan; Hu, Fengqin; Zhao, Yong Sheng

2017-03-09

We demonstrate the fabrication of organic high Q active whispering-gallery-mode (WGM) resonators from π-conjugated polymer by a controlled emulsion-solvent-evaporation method, which can simultaneously provide optical gain and act as an effective resonant cavity. By measuring the shift of their lasing modes on exposure to organic vapor, we successfully monitored the slight concentration variation in the chemical gas. These microlaser sensors demonstrated high detection sensitivity and good signal repeatability under continuous chemical gas treatments. The results offer an effective strategy to design miniaturized optical sensors.

Do Stress Trajectories Predict Mortality in Older Men? Longitudinal Findings from the VA Normative Aging Study

PubMed Central

Aldwin, Carolyn M.; Molitor, Nuoo-Ting; Avron, Spiro; Levenson, Michael R.; Molitor, John; Igarashi, Heidi

2011-01-01

We examined long-term patterns of stressful life events (SLE) and their impact on mortality contrasting two theoretical models: allostatic load (linear relationship) and hormesis (inverted U relationship) in 1443 NAS men (aged 41–87 in 1985; M = 60.30, SD = 7.3) with at least two reports of SLEs over 18 years (total observations = 7,634). Using a zero-inflated Poisson growth mixture model, we identified four patterns of SLE trajectories, three showing linear decreases over time with low, medium, and high intercepts, respectively, and one an inverted U, peaking at age 70. Repeating the analysis omitting two health-related SLEs yielded only the first three linear patterns. Compared to the low-stress group, both the moderate and the high-stress groups showed excess mortality, controlling for demographics and health behavior habits, HRs = 1.42 and 1.37, ps <.01 and <.05. The relationship between stress trajectories and mortality was complex and not easily explained by either theoretical model. PMID:21961066

Miniature protein ligands for EVH1 domains: Interplay between affinity, specificity, and cell motility⊥

PubMed Central

Holtzman, Jennifer H.; Woronowicz, Kamil; Golemi-Kotra, Dasantila; Schepartz, Alanna

2008-01-01

Dynamic rearrangements of the actin cytoskeleton power cell motility in contexts ranging from intracellular microbial pathogenesis to axon guidance. The Ena/VASP family proteins--Mena, VASP, and Evl--are believed to control cell motility by serving as a direct link between signaling events and the actin cytoskeleton. Our lab has previously reported a novel miniature protein, pGolemi, which binds with high affinity to the EVH1 domain of Mena (Mena1-112) but not to those of VASP (VASP1-115) or Evl (Evl1-115) and also causes an unusual defect in actin-driven L. monocytogenes motility. Here, we use scanning mutagenesis to examine the effects of single amino acid changes within pGolemi on EVH1 domain affinity and specificity, miniature protein secondary structure, and L. monocytogenes motility. The data suggest that pGolemi contains the expected aPP-like fold and binds Mena1-112 in a manner highly analogous to the proline-rich repeat region of L. monocytogenes ActA protein. Residues throughout pGolemi contribute to both EVH1 domain affinity and paralog specificity. Moreover, the affinities of pGolemi variants for Mena1-112 correlate with selectivity against the EVH1 domains of VASP and Evl. In L. monocytogenes motility assays, speed and speed variability correlate strongly with EVH1 paralog specificity, suggesting that the Ena/VASP paralogs do not play equivalent roles in the process of L. monocytogenes actin tail maturation. PMID:17973491

Emergence of a new human adenovirus type 4 (Ad4) genotype: identification of a novel inverted terminal repeated (ITR) sequence from majority of Ad4 isolates from US military recruits.

PubMed

Houng, Huo-Shu H; Clavio, Sarah; Graham, Katherine; Kuschner, Robert; Sun, Wellington; Russell, Kevin L; Binn, Leonard N

2006-04-01

Ad4 is the principal etiological agent of acute respiratory disease (ARD) in the US military. Discovery of the novel 208bp inverted terminal repeated (ITR) sequence from a recent Ad4 Jax78 field isolate was totally distinct from the analogous 116bp ITR of Ad4 prototype. To investigate the origin and distribution of the novel Ad4 ITR sequence from ARD infections. Direct sequencing of ligated Ad ITR termini. The new Ad4 ITR was highly homologous with the ITRs of human Ad subgroup B. The left post-ITR region of Ad4 Jax78 was found to be highly homologous to the corresponding region of subgroup B Ads: 81% for Ad11 and 98% for Ad3 and Ad7. The right post-ITR region of Ad4 Jax78 contained a truncated classic ITR of the Ad4 prototype. The Ad4 Jax78 ITR most likely evolved from Ad4 prototype by substituting the Ad4 prototype ITR with the subgroup B Ads ITR. The ITR-based PCR assays developed from this study can be used to distinguish the new Ad4 genotype from the classical Ad4 prototype. The new Ad4 genotype was first detected in 1976 from Georgia, USA, and is the main causative agent of ARD infections in US military population.

The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species

PubMed Central

Park, Inkyu; Kim, Wook-jin; Yang, Sungyu; Yeo, Sang-Min; Li, Hulin

2017-01-01

Aconitum species (belonging to the Ranunculaceae) are well known herbaceous medicinal ingredients and have great economic value in Asian countries. However, there are still limited genomic resources available for Aconitum species. In this study, we sequenced the chloroplast (cp) genomes of two Aconitum species, A. coreanum and A. carmichaelii, using the MiSeq platform. The two Aconitum chloroplast genomes were 155,880 and 157,040 bp in length, respectively, and exhibited LSC and SSC regions separated by a pair of inverted repeat regions. Both cp genomes had 38% GC content and contained 131 unique functional genes including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene order, content, and orientation of the two Aconitum cp genomes exhibited the general structure of angiosperms, and were similar to those of other Aconitum species. Comparison of the cp genome structure and gene order with that of other Aconitum species revealed general contraction and expansion of the inverted repeat regions and single copy boundary regions. Divergent regions were also identified. In phylogenetic analysis, Aconitum species positon among the Ranunculaceae was determined with other family cp genomes in the Ranunculales. We obtained a barcoding target sequence in a divergent region, ndhC–trnV, and successfully developed a SCAR (sequence characterized amplified region) marker for discrimination of A. coreanum. Our results provide useful genetic information and a specific barcode for discrimination of Aconitum species. PMID:28863163

The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species.

PubMed

Park, Inkyu; Kim, Wook-Jin; Yang, Sungyu; Yeo, Sang-Min; Li, Hulin; Moon, Byeong Cheol

2017-01-01

Aconitum species (belonging to the Ranunculaceae) are well known herbaceous medicinal ingredients and have great economic value in Asian countries. However, there are still limited genomic resources available for Aconitum species. In this study, we sequenced the chloroplast (cp) genomes of two Aconitum species, A. coreanum and A. carmichaelii, using the MiSeq platform. The two Aconitum chloroplast genomes were 155,880 and 157,040 bp in length, respectively, and exhibited LSC and SSC regions separated by a pair of inverted repeat regions. Both cp genomes had 38% GC content and contained 131 unique functional genes including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene order, content, and orientation of the two Aconitum cp genomes exhibited the general structure of angiosperms, and were similar to those of other Aconitum species. Comparison of the cp genome structure and gene order with that of other Aconitum species revealed general contraction and expansion of the inverted repeat regions and single copy boundary regions. Divergent regions were also identified. In phylogenetic analysis, Aconitum species positon among the Ranunculaceae was determined with other family cp genomes in the Ranunculales. We obtained a barcoding target sequence in a divergent region, ndhC-trnV, and successfully developed a SCAR (sequence characterized amplified region) marker for discrimination of A. coreanum. Our results provide useful genetic information and a specific barcode for discrimination of Aconitum species.

A Simple Retroelement Based Knock-Down System in Dictyostelium: Further Insights into RNA Interference Mechanisms.

PubMed

Friedrich, Michael; Meier, Doreen; Schuster, Isabelle; Nellen, Wolfgang

2015-01-01

We have previously shown that the most abundant Dictyostelium discoideum retroelement DIRS-1 is suppressed by RNAi mechanisms. Here we provide evidence that both inverted terminal repeats have strong promoter activity and that bidirectional expression apparently generates a substrate for Dicer. A cassette containing the inverted terminal repeats and a fragment of a gene of interest was sufficient to activate the RNAi response, resulting in the generation of ~21 nt siRNAs, a reduction of mRNA and protein expression of the respective endogene. Surprisingly, no transitivity was observed on the endogene. This was in contrast to previous observations, where endogenous siRNAs caused spreading on an artificial transgene. Knock-down was successful on seven target genes that we examined. In three cases a phenotypic analysis proved the efficiency of the approach. One of the target genes was apparently essential because no knock-out could be obtained; the RNAi mediated knock-down, however, resulted in a very slow growing culture indicating a still viable reduction of gene expression. ADVANTAGES OF THE DIRS-1–RNAI SYSTEM: The knock-down system required a short DNA fragment (~400 bp) of the target gene as an initial trigger. Further siRNAs were generated by RdRPs since we have shown some siRNAs with a 5'-triphosphate group. Extrachromosomal vectors facilitate the procedure and allowed for molecular and phenotypic analysis within one week. The system provides an efficient and rapid method to reduce protein levels including those of essential genes.

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

PubMed Central

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

2013-01-01

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. PMID:23648487

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.

Characterizations and Electrical Modelling of Sensory Samples Formed from Synthesized Vanadium (V) Oxide and Copper Oxide Graphene Quantum Tunneling Composites (GQTC) Applied in Electrotribology

PubMed Central

Habdank-Wojewódzki, Tadeusz; Habdank, Josef; Cwik, Przemyslaw; Zimowski, Slawomir

2016-01-01

CuO and V2O5 graphene quantum tunneling composites (GQTC) presented in this article were produced and their sensory properties were analyzed. The composites were synthesised using two stage high-power milling process, which resulted in materials that have good temeprature and pressure sensory properties. Described production process defines internal structure of materials such that when used as sensor in the desired range, it exhibits a strong percolation effect. The experiment, with controlled changing physical conditions during electrotribological measurement, enabled analyzing of the composites’ conductivity as a function of the sensory properties: applied temperature, pressure, tangential force and wear. The sensory characteristic was successfully modelled by invertible generalized equations, and used to create sensor capable of estimating temperature or pressure in the real time. The developed materials have the potential to be applied in the areas where miniaturization is essential, due to the materials exhibiting good sensory properties in mini and micro scale. PMID:26742044

Characterizations and Electrical Modelling of Sensory Samples Formed from Synthesized Vanadium (V) Oxide and Copper Oxide Graphene Quantum Tunneling Composites (GQTC) Applied in Electrotribology.

PubMed

Habdank-Wojewódzki, Tadeusz; Habdank, Josef; Cwik, Przemyslaw; Zimowski, Slawomir

2016-01-05

CuO and V₂O₅ graphene quantum tunneling composites (GQTC) presented in this article were produced and their sensory properties were analyzed. The composites were synthesised using two stage high-power milling process, which resulted in materials that have good temeprature and pressure sensory properties. Described production process defines internal structure of materials such that when used as sensor in the desired range, it exhibits a strong percolation effect. The experiment, with controlled changing physical conditions during electrotribological measurement, enabled analyzing of the composites' conductivity as a function of the sensory properties: applied temperature, pressure, tangential force and wear. The sensory characteristic was successfully modelled by invertible generalized equations, and used to create sensor capable of estimating temperature or pressure in the real time. The developed materials have the potential to be applied in the areas where miniaturization is essential, due to the materials exhibiting good sensory properties in mini and micro scale.

Multi-foci metalens for spin and orbital angular momentum interaction

NASA Astrophysics Data System (ADS)

Mei, Shengtao; Mehmood, M. Q.; Huang, Kun; Qiu, Cheng-Wei

2015-09-01

The development of metasurface, capable of controlling wave-fronts through interfacial phase discontinuity, offers a fascinating methodology for designing two dimensional miniaturized optical devices. Owing to an additional advantage of the enhanced useful transmission via Bainet-inverted matasurface, we exploit them to demonstrate an intriguing concept of merging the phase-profiles of two distinct optical devices, a lens and a spiral phase plate, to realize an ultrathin nanostructured optical vortex lens. The proposed device can has multiple focal planes along the longitudinal direction; whereas the number of focal plans, corresponding topological charges and focal lengths can readily be tailored to meet any desired requirements. Meanwhile, the dual-polarity feature of the optical vertex metalens exhibits spin controlled real and virtual focal plans, while dispersionless aptitude of nanobars enables its working over the broadband. The concept unveils a novel way of employing metasurface, to engraft the phase profiles of multiple bulk devices, to achieve unique functionalities for promising applications in integrated photonics.

Vertical Silicon Nanowire Field Effect Transistors with Nanoscale Gate-All-Around

NASA Astrophysics Data System (ADS)

Guerfi, Youssouf; Larrieu, Guilhem

2016-04-01

Nanowires are considered building blocks for the ultimate scaling of MOS transistors, capable of pushing devices until the most extreme boundaries of miniaturization thanks to their physical and geometrical properties. In particular, nanowires' suitability for forming a gate-all-around (GAA) configuration confers to the device an optimum electrostatic control of the gate over the conduction channel and then a better immunity against the short channel effects (SCE). In this letter, a large-scale process of GAA vertical silicon nanowire (VNW) MOSFETs is presented. A top-down approach is adopted for the realization of VNWs with an optimum reproducibility followed by thin layer engineering at nanoscale. Good overall electrical performances were obtained, with excellent electrostatic behavior (a subthreshold slope (SS) of 95 mV/dec and a drain induced barrier lowering (DIBL) of 25 mV/V) for a 15-nm gate length. Finally, a first demonstration of dual integration of n-type and p-type VNW transistors for the realization of CMOS inverter is proposed.

Optical sensor for fluoride determination in tea sample based on evanescent-wave interaction and fiber-optic integration.

PubMed

Xiong, Yan; Wu, Jiayi; Wang, Qing; Xu, Jing; Fang, Shenwen; Chen, Jie; Duan, Ming

2017-11-01

In this work, a miniaturized optical sensor was developed for fluoride determination in tea samples to evaluate their specific risks of fluorosis for public health based on evanescent-wave interaction. The sensor design was integrated on the optical fiber by utilizing the evanescent wave produced on the fiber surface to react with sensing reagents. According to the absorption change at 575nm, fluoride could be determined by colorimetric method and evaluated by Beer's law. With improved performances of small detection volume (1.2μL), fast analysis (0.41min), wide linear range (0.01-1.4mgL -1 ), low detection limit (3.5μgL -1 , 3σ) and excellent repeatability (2.34%), the sensor has been applied to fluoride determination in six different tea samples. Conventional spectrophotometry and ion chromatography were employed to validate the sensor's accuracy and potential application. Furthermore, this sensor fabrication provided a miniaturized colorimetric detection platform for other hazardous species monitoring based on evanescent wave interaction. Copyright © 2017 Elsevier B.V. All rights reserved.

Ion pair-based liquid-phase microextraction combined with cuvetteless UV-vis micro-spectrophotometry as a miniaturized assay for monitoring ammonia in waters.

PubMed

Senra-Ferreiro, Sonia; Pena-Pereira, Francisco; Costas-Mora, Isabel; Romero, Vanesa; Lavilla, Isela; Bendicho, Carlos

2011-09-15

A miniaturized method based on liquid-phase microextraction (LPME) in combination with microvolume UV-vis spectrophotometry for monitoring ammonia in waters is proposed. The methodology is based on the extraction of the ion pair formed between the blue indophenol obtained according to the Berthelot reaction and a quaternary ammonium salt into a microvolume of organic solvent. Experimental parameters affecting the LPME performance such as type and concentration of the quaternary ammonium ion salt required to form the ion pair, type and volume of extractant solvent, effect of disperser solvent, ionic strength and extraction time, were optimized. A detection limit of 5.0 μg L(-1) ammonia and an enrichment factor of 30 can be attained after a microextraction time of 4 min. The repeatability, expressed as relative standard deviation, was 7.6% (n=7). The proposed method can be successfully applied to the determination of trace amounts of ammonia in several environmental water samples. Copyright © 2011 Elsevier B.V. All rights reserved.

The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.

PubMed

Kang, Jong-Soo; Lee, Byoung Yoon; Kwak, Myounghai

2017-01-01

The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.

Knowing how you are feeling depends on what's on my mind: Cognitive load and expression categorization.

PubMed

Ahmed, Lubna

2018-03-01

The ability to correctly interpret facial expressions is key to effective social interactions. People are well rehearsed and generally very efficient at correctly categorizing expressions. However, does their ability to do so depend on how cognitively loaded they are at the time? Using repeated-measures designs, we assessed the sensitivity of facial expression categorization to cognitive resources availability by measuring people's expression categorization performance during concurrent low and high cognitive load situations. In Experiment1, participants categorized the 6 basic upright facial expressions in a 6-automated-facial-coding response paradigm while maintaining low or high loading information in working memory (N = 40; 60 observations per load condition). In Experiment 2, they did so for both upright and inverted faces (N = 46; 60 observations per load and inversion condition). In both experiments, expression categorization for upright faces was worse during high versus low load. Categorization rates actually improved with increased load for the inverted faces. The opposing effects of cognitive load on upright and inverted expressions are explained in terms of a cognitive load-related dispersion in the attentional window. Overall, the findings support that expression categorization is sensitive to cognitive resources availability and moreover suggest that, in this paradigm, it is the perceptual processing stage of expression categorization that is affected by cognitive load. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome.

PubMed

Sabot, F; Schulman, A H

2006-12-01

LTR (long terminal repeat) retrotransposons are the main components of higher plant genomic DNA. They have shaped their host genomes through insertional mutagenesis and by effects on genome size, gene expression and recombination. These Class I transposable elements are closely related to retroviruses such as the HIV by their structure and presumptive life cycle. However, the retrotransposon life cycle has been closely investigated in few systems. For retroviruses and retrotransposons, individual defective copies can parasitize the activity of functional ones. However, some LTR retrotransposon groups as a whole, such as large retrotransposon derivatives and terminal repeats in miniature, are non-autonomous even though their genomic insertion patterns remain polymorphic between organismal accessions. Here, we examine what is known of the retrotransposon life cycle in plants, and in that context discuss the role of parasitism and complementation between and within retrotransposon groups.

Oligonucleotide Microarray Analysis of Dietary-Induced Hyperlipidemia Gene Expression Profiles in Miniature Pigs

PubMed Central

Takahashi, Junko; Waki, Shiori; Matsumoto, Rena; Odake, Junji; Miyaji, Takayuki; Tottori, Junichi; Iwanaga, Takehiro; Iwahashi, Hitoshi

2012-01-01

Background Hyperlipidemia animal models have been established, but complete gene expression profiles of the transition from normal lipid levels have not been obtained. Miniature pigs are useful model animals for gene expression studies on dietary-induced hyperlipidemia because they have a similar anatomy and digestive physiology to humans, and blood samples can be obtained from them repeatedly. Methodology Two typical dietary treatments were used for dietary-induced hyperlipidemia models, by using specific pathogen-free (SPF) Clawn miniature pigs. One was a high-fat and high-cholesterol diet (HFCD) and the other was a high-fat, high-cholesterol, and high-sucrose diet (HFCSD). Microarray analyses were conducted from whole blood samples during the dietary period and from white blood cells at the end of the dietary period to evaluate the transition of expression profiles of the two dietary models. Principal Findings Variations in whole blood gene expression intensity within the HFCD or the HFCSD group were in the same range as the controls provide with normal diet at all periods. This indicates uniformity of dietary-induced hyperlipidemia for our dietary protocols. Gene ontology- (GO) based functional analyses revealed that characteristics of the common changes between HFCD and HFCSD were involved in inflammatory responses and reproduction. The correlation coefficient between whole blood and white blood cell expression profiles at 27 weeks with the HFCSD diet was significantly lower than that of the control and HFCD diet groups. This may be due to the effects of RNA originating from the tissues and/or organs. Conclusions No statistically significant differences in fasting plasma lipids and glucose levels between the HFCD and HFCSD groups were observed. However, blood RNA analyses revealed different characteristics corresponding to the dietary protocols. In this study, whole blood RNA analyses proved to be a useful tool to evaluate transitions in dietary-induced hyperlipidemia gene expression profiles in miniature pigs. PMID:22662175

The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms

PubMed Central

Bausher, Michael G; Singh, Nameirakpam D; Lee, Seung-Bum; Jansen, Robert K; Daniell, Henry

2006-01-01

Background The production of Citrus, the largest fruit crop of international economic value, has recently been imperiled due to the introduction of the bacterial disease Citrus canker. No significant improvements have been made to combat this disease by plant breeding and nuclear transgenic approaches. Chloroplast genetic engineering has a number of advantages over nuclear transformation; it not only increases transgene expression but also facilitates transgene containment, which is one of the major impediments for development of transgenic trees. We have sequenced the Citrus chloroplast genome to facilitate genetic improvement of this crop and to assess phylogenetic relationships among major lineages of angiosperms. Results The complete chloroplast genome sequence of Citrus sinensis is 160,129 bp in length, and contains 133 genes (89 protein-coding, 4 rRNAs and 30 distinct tRNAs). Genome organization is very similar to the inferred ancestral angiosperm chloroplast genome. However, in Citrus the infA gene is absent. The inverted repeat region has expanded to duplicate rps19 and the first 84 amino acids of rpl22. The rpl22 gene in the IRb region has a nonsense mutation resulting in 9 stop codons. This was confirmed by PCR amplification and sequencing using primers that flank the IR/LSC boundaries. Repeat analysis identified 29 direct and inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Comparison of protein-coding sequences with expressed sequence tags revealed six putative RNA edits, five of which resulted in non-synonymous modifications in petL, psbH, ycf2 and ndhA. Phylogenetic analyses using maximum parsimony (MP) and maximum likelihood (ML) methods of a dataset composed of 61 protein-coding genes for 30 taxa provide strong support for the monophyly of several major clades of angiosperms, including monocots, eudicots, rosids and asterids. The MP and ML trees are incongruent in three areas: the position of Amborella and Nymphaeales, relationship of the magnoliid genus Calycanthus, and the monophyly of the eurosid I clade. Both MP and ML trees provide strong support for the monophyly of eurosids II and for the placement of Citrus (Sapindales) sister to a clade including the Malvales/Brassicales. Conclusion This is the first complete chloroplast genome sequence for a member of the Rutaceae and Sapindales. Expansion of the inverted repeat region to include rps19 and part of rpl22 and presence of two truncated copies of rpl22 is unusual among sequenced chloroplast genomes. Availability of a complete Citrus chloroplast genome sequence provides valuable information on intergenic spacer regions and endogenous regulatory sequences for chloroplast genetic engineering. Phylogenetic analyses resolve relationships among several major clades of angiosperms and provide strong support for the monophyly of the eurosid II clade and the position of the Sapindales sister to the Brassicales/Malvales. PMID:17010212

An L-band SAR for repeat pass deformation measurements on a UAV platform

NASA Technical Reports Server (NTRS)

Hensley, Scott; Lou, Yunling; Rosen, Paul; Wheeler, Kevin; Zebker, Howard; Madsen, Soren; Miller, Tim; Hoffman, Jim; Farra, Don

2003-01-01

We are proposing to develop a miniaturized polarimetric L-band synthetic aperture radar (SAR) for repeat-pass differential interferometric measurements of deformation for rapidly deforming surfaces of geophysical interest such as volcanoes or earthquakes that is to be flown on a unmanned aerial vehicle (UAV) or minimally piloted vehicle (MPV). Upon surveying the capabilities and availabilities of such aircraft, the Proteus aircraft and the ALTAIR UAV appear to meet our criteria in terms of payload capabilities, flying altitude, and endurance. To support the repeat pass deformation capability it is necessary to control flight track capability of the aircraft to be within a specified 10 m tube with a goal of 1 m. This requires real-time GPS control of the autopilot to achieve these objectives that has not been demonstrated on these aircraft. Based on the Proteus and ALTAIR's altitude of 13.7 km (45,000 ft), we are designing a fully polarimetric L-band radar with 80 MHz bandwidth and a 16 km range swath. The radar will have an active electronic beam steering antenna to achieve a Doppler centroid stability that is necessary for repeat-pass interferometry. This paper presents some of the trade studies for the platform, instrument and the expected science.

The complete chloroplast genome sequence of Dendrobium officinale.

PubMed

Yang, Pei; Zhou, Hong; Qian, Jun; Xu, Haibin; Shao, Qingsong; Li, Yonghua; Yao, Hui

2016-01-01

The complete chloroplast sequence of Dendrobium officinale, an endangered and economically important traditional Chinese medicine, was reported and characterized. The genome size is 152,018 bp, with 37.5% GC content. A pair of inverted repeats (IRs) of 26,284 bp are separated by a large single-copy region (LSC, 84,944 bp) and a small single-copy region (SSC, 14,506 bp). The complete cp DNA contains 83 protein-coding genes, 39 tRNA genes and 8 rRNA genes. Fourteen genes contained one or two introns.

Multiplexed single-molecule force spectroscopy using a centrifuge.

PubMed

Yang, Darren; Ward, Andrew; Halvorsen, Ken; Wong, Wesley P

2016-03-17

We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise.

Multiplexed single-molecule force spectroscopy using a centrifuge

PubMed Central

Yang, Darren; Ward, Andrew; Halvorsen, Ken; Wong, Wesley P.

2016-01-01

We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise. PMID:26984516

Note: An improved solenoid driver valve for miniature shock tubes.

PubMed

Lynch, P T

2016-05-01

A solenoid driver valve has been built to improve the operating performance of diaphragmless shock tubes, which are used for high pressure, high temperature chemical kinetics, and fluid mechanics studies. For shock tube driver application, the most important characteristics are those of sealing, strength, and quality of the generated shock waves and repeatability of opening characteristics and therefore subsequent post-shock conditions. The main features of the new driver valve are a face o-ring sealing design of the valve, the large internal volume, and through inserts near the solenoid core: adjustable opening characteristics of the valve.

Abr1, a Transposon-Like Element in the Genome of the Cultivated Mushroom Agaricus bisporus (Lange) Imbach

PubMed Central

Sonnenberg, Anton S. M.; Baars, Johan J. P.; Mikosch, Thomas S. P.; Schaap, Peter J.; Van Griensven, Leo J. L. D.

1999-01-01

A 300-bp repetitive element was found in the genome of the white button mushroom, Agaricus bisporus, and designated Abr1. It is present in ∼15 copies per haploid genome in the commercial strain Horst U1. Analysis of seven copies showed 89 to 97% sequence identity. The repeat has features typical of class II transposons (i.e., terminal inverted repeats, subterminal repeats, and a target site duplication of 7 bp). The latter shows a consensus sequence. When used as probe on Southern blots, Abr1 identifies relatively little variation within traditional and present-day commercial strains, indicating that most strains are identical or have a common origin. In contrast to these cultivars, high variation is found among field-collected strains. Furthermore, a remarkable difference in copy numbers of Abr1 was found between A. bisporus isolates with a secondarily homothallic life cycle and those with a heterothallic life cycle. Abr1 is a type II transposon not previously reported in basidiomycetes and appears to be useful for the identification of strains within the species A. bisporus. PMID:10427018

Genotyping and Molecular Identification of Date Palm Cultivars Using Inter-Simple Sequence Repeat (ISSR) Markers.

PubMed

Ayesh, Basim M

2017-01-01

Molecular markers are credible for the discrimination of genotypes and estimation of the extent of genetic diversity and relatedness in a set of genotypes. Inter-simple sequence repeat (ISSR) markers rapidly reveal high polymorphic fingerprints and have been used frequently to determine the genetic diversity among date palm cultivars. This chapter describes the application of ISSR markers for genotyping of date palm cultivars. The application involves extraction of genomic DNA from the target cultivars with reliable quality and quantity. Subsequently the extracted DNA serves as a template for amplification of genomic regions flanked by inverted simple sequence repeats using a single primer. The similarity of each pair of samples is measured by calculating the number of mono- and polymorphic bands revealed by gel electrophoresis. Matrices constructed for similarity and genetic distance are used to build a phylogenetic tree and cluster analysis, to determine the molecular relatedness of cultivars. The protocol describes 3 out of 9 tested primers consistently amplified 31 loci in 6 date palm cultivars, with 28 polymorphic loci.

Mre11-Sae2 and RPA Collaborate to Prevent Palindromic Gene Amplification.

PubMed

Deng, Sarah K; Yin, Yi; Petes, Thomas D; Symington, Lorraine S

2015-11-05

Foldback priming at DNA double-stranded breaks is one mechanism proposed to initiate palindromic gene amplification, a common feature of cancer cells. Here, we show that small (5-9 bp) inverted repeats drive the formation of large palindromic duplications, the major class of chromosomal rearrangements recovered from yeast cells lacking Sae2 or the Mre11 nuclease. RPA dysfunction increased the frequency of palindromic duplications in Sae2 or Mre11 nuclease-deficient cells by ∼ 1,000-fold, consistent with intra-strand annealing to create a hairpin-capped chromosome that is subsequently replicated to form a dicentric isochromosome. The palindromic duplications were frequently associated with duplication of a second chromosome region bounded by a repeated sequence and a telomere, suggesting the dicentric chromosome breaks and repairs by recombination between dispersed repeats to acquire a telomere. We propose secondary structures within single-stranded DNA are potent instigators of genome instability, and RPA and Mre11-Sae2 play important roles in preventing their formation and propagation, respectively. Copyright © 2015 Elsevier Inc. All rights reserved.

The 28S–18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences, length heterogeneity, putative processing sites and potential interactions between U3 small nucleolar RNA and the ribosomal RNA precursor

PubMed Central

Schnare, Murray N.; Collings, James C.; Spencer, David F.; Gray, Michael W.

2000-01-01

In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from ∼11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains tandemly repeated copies of a 19mer sequence. The IGS also contains four copies of an ∼55 nt repeat that has an internal inverted repeat and is also present in the IGS of Leishmania species. We have mapped the C.fasciculata transcription initiation site as well as two other reverse transcriptase stop sites that may be analogous to the A0 and A′ pre-rRNA processing sites within the 5′ external transcribed spacer (ETS) of other eukaryotes. Features that could influence processing at these sites include two stretches of conserved primary sequence and three secondary structure elements present in the 5′ ETS. We also characterized the C.fasciculata U3 snoRNA, which has the potential for base-pairing with pre-rRNA sequences. Finally, we demonstrate that biosynthesis of large subunit rRNA in both C.fasciculata and Trypanosoma brucei involves 3′-terminal addition of three A residues that are not present in the corresponding DNA sequences. PMID:10982863

Highly Sensitive and Long Term Stable Electrochemical Microelectrodes for Implantable Glucose Monitoring Devices

NASA Astrophysics Data System (ADS)

Qiang, Liangliang

A miniature wireless implantable electrochemical glucose system for continuous glucose monitoring with good selectivity, sensitivity, linearity and long term stability was developed. First, highly sensitive, long-term stable and reusable planar H2O2 microelectrodes have been fabricated by microlithography. These electrodes composed of a 300 nm Pt black layer situated on a 5 um thick Au layer, provide effective protection to the underlying chromium adhesion layer. Using repeated cyclic voltammetric sweeps in flowing buffer solution, highly sensitive Pt black working electrodes were realized with five-decade linear dynamic range and low detection limit (10 nM) for H2O2 at low oxidation potentials. Second, a highly sensitive, low cost and flexible microwire biosensor was described using 25-mum thick gold wire as working electrode together with 125-mum thick Pt/Ir and Ag wires as counter and reference electrode, embedded within a PDMS-filled polyethylene tube. Surface area and activity of sensor was enhanced by converting gold electrode to nanoporous configuration followed by electrodeposition of platinum black. Glucose oxidase based biosensors by electrodeposition of poly(o-phenylenediamine) and glucose oxidase on the working electrode, displayed a higher glucose sensitivity (1.2 mA mM-1 cm-2) than highest literature reported. In addition it exhibits wide detection range (up to 20 mM) and selectivity (>95%). Third, novel miniaturized and flexible microelectrode arrays with 8 of 25 mum electrodes displayed the much needed 3D diffusion profiles similar to a single 25 mum microelectrode, but with one order increase in current levels. These microelectrode arrays displayed a H2O2 sensitivity of 13 mA mM-1 cm-2, a wide dynamic range of 100 nM to 10 mM, limit of detection of 10 nM. These microwire based edge plane microsensors incorporated flexibility, miniaturization and low operation potential are an promising approach for continuous in vivo metabolic monitoring. Fourth, homemade miniature wireless potentisotat was fabricated based on low power consumption integrated circuits and surface mount parts. The miniature wireless potentisotat with up to two week life-time for continuous glucose sensing has a size less than 9x22x10 mm and weight ˜3.4 grams. Primary in vivo experiment showed homemade system has the exactly same respond and trend as commercial glucose meter.

A high-throughput lab-on-a-chip interface for zebrafish embryo tests in drug discovery and ecotoxicology

NASA Astrophysics Data System (ADS)

Zhu, Feng; Akagi, Jin; Hall, Chris J.; Crosier, Kathryn E.; Crosier, Philip S.; Delaage, Pierre; Wlodkowic, Donald

2013-12-01

Drug discovery screenings performed on zebrafish embryos mirror with a high level of accuracy. The tests usually performed on mammalian animal models, and the fish embryo toxicity assay (FET) is one of the most promising alternative approaches to acute ecotoxicity testing with adult fish. Notwithstanding this, conventional methods utilising 96-well microtiter plates and manual dispensing of fish embryos are very time-consuming. They rely on laborious and iterative manual pipetting that is a main source of analytical errors and low throughput. In this work, we present development of a miniaturised and high-throughput Lab-on-a-Chip (LOC) platform for automation of FET assays. The 3D high-density LOC array was fabricated in poly-methyl methacrylate (PMMA) transparent thermoplastic using infrared laser micromachining while the off-chip interfaces were fabricated using additive manufacturing processes (FDM and SLA). The system's design facilitates rapid loading and immobilization of a large number of embryos in predefined clusters of traps during continuous microperfusion of drugs/toxins. It has been conceptually designed to seamlessly interface with both upright and inverted fluorescent imaging systems and also to directly interface with conventional microtiter plate readers that accept 96-well plates. We also present proof-of-concept interfacing with a high-speed imaging cytometer Plate RUNNER HD® capable of multispectral image acquisition with resolution of up to 8192 x 8192 pixels and depth of field of about 40 μm. Furthermore, we developed a miniaturized and self-contained analytical device interfaced with a miniaturized USB microscope. This system modification is capable of performing rapid imaging of multiple embryos at a low resolution for drug toxicity analysis.

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.

A variant Tc4 transposable element in the nematode C. elegans could encode a novel protein.

PubMed Central

Li, W; Shaw, J E

1993-01-01

A variant C. elegans Tc4 transposable element, Tc4-rh1030, has been sequenced and is 3483 bp long. The Tc4 element that had been analyzed previously is 1605 bp long, consists of two 774-bp nearly perfect inverted terminal repeats connected by a 57-bp loop, and lacks significant open reading frames. In Tc4-rh1030, by comparison, a 2343-bp novel sequence is present in place of a 477-bp segment in one of the inverted repeats. The novel sequence of Tc4-rh1030 is present about five times per haploid genome and is invariably associated with Tc4 elements; we have used the designation Tc4v to denote this variant subfamily of Tc4 elements. Sequence analysis of three cDNA clones suggests that a Tc4v element contains at least five exons that could encode a novel basic protein of 537 amino acid residues. On northern blots, a 1.6-kb Tc4v-specific transcript was detected in the mutator strain TR679 but not in the wild-type strain N2; Tc4 elements are known to transpose in TR679 but appear to be quiescent in N2. We have analyzed transcripts produced by an unc-33 gene that has the Tc4-rh1030 insertional mutation in its transcribed region; all or almost all of the Tc4v sequence is frequently spliced out of the mutant unc-33 transcripts, sometimes by means of non-consensus splice acceptor sites. Images PMID:8382791

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

Xer1-Mediated Site-Specific DNA Inversions and Excisions in Mycoplasma agalactiae▿ ‡

PubMed Central

Czurda, Stefan; Jechlinger, Wolfgang; Rosengarten, Renate; Chopra-Dewasthaly, Rohini

2010-01-01

Surface antigen variation in Mycoplasma agalactiae, the etiologic agent of contagious agalactia in sheep and goats, is governed by site-specific recombination within the vpma multigene locus encoding the Vpma family of variable surface lipoproteins. This high-frequency Vpma phase switching was previously shown to be mediated by a Xer1 recombinase encoded adjacent to the vpma locus. In this study, it was demonstrated in Escherichia coli that the Xer1 recombinase is responsible for catalyzing vpma gene inversions between recombination sites (RS) located in the 5′-untranslated region (UTR) in all six vpma genes, causing cleavage and strand exchange within a 21-bp conserved region that serves as a recognition sequence. It was further shown that the outcome of the site-specific recombination event depends on the orientation of the two vpma RS, as direct or inverted repeats. While recombination between inverted vpma RS led to inversions, recombination between direct repeat vpma RS led to excisions. Using a newly developed excision assay based on the lacZ reporter system, we were able to successfully demonstrate under native conditions that such Xer1-mediated excisions can indeed also occur in the M. agalactiae type strain PG2, whereas they were not observed in the control xer1-disrupted VpmaY phase-locked mutant (PLMY), which lacks Xer1 recombinase. Unless there are specific regulatory mechanisms preventing such excisions, this might be the cost that the pathogen has to render at the population level for maintaining this high-frequency phase variation machinery. PMID:20562305

A microfluidic reciprocating intracochlear drug delivery system with reservoir and active dose control

PubMed Central

Kim, Ernest S.; Gustenhoven, Erich; Mescher, Mark J.; Pararas, Erin E. Leary; Smith, Kim A.; Spencer, Abigail J.; Tandon, Vishal; Borenstein, Jeffrey T.; Fiering, Jason

2014-01-01

Reciprocating microfluidic drug delivery, as compared to steady or pulsed infusion, has unique features which may be advantageous in many therapeutic applications. We have previously described a device, designed for wearable use in small animal models, which periodically infuses then withdraws a sub-microliter volume of drug solution to and from the endogenous fluid of the inner ear. This delivery approach results in zero net volume of liquid transfer while enabling mass transport of compounds to the cochlea by means of diffusion and mixing. We report here on an advanced wearable delivery system aimed at further miniaturization and complex dose protocols. Enhancements to the system include the incorporation of a planar micropump to generate reciprocating flow and a novel drug reservoir which maintains zero net volume delivery and permits programmable modulation of the drug concentration in the infused bolus. The reciprocating pump is fabricated from laminated polymer films and employs a miniature electromagnetic actuator to meet the size and weight requirements of a head-mounted in vivo guinea pig testing system. The reservoir comprises a long microchannel in series with a micropump, connected in parallel with the reciprocating flow network. We characterized in vitro the response and repeatability of the planar pump and compared the results with a lumped element simulation. We also characterized the performance of the reservoir, including repeatability of dosing and range of dose modulation. Acute in vivo experiments were performed in which the reciprocating pump was used to deliver a test compound to the cochlea of anesthetized guinea pigs to evaluate short-term safety and efficacy of the system. These advances are key steps toward realization of an implantable device for long-term therapeutic applications in humans. PMID:24302432

Minimal and Contributing Sequence Determinants of the cis-Acting Locus of Transfer (clt) of Streptomycete Plasmid pIJ101 Occur within an Intrinsically Curved Plasmid Region

PubMed Central

Ducote, Matthew J.; Prakash, Shubha; Pettis, Gregg S.

2000-01-01

Efficient interbacterial transfer of streptomycete plasmid pIJ101 requires the pIJ101 tra gene, as well as a cis-acting plasmid function known as clt. Here we show that the minimal pIJ101 clt locus consists of a sequence no greater than 54 bp in size that includes essential inverted-repeat and direct-repeat sequences and is located in close proximity to the 3′ end of the korB regulatory gene. Evidence that sequences extending beyond the minimal locus and into the korB open reading frame influence clt transfer function and demonstration that clt-korB sequences are intrinsically curved raise the possibility that higher-order structuring of DNA and protein within this plasmid region may be an inherent feature of efficient pIJ101 transfer. PMID:11073933

Minimal and contributing sequence determinants of the cis-acting locus of transfer (clt) of streptomycete plasmid pIJ101 occur within an intrinsically curved plasmid region.

PubMed

Ducote, M J; Prakash, S; Pettis, G S

2000-12-01

Efficient interbacterial transfer of streptomycete plasmid pIJ101 requires the pIJ101 tra gene, as well as a cis-acting plasmid function known as clt. Here we show that the minimal pIJ101 clt locus consists of a sequence no greater than 54 bp in size that includes essential inverted-repeat and direct-repeat sequences and is located in close proximity to the 3' end of the korB regulatory gene. Evidence that sequences extending beyond the minimal locus and into the korB open reading frame influence clt transfer function and demonstration that clt-korB sequences are intrinsically curved raise the possibility that higher-order structuring of DNA and protein within this plasmid region may be an inherent feature of efficient pIJ101 transfer.

Evidence for large inversion polymorphisms in the human genome from HapMap data

PubMed Central

Bansal, Vikas; Bashir, Ali; Bafna, Vineet

2007-01-01

Knowledge about structural variation in the human genome has grown tremendously in the past few years. However, inversions represent a class of structural variation that remains difficult to detect. We present a statistical method to identify large inversion polymorphisms using unusual Linkage Disequilibrium (LD) patterns from high-density SNP data. The method is designed to detect chromosomal segments that are inverted (in a majority of the chromosomes) in a population with respect to the reference human genome sequence. We demonstrate the power of this method to detect such inversion polymorphisms through simulations done using the HapMap data. Application of this method to the data from the first phase of the International HapMap project resulted in 176 candidate inversions ranging from 200 kb to several megabases in length. Our predicted inversions include an 800-kb polymorphic inversion at 7p22, a 1.1-Mb inversion at 16p12, and a novel 1.2-Mb inversion on chromosome 10 that is supported by the presence of two discordant fosmids. Analysis of the genomic sequence around inversion breakpoints showed that 11 predicted inversions are flanked by pairs of highly homologous repeats in the inverted orientation. In addition, for three candidate inversions, the inverted orientation is represented in the Celera genome assembly. Although the power of our method to detect inversions is restricted because of inherently noisy LD patterns in population data, inversions predicted by our method represent strong candidates for experimental validation and analysis. PMID:17185644

An inverted metamorphic field gradient in the central Brooks Range, Alaska and implications for exhumation of high-pressure/low-temperature metamorphic rocks

USGS Publications Warehouse

Patrick, B.; Till, A.B.; Dinklage, W.S.

1994-01-01

During exhumation of the Brooks Range internal zone, amphibolite-facies rocks were emplaced atop the blueschist/greenschist facies schist belt. The resultant inverted metamorphic field gradient is mappable as a series of isograds encountered as one traverses up structural section. Amphibolite-facies metamorphism occurred at ??? 110 Ma as determined from 40Ar 39Ar analysis of hornblende. This contrasts with 40Ar 39Ar phengite cooling ages from the uderlying schist belt, which are clearly older (by 17-22 m.y.). Fabrics in both the amphibolite-facies rocks and schist belt are characterized by repeated cycles of N-vergent crenulation and transposition that was likely associated with out-of-sequence ductile thrusting in the internal zone of the Brooks Range orogen. Contractional deformation occurred in an overall environment of foreland-directed tectonic transport, broadly synchronous with exhumation of the internal zone, and shortening within the thin-skinned fold and thrust belt. These data are inconsistent with a recently postulated mid-Cretaceous episode of lithospheric extension in northern Alaska. ?? 1994.

Assessment of Ductile-to-Brittle Transition Behavior of Localized Microstructural Regions in a Friction-Stir Welded X80 Pipeline Steel with Miniaturized Charpy V-Notch Testing

NASA Astrophysics Data System (ADS)

Avila, Julian A.; Lucon, Enrico; Sowards, Jeffrey; Mei, Paulo Roberto; Ramirez, Antonio J.

2016-06-01

Friction-stir welding (FSW) is an alternative welding process for pipelines. This technology offers sound welds, good repeatability, and excellent mechanical properties. However, it is of paramount importance to determine the toughness of the welds at low temperatures in order to establish the limits of this technology. Ductile-to-brittle transition curves were generated in the present study by using a small-scale instrumented Charpy machine and miniaturized V-notch specimens (Kleinstprobe, KLST); notches were located in base metal, heat-affected, stirred, and hard zones within a FSW joint of API-5L X80 Pipeline Steel. Specimens were tested at temperatures between 77 K (-196 °C) and 298 K (25 °C). Based on the results obtained, the transition temperatures for the base material and heat-affected zone were below 173 K (-100 °C); conversely, for the stirred and hard zones, it was located around 213 K (-60 °C). Fracture surfaces were characterized and showed a ductile fracture mechanism at high impact energies and a mixture of ductile and brittle mechanisms at low impact energies.

Hybrid molecularly imprinted polymers synthesized with 3-aminopropyltriethoxysilane-methacrylic acid monomer for miniaturized solid-phase extraction: A new and economical sample preparation strategy for determination of acyclovir in urine.

PubMed

Yan, Hongyuan; Wang, Mingyu; Han, Yehong; Qiao, Fengxia; Row, Kyung Ho

2014-06-13

The miniaturized molecularly imprinted solid-phase extraction (mini-MISPE) coupled with high-performance liquid chromatography was proposed for the determination of acyclovir in urine. 1.5-mL tapered plastic centrifuge tube filled with hybrid molecularly imprinted polymers (HMIPs) was used as the cartridge of mini-MISPE, and the HMIPs synthesized with 3-aminopropyltriethoxy silane-methacrylic acid as monomer exhibited good recognition and selectivity for acyclovir. Under the optimized condition, good linear calibration was obtained in a range of 0.5-15μgmL(-1) with the correlation coefficient of 0.9994, and the recoveries at three spiked levels were 91.6-103.3% in urine with the relative standard deviation (RSD) of ≤3.5%. Excellent intra-day and inter-day repeatability were achieved with RSD of ≤2.6% and 4.0% in three different concentrations. This method combined the advantages of HMIPs and mini-MISPE, and it could become an alternative tool for analyzing the residues of acyclovir in complex urine matrices. Copyright © 2014 Elsevier B.V. All rights reserved.

The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms

PubMed Central

Lee, Seung-Bum; Kaittanis, Charalambos; Jansen, Robert K; Hostetler, Jessica B; Tallon, Luke J; Town, Christopher D; Daniell, Henry

2006-01-01

Background Cotton (Gossypium hirsutum) is the most important fiber crop grown in 90 countries. In 2004–2005, US farmers planted 79% of the 5.7-million hectares of nuclear transgenic cotton. Unfortunately, genetically modified cotton has the potential to hybridize with other cultivated and wild relatives, resulting in geographical restrictions to cultivation. However, chloroplast genetic engineering offers the possibility of containment because of maternal inheritance of transgenes. The complete chloroplast genome of cotton provides essential information required for genetic engineering. In addition, the sequence data were used to assess phylogenetic relationships among the major clades of rosids using cotton and 25 other completely sequenced angiosperm chloroplast genomes. Results The complete cotton chloroplast genome is 160,301 bp in length, with 112 unique genes and 19 duplicated genes within the IR, containing a total of 131 genes. There are four ribosomal RNAs, 30 distinct tRNA genes and 17 intron-containing genes. The gene order in cotton is identical to that of tobacco but lacks rpl22 and infA. There are 30 direct and 24 inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Most of the direct repeats are within intergenic spacer regions, introns and a 72 bp-long direct repeat is within the psaA and psaB genes. Comparison of protein coding sequences with expressed sequence tags (ESTs) revealed nucleotide substitutions resulting in amino acid changes in ndhC, rpl23, rpl20, rps3 and clpP. Phylogenetic analysis of a data set including 61 protein-coding genes using both maximum likelihood and maximum parsimony were performed for 28 taxa, including cotton and five other angiosperm chloroplast genomes that were not included in any previous phylogenies. Conclusion Cotton chloroplast genome lacks rpl22 and infA and contains a number of dispersed direct and inverted repeats. RNA editing resulted in amino acid changes with significant impact on their hydropathy. Phylogenetic analysis provides strong support for the position of cotton in the Malvales in the eurosids II clade sister to Arabidopsis in the Brassicales. Furthermore, there is strong support for the placement of the Myrtales sister to the eurosid I clade, although expanded taxon sampling is needed to further test this relationship. PMID:16553962

Mutational Dynamics of Aroid Chloroplast Genomes

PubMed Central

Ahmed, Ibrar; Biggs, Patrick J.; Matthews, Peter J.; Collins, Lesley J.; Hendy, Michael D.; Lockhart, Peter J.

2012-01-01

A characteristic feature of eukaryote and prokaryote genomes is the co-occurrence of nucleotide substitution and insertion/deletion (indel) mutations. Although similar observations have also been made for chloroplast DNA, genome-wide associations have not been reported. We determined the chloroplast genome sequences for two morphotypes of taro (Colocasia esculenta; family Araceae) and compared these with four publicly available aroid chloroplast genomes. Here, we report the extent of genome-wide association between direct and inverted repeats, indels, and substitutions in these aroid chloroplast genomes. We suggest that alternative but not mutually exclusive hypotheses explain the mutational dynamics of chloroplast genome evolution. PMID:23204304

The complete chloroplast genome sequence of Hibiscus syriacus.

PubMed

Kwon, Hae-Yun; Kim, Joon-Hyeok; Kim, Sea-Hyun; Park, Ji-Min; Lee, Hyoshin

2016-09-01

The complete chloroplast genome sequence of Hibiscus syriacus L. is presented in this study. The genome is composed of 161 019 bp in length, with a typical circular structure containing a pair of inverted repeats of 25 745 bp of length separated by a large single-copy region and a small single-copy region of 89 698 bp and 19 831 bp of length, respectively. The overall GC content is 36.8%. One hundred and fourteen genes were annotated, including 81 protein-coding genes, 4 ribosomal RNA genes and 29 transfer RNA genes.

An automated miniaturized Haploscope for testing binocular visual function

NASA Technical Reports Server (NTRS)

Decker, T. A.; Williams, R. E.; Kuether, C. L.; Wyman-Cornsweet, D.

1976-01-01

A computer-controlled binocular vision testing device has been developed as one part of a system designed for NASA to test the vision of astronauts during spaceflight. The device, called the Mark III Haploscope, utilizes semi-automated psychophysical test procedures to measure visual acuity, stereopsis, phorias, fixation disparity and accommodation/convergence relationships. All tests are self-administered, yield quantitative data and may be used repeatedly without subject memorization. Future applications of this programmable, compact device include its use as a clinical instrument to perform routine eye examinations or vision screening, and as a research tool to examine the effects of environment or work-cycle upon visual function.

Direct-Write Printing on Three-Dimensional Geometries for Miniaturized Detector and Electronic Assemblies

NASA Technical Reports Server (NTRS)

Paquette, Beth; Samuels, Margaret; Chen, Peng

2017-01-01

Direct-write printing techniques will enable new detector assemblies that were not previously possible with traditional assembly processes. Detector concepts were manufactured using this technology to validate repeatability. Additional detector applications and printed wires on a 3-dimensional magnetometer bobbin will be designed for print. This effort focuses on evaluating performance for direct-write manufacturing techniques on 3-dimensional surfaces. Direct-write manufacturing has the potential to reduce mass and volume for fabrication and assembly of advanced detector concepts by reducing trace widths down to 10 microns, printing on complex geometries, allowing new electronic concept production, and reduced production times of complex those electronics.

Deletion of a 77-base-pair inverted repeat element alters the synthesis of surface polysaccharides in Porphyromonas gingivalis.

PubMed

Bainbridge, Brian W; Hirano, Takanori; Grieshaber, Nicole; Davey, Mary E

2015-04-01

Bacterial cell surface glycans, such as capsular polysaccharides and lipopolysaccharides (LPS), influence host recognition and are considered key virulence determinants. The periodontal pathogen Porphyromonas gingivalis is known to display at least three different types of surface glycans: O-LPS, A-LPS, and K-antigen capsule. We have shown that PG0121 (in strain W83) encodes a DNABII histone-like protein and that this gene is transcriptionally linked to the K-antigen capsule synthesis genes, generating a large ∼19.4-kb transcript (PG0104-PG0121). Furthermore, production of capsule is deficient in a PG0121 mutant strain. In this study, we report on the identification of an antisense RNA (asRNA) molecule located within a 77-bp inverted repeat (77bpIR) element located near the 5' end of the locus. We show that overexpression of this asRNA decreases the amount of capsule produced, indicating that this asRNA can impact capsule synthesis in trans. We also demonstrate that deletion of the 77bpIR element and thereby synthesis of the large 19.4-kb transcript also diminishes, but does not eliminate, capsule synthesis. Surprisingly, LPS structures were also altered by deletion of the 77bpIR element, and reactivity to monoclonal antibodies specific to both O-LPS and A-LPS was eliminated. Additionally, reduced reactivity to these antibodies was also observed in a PG0106 mutant, indicating that this putative glycosyltransferase, which is required for capsule synthesis, is also involved in LPS synthesis in strain W83. We discuss our finding in the context of how DNABII proteins, an antisense RNA molecule, and the 77bpIR element may modulate expression of surface polysaccharides in P. gingivalis. The periodontal pathogen Porphyromonas gingivalis displays at least three different types of cell surface glycans: O-LPS, A-LPS, and K-antigen capsule. We have shown using Northern analysis that the K-antigen capsule locus encodes a large transcript (∼19.4 kb), encompassing a 77-bp inverted repeat (77bpIR) element near the 5' end. Here, we report on the identification of an antisense RNA (asRNA) encoded within the 77bpIR. We show that overexpression of this asRNA or deletion of the element decreases the amount of capsule. LPS structures were also altered by deletion of the 77bpIR, and reactivity to monoclonal antibodies to both O-LPS and A-LPS was eliminated. Our data indicate that the 77bpIR element is involved in modulating both LPS and capsule synthesis in P. gingivalis. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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

PubMed Central

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

2015-01-01

ABSTRACT Bacterial cell surface glycans, such as capsular polysaccharides and lipopolysaccharides (LPS), influence host recognition and are considered key virulence determinants. The periodontal pathogen Porphyromonas gingivalis is known to display at least three different types of surface glycans: O-LPS, A-LPS, and K-antigen capsule. We have shown that PG0121 (in strain W83) encodes a DNABII histone-like protein and that this gene is transcriptionally linked to the K-antigen capsule synthesis genes, generating a large ∼19.4-kb transcript (PG0104-PG0121). Furthermore, production of capsule is deficient in a PG0121 mutant strain. In this study, we report on the identification of an antisense RNA (asRNA) molecule located within a 77-bp inverted repeat (77bpIR) element located near the 5′ end of the locus. We show that overexpression of this asRNA decreases the amount of capsule produced, indicating that this asRNA can impact capsule synthesis in trans. We also demonstrate that deletion of the 77bpIR element and thereby synthesis of the large 19.4-kb transcript also diminishes, but does not eliminate, capsule synthesis. Surprisingly, LPS structures were also altered by deletion of the 77bpIR element, and reactivity to monoclonal antibodies specific to both O-LPS and A-LPS was eliminated. Additionally, reduced reactivity to these antibodies was also observed in a PG0106 mutant, indicating that this putative glycosyltransferase, which is required for capsule synthesis, is also involved in LPS synthesis in strain W83. We discuss our finding in the context of how DNABII proteins, an antisense RNA molecule, and the 77bpIR element may modulate expression of surface polysaccharides in P. gingivalis. IMPORTANCE The periodontal pathogen Porphyromonas gingivalis displays at least three different types of cell surface glycans: O-LPS, A-LPS, and K-antigen capsule. We have shown using Northern analysis that the K-antigen capsule locus encodes a large transcript (∼19.4 kb), encompassing a 77-bp inverted repeat (77bpIR) element near the 5′ end. Here, we report on the identification of an antisense RNA (asRNA) encoded within the 77bpIR. We show that overexpression of this asRNA or deletion of the element decreases the amount of capsule. LPS structures were also altered by deletion of the 77bpIR, and reactivity to monoclonal antibodies to both O-LPS and A-LPS was eliminated. Our data indicate that the 77bpIR element is involved in modulating both LPS and capsule synthesis in P. gingivalis. PMID:25622614

Evidence that meiotic pairing starts at the telomeres: Molecular analysis of recombination in a family with a pericentric X chromosome inversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shashi, V.; Allinson, P.S.; Golden, W.L.

1994-09-01

Recent studies in yeast have shown that telomeres rather than centromeres lead in chromosome movement just prior to meiosis and may have a role in recombination. Cytological studies of meiosis in Drosophila and mice have shown that in pericentric inversion heterozygotes there is lack of loop formation, with recobmination seen only outside the inversion. In a family with Duchenne muscular dystrophy (DMD) we recognized that only affected males and carrier females had a pericentric X chromosome inversion (inv X(p11.4;q26)). Since the short arm inversion breakpoint was proximal to the DMD locus, it could not be implicated in the mutational eventmore » causing DMD. There was no history of infertility, recurrent miscarriages or liveborn unbalanced females to suggest there was recombination within the inversion. We studied 22 members over three generations to understand the pattern of meiotic recombination between the normal and the inverted X chromosome. In total, 17 meioses involving the inverted X chromosome in females were studied by cytogenetic analysis and 16 CA repeat polymorphisms along the length of the X chromosome. Results: (a) There was complete concordance between the segregation of the DMD mutation and the inverted X chromosome. (b) On DNA analysis, there was complete absence of recombination within the inverted segment. We also found no recombination at the DMD locus. Recombination was seen only at Xp22 and Xq27-28. (c) Recombination was seen in the same individual at both Xp22 and Xq27-28 without recombination otherwise. Conclusions: (1) Pericentric X inversions reduce the genetic map length of the chromosome, with the physical map length being normal. (2) Meiotic X chromosome pairing in this family is initiated at the telomeres. (3) Following telomeric pairing in pericentric X chromosome inversions, there is inhibition of recombination within the inversion and adjacent regions.« less

One hundred fold increase in current carrying capacity in a carbon nanotube–copper composite

PubMed Central

Subramaniam, Chandramouli; Yamada, Takeo; Kobashi, Kazufumi; Sekiguchi, Atsuko; Futaba, Don N.; Yumura, Motoo; Hata, Kenji

2013-01-01

Increased portability, versatility and ubiquity of electronics devices are a result of their progressive miniaturization, requiring current flow through narrow channels. Present-day devices operate close to the maximum current-carrying-capacity (that is, ampacity) of conductors (such as copper and gold), leading to decreased lifetime and performance, creating demand for new conductors with higher ampacity. Ampacity represents the maximum current-carrying capacity of the object that depends both on the structure and material. Here we report a carbon nanotube–copper composite exhibiting similar conductivity (2.3–4.7 × 105 S cm−1) as copper (5.8 × 105 S cm−1), but with a 100-times higher ampacity (6 × 108 A cm−2). Vacuum experiments demonstrate that carbon nanotubes suppress the primary failure pathways in copper as observed by the increased copper diffusion activation energy (∼2.0 eV) in carbon nanotube–copper composite, explaining its higher ampacity. This is the only material with both high conductivity and high ampacity, making it uniquely suited for applications in microscale electronics and inverters. PMID:23877359

One hundred fold increase in current carrying capacity in a carbon nanotube-copper composite

NASA Astrophysics Data System (ADS)

Subramaniam, Chandramouli; Yamada, Takeo; Kobashi, Kazufumi; Sekiguchi, Atsuko; Futaba, Don N.; Yumura, Motoo; Hata, Kenji

2013-07-01

Increased portability, versatility and ubiquity of electronics devices are a result of their progressive miniaturization, requiring current flow through narrow channels. Present-day devices operate close to the maximum current-carrying-capacity (that is, ampacity) of conductors (such as copper and gold), leading to decreased lifetime and performance, creating demand for new conductors with higher ampacity. Ampacity represents the maximum current-carrying capacity of the object that depends both on the structure and material. Here we report a carbon nanotube-copper composite exhibiting similar conductivity (2.3-4.7 × 105Scm-1) as copper (5.8 × 105Scm-1), but with a 100-times higher ampacity (6 × 108Acm-2). Vacuum experiments demonstrate that carbon nanotubes suppress the primary failure pathways in copper as observed by the increased copper diffusion activation energy (~2.0eV) in carbon nanotube-copper composite, explaining its higher ampacity. This is the only material with both high conductivity and high ampacity, making it uniquely suited for applications in microscale electronics and inverters.

Development of a Practical Broadband Active Vibration Control System

NASA Technical Reports Server (NTRS)

Schiller, Noah H.; Perey, Daniel F.; Cabell, Randolph H.

2011-01-01

The goal of this work is to develop robust, lightweight, and low-power control units that can be used to suppress structural vibration in flexible aerospace structures. In particular, this paper focuses on active damping, which is implemented using compact decentralized control units distributed over the structure. Each control unit consists of a diamond-shaped piezoelectric patch actuator, three miniature accelerometers, and analog electronics. The responses from the accelerometers are added together and then integrated to give a signal proportional to velocity. The signal is then inverted, amplified, and applied to the actuator, which generates a control force that is out of phase with the measured velocity. This paper describes the development of the control system, including a detailed description of the control and power electronics. The paper also presents experimental results acquired on a Plexiglas window blank. Five identical control units installed around the perimeter of the window achieved 10 dB peak reductions and a 2.4 dB integrated reduction of the spatially averaged velocity of the window between 500 and 3000 Hz.

Novel concept for driving the linear compressor of a micro-miniature split Stirling cryogenic cooler

NASA Astrophysics Data System (ADS)

Maron, V.; Veprik, A.; Finkelstein, L.; Vilenchik, H.; Ziv, I.; Pundak, N.

2009-05-01

New methods of carrying out homeland security and antiterrorist operations call for the development of a new generation of mechanically cooled, portable, battery powered infrared imagers, relying on micro-miniature Stirling cryogenic coolers of rotary or linear types. Since split Stirling linearly driven micro-miniature cryogenic coolers have inherently longer life spans, low vibration export and better aural stealth as compared to their rotary driven rivals, they are more suitable for the above applications. The performance of such cryogenic coolers depends strongly on the efficacy of their electronic drivers. In a traditional approach, the PWM power electronics produce the fixed frequency tonal driving voltage/current, the magnitude of which is modulated via a PID control law so as to maintain the desired focal plane array temperature. The disadvantage of such drivers is that they draw high ripple current from the system's power bus. This results in the need for an oversized DC power supply (battery packs) and power electronic components, low efficiency due to excessive conductive losses and high residual electromagnetic interference which in turn degrades the performance of other systems connected to the same power bus. Without either an active line filter or large and heavy passive filtering, other electronics can not be powered from the same power bus, unless they incorporate heavy filtering at their inputs. The authors present the results of a feasibility study towards developing a novel "pumping" driver consuming essentially constant instant battery power/current without making use of an active or passive filter. In the tested setup, the driver relies on a bidirectional controllable bridge, invertible with the driving frequency, and a fast regulated DC/DC converter which maintains a constant level of current consumed from the DC power supply and thus operates in input current control mode. From the experimental results, the steady-state power consumed by the linear compressor remains the same as compared with the traditional sine wave driver, the voltage and current drawn from the battery pack is essentially free of low frequency ripple (this without use of any kind of filtering) and the overall coefficient of performance of the driver is in excess of 94% over the entire working range of supply voltages. Such a driver free of sine forming PWM stage and have reduced power peaks in all power conversion components.

The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae

PubMed Central

Zheng, Renhua; Xu, Haibin; Zhou, Yanwei; Li, Meiping; Lu, Fengjuan; Dong, Yini; Liu, Xin; Chen, Jinhui; Shi, Jisen

2016-01-01

Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild. PMID:27560965

Inheritance of congenital cataracts and microphthalmia in the Miniature Schnauzer.

PubMed

Gelatt, K N; Samuelson, D A; Bauer, J E; Das, N D; Wolf, E D; Barrie, K P; Andresen, T L

1983-06-01

Congenital cataracts and microphthalmia in the Miniature Schnauzer were inherited as an autosomal recessive trait. Eighteen matings of affected X affected Miniature Schnauzers resulted in 87 offspring with congenital cataracts and microphthalmia (49 males/38 females). Two matings of congenital cataractous and microphthalmic Miniature Schnauzers (2 females) X a normal Miniature Schnauzer (1 male) yielded 11 clinically normal Miniature Schnauzers (7 males/4 females). Eighteen matings of congenital cataractous and microphthalmic Miniature Schnauzers (6 males) X carrier Miniature Schnauzers (9 females) produced 81 offspring; 39 exhibited congenital cataracts and microphthalmia (20 males/19 females) and 42 had clinically normal eyes (17 males/25 females).

A Dynamic Tandem Repeat in Monocotyledons Inferred from a Comparative Analysis of Chloroplast Genomes in Melanthiaceae.

PubMed

Do, Hoang Dang Khoa; Kim, Joo-Hwan

2017-01-01

Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species Heloniopsis tubiflora (Korea) and Xerophyllum tenax (USA) to cover the gap between molecular data and explore "hot spots" for genomic events in Melanthiaceae. Comparative analysis of 23 complete cpDNA sequences revealed that there were different stages of deletion in the rps16 region across the Melanthiaceae. Based on the partial or complete loss of rps16 gene in cpDNA, we have firstly reported potential molecular markers for recognizing two sections ( Veratrum and Fuscoveratrum ) of Veratrum . Melathiaceae exhibits a significant change in the junction between large single copy and inverted repeat regions, ranging from trnH_GUG to a part of rps3 . Our results show an accumulation of tandem repeats in the rpl23-ycf2 regions of cpDNAs. Small conserved sequences exist and flank tandem repeats in further observation of this region across most of the examined taxa of Liliales. Therefore, we propose three scenarios in which different small repeated sequences were used during SSM events to generate newly distinct types of repeats. Occasionally, prior to the SSM process, point mutation event and double strand break repair occurred and induced the formation of initial repeat units which are indispensable in the SSM process. SSM may have likely occurred more frequently for short repeats than for long repeat sequences in tribe Parideae (Melanthiaceae, Liliales). Collectively, these findings add new evidence of dynamic results from SSM in chloroplast genomes which can be useful for further evolutionary studies in angiosperms. Additionally, genomics events in cpDNA are potential resources for mining molecular markers in Liliales.

Office Chromatography: Precise printing of sample solutions on miniaturized thin-layer phases and utilization for scanning Direct Analysis in Real Time mass spectrometry.

PubMed

Häbe, Tim T; Morlock, Gertrud E

2015-09-25

Office Chromatography combines achievements in office technologies with miniaturized planar chromatography. In the life sciences, printing of materials became an accepted technique, whereas in separation science, the use of printers for chromatography is at its infancy. A bubble-jet printer was modified for exact application on miniaturized plates. Technical modifications included the removal of all unnecessary parts and the improvement of the positioning system, purge unit and sample supply system. Evaluation was performed via a slide scanner and image evaluation software. Printing of a food dye mixture solution (n=5) led to a calculated mean deposition volume of 13±1nL/mm(2) per print-cycle. A mean determination coefficient (R(2); n=5) of 0.9990 was obtained for application of increasing volumes, executed via increasing band widths of 50-200μm (corresponding to 2-8nL). Using larger band widths and multiple print jobs, deposition volumes of up to the microliter scale represented an alternative to cost-intensive standard equipment. After print, separation, detection and digital evaluation of five food dyes, mean R(2) (n=5) were obtained between 0.9977 and 0.9995. The accuracy of printing was proven by mean recovery rates of 101-105% with repeatabilities of 3-7% (%RSD, n=5). The transfer to nanostructured ultrathin-layer plates proved the synergetic potential of these fields of research. First, this modified printer was suited for printing of finely graduated scales of three preservatives for determination of the spatial resolution of scanning Direct Analysis in Real Time mass spectrometry. Copyright © 2015 Elsevier B.V. All rights reserved.

Systematic Design of a Magnetically Levitated Brushless DC Motor for a Reversible Rotary Intra-Aortic Blood Pump.

PubMed

Wang, Yaxin; Logan, Thomas G; Smith, P Alex; Hsu, Po-Lin; Cohn, William E; Xu, Liping; McMahon, Richard A

2017-10-01

The IntraVAD is a miniature intra-aortic ventricular assist device (VAD) designed to work in series with the compromised left ventricle. A reverse-rotation control (RRc) mode has been developed to increase myocardial perfusion and reduce ventricular volume. The RRc mode includes forward rotation in systole and reverse rotation in diastole, which requires the IntraVAD to periodically reverse its rotational direction in synchrony with the cardiac cycle. This periodic reversal leads to changes in pressure force over the impeller, which makes the entire system less stable. To eliminate the mechanical wear of a contact bearing and provide active control over the axial position of the rotor, a miniature magnetically levitated bearing (i.e., the PM-Coil module) composed of two concentric permanent magnetic (PM) rings and a pair of coils-one on each side-was proposed to provide passive radial and active axial rotor stabilization. In the early design stage, the numerical finite element method (FEM) was used to optimize the geometry of the brushless DC (BLDC) motor and the maglev module, but constructing a new model each time certain design parameters were adjusted required substantial computation time. Because the design criteria for the module had to be modified to account for the magnetic force produced by the motor and for the hemodynamic changes associated with pump operation, a simplified analytic expression was derived for the expected magnetic forces. Suitable bearings could then be designed capable of overcoming these forces without repeating the complicated FEM simulation for the motor. Using this method at the initial design stage can inform the design of the miniature maglev BLDC motor for the proposed pulsatile axial-flow VAD. © 2017 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Serum C-reactive protein concentrations in healthy Miniature Schnauzer dogs.

PubMed

Wong, Valerie M; Kidney, Beverly A; Snead, Elisabeth C R; Myers, Sherry L; Jackson, Marion L

2011-09-01

C-reactive protein (CRP) is a sensitive marker for inflammation in people and dogs. In people, an association between CRP concentration and atherosclerosis has been reported. Atherosclerosis is rare in dogs, but the Miniature Schnauzer breed may be at increased risk for developing this vascular disease. It is not known if CRP concentrations in Miniature Schnauzer dogs differ from those in other dog breeds. Our objectives were to validate an automated human CRP assay for measuring CRP in dogs and compare CRP concentrations in healthy Miniature Schnauzer dogs with those in non-Miniature Schnauzer breeds. Sera from 37 non-Miniature Schnauzer dogs with inflammatory disease were pooled and used to validate a human CRP immunoturbidimetric assay for measuring canine CRP. Blood was collected from 20 healthy Miniature Schnauzer dogs and 41 healthy dogs of other breeds. Median serum CRP concentration of healthy Miniature Schnauzer dogs was compared with that of healthy non-Miniature Schnauzer dogs. The human CRP assay measured CRP reliably with linearity between 0 and 20 mg/L. CRP concentration for healthy Miniature Schnauzer dogs (median 4.0 mg/L, minimum-maximum 0-18.2 mg/L) was significantly higher than for the healthy non-Miniature Schnauzer dogs (median 0.1 mg/L, minimum-maximum 0-10.7 mg/L); 17 of the 20 Miniature Schnauzer dogs had values that overlapped with those of the non-Miniature Schnauzer dogs. Median CRP concentration of Miniature Schnauzer dogs was slightly higher than that of other breeds of dogs. A relationship between higher CRP concentration in Miniature Schnauzer dogs and idiopathic hyperlipidemia, pancreatitis, and possible increased risk for atherosclerosis remains to be determined. ©2011 American Society for Veterinary Clinical Pathology.

Endogenous siRNAs and noncoding RNA-derived small RNAs are expressed in adult mouse hippocampus and are up-regulated in olfactory discrimination training.

PubMed

Smalheiser, Neil R; Lugli, Giovanni; Thimmapuram, Jyothi; Cook, Edwin H; Larson, John

2011-01-01

We previously proposed that endogenous siRNAs may regulate synaptic plasticity and long-term gene expression in the mammalian brain. Here, a hippocampal-dependent task was employed in which adult mice were trained to execute a nose-poke in a port containing one of two simultaneously present odors in order to obtain a reward. Mice demonstrating olfactory discrimination training were compared to pseudo-training and nose-poke control groups; size-selected hippocampal RNA was subjected to Illumina deep sequencing. Sequences that aligned uniquely and exactly to the genome without uncertain nucleotide assignments, within exons or introns of MGI annotated genes, were examined further. The data confirm that small RNAs having features of endogenous siRNAs are expressed in brain; that many of them derive from genes that regulate synaptic plasticity (and have been implicated in neuropsychiatric diseases); and that hairpin-derived endo-siRNAs and the 20- to 23-nt size class of small RNAs show a significant increase during an early stage of training. The most abundant putative siRNAs arose from an intronic inverted repeat within the SynGAP1 locus; this inverted repeat was a substrate for dicer in vitro, and SynGAP1 siRNA was specifically associated with Argonaute proteins in vivo. Unexpectedly, a dramatic increase with training (more than 100-fold) was observed for a class of 25- to 30-nt small RNAs derived from specific sites within snoRNAs and abundant noncoding RNAs (Y1 RNA, RNA component of mitochondrial RNAse P, 28S rRNA, and 18S rRNA). Further studies are warranted to characterize the role(s) played by endogenous siRNAs and noncoding RNA-derived small RNAs in learning and memory.

The first complete chloroplast genome sequence of a lycophyte,Huperzia lucidula (Lycopodiaceae)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolf, Paul G.; Karol, Kenneth G.; Mandoli, Dina F.

2005-02-01

We used a unique combination of techniques to sequence the first complete chloroplast genome of a lycophyte, Huperzia lucidula. This plant belongs to a significant clade hypothesized to represent the sister group to all other vascular plants. We used fluorescence-activated cell sorting (FACS) to isolate the organelles, rolling circle amplification (RCA) to amplify the genome, and shotgun sequencing to 8x depth coverage to obtain the complete chloroplast genome sequence. The genome is 154,373bp, containing inverted repeats of 15,314 bp each, a large single-copy region of 104,088 bp, and a small single-copy region of 19,671 bp. Gene order is more similarmore » to those of mosses, liverworts, and hornworts than to gene order for other vascular plants. For example, the Huperziachloroplast genome possesses the bryophyte gene order for a previously characterized 30 kb inversion, thus supporting the hypothesis that lycophytes are sister to all other extant vascular plants. The lycophytechloroplast genome data also enable a better reconstruction of the basaltracheophyte genome, which is useful for inferring relationships among bryophyte lineages. Several unique characters are observed in Huperzia, such as movement of the gene ndhF from the small single copy region into the inverted repeat. We present several analyses of evolutionary relationships among land plants by using nucleotide data, amino acid sequences, and by comparing gene arrangements from chloroplast genomes. The results, while still tentative pending the large number of chloroplast genomes from other key lineages that are soon to be sequenced, are intriguing in themselves, and contribute to a growing comparative database of genomic and morphological data across the green plants.« less

Nucleotide sequence of the gene for the Mr 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of Mr 38,950

PubMed Central

Zurawski, Gerard; Bohnert, Hans J.; Whitfeld, Paul R.; Bottomley, Warwick

1982-01-01

The gene for the so-called Mr 32,000 rapidly labeled photosystem II thylakoid membrane protein (here designated psbA) of spinach (Spinacia oleracea) chloroplasts is located on the chloroplast DNA in the large single-copy region immediately adjacent to one of the inverted repeat sequences. In this paper we show that the size of the mRNA for this protein is ≈ 1.25 kilobases and that the direction of transcription is towards the inverted repeat unit. The nucleotide sequence of the gene and its flanking regions is presented. The only large open reading frame in the sequence codes for a protein of Mr 38,950. The nucleotide sequence of psbA from Nicotiana debneyi also has been determined, and comparison of the sequences from the two species shows them to be highly conserved (>95% homology) throughout the entire reading frame. Conservation of the amino acid sequence is absolute, there being no changes in a total of 353 residues. This leads us to conclude that the primary translation product of psbA must be a protein of Mr 38,950. The protein is characterized by the complete absence of lysine residues and is relatively rich in hydrophobic amino acids, which tend to be clustered. Transcription of spinach psbA starts about 86 base pairs before the first ATG codon. Immediately upstream from this point there is a sequence typical of that found in E. coli promoters. An almost identical sequence occurs in the equivalent region of N. debneyi DNA. Images PMID:16593262

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

PubMed Central

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

2014-01-01

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

Regulation of ecmF gene expression and genetic hierarchy among STATa, CudA, and MybC on several prestalk A-specific gene expressions in Dictyostelium.

PubMed

Saga, Yukika; Inamura, Tomoka; Shimada, Nao; Kawata, Takefumi

2016-05-01

STATa, a Dictyostelium homologue of metazoan signal transducer and activator of transcription, is important for the organizer function in the tip region of the migrating Dictyostelium slug. We previously showed that ecmF gene expression depends on STATa in prestalk A (pstA) cells, where STATa is activated. Deletion and site-directed mutagenesis analysis of the ecmF/lacZ fusion gene in wild-type and STATa null strains identified an imperfect inverted repeat sequence, ACAAATANTATTTGT, as a STATa-responsive element. An upstream sequence element was required for efficient expression in the rear region of pstA zone; an element downstream of the inverted repeat was necessary for sufficient prestalk expression during culmination. Band shift analyses using purified STATa protein detected no sequence-specific binding to those ecmF elements. The only verified upregulated target gene of STATa is cudA gene; CudA directly activates expL7 gene expression in prestalk cells. However, ecmF gene expression was almost unaffected in a cudA null mutant. Several previously reported putative STATa target genes were also expressed in cudA null mutant but were downregulated in STATa null mutant. Moreover, mybC, which encodes another transcription factor, belonged to this category, and ecmF expression was downregulated in a mybC null mutant. These findings demonstrate the existence of a genetic hierarchy for pstA-specific genes, which can be classified into two distinct STATa downstream pathways, CudA dependent and independent. The ecmF expression is indirectly upregulated by STATa in a CudA-independent activation manner but dependent on MybC, whose expression is positively regulated by STATa. © 2016 Japanese Society of Developmental Biologists.

The Complete Chloroplast Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction

PubMed Central

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 (IRA). This loss event should have occurred and led to the contraction of IRs after ginkgos diverged from other gymnosperms. A novel cluster of three transfer RNA (tRNA) genes, trnY-AUA, trnC-ACA, and trnSeC-UCA, was predicted to be located between trnC-GCA and rpoB of the large single-copy region. Our phylogenetic analysis strongly suggests that the three predicted tRNA genes are duplicates of trnC-GCA. Interestingly, in ginkgo cpDNA, the loss of one ycf2 copy does not significantly elevate the synonymous rate (Ks) of the retained copy, which disagrees with the view of Perry and Wolfe (2002) that one of the two-copy genes is subjected to elevated Ks when its counterpart has been lost. We hypothesize that the loss of one ycf2 is likely recent, and therefore, the acquired Ks of the retained copy is low. Our data reveal that ginkgo possesses several unique features that contribute to our understanding of the cpDNA evolution in seed plants. PMID:22403032

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

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.

The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots

PubMed Central

Niu, Zhitao; Xue, Qingyun; Zhu, Shuying; Sun, Jing; Liu, Wei; Ding, Xiaoyu

2017-01-01

Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome) and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented. In this study, we compared 53 orchid plastomes, including four newly sequenced ones, that represent four remote genera: Dendrobium, Goodyera, Paphiopedilum, and Vanilla. These differ from one another not only in their lengths of inverted repeats and small single copy regions but also in their retention of ndh genes. Comparative analyses of the plastomes revealed that the expansion of inverted repeats in Paphiopedilum and Vanilla is associated with a loss of ndh genes. In orchid plastomes, mutational hotspots are genus specific. After having carefully examined the data, we propose that the three loci 5′trnK-rps16, trnS-trnG, and rps16-trnQ might be powerful markers for genera within Epidendroideae, and clpP-psbB and rps16-trnQ might be markers for genera within Cypripedioideae. After analyses of a partitioned dataset, we found that our plastid phylogenomic trees were congruent in a topology where two one-stamened subfamilies (i.e., Epidendroideae and Orchidoideae) were sisters to a multi-stamened subfamily (i.e., Cypripedioideae) rather than to the other one-stamened subfamily (Vanilloideae), suggesting that the living one-stamened orchids are paraphyletic. PMID:28515737

Analysis of the siRNA-Mediated Gene Silencing Process Targeting Three Homologous Genes Controlling Soybean Seed Oil Quality.

PubMed

Lu, Sha; Yin, Xiaoyan; Spollen, William; Zhang, Ning; Xu, Dong; Schoelz, James; Bilyeu, Kristin; Zhang, Zhanyuan J

2015-01-01

In the past decade, RNA silencing has gained significant attention because of its success in genomic scale research and also in the genetic improvement of crop plants. However, little is known about the molecular basis of siRNA processing in association with its target transcript. To reveal this process for improving hpRNA-mediated gene silencing in crop plants, the soybean GmFAD3 gene family was chosen as a test model. We analyzed RNAi mutant soybean lines in which three members of the GmFAD3 gene family were silenced. The silencing levels of FAD3A, FAD3B and FAD3C were correlated with the degrees of sequence homology between the inverted repeat of hpRNA and the GmFAD3 transcripts in the RNAi lines. Strikingly, transgenes in two of the three RNAi lines were heavily methylated, leading to a dramatic reduction of hpRNA-derived siRNAs. Small RNAs corresponding to the loop portion of the hairpin transcript were detected while much lower levels of siRNAs were found outside of the target region. siRNAs generated from the 318-bp inverted repeat were found to be diced much more frequently at stem sequences close to the loop and associated with the inferred cleavage sites on the target transcripts, manifesting "hot spots". The top candidate hpRNA-derived siRNA share certain sequence features with mature miRNA. This is the first comprehensive and detailed study revealing the siRNA-mediated gene silencing mechanism in crop plants using gene family GmFAD3 as a test model.

Characterization of IntA, a Bidirectional Site-Specific Recombinase Required for Conjugative Transfer of the Symbiotic Plasmid of Rhizobium etli CFN42

PubMed Central

Hernández-Tamayo, Rogelio; Sohlenkamp, Christian; Puente, José Luis; Brom, Susana

2013-01-01

Site-specific recombination occurs at short specific sequences, mediated by the cognate recombinases. IntA is a recombinase from Rhizobium etli CFN42 and belongs to the tyrosine recombinase family. It allows cointegration of plasmid p42a and the symbiotic plasmid via site-specific recombination between attachment regions (attA and attD) located in each replicon. Cointegration is needed for conjugative transfer of the symbiotic plasmid. To characterize this system, two plasmids harboring the corresponding attachment sites and intA were constructed. Introduction of these plasmids into R. etli revealed IntA-dependent recombination events occurring at high frequency. Interestingly, IntA promotes not only integration, but also excision events, albeit at a lower frequency. Thus, R. etli IntA appears to be a bidirectional recombinase. IntA was purified and used to set up electrophoretic mobility shift assays with linear fragments containing attA and attD. IntA-dependent retarded complexes were observed only with fragments containing either attA or attD. Specific retarded complexes, as well as normal in vivo recombination abilities, were seen even in derivatives harboring only a minimal attachment region (comprising the 5-bp central region flanked by 9- to 11-bp inverted repeats). DNase I-footprinting assays with IntA revealed specific protection of these zones. Mutations that disrupt the integrity of the 9- to 11-bp inverted repeats abolish both specific binding and recombination ability, while mutations in the 5-bp central region severely reduce both binding and recombination. These results show that IntA is a bidirectional recombinase that binds to att regions without requiring neighboring sequences as enhancers of recombination. PMID:23935046

Analysis of ADP-glucose pyrophosphorylase expression during turion formation induced by abscisic acid in Spirodela polyrhiza (greater duckweed)

PubMed Central

2012-01-01

Background Aquatic plants differ in their development from terrestrial plants in their morphology and physiology, but little is known about the molecular basis of the major phases of their life cycle. Interestingly, in place of seeds of terrestrial plants their dormant phase is represented by turions, which circumvents sexual reproduction. However, like seeds turions provide energy storage for starting the next growing season. Results To begin a characterization of the transition from the growth to the dormant phase we used abscisic acid (ABA), a plant hormone, to induce controlled turion formation in Spirodela polyrhiza and investigated their differentiation from fronds, representing their growth phase, into turions with respect to morphological, ultra-structural characteristics, and starch content. Turions were rich in anthocyanin pigmentation and had a density that submerged them to the bottom of liquid medium. Transmission electron microscopy (TEM) of turions showed in comparison to fronds shrunken vacuoles, smaller intercellular space, and abundant starch granules surrounded by thylakoid membranes. Turions accumulated more than 60% starch in dry mass after two weeks of ABA treatment. To further understand the mechanism of the developmental switch from fronds to turions, we cloned and sequenced the genes of three large-subunit ADP-glucose pyrophosphorylases (APLs). All three putative protein and exon sequences were conserved, but the corresponding genomic sequences were extremely variable mainly due to the invasion of miniature inverted-repeat transposable elements (MITEs) into introns. A molecular three-dimensional model of the SpAPLs was consistent with their regulatory mechanism in the interaction with the substrate (ATP) and allosteric activator (3-PGA) to permit conformational changes of its structure. Gene expression analysis revealed that each gene was associated with distinct temporal expression during turion formation. APL2 and APL3 were highly expressed in earlier stages of turion development, while APL1 expression was reduced throughout turion development. Conclusions These results suggest that the differential expression of APLs could be used to enhance energy flow from photosynthesis to storage of carbon in aquatic plants, making duckweeds a useful alternative biofuel feedstock. PMID:22235974

Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae.

PubMed

Dai, Shutao; Hou, Jinna; Long, Yan; Wang, Jing; Li, Cong; Xiao, Qinqin; Jiang, Xiaoxue; Zou, Xiaoxiao; Zou, Jun; Meng, Jinling

2015-06-19

Miniature inverted repeat transposable elements (MITEs) are important components of eukaryotic genomes, with hundreds of families and many copies, which may play important roles in gene regulation and genome evolution. However, few studies have investigated the molecular mechanisms involved. In our previous study, a Tourist-like MITE, Monkey King, was identified from the promoter region of a flowering time gene, BnFLC.A10, in Brassica napus. Based on this MITE, the characteristics and potential roles on gene regulation of the MITE family were analyzed in Brassicaceae. The characteristics of the Tourist-like MITE family Monkey King in Brassicaceae, including its distribution, copies and insertion sites in the genomes of major Brassicaceae species were analyzed in this study. Monkey King was actively amplified in Brassica after divergence from Arabidopsis, which was indicated by the prompt increase in copy number and by phylogenetic analysis. The genomic variations caused by Monkey King insertions, both intra- and inter-species in Brassica, were traced by PCR amplification. Genomic sequence analysis showed that most complete Monkey King elements are located in gene-rich regions, less than 3kb from genes, in both the B. rapa and A. thaliana genomes. Sixty-seven Brassica expressed sequence tags carrying Monkey King fragments were also identified from the NCBI database. Bisulfite sequencing identified specific DNA methylation of cytosine residues in the Monkey King sequence. A fragment containing putative TATA-box motifs in the MITE sequence could bind with nuclear protein(s) extracted from leaves of B. napus plants. A Monkey King-related microRNA, bna-miR6031, was identified in the microRNA database. In transgenic A. thaliana, when the Monkey King element was inserted upstream of 35S promoter, the promoter activity was weakened. Monkey King, a Brassicaceae Tourist-like MITE family, has amplified relatively recently and has induced intra- and inter-species genomic variations in Brassica. Monkey King elements are most abundant in the vicinity of genes and may have a substantial effect on genome-wide gene regulation in Brassicaceae. Monkey King insertions potentially regulate gene expression and genome evolution through epigenetic modification and new regulatory motif production.

Molecular cloning and long terminal repeat sequences of human endogenous retrovirus genes related to types A and B retrovirus genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ono, M.

1986-06-01

By using a DNA fragment primarily encoding the reverse transcriptase (pol) region of the Syrian hamster intracisternal A particle (IAP; type A retrovirus) gene as a probe, human endogenous retrovirus genes, tentatively termed HERV-K genes, were cloned from a fetal human liver gene library. Typical HERV-K genes were 9.1 or 9.4 kilobases in length, having long terminal repeats (LTRs) of ca. 970 base pairs. Many structural features commonly observed on the retrovirus LTRs, such as the TATAA box, polyadenylation signal, and terminal inverted repeats, were present on each LTR, and a lysine (K) tRNA having a CUU anticodon was identifiedmore » as a presumed primer tRNA. The HERV-K LTR, however, had little sequence homology to either the IAP LTR or other typical oncovirus LTRs. By filter hybridization, the number of HERV-K genes was estimated to be ca. 50 copies per haploid human genome. The cloned mouse mammary tumor virus (type B) gene was found to hybridize with both the HERV-K and IAP genes to essentially the same extent.« less

Reducing uncertainties in the velocities determined by inversion of phase velocity dispersion curves using synthetic seismograms

NASA Astrophysics Data System (ADS)

Hosseini, Seyed Mehrdad

Characterizing the near-surface shear-wave velocity structure using Rayleigh-wave phase velocity dispersion curves is widespread in the context of reservoir characterization, exploration seismology, earthquake engineering, and geotechnical engineering. This surface seismic approach provides a feasible and low-cost alternative to the borehole measurements. Phase velocity dispersion curves from Rayleigh surface waves are inverted to yield the vertical shear-wave velocity profile. A significant problem with the surface wave inversion is its intrinsic non-uniqueness, and although this problem is widely recognized, there have not been systematic efforts to develop approaches to reduce the pervasive uncertainty that affects the velocity profiles determined by the inversion. Non-uniqueness cannot be easily studied in a nonlinear inverse problem such as Rayleigh-wave inversion and the only way to understand its nature is by numerical investigation which can get computationally expensive and inevitably time consuming. Regarding the variety of the parameters affecting the surface wave inversion and possible non-uniqueness induced by them, a technique should be established which is not controlled by the non-uniqueness that is already affecting the surface wave inversion. An efficient and repeatable technique is proposed and tested to overcome the non-uniqueness problem; multiple inverted shear-wave velocity profiles are used in a wavenumber integration technique to generate synthetic time series resembling the geophone recordings. The similarity between synthetic and observed time series is used as an additional tool along with the similarity between the theoretical and experimental dispersion curves. The proposed method is proven to be effective through synthetic and real world examples. In these examples, the nature of the non-uniqueness is discussed and its existence is shown. Using the proposed technique, inverted velocity profiles are estimated and effectiveness of this technique is evaluated; in the synthetic example, final inverted velocity profile is compared with the initial target velocity model, and in the real world example, final inverted shear-wave velocity profile is compared with the velocity model from independent measurements in a nearby borehole. Real world example shows that it is possible to overcome the non-uniqueness and distinguish the representative velocity profile for the site that also matches well with the borehole measurements.

Biomolecular and structural analyses of cauliflower-like DNAs by ultraviolet, circular dichroism, and fluorescence spectroscopies in comparison with natural DNA.

PubMed

Gill, Pooria; Ranjbar, Bijan; Saber, Reza; Khajeh, Khosro; Mohammadian, Mehdi

2011-07-01

Cauliflower-like DNAs are stem-loop DNAs that are fabricated periodically in inverted repetitions from deoxyribonucleic acid phosphates (dNTPs) by loop-mediated isothermal amplification (LAMP). Cauliflower-like DNAs have ladder-shape behaviors on gel electrophoresis, and increasing the time of LAMP leads to multiplying the repetitions, stem-loops, and electrophoretic bands. Cauliflower-like DNAs were fabricated via LAMP using two loop primers, two bumper primers, dNTPs, a λ-phage DNA template, and a Bst DNA polymerase in 75- and 90-min periods. These times led to manufacturing two types of cauliflower-like DNAs with different contents of inverted repetitions and stem-loops, which were clearly indicated by two comparable electrophoresis patterns in agarose gel. LAMP-fabricated DNAs and natural dsB-DNA (salmon genomic DNA) were dialyzed in Gomori phosphate buffer (10 mM, pH 7.4) to be isolated from salts, nucleotides, and primers. Dialyzed DNAs were studied using UV spectroscopy, circular dichroism spectropolarimetry, and fluorescence spectrophotometry. Structural analyses indicated reduction of the molecular ellipticity and extinction coefficients in comparison with B-DNA. Also, cauliflower-like DNAs demonstrated less intrinsic and more extrinsic fluorescence in comparison with natural DNA. The overwinding and lengthening of the cauliflower-like configurations of LAMP DNAs led to changes in physical parameters of this type of DNA in comparison with natural DNA. The results obtained introduced new biomolecular characteristics of DNA macromolecules fabricated within a LAMP process and show the effects of more inverted repeats and stem-loops, which are manufactured by lengthening the process.

Capturing Postseismic Processes of the 2016 Mw 7.1 Kumamoto Earthquake, Japan, Using Dense, Continuous GPS and Short-repeat Time ALOS-2 InSAR Data: Implications for the Shallow Slip Deficit Problem

NASA Astrophysics Data System (ADS)

Milliner, C. W. D.; Burgmann, R.; Wang, T.; Inbal, A.; Bekaert, D. P.; Liang, C.; Fielding, E. J.

2017-12-01

Separating the contribution of shallow coseismic slip from rapidly decaying, postseismic afterslip in surface rupturing events has been difficult to resolve due to the typically sparse configuration of GPS networks and long-repeat time of InSAR acquisitions. Whether shallow fault motion along surface ruptures is a result of coseismic slip, or largely a product of rapid afterslip occurring within the first minutes to days, has significant implications for our understanding of the mechanics and frictional behavior of faulting in the shallow crust. To test this behavior in the case of a major surface rupturing event, we attempt to quantify the co- and postseismic slip of the 2016 Mw 7.1 Kumamoto earthquake sequence using a dense and continuous GPS network ( 10 km spacing), with short-repeat time, ALOS-2 InSAR data. Using the Network Inversion Filter method, we jointly invert the GPS and InSAR data to obtain a time history of afterslip in the first minutes to months following the mainshock. From our initial results, we find no clear evidence of significant shallow afterslip (i.e., no observable slip > 30 cm at depths of < 3 km, a minimum resolvable value), that could account for the 1 m of coseismic deficit of shallow slip inferred from our static finite-fault inversion. Our results show, aside from significant volumetric changes related to poroelastic processes, the majority of shallow fault slip was largely complete after rupture cessation. We also attempt to improve our coseismic slip model by implementing a method that inverts changes in seismicity rates for coseismic slip, helping constrain parts of the model space at depth where geodetic data loses resolving power. The use of geodetic data with the ability to resolve near-field, coseismic deformation and rapidly decaying postseismic processes will aid in our understanding of the frictional properties of shallow faulting, giving more reliable predictions for ground motion simulations and seismic hazard assessments.

The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae

PubMed Central

de Cambiaire, Jean-Charles; Otis, Christian; Turmel, Monique; Lemieux, Claude

2007-01-01

Background In the Chlorophyta – the green algal phylum comprising the classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae – the chloroplast genome displays a highly variable architecture. While chlorophycean chloroplast DNAs (cpDNAs) deviate considerably from the ancestral pattern described for the prasinophyte Nephroselmis olivacea, the degree of remodelling sustained by the two ulvophyte cpDNAs completely sequenced to date is intermediate relative to those observed for chlorophycean and trebouxiophyte cpDNAs. Chlorella vulgaris (Chlorellales) is currently the only photosynthetic trebouxiophyte whose complete cpDNA sequence has been reported. To gain insights into the evolutionary trends of the chloroplast genome in the Trebouxiophyceae, we sequenced cpDNA from the filamentous alga Leptosira terrestris (Ctenocladales). Results The 195,081-bp Leptosira chloroplast genome resembles the 150,613-bp Chlorella genome in lacking a large inverted repeat (IR) but differs greatly in gene order. Six of the conserved genes present in Chlorella cpDNA are missing from the Leptosira gene repertoire. The 106 conserved genes, four introns and 11 free standing open reading frames (ORFs) account for 48.3% of the genome sequence. This is the lowest gene density yet observed among chlorophyte cpDNAs. Contrary to the situation in Chlorella but similar to that in the chlorophycean Scenedesmus obliquus, the gene distribution is highly biased over the two DNA strands in Leptosira. Nine genes, compared to only three in Chlorella, have significantly expanded coding regions relative to their homologues in ancestral-type green algal cpDNAs. As observed in chlorophycean genomes, the rpoB gene is fragmented into two ORFs. Short repeats account for 5.1% of the Leptosira genome sequence and are present mainly in intergenic regions. Conclusion Our results highlight the great plasticity of the chloroplast genome in the Trebouxiophyceae and indicate that the IR was lost on at least two separate occasions. The intriguing similarities of the derived features exhibited by Leptosira cpDNA and its chlorophycean counterparts suggest that the same evolutionary forces shaped the IR-lacking chloroplast genomes in these two algal lineages. PMID:17610731

Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms.

PubMed

Ruhlman, Tracey; Lee, Seung-Bum; Jansen, Robert K; Hostetler, Jessica B; Tallon, Luke J; Town, Christopher D; Daniell, Henry

2006-08-31

Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombinant proteins in carrot have had limited success in terms of protein accumulation in the edible tap roots. Plastid genetic engineering offers the potential to overcome this limitation, as demonstrated by the accumulation of BADH in chromoplasts of carrot taproots to confer exceedingly high levels of salt resistance. The complete plastid genome of carrot provides essential information required for genetic engineering. Additionally, the sequence data add to the rapidly growing database of plastid genomes for assessing phylogenetic relationships among angiosperms. The complete carrot plastid genome is 155,911 bp in length, with 115 unique genes and 21 duplicated genes within the IR. There are four ribosomal RNAs, 30 distinct tRNA genes and 18 intron-containing genes. Repeat analysis reveals 12 direct and 2 inverted repeats > or = 30 bp with a sequence identity > or = 90%. Phylogenetic analysis of nucleotide sequences for 61 protein-coding genes using both maximum parsimony (MP) and maximum likelihood (ML) were performed for 29 angiosperms. Phylogenies from both methods provide strong support for the monophyly of several major angiosperm clades, including monocots, eudicots, rosids, asterids, eurosids II, euasterids I, and euasterids II. The carrot plastid genome contains a number of dispersed direct and inverted repeats scattered throughout coding and non-coding regions. This is the first sequenced plastid genome of the family Apiaceae and only the second published genome sequence of the species-rich euasterid II clade. Both MP and ML trees provide very strong support (100% bootstrap) for the sister relationship of Daucus with Panax in the euasterid II clade. These results provide the best taxon sampling of complete chloroplast genomes and the strongest support yet for the sister relationship of Caryophyllales to the asterids. The availability of the complete plastid genome sequence should facilitate improved transformation efficiency and foreign gene expression in carrot through utilization of endogenous flanking sequences and regulatory elements.

New approaches to provide ride-through for critical loads in electric power distribution systems

NASA Astrophysics Data System (ADS)

Montero-Hernandez, Oscar C.

2001-07-01

The extensive use of electronic circuits has enabled modernization, automation, miniaturization, high quality, low cost, and other achievements regarding electric loads in the last decades. However, modern electronic circuits and systems are extremely sensitive to disturbances from the electric power supply. In fact, the rate at which these disturbances happen is considerable as has been documented in recent years. In response to the power quality concerns presented previously, this dissertation is proposing new approaches to provide ride-through for critical loads during voltage disturbances with emphasis on voltage sags. In this dissertation, a new approach based on an AC-DC-AC system is proposed to provide ride-through for critical loads connected in buildings and/or an industrial system. In this approach, a three-phase IGBT inverter with a built in Dc-link voltage regulator is suitably controlled along with static by-pass switches to provide continuous power to critical loads. During a disturbance, the input utility source is disconnected and the power from the inverter is connected to the load. The remaining voltage in the AC supply is converted to DC and compensated before being applied to the inverter and the load. After detecting normal utility conditions, power from the utility is restored to the critical load. In order to achieve an extended ride-through capability a second approach is introduced. In this case, the Dc-link voltage regulator is performed by a DC-DC Buck-Boost converter. This new approach has the capability to mitigate voltage variations below and above the nominal value. In the third approach presented in this dissertation, a three-phase AC to AC boost converter is investigated. This converter provides a boosting action for the utility input voltages, right before they are applied to the load. The proposed Pulse Width Modulation (PWM) control strategy ensures independent control of each phase and compensates for both single-phase or poly-phase voltage sags. Algorithms capable of detecting voltage disturbances such as voltage sags, voltage swells, flicker, frequency change, and harmonics in a fast and reliable way are investigated and developed in this dissertation as an essential part of the approaches previously described. Simulation and experimental work has been done to validate the feasibility of all approaches under the most common voltage disturbances such as single-phase voltage sags and three-phase voltage sags.

The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species.

PubMed

Chen, Caihui; Zheng, Yongjie; Liu, Sian; Zhong, Yongda; Wu, Yanfang; Li, Jiang; Xu, Li-An; Xu, Meng

2017-01-01

Cinnamomum camphora , a member of the Lauraceae family, is a valuable aromatic and timber tree that is indigenous to the south of China and Japan. All parts of Cinnamomum camphora have secretory cells containing different volatile chemical compounds that are utilized as herbal medicines and essential oils. Here, we reported the complete sequencing of the chloroplast genome of Cinnamomum camphora using illumina technology. The chloroplast genome of Cinnamomum camphora is 152,570 bp in length and characterized by a relatively conserved quadripartite structure containing a large single copy region of 93,705 bp, a small single copy region of 19,093 bp and two inverted repeat (IR) regions of 19,886 bp. Overall, the genome contained 123 coding regions, of which 15 were repeated in the IR regions. An analysis of chloroplast sequence divergence revealed that the small single copy region was highly variable among the different genera in the Lauraceae family. A total of 40 repeat structures and 83 simple sequence repeats were detected in both the coding and non-coding regions. A phylogenetic analysis indicated that Calycanthus is most closely related to Lauraceae , both being members of Laurales , which forms a sister group to Magnoliids . The complete sequence of the chloroplast of Cinnamomum camphora will aid in in-depth taxonomical studies of the Lauraceae family in the future. The genetic sequence information will also have valuable applications for chloroplast genetic engineering.

Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates.

PubMed

Weng, Mao-Lun; Blazier, John C; Govindu, Madhumita; Jansen, Robert K

2014-03-01

Geraniaceae plastid genomes are highly rearranged, and each of the four genera already sequenced in the family has a distinct genome organization. This study reports plastid genome sequences of six additional species, Francoa sonchifolia, Melianthus villosus, and Viviania marifolia from Geraniales, and Pelargonium alternans, California macrophylla, and Hypseocharis bilobata from Geraniaceae. These genome sequences, combined with previously published species, provide sufficient taxon sampling to reconstruct the ancestral plastid genome organization of Geraniaceae and the rearrangements unique to each genus. The ancestral plastid genome of Geraniaceae has a 4 kb inversion and a reduced, Pelargonium-like small single copy region. Our ancestral genome reconstruction suggests that a few minor rearrangements occurred in the stem branch of Geraniaceae followed by independent rearrangements in each genus. The genomic comparison demonstrates that a series of inverted repeat boundary shifts and inversions played a major role in shaping genome organization in the family. The distribution of repeats is strongly associated with breakpoints in the rearranged genomes, and the proportion and the number of large repeats (>20 bp and >60 bp) are significantly correlated with the degree of genome rearrangements. Increases in the degree of plastid genome rearrangements are correlated with the acceleration in nonsynonymous substitution rates (dN) but not with synonymous substitution rates (dS). Possible mechanisms that might contribute to this correlation, including DNA repair system and selection, are discussed.

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes.

PubMed

Cer, Regina Z; Bruce, Kevin H; Mudunuri, Uma S; Yi, Ming; Volfovsky, Natalia; Luke, Brian T; Bacolla, Albino; Collins, Jack R; Stephens, Robert M

2011-01-01

Although the capability of DNA to form a variety of non-canonical (non-B) structures has long been recognized, the overall significance of these alternate conformations in biology has only recently become accepted en masse. In order to provide access to genome-wide locations of these classes of predicted structures, we have developed non-B DB, a database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides the most complete list of alternative DNA structure predictions available, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively. The database also contains motifs predicted to form static DNA bends, short tandem repeats and homo(purine•pyrimidine) tracts that have been associated with disease. The database has been built using the latest releases of the human, chimp, dog, macaque and mouse genomes, so that the results can be compared directly with other data sources. In order to make the data interpretable in a genomic context, features such as genes, single-nucleotide polymorphisms and repetitive elements (SINE, LINE, etc.) have also been incorporated. The database is accessed through query pages that produce results with links to the UCSC browser and a GBrowse-based genomic viewer. It is freely accessible at http://nonb.abcc.ncifcrf.gov.

Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei

PubMed Central

2012-01-01

Background At the core of the RNA interference (RNAi) pathway in Trypanosoma brucei is a single Argonaute protein, TbAGO1, with an established role in controlling retroposon and repeat transcripts. Recent evidence from higher eukaryotes suggests that a variety of genomic sequences with the potential to produce double-stranded RNA are sources for small interfering RNAs (siRNAs). Results To test whether such endogenous siRNAs are present in T. brucei and to probe the individual role of the two Dicer-like enzymes, we affinity purified TbAGO1 from wild-type procyclic trypanosomes, as well as from cells deficient in the cytoplasmic (TbDCL1) or nuclear (TbDCL2) Dicer, and subjected the bound RNAs to Illumina high-throughput sequencing. In wild-type cells the majority of reads originated from two classes of retroposons. We also considerably expanded the repertoire of trypanosome siRNAs to encompass a family of 147-bp satellite-like repeats, many of the regions where RNA polymerase II transcription converges, large inverted repeats and two pseudogenes. Production of these newly described siRNAs is strictly dependent on the nuclear DCL2. Notably, our data indicate that putative centromeric regions, excluding the CIR147 repeats, are not a significant source for endogenous siRNAs. Conclusions Our data suggest that endogenous RNAi targets may be as evolutionarily old as the mechanism itself. PMID:22925482

Comparative Chloroplast Genomes of Pinaceae: Insights into the Mechanism of Diversified Genomic Organizations

PubMed Central

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

2011-01-01

Abstract Pinaceae, the largest family of conifers, has diversified organizations of chloroplast genomes (cpDNAs) with the two typical inverted repeats (IRs) highly reduced. To unravel the mechanism of this genomic diversification, we examined the cpDNA organizations from 53 species of the ten Pinaceous genera, including those of Larix decidua (122,474 bp), Picea morrisonicola (124,168 bp), and Pseudotsuga wilsoniana (122,513 bp), which were firstly elucidated. The results uncovered four distinct cpDNA forms (A−C and P) that are due to rearrangements of two ∼20 and ∼21 kb specific fragments. The C form was documented for the first time and the A form might be the most ancestral one. In addition, only the individuals of Ps. macrocarpa and Ps. wilsoniana were detected to have isomeric cpDNA forms. Three types (types 1−3) of Pinaceae-specific repeats situated nearby the rearranged fragments were found to be syntenic. We hypothesize that type 1 (949 ± 343 bp) and type 3 (608 ± 73 bp) repeats are substrates for homologous recombination (HR), whereas type 2 repeats are likely inactive for HR because of their relatively short sizes (151 ± 30 bp). Conversions among the four distinct forms may be achieved by HR and mediated by type 1 or 3 repeats, thus resulting in increased diversity of cpDNA organizations. We propose that in the Pinaceae cpDNAs, the reduced IRs have lost HR activity, then decreasing the diversity of cpDNA organizations, but the specific repeats that the evolution endowed Pinaceae complement the reduced IRs and increase the diversity of cpDNA organizations. PMID:21402866

General survey of hAT transposon superfamily with highlight on hobo element in Drosophila.

PubMed

Ladevèze, Véronique; Chaminade, Nicole; Lemeunier, Françoise; Periquet, Georges; Aulard, Sylvie

2012-09-01

The hAT transposons, very abundant in all kingdoms, have a common evolutionary origin probably predating the plant-fungi-animal divergence. In this paper we present their general characteristics. Members of this superfamily belong to Class II transposable elements. hAT elements share transposase, short terminal inverted repeats and eight base-pairs duplication of genomic target. We focus on hAT elements in Drosophila, especially hobo. Its distribution, dynamics and impact on genome restructuring in laboratory strains as well as in natural populations are reported. Finally, the evolutionary history of hAT elements, their domestication and use as transgenic tools are discussed.

The complete chloroplast genome sequence of the medicinal plant Andrographis paniculata.

PubMed

Ding, Ping; Shao, Yanhua; Li, Qian; Gao, Junli; Zhang, Runjing; Lai, Xiaoping; Wang, Deqin; Zhang, Huiye

2016-07-01

The complete chloroplast genome of Andrographis paniculata, an important medicinal plant with great economic value, has been studied in this article. The genome size is 150,249 bp in length, with 38.3% GC content. A pair of inverted repeats (IRs, 25,300 bp) are separated by a large single copy region (LSC, 82,459 bp) and a small single-copy region (SSC, 17,190 bp). The chloroplast genome contains 114 unique genes, 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. In these genes, 15 genes contained 1 intron and 3 genes comprised of 2 introns.

The complete chloroplast genome sequence of Dianthus superbus var. longicalycinus.

PubMed

Gurusamy, Raman; Lee, Do-Hyung; Park, SeonJoo

2016-05-01

The complete chloroplast genome (cpDNA) sequence of Dianthus superbus var. longicalycinus is an economically important traditional Chinese medicine was reported and characterized. The cpDNA of Dianthus superbus var. longicalycinus is 149,539 bp, with 36.3% GC content. A pair of inverted repeats (IRs) of 24,803 bp is separated by a large single-copy region (LSC, 82,805 bp) and a small single-copy region (SSC, 17,128 bp). It encodes 85 protein-coding genes, 36 tRNA genes and 8 rRNA genes. Of 129 individual genes, 13 genes encoded one intron and three genes have two introns.

Complete plastid genome of Astragalus mongholicus var. nakaianus (Fabaceae).

PubMed

Choi, In-Su; Kim, Joo-Hwan; Choi, Byoung-Hee

2016-07-01

The first complete plastid genome (plastome) of the largest angiosperm genus, Astragalus, was sequenced for the Korean endangered endemic species A. mongholicus var. nakaianus. Its genome is relatively short (123,633 bp) because it lacks an Inverted Repeat (IR) region. It comprises 110 genes, including four unique rRNAs, 30 tRNAs, and 76 protein-coding genes. Similar to other closely related plastomes, rpl22 and rps16 are absent. The putative pseudogene with abnormal stop codons is atpE. This plastome has no additional inversions when compared with highly variable plastomes from IRLC tribes Fabeae and Trifolieae. Our phylogenetic analysis confirms the non-monophyly of Galegeae.

The complete chloroplast genome sequence of Dendrobium nobile.

PubMed

Yan, Wenjin; Niu, Zhitao; Zhu, Shuying; Ye, Meirong; Ding, Xiaoyu

2016-11-01

The complete chloroplast (cp) genome sequence of Dendrobium nobile, an endangered and traditional Chinese medicine with important economic value, is presented in this article. The total genome size is 150,793 bp, containing a large single copy (LSC) region (84,939 bp) and a small single copy region (SSC) (13,310 bp) which were separated by two inverted repeat (IRs) regions (26,272 bp). The overall GC contents of the plastid genome were 38.8%. In total, 130 unique genes were annotated and they were consisted of 76 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Fourteen genes contained one or two introns.

Adenovirus sequences required for replication in vivo.

PubMed Central

Wang, K; Pearson, G D

1985-01-01

We have studied the in vivo replication properties of plasmids carrying deletion mutations within cloned adenovirus terminal sequences. Deletion mapping located the adenovirus DNA replication origin entirely within the first 67 bp of the adenovirus inverted terminal repeat. This region could be further subdivided into two functional domains: a minimal replication origin and an adjacent auxillary region which boosted the efficiency of replication by more than 100-fold. The minimal origin occupies the first 18 to 21 bp and includes sequences conserved between all adenovirus serotypes. The adjacent auxillary region extends past nucleotide 36 but not past nucleotide 67 and contains the binding site for nuclear factor I. Images PMID:2991857

A re-examination of the mere exposure effect: The influence of repeated exposure on recognition, familiarity, and liking.

PubMed

Montoya, R Matthew; Horton, Robert S; Vevea, Jack L; Citkowicz, Martyna; Lauber, Elissa A

2017-05-01

To evaluate the veracity of models of the mere exposure effect and to understand the processes that moderate the effect, we conducted a meta-analysis of the influence of repeated exposure on liking, familiarity, recognition, among other evaluations. We estimated parameters from 268 curve estimates drawn from 81 articles and revealed that the mere exposure effect was characterized by a positive slope and negative quadratic effect consistent with an inverted-U shaped curve. In fact, such curves were associated with (a) all visual, but not auditory stimuli; (b) exposure durations shorter than 10 s and longer than 1 min; (c) both homogeneous and heterogeneous presentation types; and (d) ratings that were taken after all stimuli were presented. We conclude that existing models for the mere exposure effect do not adequately account for the findings, and we provide a framework to help guide future research. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Computational Analysis of Mouse piRNA Sequence and Biogenesis

PubMed Central

Betel, Doron; Sheridan, Robert; Marks, Debora S; Sander, Chris

2007-01-01

The recent discovery of a new class of 30-nucleotide long RNAs in mammalian testes, called PIWI-interacting RNA (piRNA), with similarities to microRNAs and repeat-associated small interfering RNAs (rasiRNAs), has raised puzzling questions regarding their biogenesis and function. We report a comparative analysis of currently available piRNA sequence data from the pachytene stage of mouse spermatogenesis that sheds light on their sequence diversity and mechanism of biogenesis. We conclude that (i) there are at least four times as many piRNAs in mouse testes than currently known; (ii) piRNAs, which originate from long precursor transcripts, are generated by quasi-random enzymatic processing that is guided by a weak sequence signature at the piRNA 5′ends resulting in a large number of distinct sequences; and (iii) many of the piRNA clusters contain inverted repeats segments capable of forming double-strand RNA fold-back segments that may initiate piRNA processing analogous to transposon silencing. PMID:17997596

SV40 host-substituted variants: a new look at the monkey DNA inserts and recombinant junctions.

PubMed

Singer, Maxine; Winocour, Ernest

2011-04-10

The available monkey genomic data banks were examined in order to determine the chromosomal locations of the host DNA inserts in 8 host-substituted SV40 variant DNAs. Five of the 8 variants contained more than one linked monkey DNA insert per tandem repeat unit and in all cases but one, the 19 monkey DNA inserts in the 8 variants mapped to different locations in the monkey genome. The 50 parental DNAs (32 monkey and 18 SV40 DNA segments) which spanned the crossover and flanking regions that participated in monkey/monkey and monkey/SV40 recombinations were characterized by substantial levels of microhomology of up to 8 nucleotides in length; the parental DNAs also exhibited direct and inverted repeats at or adjacent to the crossover sequences. We discuss how the host-substituted SV40 variants arose and the nature of the recombination mechanisms involved. Copyright © 2011 Elsevier Inc. All rights reserved.

In vivo measurement of spinal column viscoelasticity--an animal model.

PubMed

Hult, E; Ekström, L; Kaigle, A; Holm, S; Hansson, T

1995-01-01

The goal of this study was to measure the in vivo viscoelastic response of spinal motion segments loaded in compression using a porcine model. Nine pigs were used in the study. The animals were anaesthetized and, using surgical techniques, four intrapedicular screws were inserted into the vertebrae of the L2-L3 motion segment. A miniaturized servohydraulic exciter capable of compressing the motion segment was mounted on to the screws. In six animals, a loading scheme consisting of 50 N and 100 N of compression, each applied for 10 min, was used. Each loading period was followed by 10 min restitution with zero load. The loading scheme was repeated four times. Three animals were examined for stiffening effects by consecutively repeating eight times 50 N loading for 5 min followed by 5 min restitution with zero load. This loading scheme was repeated using a 100 N load level. The creep-recovery behavior of the motion segment was recorded continuously. Using non-linear regression techniques, the experimental data were used for evaluating the parameters of a three-parameter standard linear solid model. Correlation coefficients of the order of 0.85 or higher were obtained for the three independent parameters of the model. A survey of the data shows that the viscous deformation rate was a function of the load level. Also, repeated loading at 100 N seemed to induce long-lasting changes in the viscoelastic properties of the porcine lumbar motion segment.

Complete chloroplast genome of Trachelium caeruleum: extensiverearrangements are associated with repeats and tRNAs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haberle, Rosemarie C.; Fourcade, Matthew L.; Boore, Jeffrey L.

2006-01-09

Chloroplast genome structure, gene order and content arehighly conserved in land plants. We sequenced the complete chloroplastgenome sequence of Trachelium caeruleum (Campanulaceae) a member of anangiosperm family known for highly rearranged chloroplast genomes. Thetotal genome size is 162,321 bp with an IR of 27,273 bp, LSC of 100,113bp and SSC of 7,661 bp. The genome encodes 115 unique genes, with 19duplicated in the IR, a tRNA (trnI-CAU) duplicated once in the LSC and aprotein coding gene (psbJ) duplicated twice, for a total of 137 genes.Four genes (ycf15, rpl23, infA and accD) are truncated and likelynonfunctional; three others (clpP, ycf1 andmore » ycf2) are so highly divergedthat they may now be pseudogenes. The most conspicuous feature of theTrachelium genome is the presence of eighteen internally unrearrangedblocks of genes that have been inverted or relocated within the genome,relative to the typical gene order of most angiosperm chloroplastgenomes. Recombination between repeats or tRNAs has been suggested as twomeans of chloroplast genome rearrangements. We compared the relativenumber of repeats in Trachelium to eight other angiosperm chloroplastgenomes, and evaluated the location of repeats and tRNAs in relation torearrangements. Trachelium has the highest number and largest repeats,which are concentrated near inversion endpoints or other rearrangements.tRNAs occur at many but not all inversion endpoints. There is likely nosingle mechanism responsible for the remarkable number of alterations inthis genome, but both repeats and tRNAs are clearly associated with theserearrangements. Land plant chloroplast genomes are highly conserved instructure, gene order and content. The chloroplast genomes of ferns, thegymnosperm Ginkgo, and most angiosperms are nearly collinear, reflectingthe gene order in lineages that diverged from lycopsids and the ancestralchloroplast gene order over 350 million years ago (Raubeson and Jansen,1992). Although earlier mapping studies identified a number of taxa inwhich several rearrangements have occurred (reviewed in Raubeson andJansen, 2005), an extraordinary number of chloroplast genome alterationsare concentrated in several families in the angiosperm order Asterales(sensu APGII, Bremer et al., 2003). Gene mapping studies ofrepresentatives of the Campanulaceae (Cosner, 1993; Cosner et al.,1997,2004) and Lobeliaceae (Knox et al., 1993; Knox and Palmer, 1999)identified large inversions, contraction and expansion of the invertedrepeat regions, and several insertions and deletions in the cpDNAs ofthese closely related taxa. Detailed restriction site and gene mapping ofthe chloroplast genome of Trachelium caeruleum (Campanulaceae) identifiedseven to ten large inversions, families of repeats associated withrearrangements, possible transpositions, and even the disruption ofoperons (Cosner et al., 1997). Seventeen other members of theCampanulaceae were mapped and exhibit many additional rearrangements(Cosner et al., 2004). What happened in this lineage that made itsusceptible to so many chloroplast genome rearrangements? How do normallyvery conserved chloroplast genomes change? The cause of rearrangements inthis group is unclear based on the limited resolution available withmapping techniques. Several mechanisms have been proposed to explain howrearrangements occur: recombination between repeats, transposition, ortemporary instability due to loss of the inverted repeat (Raubeson andJansen, 2005). Sequencing whole chloroplast genomes within theCampanulaceae offers a unique opportunity to examine both the extent andmechanisms of rearrangements within a phylogenetic framework.We reporthere the first complete chloroplast genome sequence of a member of theCampanulaceae, Trachelium caeruleum. This work will serve as a benchmarkfor subsequent, comparative sequencing and analysis of other members ofthis family and close relatives, with the goal of further understandingchloroplast genome evolution. We confirmed features previously identifiedthrough mapping, and discovered many additional structural changes,including several partial to entire gene duplications, deterioration ofat least four normally conserved chloroplast genes into gene fragments,and the nature and position of numerous repeat elements at or nearinversion endpoints. The focus of this paper is on analyses of sequencesat or near these rearrangements in Trachelium caeruleum. Inversions arebelieved to occur due to the presence of repeat elements subject tohomologous recombination (Palmer, 1991; Knox et al., 1993). Repeats mayfacilitate inversions or other genome rearrangements (Achaz et al.,2003), and higher incidences of repeats have been correlated with greaternumbers of rearrangements (Rocha, 2003). Alternatively, repeats mayproliferate within a genome asa result of DNA strand repair mechanismsfollowing a rearrangement event such as an inversion. Gene« less

Small Scaffolds, Big Potential: Developing Miniature Proteins as Therapeutic Agents.

PubMed

Holub, Justin M

2017-09-01

Preclinical Research Miniature proteins are a class of oligopeptide characterized by their short sequence lengths and ability to adopt well-folded, three-dimensional structures. Because of their biomimetic nature and synthetic tractability, miniature proteins have been used to study a range of biochemical processes including fast protein folding, signal transduction, catalysis and molecular transport. Recently, miniature proteins have been gaining traction as potential therapeutic agents because their small size and ability to fold into defined tertiary structures facilitates their development as protein-based drugs. This research overview discusses emerging developments involving the use of miniature proteins as scaffolds to design novel therapeutics for the treatment and study of human disease. Specifically, this review will explore strategies to: (i) stabilize miniature protein tertiary structure; (ii) optimize biomolecular recognition by grafting functional epitopes onto miniature protein scaffolds; and (iii) enhance cytosolic delivery of miniature proteins through the use of cationic motifs that facilitate endosomal escape. These objectives are discussed not only to address challenges in developing effective miniature protein-based drugs, but also to highlight the tremendous potential miniature proteins hold for combating and understanding human disease. Drug Dev Res 78 : 268-282, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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 are...

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 are...

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 are...

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 are...

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 are...

Addressable inverter matrix for process and device characterization

NASA Technical Reports Server (NTRS)

Buehler, M. G.; Sayah, H. R.

1985-01-01

The addressable inverter matrix consists of 222 inverters each accessible with the aid of a shift register. The structure has proven useful in characterizing the variability of inverter transfer curves and in diagnosing processing faults. For good 3-micron CMOS bulk inverters investigated, the percent standard deviation of the inverter threshold voltage was less than one percent and the inverter gain (the slope of the inverter transfer curve at the inverter threshold vltage) was less than 3 percent. The average noise margin for the inverters was near 2 volts for a power supply voltage of 5 volts. The specific faults studied included undersize pull-down transistor widths and various open contacts in the matrix.

Addressable inverter matrix for process and device characterization

NASA Technical Reports Server (NTRS)

Buehler, M. G.; Sayah, H. R.

1985-01-01

The addressable inverter matrix consists of 222 inverters each accessible with the aid of a shift register. The structure has proven useful in characterizing the variability of inverter transfer curves and in diagnosing processing faults. For good 3-micron CMOS bulk inverters investigated in this study, the percent standard deviation of the inverter threshold voltage was less than one percent and the inverter gain (the slope of the inverter transfer curve at the inverter threshold voltage) was less than 3 percent. The average noise margin for the inverters was near 2 volts for a power supply voltage of 5 volts. The specific faults studied included undersize pull-down transistor widths and various open contacts in the matrix.

Gene-for-genes interactions between cotton R genes and Xanthomonas campestris pv. malvacearum avr genes.

PubMed

De Feyter, R; Yang, Y; Gabriel, D W

1993-01-01

Six plasmid-borne avirulence (avr) genes were previously cloned from strain XcmH of the cotton pathogen, Xanthomonas campestris pv. malvacearum. We have now localized all six avr genes on the cloned fragments by subcloning and Tn5-gusA insertional mutagenesis. None of these avr genes appeared to exhibit exclusively gene-for-gene patterns of interactions with cotton R genes, and avrB4 was demonstrated to confer avr gene-for-R genes (plural) avirulence to X. c. pv. malvacearum on congenic cotton lines carrying either of two different resistance loci, B1 or B4. Furthermore, the B1 locus appeared to confer R gene-for-avr genes resistance to cotton against isogenic X. c. pv. malvacearum strains carrying any one of three avr genes: avrB4, avrb6, or avrB102. Restriction enzyme, Southern blot hybridization, and DNA sequence analyses showed that the XcmH avr genes are all highly similar to each other, to avrBs3 and avrBsP from the pepper pathogen X. c. pv. vesicatoria, and to the host-specific virulence gene pthA from the citrus pathogen X. citri. The XcmH avr genes differed primarily in the multiplicity of a tandemly repeated 102-base pair motif within the central portions of the genes, repeated from 14 to 23 times in members of this gene family. The complete nucleotide sequence of avrb6 revealed that it is 97% identical in DNA sequence to avrB4, avrBs3, avrBsP, and pthA and that 62-bp inverted terminal repeats mark the boundaries of homology between avrb6 and all members of this Xanthomonas virulence/avirulence gene family sequenced to date. The terminal 38 bp of both inverted repeats are highly similar to the 38-bp consensus terminal sequence of the Tn3 family of transposons. Up to 11 members of the avr gene family appear to be present in North American strains of X. c. pv. malvacearum, including XcmH. The high level of homology observed among these avr genes and their presence in multiple copies may explain the gene-for-genes interactions and also the observed high frequencies (10(-3) to 10(-4) per locus) of X. c. pv. malvacearum race change mutations. Five spontaneous race change mutants of XcmH suffered avr locus deletions, strongly indicating intergenic recombination as the primary mechanism for generating new races in X. c. pv. malvacearum.

Effect of recipient breed on delivery rate of cloned miniature pig.

PubMed

Koo, Ok Jae; Park, Hee Jung; Kwon, Dae Kee; Kang, Jung Taek; Jang, Goo; Lee, Byeong Chun

2009-08-01

The miniature pig is regarded as a better organ donor breed for xenotransplantation than other pig breeds because the size of their organs is similar to that of humans. To improve efficiency of cloned miniature pig production, we analysed the effect of breed difference between donor cells and embryo recipients on pregnancy rate and delivery rate. Cloned porcine embryos derived from domestic or miniature pig donor cells were transferred to domestic or miniature recipient pigs. Delivery rate was significantly higher when embryos reconstructed with miniature pig donor cells were transferred to miniature pig recipients as compared with that of embryos transferred to domestic pig recipients. However, pregnancy rates were similar between the two groups. The breed of donor cells, but not of embryo recipients, seems likely to affect litter size. From a 13 610 gene cDNA microarray, 1551 (11.7%) genes showed significantly different levels of expression between the fetuses of the two breeds. Vascular endothelial growth factor and c-kit ligand genes related to implantation and maintenance of pregnancy were significantly down-regulated in miniature pigs. In conclusion, the differential gene expression in fetuses interferes with proper fetal/maternal interactions, and results in late-stage pregnancy loss. Our results indicate that the miniature pig is the preferred embryo recipient breed than domestic pig for producing cloned miniature piglets.

Amplified DNAs in laboratory stocks of Leishmania tarentolae: extrachromosomal circles structurally and functionally similar to the inverted-H-region amplification of methotrexate-resistant Leishmania major

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrillo-Peixoto, M.L.; Beverley, S.M.

1988-12-01

We describe the structure of amplified DNA that was discovered in two laboratory stocks of the protozoan parasite Leishmania tarentolae. Restriction mapping and molecular cloning revealed that a region of 42 kilobases was amplified 8- to 30-fold in these lines. Southern blot analyses of digested DNAs or chromosomes separated by pulsed-field electrophoresis showed that the amplified DNA corresponded to the H region, a locus defined originally by its amplification in methotrexate-resistant Leishmania major. Similarities between the amplified DNA of the two species included (i) extensive cross-hybridization; (ii) approximate conservation of sequence order; (iii) extrachromosomal localization; (iv) an overall inverted, head-to-headmore » configuration as a circular 140-kilobase tetrameric molecule; (v) two regions of DNA sequence rearrangement, each of which was closely associated with the two centers of the inverted repeats; (vi) association with methotrexate resistance; and (vii) phenotypically conservative amplification, in which the wild-type chromosomal arrangement was retained without apparent modification. Our data showed that amplified DNA mediating drug resistance arose in unselected L. tarentolae, although the pressures leading to apparently spontaneous amplification and maintenance of the H region are not known. The simple structure and limited extent of DNA amplified in these and other Leishmania lines suggests that the study of gene amplification in Leishmania spp. offers an attractive model system for the study of amplification in cultured mammalian cells and tumors. We also introduced a method for measuring the size of large circular DNAs, using gamma-irradiation to introduce limited double-strand breaks followed by sizing of the linear DNAs by pulsed-field electrophoresis.« less

Overload protection system for power inverter

NASA Technical Reports Server (NTRS)

Nagano, S. (Inventor)

1977-01-01

An overload protection system for a power inverter utilized a first circuit for monitoring current to the load from the power inverter to detect an overload and a control circuit to shut off the power inverter, when an overload condition was detected. At the same time, a monitoring current inverter was turned on to deliver current to the load at a very low power level. A second circuit monitored current to the load, from the monitoring current inverter, to hold the power inverter off through the control circuit, until the overload condition was cleared so that the control circuit may be deactivated in order for the power inverter to be restored after the monitoring current inverter is turned off completely.

Epistasis between dopamine regulating genes identifies a nonlinear response of the human hippocampus during memory tasks.

PubMed

Bertolino, Alessandro; Di Giorgio, Annabella; Blasi, Giuseppe; Sambataro, Fabio; Caforio, Grazia; Sinibaldi, Lorenzo; Latorre, Valeria; Rampino, Antonio; Taurisano, Paolo; Fazio, Leonardo; Romano, Raffaella; Douzgou, Sofia; Popolizio, Teresa; Kolachana, Bhaskar; Nardini, Marcello; Weinberger, Daniel R; Dallapiccola, Bruno

2008-08-01

Dopamine modulation of neuronal activity in prefrontal cortex maps to an inverted U-curve. Dopamine is also an important factor in regulation of hippocampal mediated memory processing. Here, we investigated the effect of genetic variation of dopamine inactivation via catechol-O-methyltransferase (COMT) and the dopamine transporter (DAT) on hippocampal activity in healthy humans during different memory conditions. Using blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) in 82 subjects matched for a series of demographic and genetic variables, we studied the effect of the COMT valine (Val)(158)methionine (Met) and the DAT 3' variable number tandem repeat (VNTR) polymorphisms on function of the hippocampus during encoding of recognition memory and during working memory. Our results consistently demonstrated a double dissociation so that DAT 9-repeat carrier alleles modulated activity in the hippocampus in the exact opposite direction of DAT 10/10-repeat alleles based on COMT Val(158)Met genotype during different memory conditions. Similar results were evident in ventrolateral and dorsolateral prefrontal cortex. These findings suggest that genetically determined dopamine signaling during memory processing maps to a nonlinear relationship also in the hippocampus. Our data also demonstrate in human brain epistasis of two genes implicated in dopamine signaling on brain activity during different memory conditions.

Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus.

PubMed

Lei, Wanjun; Ni, Dapeng; Wang, Yujun; Shao, Junjie; Wang, Xincun; Yang, Dan; Wang, Jinsheng; Chen, Haimei; Liu, Chang

2016-02-22

Astragalus membranaceus is an important medicinal plant in Asia. Several of its varieties have been used interchangeably as raw materials for commercial production. High resolution genetic markers are in urgent need to distinguish these varieties. Here, we sequenced and analyzed the chloroplast genome of A. membranaceus (Fisch.) Bunge var. mongholicus (Bunge) P.K. Hsiao using the next generation DNA sequencing technology. The genome was assembled using Abyss and then subjected to gene prediction using CPGAVAS and repeat analysis using MISA, Tandem Repeats Finder, and REPuter. Finally, the genome was subjected phylogenetic and comparative genomic analyses. The complete genome is 123,582 bp long, containing only one copy of the inverted repeat. Gene prediction revealed 110 genes encoding 76 proteins, 30 tRNAs, and four rRNAs. Five intra-specific hypermutation loci were identified, three of which are heteroplasmic. Furthermore, three gene losses and two large inversions were identified. Comparative genomic analyses demonstrated the dynamic nature of the Papilionoideae chloroplast genomes, which showed occurrence of numerous hypermutation loci, frequent gene losses, and fragment inversions. Results obtained herein elucidate the complex evolutionary history of chloroplast genomes and have laid the foundation for the identification of genetic markers to distinguish A. membranaceus varieties.

The complete chloroplast genome of Gentiana straminea (Gentianaceae), an endemic species to the Sino-Himalayan subregion.

PubMed

Ni, Lianghong; Zhao, Zhili; Xu, Hongxi; Chen, Shilin; Dorje, Gaawe

2016-02-15

Endemic to the Sino-Himalayan subregion, the medicinal alpine plant Gentiana straminea is a threatened species. The genetic and molecular data about it is deficient. Here we report the complete chloroplast (cp) genome sequence of G. straminea, as the first sequenced member of the family Gentianaceae. The cp genome is 148,991bp in length, including a large single copy (LSC) region of 81,240bp, a small single copy (SSC) region of 17,085bp and a pair of inverted repeats (IRs) of 25,333bp. It contains 112 unique genes, including 78 protein-coding genes, 30 tRNAs and 4 rRNAs. The rps16 gene lacks exon2 between trnK-UUU and trnQ-UUG, which is the first rps16 pseudogene found in the nonparasitic plants of Asterids clade. Sequence analysis revealed the presence of 13 forward repeats, 13 palindrome repeats and 39 simple sequence repeats (SSRs). An entire cp genome comparison study of G. straminea and four other species in Gentianales was carried out. Phylogenetic analyses using maximum likelihood (ML) and maximum parsimony (MP) were performed based on 69 protein-coding genes from 36 species of Asterids. The results strongly supported the position of Gentianaceae as one member of the order Gentianales. The complete chloroplast genome sequence will provide intragenic information for its conservation and contribute to research on the genetic and phylogenetic analyses of Gentianales and Asterids. Copyright © 2015 Elsevier B.V. All rights reserved.

Gas tube-switched high voltage DC power converter

DOEpatents

She, Xu; Bray, James William; Sommerer, Timothy John; Chokhawala, Rahul

2018-05-15

A direct current (DC)-DC converter includes a transformer and a gas tube-switched inverter circuit. The transformer includes a primary winding and a secondary winding. The gas tube-switched inverter circuit includes first and second inverter load terminals and first and second inverter input terminals. The first and second inverter load terminals are coupled to the primary winding. The first and second inverter input terminals are couplable to a DC node. The gas tube-switched inverter circuit further includes a plurality of gas tube switches respectively coupled between the first and second inverter load terminals and the first and second inverter input terminals. The plurality of gas tube switches is configured to operate to generate an alternating current (AC) voltage at the primary winding.

Space biology initiative program definition review. Trade study 3: Hardware miniaturization versus cost

NASA Technical Reports Server (NTRS)

Jackson, L. Neal; Crenshaw, John, Sr.; Davidson, William L.; Herbert, Frank J.; Bilodeau, James W.; Stoval, J. Michael; Sutton, Terry

1989-01-01

The optimum hardware miniaturization level with the lowest cost impact for space biology hardware was determined. Space biology hardware and/or components/subassemblies/assemblies which are the most likely candidates for application of miniaturization are to be defined and relative cost impacts of such miniaturization are to be analyzed. A mathematical or statistical analysis method with the capability to support development of parametric cost analysis impacts for levels of production design miniaturization are provided.

NASA Tech Briefs, October 2004

NASA Technical Reports Server (NTRS)

2004-01-01

Topics include: Relative-Motion Sensors and Actuators for Two Optical Tables; Improved Position Sensor for Feedback Control of Levitation; Compact Tactile Sensors for Robot Fingers; Improved Ion-Channel Biosensors; Suspended-Patch Antenna With Inverted, EM-Coupled Feed; System Would Predictively Preempt Traffic Lights for Emergency Vehicles; Optical Position Encoders for High or Low Temperatures; Inter-Valence-Subband/Conduction-Band-Transport IR Detectors; Additional Drive Circuitry for Piezoelectric Screw Motors; Software for Use with Optoelectronic Measuring Tool; Coordinating Shared Activities; Software Reduces Radio-Interference Effects in Radar Data; Using Iron to Treat Chlorohydrocarbon-Contaminated Soil; Thermally Insulating, Kinematic Tensioned-Fiber Suspension; Back Actuators for Segmented Mirrors and Other Applications; Mechanism for Self-Reacted Friction Stir Welding; Lightweight Exoskeletons with Controllable Actuators; Miniature Robotic Submarine for Exploring Harsh Environments; Electron-Spin Filters Based on the Rashba Effect; Diffusion-Cooled Tantalum Hot-Electron Bolometer Mixers; Tunable Optical True-Time Delay Devices Would Exploit EIT; Fast Query-Optimized Kernel-Machine Classification; Indentured Parts List Maintenance and Part Assembly Capture Tool - IMPACT; An Architecture for Controlling Multiple Robots; Progress in Fabrication of Rocket Combustion Chambers by VPS; CHEM-Based Self-Deploying Spacecraft Radar Antennas; Scalable Multiprocessor for High-Speed Computing in Space; and Simple Systems for Detecting Spacecraft Meteoroid Punctures.

The design of common aperture and multi-band optical system based on day light telescope

NASA Astrophysics Data System (ADS)

Chen, Jiao; Wang, Ling; Zhang, Bo; Teng, Guoqi; Wang, Meng

2017-02-01

As the development of electro-optical weapon system, the technique of common path and multi-sensor are used popular, and becoming a trend. According to the requirement of miniaturization and lightweight for electro-optical stabilized sighting system, a day light telescope/television viewing-aim system/ laser ranger has been designed in this thesis, which has common aperture. Thus integration scheme of multi-band and common aperture has been adopted. A day light telescope has been presented, which magnification is 8, field of view is 6°, and distance of exit pupil is more than 20mm. For 1/3" CCD, television viewing-aim system which has 156mm focal length, has been completed. In addition, laser ranging system has been designed, with 10km raging distance. This paper outlines its principle which used day light telescope as optical reference of correcting the optical axis. Besides, by means of shared objective, reserved image with inverting prism and coating beam-splitting film on the inclined plane of the cube prism, the system has been applied to electro-optical weapon system, with high-resolution of imaging and high-precision ranging.

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)

Traceable Co-C eutectic points for thermocouple calibration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jahan, F.; Ballico, M. J.

2013-09-11

National Measurement Institute of Australia (NMIA) has developed a miniature crucible design suitable for measurement by both thermocouples and radiation thermometry, and has established an ensemble of five Co-C eutectic-point cells based on this design. The cells in this ensemble have been individually calibrated using both ITS-90 radiation thermometry and thermocouples calibrated on the ITS-90 by the NMIA mini-coil methodology. The assigned ITS-90 temperatures obtained using these different techniques are both repeatable and consistent, despite the use of different furnaces and measurement conditions. The results demonstrate that, if individually calibrated, such cells can be practically used as part of amore » national traceability scheme for thermocouple calibration, providing a useful intermediate calibration point between Cu and Pd.« less

A multichannel implantable telemetry system for flow, pressure, and ECG measurements

NASA Technical Reports Server (NTRS)

Fryer, T. B.; Sandler, H.; Freund, W.; Mccutcheon, E. P.; Carlson, E. L.

1975-01-01

The design, principles of operation, and performance of an implantable miniaturized (48 cu cm in volume) multiplex telemetry system for simultaneous measurement of up to eight physiological parameters (including cardiovascular data) are described. Integrated circuits are used to reduce the size, complexity, and cost of fabrication. Power consumption is reduced using recently developed complementary MOS devices. PWM technique is selected as it is relatively easy to implement, lends itself to ICs, and provides an accurate means of transmitting data. The system is totally implantable within the chest of a test animal, with no wire penetrating through the skin. It is shown that the described system permits repeated measurement of the physiological effects of a variety of interventions in awake unanesthetized animals.

Collection, quality control and delivery of ground-based magnetic data during ESA's Swarm mission

NASA Astrophysics Data System (ADS)

Macmillan, Susan; Humphries, Thomas; Flower, Simon; Swan, Anthony

2016-04-01

Ground-based magnetic data are used in a variety of ways when analysing satellite data. Selecting satellite data often involves the use of magnetic disturbance indices derived from ground-based stations and inverting satellite magnetic data for models of fields from various sources often requires ground-based data. Ground-based data can also be valuable independent data for validation purposes. We summarise data collection and quality control procedures in place at the British Geological Survey for global ground-based observatory and repeat station data. Whilst ongoing participation in the ICSU World Data System and INTERMAGNET facilitates this work, additional procedures have been specially developed for the Swarm mission. We describe these in detail.

Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses

PubMed Central

Chew, David S. H.; Choi, Kwok Pui; Leung, Ming-Ying

2005-01-01

Many empirical studies show that there are unusual clusters of palindromes, closely spaced direct and inverted repeats around the replication origins of herpesviruses. In this paper, we introduce two new scoring schemes to quantify the spatial abundance of palindromes in a genomic sequence. Based on these scoring schemes, a computational method to predict the locations of replication origins is developed. When our predictions are compared with 39 known or annotated replication origins in 19 herpesviruses, close to 80% of the replication origins are located within 2% of the genome length. A list of predicted locations of replication origins in all the known herpesviruses with complete genome sequences is reported. PMID:16141192

The complete chloroplast genomes of two Wisteria species, W. floribunda and W. sinensis (Fabaceae).

PubMed

Kim, Na-Rae; Kim, Kyunghee; Lee, Sang-Choon; Lee, Jung-Hoon; Cho, Seong-Hyun; Yu, Yeisoo; Kim, Young-Dong; Yang, Tae-Jin

2016-11-01

Wisteria floribunda and Wisteria sinensis are ornamental woody vines in the Fabaceae. The complete chloroplast genome sequences of the two species were generated by de novo assembly using whole genome next generation sequences. The chloroplast genomes of W. floribunda and W. sinensis were 130 960 bp and 130 561 bp long, respectively, and showed inverted repeat (IR)-lacking structures as those reported in IRLC in the Fabaceae. The chloroplast genomes of both species contained same number of protein-coding sequences (77), tRNA genes (30), and rRNA genes (4). The phylogenetic analysis with the reported chloroplast genomes confirmed close taxonomical relationship of W. floribunda and W. sinensis.

Reduced-Order Structure-Preserving Model for Parallel-Connected Three-Phase Grid-Tied Inverters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Brian B; Purba, Victor; Jafarpour, Saber

Next-generation power networks will contain large numbers of grid-connected inverters satisfying a significant fraction of system load. Since each inverter model has a relatively large number of dynamic states, it is impractical to analyze complex system models where the full dynamics of each inverter are retained. To address this challenge, we derive a reduced-order structure-preserving model for parallel-connected grid-tied three-phase inverters. Here, each inverter in the system is assumed to have a full-bridge topology, LCL filter at the point of common coupling, and the control architecture for each inverter includes a current controller, a power controller, and a phase-locked loopmore » for grid synchronization. We outline a structure-preserving reduced-order inverter model with lumped parameters for the setting where the parallel inverters are each designed such that the filter components and controller gains scale linearly with the power rating. By structure preserving, we mean that the reduced-order three-phase inverter model is also composed of an LCL filter, a power controller, current controller, and PLL. We show that the system of parallel inverters can be modeled exactly as one aggregated inverter unit and this equivalent model has the same number of dynamical states as any individual inverter in the system. Numerical simulations validate the reduced-order model.« less

The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng.

PubMed

Chen, Jinhui; Hao, Zhaodong; Xu, Haibin; Yang, Liming; Liu, Guangxin; Sheng, Yu; Zheng, Chen; Zheng, Weiwei; Cheng, Tielong; Shi, Jisen

2015-01-01

Metasequoia glyptostroboides Hu et Cheng is the only species in the genus Metasequoia Miki ex Hu et Cheng, which belongs to the Cupressaceae family. There were around 10 species in the Metasequoia genus, which were widely spread across the Northern Hemisphere during the Cretaceous of the Mesozoic and in the Cenozoic. M. glyptostroboides is the only remaining representative of this genus. Here, we report the complete chloroplast (cp) genome sequence and the cp genomic features of M. glyptostroboides. The M. glyptostroboides cp genome is 131,887 bp in length, with a total of 117 genes comprised of 82 protein-coding genes, 31 tRNA genes and four rRNA genes. In this genome, 11 forward repeats, nine palindromic repeats, and 15 tandem repeats were detected. A total of 188 perfect microsatellites were detected through simple sequence repeat (SSR) analysis and these were distributed unevenly within the cp genome. Comparison of the cp genome structure and gene order to those of several other land plants indicated that a copy of the inverted repeat (IR) region, which was found to be IR region A (IRA), was lost in the M. glyptostroboides cp genome. The five most divergent and five most conserved genes were determined and further phylogenetic analysis was performed among plant species, especially for related species in conifers. Finally, phylogenetic analysis demonstrated that M. glyptostroboides is a sister species to Cryptomeria japonica (L. F.) D. Don and to Taiwania cryptomerioides Hayata. The complete cp genome sequence information of M. glyptostroboides will be great helpful for further investigations of this endemic relict woody plant and for in-depth understanding of the evolutionary history of the coniferous cp genomes, especially for the position of M. glyptostroboides in plant systematics and evolution.

The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng

PubMed Central

Chen, Jinhui; Hao, Zhaodong; Xu, Haibin; Yang, Liming; Liu, Guangxin; Sheng, Yu; Zheng, Chen; Zheng, Weiwei; Cheng, Tielong; Shi, Jisen

2015-01-01

Metasequoia glyptostroboides Hu et Cheng is the only species in the genus Metasequoia Miki ex Hu et Cheng, which belongs to the Cupressaceae family. There were around 10 species in the Metasequoia genus, which were widely spread across the Northern Hemisphere during the Cretaceous of the Mesozoic and in the Cenozoic. M. glyptostroboides is the only remaining representative of this genus. Here, we report the complete chloroplast (cp) genome sequence and the cp genomic features of M. glyptostroboides. The M. glyptostroboides cp genome is 131,887 bp in length, with a total of 117 genes comprised of 82 protein-coding genes, 31 tRNA genes and four rRNA genes. In this genome, 11 forward repeats, nine palindromic repeats, and 15 tandem repeats were detected. A total of 188 perfect microsatellites were detected through simple sequence repeat (SSR) analysis and these were distributed unevenly within the cp genome. Comparison of the cp genome structure and gene order to those of several other land plants indicated that a copy of the inverted repeat (IR) region, which was found to be IR region A (IRA), was lost in the M. glyptostroboides cp genome. The five most divergent and five most conserved genes were determined and further phylogenetic analysis was performed among plant species, especially for related species in conifers. Finally, phylogenetic analysis demonstrated that M. glyptostroboides is a sister species to Cryptomeria japonica (L. F.) D. Don and to Taiwania cryptomerioides Hayata. The complete cp genome sequence information of M. glyptostroboides will be great helpful for further investigations of this endemic relict woody plant and for in-depth understanding of the evolutionary history of the coniferous cp genomes, especially for the position of M. glyptostroboides in plant systematics and evolution. PMID:26136762

Production of cloned NIBS (Nippon Institute for Biological Science) and α-1, 3-galactosyltransferase knockout MGH miniature pigs by somatic cell nuclear transfer using the NIBS breed as surrogates.

PubMed

Shimatsu, Yoshiki; Yamada, Kazuhiko; Horii, Wataru; Hirakata, Atsushi; Sakamoto, Yuji; Waki, Shiori; Sano, Junichi; Saitoh, Toshiki; Sahara, Hisashi; Shimizu, Akira; Yazawa, Hajime; Sachs, David H; Nunoya, Tetsuo

2013-01-01

Nuclear transfer (NT) technologies offer a means for producing the genetically modified pigs necessary to develop swine models for mechanistic studies of disease processes as well as to serve as organ donors for xenotransplantation. Most previous studies have used commercial pigs as surrogates. In this study, we established a cloning technique for miniature pigs by somatic cell nuclear transfer (SCNT) using Nippon Institute for Biological Science (NIBS) miniature pigs as surrogates. Moreover, utilizing this technique, we have successfully produced an α-1, 3-galactosyltransferase knockout (GalT-KO) miniature swine. Fibroblasts procured from a NIBS miniature pig fetus were injected into 1312 enucleated oocytes. The cloned embryos were transferred to 11 surrogates of which five successfully delivered 13 cloned offspring; the production efficiency was 1.0% (13/1312). In a second experiment, lung fibroblasts obtained from neonatal GalT-KO MGH miniature swine were used as donor cells and 1953 cloned embryos were transferred to 12 surrogates. Six cloned offspring were born from five surrogates, a production efficiency of 0.3% (6/1953). These results demonstrate successful establishment of a miniature pig cloning technique by SCNT using NIBS miniature pigs as surrogates. To our knowledge, this is the first demonstration of successful production of GalT-KO miniature swine using miniature swine surrogates. This technique could help to ensure a stable supply of the cloned pigs through the use of miniature pig surrogates and could expand production in countries with limited space or in facilities with special regulations such as specific pathogen-free or good laboratory practice. © 2013 John Wiley & Sons A/S.

Production of cloned NIBS (Nippon Institute for Biological Science) and α-1, 3-galactosyltransferase knockout MGH miniature pigs by somatic cell nuclear transfer using the NIBS breed as surrogates

PubMed Central

Shimatsu, Yoshiki; Yamada, Kazuhiko; Horii, Wataru; Hirakata, Atsushi; Sakamoto, Yuji; Waki, Shiori; Sano, Junichi; Saitoh, Toshiki; Sahara, Hisashi; Shimizu, Akira; Yazawa, Hajime; Sachs, David H.; Nunoya, Tetsuo

2013-01-01

Background Nuclear transfer (NT) technologies offer a means for producing the genetically modified pigs necessary to develop swine models for mechanistic studies of disease processes as well as to serve as organ donors for xenotransplantation. Most previous studies have used commercial pigs as surrogates. Method and Results In this study, we established a cloning technique for miniature pigs by somatic cell nuclear transfer (SCNT) using Nippon Institute for Biological Science (NIBS) miniature pigs as surrogates. Moreover, utilizing this technique, we have successfully produced an α-1, 3-galactosyltransferase knockout (GalT-KO) miniature swine. Fibroblasts procured from a NIBS miniature pig fetus were injected into 1312 enucleated oocytes. The cloned embryos were transferred to 11 surrogates of which five successfully delivered 13 cloned offspring; the production efficiency was 1.0% (13/1312). In a second experiment, lung fibroblasts obtained from neonatal GalT-KO MGH miniature swine were used as donor cells and 1953 cloned embryos were transferred to 12 surrogates. Six cloned offspring were born from five surrogates, a production efficiency of 0.3% (6/1953). Conclusions These results demonstrate successful establishment of a miniature pig cloning technique by SCNT using NIBS miniature pigs as surrogates. To our knowledge, this is the first demonstration of successful production of GalT-KO miniature swine using miniature swine surrogates. This technique could help to ensure a stable supply of the cloned pigs through the use of miniature pig surrogates and could expand production in countries with limited space or in facilities with special regulations such as specific pathogen-free or good laboratory practice. PMID:23581451

Operating temperatures of open-rack installed photovoltaic inverters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Z.; Wang, L.; Kurtz, S.

This paper presents a model for evaluating the heat-sink and component temperatures of open-rack installed photovoltaic inverters. These temperatures can be used for predicting inverter reliability. Inverter heat-sink temperatures were measured for inverters connected to three grid-connected PV (photovoltaic) test systems in Golden, Colorado, US. A model is proposed for calculating the inverter heat-sink temperature based on the ambient temperature, the ratio of the consumed power to the rated power of the inverter, and the measured wind speed. To verify and study this model, more than one year of inverter DC/AC power, irradiance, wind speed, and heat sink temperature risemore » data were collected and analyzed. The model is shown to be accurate in predicting average inverter temperatures, but will require further refinement for prediction of transient temperatures.« less

The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete.

PubMed

Goodwin, Stephen B; McCorison, Cassandra B; Cavaletto, Jessica R; Culley, David E; LaButti, Kurt; Baker, Scott E; Grigoriev, Igor V

2016-08-01

Fungi in the class Dothideomycetes often live in extreme environments or have unusual physiology. One of these, the wine cellar mold Zasmidium cellare, produces thick curtains of mycelia in cellars with high humidity, and its ability to metabolize volatile organic compounds is thought to improve air quality. Whether these abilities have affected its mitochondrial genome is not known. To fill this gap, the circular-mapping mitochondrial genome of Z. cellare was sequenced and, at only 23 743 bp, is the smallest reported for a filamentous fungus. Genes were encoded on both strands with a single change of direction, different from most other fungi but consistent with the Dothideomycetes. Other than its small size, the only unusual feature of the Z. cellare mitochondrial genome was two copies of a 110-bp sequence that were duplicated, inverted and separated by approximately 1 kb. This inverted-repeat sequence confused the assembly program but appears to have no functional significance. The small size of the Z. cellare mitochondrial genome was due to slightly smaller genes, lack of introns and non-essential genes, reduced intergenic spacers and very few ORFs relative to other fungi rather than a loss of essential genes. Whether this reduction facilitates its unusual biology remains unknown. Published by Elsevier Ltd.

Direct model-based predictive control scheme without cost function for voltage source inverters with reduced common-mode voltage

NASA Astrophysics Data System (ADS)

Kim, Jae-Chang; Moon, Sung-Ki; Kwak, Sangshin

2018-04-01

This paper presents a direct model-based predictive control scheme for voltage source inverters (VSIs) with reduced common-mode voltages (CMVs). The developed method directly finds optimal vectors without using repetitive calculation of a cost function. To adjust output currents with the CMVs in the range of -Vdc/6 to +Vdc/6, the developed method uses voltage vectors, as finite control resources, excluding zero voltage vectors which produce the CMVs in the VSI within ±Vdc/2. In a model-based predictive control (MPC), not using zero voltage vectors increases the output current ripples and the current errors. To alleviate these problems, the developed method uses two non-zero voltage vectors in one sampling step. In addition, the voltage vectors scheduled to be used are directly selected at every sampling step once the developed method calculates the future reference voltage vector, saving the efforts of repeatedly calculating the cost function. And the two non-zero voltage vectors are optimally allocated to make the output current approach the reference current as close as possible. Thus, low CMV, rapid current-following capability and sufficient output current ripple performance are attained by the developed method. The results of a simulation and an experiment verify the effectiveness of the developed method.

Complete plastid genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms

PubMed Central

Ruhlman, Tracey; Lee, Seung-Bum; Jansen, Robert K; Hostetler, Jessica B; Tallon, Luke J; Town, Christopher D; Daniell, Henry

2006-01-01

Background Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombinant proteins in carrot have had limited success in terms of protein accumulation in the edible tap roots. Plastid genetic engineering offers the potential to overcome this limitation, as demonstrated by the accumulation of BADH in chromoplasts of carrot taproots to confer exceedingly high levels of salt resistance. The complete plastid genome of carrot provides essential information required for genetic engineering. Additionally, the sequence data add to the rapidly growing database of plastid genomes for assessing phylogenetic relationships among angiosperms. Results The complete carrot plastid genome is 155,911 bp in length, with 115 unique genes and 21 duplicated genes within the IR. There are four ribosomal RNAs, 30 distinct tRNA genes and 18 intron-containing genes. Repeat analysis reveals 12 direct and 2 inverted repeats ≥ 30 bp with a sequence identity ≥ 90%. Phylogenetic analysis of nucleotide sequences for 61 protein-coding genes using both maximum parsimony (MP) and maximum likelihood (ML) were performed for 29 angiosperms. Phylogenies from both methods provide strong support for the monophyly of several major angiosperm clades, including monocots, eudicots, rosids, asterids, eurosids II, euasterids I, and euasterids II. Conclusion The carrot plastid genome contains a number of dispersed direct and inverted repeats scattered throughout coding and non-coding regions. This is the first sequenced plastid genome of the family Apiaceae and only the second published genome sequence of the species-rich euasterid II clade. Both MP and ML trees provide very strong support (100% bootstrap) for the sister relationship of Daucus with Panax in the euasterid II clade. These results provide the best taxon sampling of complete chloroplast genomes and the strongest support yet for the sister relationship of Caryophyllales to the asterids. The availability of the complete plastid genome sequence should facilitate improved transformation efficiency and foreign gene expression in carrot through utilization of endogenous flanking sequences and regulatory elements. PMID:16945140

Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species.

PubMed

Hirao, Tomonori; Watanabe, Atsushi; Kurita, Manabu; Kondo, Teiji; Takata, Katsuhiko

2008-06-23

The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms. The C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements. The observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the C. japonica cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.

A small punch test technique for characterizing the elastic modulus and fracture behavior of PMMA bone cement used in total joint replacement.

PubMed

Giddings, V L; Kurtz, S M; Jewett, C W; Foulds, J R; Edidin, A A

2001-07-01

Polymethylmethacrylate (PMMA) bone cement is used in total joint replacements to anchor implants to the underlying bone. Establishing and maintaining the integrity of bone cement is thus of critical importance to the long-term outcome of joint replacement surgery. The goal of the present study was to evaluate the suitability of a novel testing technique, the small punch or miniaturized disk bend test, to characterize the elastic modulus and fracture behavior of PMMA. We investigated the hypothesis that the crack initiation behavior of PMMA during the small punch test was sensitive to the test temperature. Miniature disk-shaped specimens, 0.5 mm thick and 6.4 mm in diameter, were prepared from PMMA and Simplex-P bone cement according to manufacturers' instructions. Testing was conducted at ambient and body temperatures, and the effect of test temperature on the elastic modulus and fracture behavior was statistically evaluated using analysis of variance. For both PMMA materials, the test temperature had a significant effect on elastic modulus and crack initiation behavior. At body temperature, the specimens exhibited "ductile" crack initiation, whereas at room temperature "brittle" crack initiation was observed. The small punch test was found to be a sensitive and repeatable test method for evaluating the mechanical behavior of PMMA. In light of the results of this study, future small punch testing should be conducted at body temperature.

Observational study: microgravity testing of a phase-change reference on the International Space Station

PubMed Central

Topham, T Shane; Bingham, Gail E; Latvakoski, Harri; Podolski, Igor; Sychev, Vladimir S; Burdakin, Andre

2015-01-01

Background: Orbital sensors to monitor global climate change during the next decade require low-drift rates for onboard thermometry, which is currently unattainable without on-orbit recalibration. Phase-change materials (PCMs), such as those that make up the ITS-90 standard, are seen as the most reliable references on the ground and could be good candidates for orbital recalibration. Space Dynamics Lab (SDL) has been developing miniaturized phase-change references capable of deployment on an orbital blackbody for nearly a decade. Aims: Improvement of orbital temperature measurements for long duration earth observing and remote sensing. Methods: To determine whether and how microgravity will affect the phase transitions, SDL conducted experiments with ITS-90 standard material (gallium, Ga) on the International Space Station (ISS) and compared the phase-change temperature with earth-based measurements. The miniature on-orbit thermal reference (MOTR) experiment launched to the ISS in November 2013 on Soyuz TMA-11M with the Expedition 38 crew and returned to Kazakhstan in March 2014 on the Soyuz TMA-10 spacecraft. Results: MOTR tested melts and freezes of Ga using repeated 6-h cycles. Melt cycles obtained on the ground before and after launch were compared with those obtained on the ISS. Conclusions: To within a few mK uncertainty, no significant difference between the melt temperature of Ga at 1 g and in microgravity was observed. PMID:28725713

Pressurized hot water extraction followed by miniaturized membrane assisted solvent extraction for the green analysis of alkylphenols in sediments.

PubMed

Salgueiro-González, N; Turnes-Carou, I; Muniategui-Lorenzo, S; López-Mahía, P; Prada-Rodríguez, D

2015-02-27

A novel and Green analytical methodology for the determination of alkylphenols (4-tert-octylphenol, 4-n-octylphenol, 4-n-nonylphenol, nonylphenol) in sediments was developed and validated. The method was based on pressurized hot water extraction (PHWE) followed by miniaturized membrane assisted solvent extraction (MASE) and liquid chromatography-electrospray ionization tandem mass spectrometry detection (LC-ESI-MS/MS). The extraction conditions were optimized by a Plackett-Burman design in order to minimize the number of assays according to Green principles. Matrix effect was studied and compensated using deuterated labeled standards as surrogate standards for the quantitation of the target compounds. The analytical features of the method were satisfactory: relative recoveries varied between 92 and 103% and repeatability and intermediate precision were <9% for all compounds. Quantitation limits of the method (MQL) ranged from 0.061 (4-n-nonylphenol) to 1.7ngg(-1) dry weight (nonylphenol). Sensitivity, selectivity, automaticity and fastness are the main advantages of the exposed methodology. Reagent consumption, analysis time and waste generation were minimized. The "greenness" of the proposed method was evaluated using an analytical Eco-Scale approach and satisfactory results were obtained. The applicability of the proposed method was demonstrated analysing sediment samples of Galicia coast (NW of Spain) and the ubiquity of alkylphenols in the environment was demonstrated. Copyright © 2015 Elsevier B.V. All rights reserved.

Observational study: microgravity testing of a phase-change reference on the International Space Station.

PubMed

Topham, T Shane; Bingham, Gail E; Latvakoski, Harri; Podolski, Igor; Sychev, Vladimir S; Burdakin, Andre

2015-01-01

Orbital sensors to monitor global climate change during the next decade require low-drift rates for onboard thermometry, which is currently unattainable without on-orbit recalibration. Phase-change materials (PCMs), such as those that make up the ITS-90 standard, are seen as the most reliable references on the ground and could be good candidates for orbital recalibration. Space Dynamics Lab (SDL) has been developing miniaturized phase-change references capable of deployment on an orbital blackbody for nearly a decade. Improvement of orbital temperature measurements for long duration earth observing and remote sensing. To determine whether and how microgravity will affect the phase transitions, SDL conducted experiments with ITS-90 standard material (gallium, Ga) on the International Space Station (ISS) and compared the phase-change temperature with earth-based measurements. The miniature on-orbit thermal reference (MOTR) experiment launched to the ISS in November 2013 on Soyuz TMA-11M with the Expedition 38 crew and returned to Kazakhstan in March 2014 on the Soyuz TMA-10 spacecraft. MOTR tested melts and freezes of Ga using repeated 6-h cycles. Melt cycles obtained on the ground before and after launch were compared with those obtained on the ISS. To within a few mK uncertainty, no significant difference between the melt temperature of Ga at 1 g and in microgravity was observed.

NREL Evaluates Advanced Solar Inverter Performance for Hawaiian Electric

Science.gov Websites

Companies | Energy Systems Integration Facility | NREL NREL Evaluates Advanced Solar Inverter Performance for Hawaiian Electric Companies NREL Evaluates Advanced Solar Inverter Performance for Hawaiian performance and impacts of today's advanced solar inverters, as well as proprietary feedback to the inverter

Inverter design for high frequency power distribution

NASA Technical Reports Server (NTRS)

King, R. J.

1985-01-01

A class of simple resonantly commutated inverters are investigated for use in a high power (100 KW - 1000 KW) high frequency (10 KHz - 20 KHz) AC power distribution system. The Mapham inverter is found to provide a unique combination of large thyristor turn-off angle and good utilization factor, much better than an alternate 'current-fed' inverter. The effects of loading the Mapham inverter entirely with rectifier loads are investigated by simulation and with an experimental 3 KW 20 KHz inverter. This inverter is found to be well suited to a power system with heavy rectifier loading.

Status and Needs of Power Electronics for Photovoltaic Inverters

NASA Astrophysics Data System (ADS)

Qin, Y. C.; Mohan, N.; West, R.; Bonn, R.

2002-06-01

Photovoltaics is the utility connected distributed energy resource (DER) that is in widespread use today. It has one element, the inverter, which is common with all DER sources except rotating generators. The inverter is required to transfer dc energy to ac energy. With all the DER technologies, (solar, wind, fuel cells, and microturbines) the inverter is still an immature product that will result in reliability problems in fielded systems. Today, the PV inverter is a costly and complex component of PV systems that produce ac power. Inverter MTFF (mean time to first failure) is currently unacceptable. Low inverter reliability contributes to unreliable fielded systems and a loss of confidence in renewable technology. The low volume of PV inverters produced restricts the manufacturing to small suppliers without sophisticated research and reliability programs or manufacturing methods. Thus, the present approach to PV inverter supply has low probability of meeting DOE reliability goals.

Reduced-Order Structure-Preserving Model for Parallel-Connected Three-Phase Grid-Tied Inverters: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Brian B; Purba, Victor; Jafarpour, Saber

Given that next-generation infrastructures will contain large numbers of grid-connected inverters and these interfaces will be satisfying a growing fraction of system load, it is imperative to analyze the impacts of power electronics on such systems. However, since each inverter model has a relatively large number of dynamic states, it would be impractical to execute complex system models where the full dynamics of each inverter are retained. To address this challenge, we derive a reduced-order structure-preserving model for parallel-connected grid-tied three-phase inverters. Here, each inverter in the system is assumed to have a full-bridge topology, LCL filter at the pointmore » of common coupling, and the control architecture for each inverter includes a current controller, a power controller, and a phase-locked loop for grid synchronization. We outline a structure-preserving reduced-order inverter model for the setting where the parallel inverters are each designed such that the filter components and controller gains scale linearly with the power rating. By structure preserving, we mean that the reduced-order three-phase inverter model is also composed of an LCL filter, a power controller, current controller, and PLL. That is, we show that the system of parallel inverters can be modeled exactly as one aggregated inverter unit and this equivalent model has the same number of dynamical states as an individual inverter in the paralleled system. Numerical simulations validate the reduced-order models.« less

Comparative study of SiC- and Si-based photovoltaic inverters

NASA Astrophysics Data System (ADS)

Ando, Yuji; Oku, Takeo; Yasuda, Masashi; Shirahata, Yasuhiro; Ushijima, Kazufumi; Murozono, Mikio

2017-01-01

This article reports comparative study of 150-300 W class photovoltaic inverters (Si inverter, SiC inverter 1, and SiC inverter 2). In these sub-kW class inverters, the ON-resistance was considered to have little influence on the efficiency. The developed SiC inverters, however, have exhibited an approximately 3% higher direct current (DC)-alternating current (AC) conversion efficiency as compared to the Si inverter. Power loss analysis indicated a reduction in the switching and reverse recovery losses of SiC metal-oxide-semiconductor field-effect transistors used for the DC-AC converter is responsible for this improvement. In the SiC inverter 2, an increase of the switching frequency up to 100 kHz achieved a state-of-the-art combination of the weight (1.25 kg) and the volume (1260 cm3) as a 150-250 W class inverter. Even though the increased switching frequency should cause the increase of the switching losses, the SiC inverter 2 exhibited an efficiency comparable to the SiC inverter 1 with a switching frequency of 20 kHz. The power loss analysis also indicated a decreased loss of the DC-DC converter built with SiC Schottky barrier diodes led to the high efficiency for its increased switching frequency. These results clearly indicated feasibility of SiC devices even for sub-kW photovoltaic inverters, which will be available for the applications where compactness and efficiency are of tremendous importance.

Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication oriP in origin function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polonskaya, Zhanna; Benham, Craig J.; Hearing, Janet

The minimal replicator of the Epstein-Barr virus (EBV) latent cycle origin of DNA replication oriP is composed of two binding sites for the Epstein-Barr virus nuclear antigen-1 (EBNA-1) and flanking inverted repeats that bind the telomere repeat binding factor TRF2. Although not required for minimal replicator activity, additional binding sites for EBNA-1 and TRF2 and one or more auxiliary elements located to the right of the EBNA-1/TRF2 sites are required for the efficient replication of oriP plasmids. Another region of oriP that is predicted to be destabilized by DNA supercoiling is shown here to be an important functional component ofmore » oriP. The ability of DNA fragments of unrelated sequence and possessing supercoiled-induced DNA duplex destabilized (SIDD) structures, but not fragments characterized by helically stable DNA, to substitute for this component of oriP demonstrates a role for the SIDD region in the initiation of oriP-plasmid DNA replication.« less

Alu Elements as Novel Regulators of Gene Expression in Type 1 Diabetes Susceptibility Genes?

PubMed

Kaur, Simranjeet; Pociot, Flemming

2015-07-13

Despite numerous studies implicating Alu repeat elements in various diseases, there is sparse information available with respect to the potential functional and biological roles of the repeat elements in Type 1 diabetes (T1D). Therefore, we performed a genome-wide sequence analysis of T1D candidate genes to identify embedded Alu elements within these genes. We observed significant enrichment of Alu elements within the T1D genes (p-value < 10e-16), which highlights their importance in T1D. Functional annotation of T1D genes harboring Alus revealed significant enrichment for immune-mediated processes (p-value < 10e-6). We also identified eight T1D genes harboring inverted Alus (IRAlus) within their 3' untranslated regions (UTRs) that are known to regulate the expression of host mRNAs by generating double stranded RNA duplexes. Our in silico analysis predicted the formation of duplex structures by IRAlus within the 3'UTRs of T1D genes. We propose that IRAlus might be involved in regulating the expression levels of the host T1D genes.

Properties of an equine herpesvirus 1 mutant devoid of the internal inverted repeat sequence of the genomic short region

PubMed Central

Ahn, ByungChul; Zhang, Yunfei; Osterrieder, Nikolaus; O'Callaghan, Dennis J.

2010-01-01

The 150 kbp genome of equine herpesvirus -1 (EHV-1) is composed of a unique long (UL) region and a unique short (Us) segment, which is flanked by identical internal and terminal repeat (IR and TR) sequences of 12.7kbp. We constructed an EHV-1 lacking the entire IR (vL11ΔIR) and showed that the IR is dispensable for EHV-1 replication but that the vL11ΔIR exhibits a smaller plaque size and delayed growth kinetics. Western blot analyses of cells infected with vL11ΔIR showed that the synthesis of viral proteins encoded by the immediate-early, early, and late genes was reduced at immediate-early and early times, but by late stages of replication reached wild type levels. Intranasal infection of CBA mice revealed that the vL11ΔIR was significantly attenuated as mice infected with the vL11ΔIR showed a reduced lung viral titer and greater ability to survive infection compared to mice infected with parental or revertant virus. PMID:21176938

Reestablishment of radiographic kidney size in Miniature Schnauzer dogs

PubMed Central

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

2016-01-01

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

Reestablishment of radiographic kidney size in Miniature Schnauzer dogs.

PubMed

Sohn, Jungmin; Yun, Sookyung; Lee, Jeosoon; Chang, Dongwoo; Choi, Mincheol; Yoon, Junghee

2017-01-10

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

Molecular characterization of a genomic region in a Lactococcus bacteriophage that is involved in its sensitivity to the phage defense mechanism AbiA.

PubMed

Dinsmore, P K; Klaenhammer, T R

1997-05-01

A spontaneous mutant of the lactococcal phage phi31 that is insensitive to the phage defense mechanism AbiA was characterized in an effort to identify the phage factor(s) involved in sensitivity of phi31 to AbiA. A point mutation was localized in the genome of the AbiA-insensitive phage (phi31A) by heteroduplex analysis of a 9-kb region. The mutation (G to T) was within a 738-bp open reading frame (ORF245) and resulted in an arginine-to-leucine change in the predicted amino acid sequence of the protein. The mutant phi31A-ORF245 reduced the sensitivity of phi31 to AbiA when present in trans, indicating that the mutation in ORF245 is responsible for the AbiA insensitivity of phi31A. Transcription of ORF245 occurs early in the phage infection cycles of phi31 and phi31A and is unaffected by AbiA. Expansion of the phi31 sequence revealed ORF169 (immediately upstream of ORF245) and ORF71 (which ends 84 bp upstream of ORF169). Two inverted repeats lie within the 84-bp region between ORF71 and ORF169. Sequence analysis of an independently isolated AbiA-insensitive phage, phi31B, identified a mutation (G to A) in one of the inverted repeats. A 118-bp fragment from phi31, encompassing the 84-bp region between ORF71 and ORF169, eliminates AbiA activity against phi31 when present in trans, establishing a relationship between AbiA and this fragment. The study of this region of phage phi31 has identified an open reading frame (ORF245) and a 118-bp DNA fragment that interact with AbiA and are likely to be involved in the sensitivity of this phage to AbiA.

Field Level RNAi-Mediated Resistance to Cassava Brown Streak Disease across Multiple Cropping Cycles and Diverse East African Agro-Ecological Locations

PubMed Central

Wagaba, Henry; Beyene, Getu; Aleu, Jude; Odipio, John; Okao-Okuja, Geoffrey; Chauhan, Raj Deepika; Munga, Theresia; Obiero, Hannington; Halsey, Mark E.; Ilyas, Muhammad; Raymond, Peter; Bua, Anton; Taylor, Nigel J.; Miano, Douglas; Alicai, Titus

2017-01-01

Cassava brown streak disease (CBSD) presents a serious threat to cassava production in East and Central Africa. Currently, no cultivars with high levels of resistance to CBSD are available to farmers. Transgenic RNAi technology was employed to combat CBSD by fusing coat protein (CP) sequences from Ugandan cassava brown streak virus (UCBSV) and Cassava brown streak virus (CBSV) to create an inverted repeat construct (p5001) driven by the constitutive Cassava vein mosaic virus promoter. Twenty-five plant lines of cultivar TME 204 expressing varying levels of small interfering RNAs (siRNAs) were established in confined field trials (CFTs) in Uganda and Kenya. Within an initial CFT at Namulonge, Uganda, non-transgenic TME 204 plants developed foliar and storage root CBSD incidences at 96–100% by 12 months after planting. In contrast, 16 of the 25 p5001 transgenic lines showed no foliar symptoms and had less than 8% of their storage roots symptomatic for CBSD. A direct positive correlation was seen between levels of resistance to CBSD and expression of transgenic CP-derived siRNAs. A subsequent CFT was established at Namulonge using stem cuttings from the initial trial. All transgenic lines established remained asymptomatic for CBSD, while 98% of the non-transgenic TME 204 stake-derived plants developed storage roots symptomatic for CBSD. Similarly, very high levels of resistance to CBSD were demonstrated by TME 204 p5001 RNAi lines grown within a CFT over a full cropping cycle at Mtwapa, coastal Kenya. Sequence analysis of CBSD causal viruses present at the trial sites showed that the transgenic lines were exposed to both CBSV and UCBSV, and that the sequenced isolates shared >90% CP identity with transgenic CP sequences expressed by the p5001 inverted repeat expression cassette. These results demonstrate very high levels of field resistance to CBSD conferred by the p5001 RNAi construct at diverse agro-ecological locations, and across the vegetative cropping cycle. PMID:28127301

Binding Sequences for RdgB, a DNA Damage-Responsive Transcriptional Activator, and Temperature-Dependent Expression of Bacteriocin and Pectin Lyase Genes in Pectobacterium carotovorum subsp. carotovorum▿ †

PubMed Central

Yamada, Kazuteru; Kaneko, Jun; Kamio, Yoshiyuki; Itoh, Yoshifumi

2008-01-01

Pectobacterium carotovorum subsp. carotovorum strain Er simultaneously produces the phage tail-like bacteriocin carotovoricin (Ctv) and pectin lyase (Pnl) in response to DNA-damaging agents. The regulatory protein RdgB of the Mor/C family of proteins activates transcription of pnl through binding to the promoter. However, the optimal temperature for the synthesis of Ctv (23°C) differs from that for synthesis of Pnl (30°C), raising the question of whether RdgB directly activates ctv transcription. Here we report that RdgB directly regulates Ctv synthesis. Gel mobility shift assays demonstrated RdgB binding to the P0, P1, and P2 promoters of the ctv operons, and DNase I footprinting determined RdgB-binding sequences (RdgB boxes) on these and on the pnl promoters. The RdgB box of the pnl promoter included a perfect 7-bp inverted repeat with high binding affinity to the regulator (Kd [dissociation constant] = 150 nM). In contrast, RdgB boxes of the ctv promoters contained an imperfect inverted repeat with two or three mismatches that consequently reduced binding affinity (Kd = 250 to 350 nM). Transcription of the rdgB and ctv genes was about doubled at 23°C compared with that at 30°C. In contrast, the amount of pnl transcription tripled at 30°C. Thus, the inverse synthesis of Ctv and Pnl as a function of temperature is apparently controlled at the transcriptional level, and reduced rdgB expression at 30°C obviously affected transcription from the ctv promoters with low-affinity RdgB boxes. Pathogenicity toward potato tubers was reduced in an rdgB knockout mutant, suggesting that the RdgAB system contributes to the pathogenicity of this bacterium, probably by activating pnl expression. PMID:18689515

Large inverted repeats within Xp11.2 are present at the breakpoints of isodicentric X chromosomes in Turner syndrome.

PubMed

Scott, Stuart A; Cohen, Ninette; Brandt, Tracy; Warburton, Peter E; Edelmann, Lisa

2010-09-01

Turner syndrome (TS) results from whole or partial monosomy X and is mediated by haploinsufficiency of genes that normally escape X-inactivation. Although a 45,X karyotype is observed in half of all TS cases, the most frequent variant TS karyotype includes the isodicentric X chromosome alone [46,X,idic(X)(p11)] or as a mosaic [46,X,idic(X)(p11)/45,X]. Given the mechanism of idic(X)(p11) rearrangement is poorly understood and breakpoint sequence information is unknown, this study sought to investigate the molecular mechanism of idic(X)(p11) formation by determining their precise breakpoint intervals. Karyotype analysis and fluorescence in situ hybridization mapping of eight idic(X)(p11) cell lines and three unbalanced Xp11.2 translocation lines identified the majority of breakpoints within a 5 Mb region, from approximately 53 to 58 Mb, in Xp11.1-p11.22, clustering into four regions. To further refine the breakpoints, a high-resolution oligonucleotide microarray (average of approximately 350 bp) was designed and array-based comparative genomic hybridization (aCGH) was performed on all 11 idic(X)(p11) and Xp11.2 translocation lines. aCGH analyses identified all breakpoint regions, including an idic(X)(p11) line with two potential breakpoints, one breakpoint shared between two idic(X)(p11) lines and two Xp translocations that shared breakpoints with idic(X)(p11) lines. Four of the breakpoint regions included large inverted repeats composed of repetitive gene clusters and segmental duplications, which corresponded to regions of copy-number variation. These data indicate that the rearrangement sites on Xp11.2 that lead to isodicentric chromosome formation and translocations are probably not random and suggest that the complex repetitive architecture of this region predisposes it to rearrangements, some of which are recurrent.

46 CFR 52.25-5 - Miniature boilers (modifies PMB-1 through PMB-21).

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false Miniature boilers (modifies PMB-1 through PMB-21). 52.25-5 Section 52.25-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING POWER BOILERS Other Boiler Types § 52.25-5 Miniature boilers (modifies PMB-1 through PMB-21). Miniature boilers must meet the applicable...

46 CFR 52.25-5 - Miniature boilers (modifies PMB-1 through PMB-21).

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 2 2014-10-01 2014-10-01 false Miniature boilers (modifies PMB-1 through PMB-21). 52.25-5 Section 52.25-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING POWER BOILERS Other Boiler Types § 52.25-5 Miniature boilers (modifies PMB-1 through PMB-21). Miniature boilers must meet the applicable...

46 CFR 52.25-5 - Miniature boilers (modifies PMB-1 through PMB-21).

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 2 2011-10-01 2011-10-01 false Miniature boilers (modifies PMB-1 through PMB-21). 52.25-5 Section 52.25-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING POWER BOILERS Other Boiler Types § 52.25-5 Miniature boilers (modifies PMB-1 through PMB-21). Miniature boilers must meet the applicable...

46 CFR 52.25-5 - Miniature boilers (modifies PMB-1 through PMB-21).

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 2 2012-10-01 2012-10-01 false Miniature boilers (modifies PMB-1 through PMB-21). 52.25-5 Section 52.25-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING POWER BOILERS Other Boiler Types § 52.25-5 Miniature boilers (modifies PMB-1 through PMB-21). Miniature boilers must meet the applicable...

46 CFR 52.25-5 - Miniature boilers (modifies PMB-1 through PMB-21).

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 2 2013-10-01 2013-10-01 false Miniature boilers (modifies PMB-1 through PMB-21). 52.25-5 Section 52.25-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING POWER BOILERS Other Boiler Types § 52.25-5 Miniature boilers (modifies PMB-1 through PMB-21). Miniature boilers must meet the applicable...

Fault-tolerant three-level inverter

DOEpatents

Edwards, John; Xu, Longya; Bhargava, Brij B.

2006-12-05

A method for driving a neutral point clamped three-level inverter is provided. In one exemplary embodiment, DC current is received at a neutral point-clamped three-level inverter. The inverter has a plurality of nodes including first, second and third output nodes. The inverter also has a plurality of switches. Faults are checked for in the inverter and predetermined switches are automatically activated responsive to a detected fault such that three-phase electrical power is provided at the output nodes.

Development of solid tunable optics for ultra-miniature imaging systems

NASA Astrophysics Data System (ADS)

Yongchao, Zou

This thesis focuses on the optimal design, fabrication and testing of solid tunable optics and exploring their applications in miniature imaging systems. It starts with the numerical modelling of such lenses, followed by the optimum design method and alignment tolerance analysis. A miniature solid tunable lens driven by a piezo actuator is then developed. To solve the problem of limited maximum optical power and tuning range in conventional lens designs, a novel multi-element solid tunable lens is proposed and developed. Inspired by the Alvarez principle, a novel miniature solid tunable dual-focus lens, which is designed using freeform surfaces and driven by one micro-electro-mechanical-systems (MEMS) rotary actuator, is demonstrated. To explore the applications of these miniature solid tunable lenses, a miniature adjustable-focus endoscope and one compact adjustable-focus camera module are developed. The adjustable-focus capability of these two miniature imaging systems is fully proved by electrically focusing targets placed at different positions.

Evaluation of the cationic trypsinogen gene for potential mutations in miniature schnauzers with pancreatitis

PubMed Central

2004-01-01

Abstract The purpose of this study was to evaluate the cationic trypsinogen gene in miniature schnauzers for possible mutations. Genetic mutations have been linked with hereditary pancreatitis in humans. Four miniature schnauzers were selected on the basis of a clinical history of pancreatitis. One healthy miniature schnauzer and 1 healthy mixed breed canine were enrolled as controls. DNA was extracted from these canines using a commercial kit. Primers were designed to amplify the entire canine cationic trypsinogen cDNA sequence. A polymerase chain reaction (PCR) was performed and products were purified and sequenced. All sequences were then compared. The healthy control canine, a healthy miniature schnauzer, and the 4 miniature schnauzers with pancreatitis showed identical sequences of the cationic trypsinogen gene to the published sequence. We conclude that, in contrast to humans with hereditary pancreatitis, mutations of the cationic trypsinogen gene do not play a major role in the genesis of pancreatitis in the miniature schnauzer. PMID:15581228

Evaluation of the cationic trypsinogen gene for potential mutations in miniature schnauzers with pancreatitis.

PubMed

Bishop, Micah A; Steiner, Jörg M; Moore, Lisa E; Williams, David A

2004-10-01

The purpose of this study was to evaluate the cationic trypsinogen gene in miniature schnauzers for possible mutations. Genetic mutations have been linked with hereditary pancreatitis in humans. Four miniature schnauzers were selected on the basis of a clinical history of pancreatitis. One healthy miniature schnauzer and 1 healthy mixed breed canine were enrolled as controls. DNA was extracted from these canines using a commercial kit. Primers were designed to amplify the entire canine cationic trypsinogen cDNA sequence. A polymerase chain reaction (PCR) was performed and products were purified and sequenced. All sequences were then compared. The healthy control canine, a healthy miniature schnauzer, and the 4 miniature schnauzers with pancreatitis showed identical sequences of the cationic trypsinogen gene to the published sequence. We conclude that, in contrast to humans with hereditary pancreatitis, mutations of the cationic trypsinogen gene do not play a major role in the genesis of pancreatitis in the miniature schnauzer.

[Comparative ultrastructural study of parotid gland, lacrimal gland and pituitary gland between miniature pig and mouse].

PubMed

Yan, Xing; Hai, Bo; Sun, Yi-lin; Zhang, Chun-mei; Wang, Song-ling

2009-02-01

To study the ultrastructure of parotid glands, lacrimal glands and pituitary glands between miniature pig and mouse. Five adult miniature pigs and 5 mice were studied. Ultrastructure of their parotid glands, lacrimal glands, and pituitary glands was observed. The secretary granules in acinar cell of miniature pig parotid glands showed higher density and more aequalis than those of mice. The cell apparatus in acinar cell of mouse parotid glands were more plentiful than those of miniature pigs. The secretary granules on blood vessel wall were richer in parotid gland of miniature pigs compared with mouse parotid gland. Lacrimal gland had the similar ultrastructure to parotid gland in these two animals. Many blood vessel antrum were found in pituitary glands of these two animals. Compared with mouse parotid glands, there are more secretary granules in acinar cells and vascular endothelial cells in miniature pig parotid glands, which might enter blood stream and have function of endocrine secretion.

21 CFR 184.1859 - Invert sugar.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Invert sugar. 184.1859 Section 184.1859 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DIRECT FOOD....1859 Invert sugar. (a) Invert sugar (CAS Reg. No. 8013-17-0) is an aqueous solution of inverted or...

Photovoltaic system with improved DC connections and method of making same

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cioffi, Philip Michael; Todorovic, Maja Harfman; Herzog, Michael Scott

A micro-inverter assembly includes a housing having an opening formed in a bottom surface thereof, and a direct current (DC)-to-alternating current (AC) micro-inverter disposed within the housing at a position adjacent to the opening. The micro-inverter assembly further includes a micro-inverter DC connector electrically coupled to the DC-to-AC micro-inverter and positioned within the opening of the housing, the micro-inverter DC connector having a plurality of exposed electrical contacts.

Frequency domain model for analysis of paralleled, series-output-connected Mapham inverters

NASA Technical Reports Server (NTRS)

Brush, Andrew S.; Sundberg, Richard C.; Button, Robert M.

1989-01-01

The Mapham resonant inverter is characterized as a two-port network driven by a selected periodic voltage. The two-port model is then used to model a pair of Mapham inverters connected in series and employing phasor voltage regulation. It is shown that the model is useful for predicting power output in paralleled inverter units, and for predicting harmonic current output of inverter pairs, using standard power flow techniques. Some sample results are compared to data obtained from testing hardware inverters.

Frequency domain model for analysis of paralleled, series-output-connected Mapham inverters

NASA Technical Reports Server (NTRS)

Brush, Andrew S.; Sundberg, Richard C.; Button, Robert M.

1989-01-01

The Mapham resonant inverter is characterized as a two-port network driven by a selected periodic voltage. The two-port model is then used to model a pair of Mapham inverters connected in series and employing phasor voltage regulation. It is shown that the model is useful for predicting power output in paralleled inverter units, and for predicting harmonic current output of inverter pairs, using standard power flow techniques. Some examples are compared to data obtained from testing hardware inverters.

Status and Needs of Power Electronics for Photovoltaic Inverters: Summary Document

NASA Astrophysics Data System (ADS)

West, R.; Mauch, K.; Qin, Y. C.; Mohan, N.; Bonn, R.

2002-05-01

Photovoltaic inverters are the most mature of any DER inverter, and their mean time to first failure (MTFF) is about five years. This is an unacceptable MTFF and will inhibit the rapid expansion of PV. With all DER technologies, (solar, wind, fuel cells, and microturbines) the inverter is still an immature product that will result in reliability problems in fielded systems. The increasing need for all of these technologies to have a reliable inverter provides a unique opportunity to address these needs with focused R&D development projects. The requirements for these inverters are so similar that modular designs with universal features are obviously the best solution for a 'next generation' inverter. A 'next generation' inverter will have improved performance, higher reliability, and improved profitability. Sandia National Laboratories has estimated that the development of a 'next generation' inverter could require approximately 20 man-years of work over an 18- to 24-month time frame, and that a government-industry partnership will greatly improve the chances of success.

Single phase inverter for a three phase power generation and distribution system

NASA Technical Reports Server (NTRS)

Lindena, S. J.

1976-01-01

A breadboard design of a single-phase inverter with sinusoidal output voltage for a three-phase power generation and distribution system was developed. The three-phase system consists of three single-phase inverters, whose output voltages are connected in a delta configuration. Upon failure of one inverter the two remaining inverters will continue to deliver three-phase power. Parallel redundancy as offered by two three-phase inverters is substituted by one three-phase inverter assembly with high savings in volume, weight, components count and complexity, and a considerable increase in reliability. The following requirements must be met: (1) Each single-phase, current-fed inverter must be capable of being synchronized to a three-phase reference system such that its output voltage remains phaselocked to its respective reference voltage. (2) Each single-phase, current-fed inverter must be capable of accepting leading and lagging power factors over a range from -0.7 through 1 to +0.7.

Cerebellar abiotrophy in a miniature schnauzer.

PubMed

Berry, Michelle L; Blas-Machado, Uriel

2003-08-01

A 3.5-month-old miniature schnauzer was presented for signs of progressive cerebellar ataxia. Necropsy revealed cerebellar abiotrophy. This is the first reported case of cerebellar abiotrophy in a purebred miniature schnauzer.

High prevalence of the c.74A>C SPINK1 variant in miniature and standard Schnauzers.

PubMed

Furrow, E; Armstrong, P J; Patterson, E E

2012-01-01

Variants in the serine protease inhibitor Kazal type 1 (SPINK1) gene have been associated with pancreatitis in Miniature Schnauzers. Replication of the association in an independent population is necessary to determine if genetic screening for SPINK1 variants should be considered in clinical practice. An association between the SPINK1 exonic variant c.74A > C and pancreatitis exists in Miniature Schnauzers. In addition, the variant is absent or rare in Standard Schnauzers, a related breed that is not reported to have an increased risk for pancreatitis. Case-control study. Seventeen Miniature Schnauzers with pancreatitis (cases), 60 mature Miniature Schnauzers with no substantial history of gastrointestinal signs in their lifetime (controls), and 31 Standard Schnauzers of unknown pancreatitis status. A PCR-RFLP assay was used to genotype dogs for the c.74A > C SPINK1 variant. Allele and genotype frequencies were reported for Schnauzers and compared between case and control Miniature Schnauzers. The c.74A > C variant was the major allele in both Schnauzer breeds with a frequency of 0.77 in Miniatures and 0.55 in Standards. The allele and genotype frequencies were similar between Miniature Schnauzers with and without a history of pancreatitis and did not impart an increased risk for pancreatitis. Genotyping a larger population of the Miniature Schnauzer breed than a previous study, along with a Standard Schnauzer cohort, demonstrated that the SPINK1 c.74A > C variant is a common polymorphism in the Schnauzer lineage. Furthermore, we were unable to confirm a relationship between the variant and clinically detectable pancreatitis in Miniature Schnauzers. Copyright © 2012 by the American College of Veterinary Internal Medicine.

An SCR inverter with an integral battery charger for electric vehicles

NASA Technical Reports Server (NTRS)

Thimmeach, D.

1983-01-01

The feasibility of incorporating an onboard battery charger into the inverter previously developed under a NASA contract is successfully demonstrated. The rated output power of the resulting isolated battery charger is 3.6 kW at 220 Vac with an 86 percent efficiency and a 95 percent power factor. Also achieved are improved inverter efficiency (from 90 to 93 percent at 15 kW motor shaft power), inverter peak power capability (from 26 to 34 kW), and reduced weight and volume of the combined inverter/charger package (47 kg, 49 x 44 x 24 cm). Some major conclusions are that using the inverter commutation circuitry to perform the battery charging function is advantageous, and that the input-commutated thyristor inverter has the potential to be an excellent inverter and battery charger for use in electric vehicle applications.

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

PubMed Central

Saski, Christopher; Lee, Seung-Bum; Fjellheim, Siri; Guda, Chittibabu; Jansen, Robert K.; Luo, Hong; Tomkins, Jeffrey; Rognli, Odd Arne; Clarke, Jihong Liu

2009-01-01

Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19–37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C–U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae. PMID:17534593

Repeated extragenic sequences in prokaryotic genomes: a proposal for the origin and dynamics of the RUP element in Streptococcus pneumoniae.

PubMed

Oggioni, M R; Claverys, J P

1999-10-01

A survey of all Streptococcus pneumoniae GenBank/EMBL DNA sequence entries and of the public domain sequence (representing more than 90% of the genome) of an S. pneumoniae type 4 strain allowed identification of 108 copies of a 107-bp-long highly repeated intergenic element called RUP (for repeat unit of pneumococcus). Several features of the element, revealed in this study, led to the proposal that RUP is an insertion sequence (IS)-derivative that could still be mobile. Among these features are: (1) a highly significant homology between the terminal inverted repeats (IRs) of RUPs and of IS630-Spn1, a new putative IS of S. pneumoniae; and (2) insertion at a TA dinucleotide, a characteristic target of several members of the IS630 family. Trans-mobilization of RUP is therefore proposed to be mediated by the transposase of IS630-Spn1. To account for the observation that RUPs are distributed among four subtypes which exhibit different degrees of sequence homogeneity, a scenario is invoked based on successive stages of RUP mobility and non-mobility, depending on whether an active transposase is present or absent. In the latter situation, an active transposase could be reintroduced into the species through natural transformation. Examination of sequences flanking RUP revealed a preferential association with ISs. It also provided evidence that RUPs promote sequence rearrangements, thereby contributing to genome flexibility. The possibility that RUP preferentially targets transforming DNA of foreign origin and subsequently favours disruption/rearrangement of exogenous sequences is discussed.

Source Repeatability of Time-Lapse Offset VSP Surveys for Monitoring CO2 Injection

NASA Astrophysics Data System (ADS)

Zhang, Z.; Huang, L.; Rutledge, J. T.; Denli, H.; Zhang, H.; McPherson, B. J.; Grigg, R.

2009-12-01

Time-lapse vertical seismic profiling (VSP) surveys have the potential to remotely track the migration of injected CO2 within a geologic formation. To accurately detect small changes due to CO2 injection, the sources of time-lapse VSP surveys must be located exactly at the same positions. However, in practice, the source locations can vary from one survey to another survey. Our numerical simulations demonstrate that a variation of a few meters in the VSP source locations can result in significant changes in time-lapse seismograms. To address the source repeatability issue, we apply double-difference tomography to downgoing waves of time-lapse offset VSP data to invert for the source locations and the velocity structures simultaneously. In collaboration with Resolute Natural Resources, Navajo National Oil and Gas Company, and the Southwest Regional Partnership on Carbon Sequestration under the support of the U.S. Department of Energy’s National Energy Technology Laboratory, one baseline and two repeat offset VSP datasets were acquired in 2007-2009 for monitoring CO2 injection at the Aneth oil field in Utah. A cemented geophone string was used to acquire the data for one zero-offset and seven offset source locations. During the data acquisition, there was some uncertainty in the repeatability of the source locations relative to the baseline survey. Our double-difference tomography results of the Aneth time-lapse VSP data show that the source locations for different surveys are separated up to a few meters. Accounting for these source location variations during VSP data analysis will improve reliability of time-lapse VSP monitoring.

Characterization of the hyperrecombination phenotype of the pol3-t mutation of Saccharomyces cerevisiae.

PubMed

Galli, Alvaro; Cervelli, Tiziana; Schiestl, Robert H

2003-05-01

The DNA polymerase delta (Pol3p/Cdc2p) allele pol3-t of Saccharomyces cerevisiae has previously been shown to increase the frequency of deletions between short repeats (several base pairs), between homologous DNA sequences separated by long inverted repeats, and between distant short repeats, increasing the frequency of genomic deletions. We found that the pol3-t mutation increased intrachromosomal recombination events between direct DNA repeats up to 36-fold and interchromosomal recombination 14-fold. The hyperrecombination phenotype of pol3-t was partially dependent on the Rad52p function but much more so on Rad1p. However, in the double-mutant rad1 Delta rad52 Delta, the pol3-t mutation still increased spontaneous intrachromosomal recombination frequencies, suggesting that a Rad1p Rad52p-independent single-strand annealing pathway is involved. UV and gamma-rays were less potent inducers of recombination in the pol3-t mutant, indicating that Pol3p is partly involved in DNA-damage-induced recombination. In contrast, while UV- and gamma-ray-induced intrachromosomal recombination was almost completely abolished in the rad52 or the rad1 rad52 mutant, there was still good induction in those mutants in the pol3-t background, indicating channeling of lesions into the above-mentioned Rad1p Rad52p-independent pathway. Finally, a heterozygous pol3-t/POL3 mutant also showed an increased frequency of deletions and MMS sensitivity at the restrictive temperature, indicating that even a heterozygous polymerase delta mutation might increase the frequency of genetic instability.

Cerebellar abiotrophy in a miniature schnauzer

PubMed Central

Berry, Michelle L.; Blas-Machado, Uriel

2003-01-01

A 3.5-month-old miniature schnauzer was presented for signs of progressive cerebellar ataxia. Necropsy revealed cerebellar abiotrophy. This is the first reported case of cerebellar abiotrophy in a purebred miniature schnauzer. PMID:13677598

Microgrid and Inverter Control and Simulator Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

2012-09-13

A collection of software that can simulate the operation of an inverter on a microgrid or control a real inverter. In addition, it can simulate the control of multiple nodes on a microgrid." Application: Simulation of inverters and microgrids; control of inverters on microgrids." The MMI submodule is designed to control custom inverter hardware, and to simulate that hardware. The INVERTER submodule is only the simulator code, and is of an earlier generation than the simulator in MMI. The MICROGRID submodule is an agent-based simulator of multiple nodes on a microgrid which presents a web interface. The WIND submodule producesmore » movies of wind data with a web interface.« less

Design and Implementation of nine level multilevel Inverter

NASA Astrophysics Data System (ADS)

Dhineshkumar, K.; Subramani, C.

2018-04-01

In this paper the solar based boost converter integrated Nine level multilevel inverter presented. It uses 7 switches to produce nine level output stepped waveform. The aim of the work to produce 9 level wave form using solar and boost converter. The conventional inverter has multiple sources and has 16 switches are required and also more number of voltage sources required. The proposed inverter required single solar panel and reduced number of switches and integrated boost converter which increase the input voltage of the inverter. The proposed inverter simulated and compared with R load using Mat lab and prototype model experimentally verified. The proposed inverter can be used in n number of solar applications.

System and method for regulating resonant inverters

DOEpatents

Stevanovic, Ljubisa Dragoljub [Clifton Park, NY; Zane, Regan Andrew [Superior, CO

2007-08-28

A technique is provided for direct digital phase control of resonant inverters based on sensing of one or more parameters of the resonant inverter. The resonant inverter control system includes a switching circuit for applying power signals to the resonant inverter and a sensor for sensing one or more parameters of the resonant inverter. The one or more parameters are representative of a phase angle. The resonant inverter control system also includes a comparator for comparing the one or more parameters to a reference value and a digital controller for determining timing of the one or more parameters and for regulating operation of the switching circuit based upon the timing of the one or more parameters.

Stability Assessment of a System Comprising a Single Machine and Inverter with Scalable Ratings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Brian B; Lin, Yashen; Gevorgian, Vahan

Synchronous machines have traditionally acted as the foundation of large-scale electrical infrastructures and their physical properties have formed the cornerstone of system operations. However, with the increased integration of distributed renewable resources and energy-storage technologies, there is a need to systematically acknowledge the dynamics of power-electronics inverters - the primary energy-conversion interface in such systems - in all aspects of modeling, analysis, and control of the bulk power network. In this paper, we assess the properties of coupled machine-inverter systems by studying an elementary system comprised of a synchronous generator, three-phase inverter, and a load. The inverter model is formulatedmore » such that its power rating can be scaled continuously across power levels while preserving its closed-loop response. Accordingly, the properties of the machine-inverter system can be assessed for varying ratios of machine-to-inverter power ratings. After linearizing the model and assessing its eigenvalues, we show that system stability is highly dependent on the inverter current controller and machine exciter, thus uncovering a key concern with mixed machine-inverter systems and motivating the need for next-generation grid-stabilizing inverter controls.« less

Small-volume multiparametric electrochemical detection at low cost polymeric devices featuring nanoelectrodes

NASA Astrophysics Data System (ADS)

Kitsara, Maria; Cirera, Josep Maria; Aller-Pellitero, Miguel; Sabaté, Neus; Punter, Jaume; Colomer-Farrarons, Jordi; Miribel-Català, Pere; del Campo, F. Javier

2015-06-01

The development of a low-cost multiparametric platform for enzymatic electrochemical biosensing that can be integrated in a disposable, energy autonomous analytical device is the target of the current work. We propose a technology to fabricate nano-electrodes and ultimately biosensors on flexible polymeric-based substrates (cyclo olefin polymer, and polyimide) using standard microfabrication (step and repeat lithography and lift-off) and rapid prototyping techniques (blade cutting). Our target is towards the fabrication of a miniaturized prototype that can work with small sample volumes in the range of 5-10μL without the need for external pumps for sample loading and handling. This device can be used for the simultaneous detection of metabolites such as glucose, cholesterol and triglycerides for the early diagnosis of diabetes.

Sequential Multiplex Analyte Capturing for Phosphoprotein Profiling*

PubMed Central

Poetz, Oliver; Henzler, Tanja; Hartmann, Michael; Kazmaier, Cornelia; Templin, Markus F.; Herget, Thomas; Joos, Thomas O.

2010-01-01

Microarray-based sandwich immunoassays can simultaneously detect dozens of proteins. However, their use in quantifying large numbers of proteins is hampered by cross-reactivity and incompatibilities caused by the immunoassays themselves. Sequential multiplex analyte capturing addresses these problems by repeatedly probing the same sample with different sets of antibody-coated, magnetic suspension bead arrays. As a miniaturized immunoassay format, suspension bead array-based assays fulfill the criteria of the ambient analyte theory, and our experiments reveal that the analyte concentrations are not significantly changed. The value of sequential multiplex analyte capturing was demonstrated by probing tumor cell line lysates for the abundance of seven different receptor tyrosine kinases and their degree of phosphorylation and by measuring the complex phosphorylation pattern of the epidermal growth factor receptor in the same sample from the same cavity. PMID:20682761

Subcritical crack growth phenomenon and fractography of barium titanate and barium titanate-based composite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hwang, H.J.; Niihara, Koichi

1997-01-15

Subcritical crack growth (SCG), the propagation of surface and subsurface flaws under subcritical stress, i.e., any stress less than that necessary to catastrophically propagate the flaw, is a general phenomenon frequently observed in ceramics. Recently, electrical devices are miniaturized and used under quite severe atmospheres. Such environments often lead to the initiation and propagation of cracks due to the repeated electrical cycling, stresses by the mismatch in thermal expansion coefficient between devices and other constituents and thermal shock. In this study, the authors fabricated BaTiO{sub 3} and BaTiO{sub 3}-based composites containing nano-sized SiC particulates. The SCG phenomenon and fractography weremore » discussed based on the data obtained from indentation-induced-fracture (IIF) method.« less

All gene-sized DNA molecules in four species of hypotrichs have the same terminal sequence and an unusual 3' terminus.

PubMed Central

Klobutcher, L A; Swanton, M T; Donini, P; Prescott, D M

1981-01-01

In hypotrichous ciliates, all of the macronuclear DNA is in the form of low molecular weight molecules with an average size of approximately 2200 base pairs. Total macronuclear DNA from four hypotrichs has been shown to have inverted terminal repeats by direct sequence analysis. In Oxytricha nova, Oxytricha sp., and Stylonychia pustulata, this terminal sequence may be written as 5'-C4A4C4A4C4 ... 3'-G4T4G4T4G4T4G4T4G4 ... In Euplotes aediculatus, the sequences is similar but differs in the lengths of the duplex region (28 base pairs) and of the putative 3' extension (14 base pairs). Also in Euplotes, a second common sequence of 5 base pairs (A-A-C-T-T-T-T-G-A-A) occurs internal to the terminal repeat and a 17-base-pair heterogeneous region: 5'-C4A4C4A4C4A4C4(X)17T-T-G-A-A ... 3'-G2T4G4T4G4T4G4T4G4T4G4(X)17A-A-C-T-T ... The length of the terminal repeat sequence for O. nova was confirmed in cloned macronuclear DNA molecules. Images PMID:6265931

Par for the Course: Students Design Their Miniature Golf Course Sculptures while Considering Functional, Technical, and Communication Elements

ERIC Educational Resources Information Center

Vassil, Darlene

2005-01-01

Designing an eighteen-hole miniature-golf course is not the typical end-of-the-year art project, but at Winfield School it's "par for the course." Students anxiously count the days to the first day of miniature golf, courtesy of the sixth-grade art classes. The design and production of the miniature gold course serves as a great motivator and…

Characterization of a new high copy Stowaway family MITE, BRAMI-1 in Brassica genome

PubMed Central

2013-01-01

Background Miniature inverted-repeat transposable elements (MITEs) are expected to play important roles in evolution of genes and genome in plants, especially in the highly duplicated plant genomes. Various MITE families and their roles in plants have been characterized. However, there have been fewer studies of MITE families and their potential roles in evolution of the recently triplicated Brassica genome. Results We identified a new MITE family, BRAMI-1, belonging to the Stowaway super-family in the Brassica genome. In silico mapping revealed that 697 members are dispersed throughout the euchromatic regions of the B. rapa pseudo-chromosomes. Among them, 548 members (78.6%) are located in gene-rich regions, less than 3 kb from genes. In addition, we identified 516 and 15 members in the 470 Mb and 15 Mb genomic shotgun sequences currently available for B. oleracea and B. napus, respectively. The resulting estimated copy numbers for the entire genomes were 1440, 1464 and 2490 in B. rapa, B. oleracea and B. napus, respectively. Concurrently, only 70 members of the related Arabidopsis ATTIRTA-1 MITE family were identified in the Arabidopsis genome. Phylogenetic analysis revealed that BRAMI-1 elements proliferated in the Brassica genus after divergence from the Arabidopsis lineage. MITE insertion polymorphism (MIP) was inspected for 50 BRAMI-1 members, revealing high levels of insertion polymorphism between and within species of Brassica that clarify BRAMI-1 activation periods up to the present. Comparative analysis of the 71 genes harbouring the BRAMI-1 elements with their non-insertion paralogs (NIPs) showed that the BRAMI-1 insertions mainly reside in non-coding sequences and that the expression levels of genes with the elements differ from those of their NIPs. Conclusion A Stowaway family MITE, named as BRAMI-1, was gradually amplified and remained present in over than 1400 copies in each of three Brassica species. Overall, 78% of the members were identified in gene-rich regions, and it is assumed that they may contribute to the evolution of duplicated genes in the highly duplicated Brassica genome. The resulting MIPs can serve as a good source of DNA markers for Brassica crops because the insertions are highly dispersed in the gene-rich euchromatin region and are polymorphic between or within species. PMID:23547712

Small is beautiful: features of the smallest insects and limits to miniaturization.

PubMed

Polilov, Alexey A

2015-01-07

Miniaturization leads to considerable reorganization of structures in insects, affecting almost all organs and tissues. In the smallest insects, comparable in size to unicellular organisms, modifications arise not only at the level of organs, but also at the cellular level. Miniaturization is accompanied by allometric changes in many organ systems. The consequences of miniaturization displayed by different insect taxa include both common and unique changes. Because the smallest insects are among the smallest metazoans and have the most complex organization among organisms of the same size, their peculiar structural features and the factors that limit their miniaturization are of considerable theoretical interest to general biology.

Recognizing the enemy within: licensing RNA-guided genome defense

PubMed Central

Dumesic, Phillip A.; Madhani, Hiten D.

2014-01-01

How do cells distinguish normal genes from transposons? Although much has been learned about RNAi-related RNA silencing pathways responsible for genome defense, this fundamental question remains. The literature points to several classes of mechanisms. In some cases, double-stranded RNA structures produced by transposon inverted repeats or antisense integration trigger endo-siRNA biogenesis. In other instances, DNA features associated with transposons—such as their unusual copy number, chromosomal arrangement, and/or chromatin environment—license RNA silencing. Finally, recent studies have identified improper transcript processing events, such as stalled pre-mRNA splicing, as signals for siRNA production. Thus, the suboptimal gene expression properties of selfish elements can enable their identification by RNA silencing pathways. PMID:24280023

Mammalian DNA enriched for replication origins is enriched for snap-back sequences.

PubMed

Zannis-Hadjopoulos, M; Kaufmann, G; Martin, R G

1984-11-15

Using the instability of replication loops as a method for the isolation of double-stranded nascent DNA, extruded DNA enriched for replication origins was obtained and denatured. Snap-back DNA, single-stranded DNA with inverted repeats (palindromic sequences), reassociates rapidly into stem-loop structures with zero-order kinetics when conditions are changed from denaturing to renaturing, and can be assayed by chromatography on hydroxyapatite. Origin-enriched nascent DNA strands from mouse, rat and monkey cells growing either synchronously or asynchronously were purified and assayed for the presence of snap-back sequences. The results show that origin-enriched DNA is also enriched for snap-back sequences, implying that some origins for mammalian DNA replication contain or lie near palindromic sequences.

Importance Sampling of Word Patterns in DNA and Protein Sequences

PubMed Central

Chan, Hock Peng; Chen, Louis H.Y.

2010-01-01

Abstract Monte Carlo methods can provide accurate p-value estimates of word counting test statistics and are easy to implement. They are especially attractive when an asymptotic theory is absent or when either the search sequence or the word pattern is too short for the application of asymptotic formulae. Naive direct Monte Carlo is undesirable for the estimation of small probabilities because the associated rare events of interest are seldom generated. We propose instead efficient importance sampling algorithms that use controlled insertion of the desired word patterns on randomly generated sequences. The implementation is illustrated on word patterns of biological interest: palindromes and inverted repeats, patterns arising from position-specific weight matrices (PSWMs), and co-occurrences of pairs of motifs. PMID:21128856

The complete chloroplast genome of a medicinal plant Epimedium koreanum Nakai (Berberidaceae).

PubMed

Lee, Jung-Hoon; Kim, Kyunghee; Kim, Na-Rae; Lee, Sang-Choon; Yang, Tae-Jin; Kim, Young-Dong

2016-11-01

Epimedium koreanum is a perennial medicinal plant distributed in Eastern Asia. The complete chloroplast genome sequences of E. koreanum was obtained by de novo assembly using whole genome next-generation sequences. The chloroplast genome of E. koreanum was 157 218 bp in length and separated into four distinct regions such as large single copy region (89 600 bp), small single copy region (17 222 bp) and a pair of inverted repeat regions (25 198 bp). The genome contained a total of 112 genes including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that E. koreanum is most closely related to Berberis bealei, a traditional medicinal plant in the Berberidaceae family.

A-to-I editing of coding and non-coding RNAs by ADARs

PubMed Central

Nishikura, Kazuko

2016-01-01

Adenosine deaminases acting on RNA (ADARs) convert adenosine to inosine in double-stranded RNA. This A-to-I editing occurs not only in protein-coding regions of mRNAs, but also frequently in non-coding regions that contain inverted Alu repeats. Editing of coding sequences can result in the expression of functionally altered proteins that are not encoded in the genome, whereas the significance of Alu editing remains largely unknown. Certain microRNA (miRNA) precursors are also edited, leading to reduced expression or altered function of mature miRNAs. Conversely, recent studies indicate that ADAR1 forms a complex with Dicer to promote miRNA processing, revealing a new function of ADAR1 in the regulation of RNA interference. PMID:26648264

Conferring virus resistance in tomato by independent RNA silencing of three tomato homologs of Arabidopsis TOM1.

PubMed

Ali, Md Emran; Ishii, Yuko; Taniguchi, Jyun-Ichi; Waliullah, Sumyya; Kobayashi, Kappei; Yaeno, Takashi; Yamaoka, Naoto; Nishiguchi, Masamichi

2018-05-01

The TOM1/TOM3 genes from Arabidopsis are involved in the replication of tobamoviruses. Tomato homologs of these genes, LeTH1, LeTH2 and LeTH3, are known. In this study, we examined transgenic tomato lines where inverted repeats of either LeTH1, LeTH2 or LeTH3 were introduced by Agrobacterium. Endogenous mRNA expression for each gene was detected in non-transgenic control plants, whereas a very low level of each of the three genes was found in the corresponding line. Small interfering RNA was detected in the transgenic lines. Each silenced line showed similar levels of tobamovirus resistance, indicating that each gene is similarly involved in virus replication.

The complete mitochondrial genome sequence of Malus hupehensis var. pinyiensis.

PubMed

Duan, Naibin; Sun, Honghe; Wang, Nan; Fei, Zhangjun; Chen, Xuesen

2016-07-01

The complete mitochondrial genome sequence of Malus hupehensis var. pinyiensis, a widely used apple rootstock, was determined using the Illumina high-throughput sequencing approach. The genome is 422,555 bp in length and has a GC content of 45.21%. It is separated by a pair of inverted repeats of 32,504 bp, to form a large single copy region of 213,055 bp and a small single copy region of 144,492 bp. The genome contains 38 protein-coding genes, four pseudogenes, 25 tRNA genes, and three rRNA genes. The genome is 25,608 bp longer than that of M. domestica, and several structural variations between these two mitogenomes were detected.

Cassandra retrotransposons carry independently transcribed 5S RNA

PubMed Central

Kalendar, Ruslan; Tanskanen, Jaakko; Chang, Wei; Antonius, Kristiina; Sela, Hanan; Peleg, Ofer; Schulman, Alan H.

2008-01-01

We report a group of TRIMs (terminal-repeat retrotransposons in miniature), which are small nonautonomous retrotransposons. These elements, named Cassandra, universally carry conserved 5S RNA sequences and associated RNA polymerase (pol) III promoters and terminators in their long terminal repeats (LTRs). They were found in all vascular plants investigated. Uniquely for LTR retrotransposons, Cassandra produces noncapped, polyadenylated transcripts from the 5S pol III promoter. Capped, read-through transcripts containing Cassandra sequences can also be detected in RNA and in EST databases. The predicted Cassandra RNA 5S secondary structures resemble those for cellular 5S rRNA, with high information content specifically in the pol III promoter region. Genic integration sites are common for Cassandra, an unusual feature for abundant retrotransposons. The 5S in each LTR produces a tandem 5S arrangement with an inter-5S spacing resembling that of cellular 5S. The distribution of 5S genes is very variable in flowering plants and may be partially explained by Cassandra activity. Cassandra thus appears both to have adapted a ubiquitous cellular gene for ribosomal RNA for use as a promoter and to parasitize an as-yet-unidentified group of retrotransposons for the proteins needed in its lifecycle. PMID:18408163

Body shape convergence driven by small size optimum in marine angelfishes.

PubMed

Frédérich, Bruno; Santini, Francesco; Konow, Nicolai; Schnitzler, Joseph; Lecchini, David; Alfaro, Michael E

2017-06-01

Convergent evolution of small body size occurs across many vertebrate clades and may reflect an evolutionary response to shared selective pressures. However it remains unclear if other aspects of phenotype undergo convergent evolution in miniaturized lineages. Here we present a comparative analysis of body size and shape evolution in marine angelfishes (Pomacanthidae), a reef fish family characterized by repeated transitions to small body size. We ask if lineages that evolve small sizes show convergent evolution in body shape. Our results reveal that angelfish lineages evolved three different stable size optima with one corresponding to the group of pygmy angelfishes ( Centropyge ). Then, we test if the observed shifts in body size are associated with changes to new adaptive peaks in shape. Our data suggest that independent evolution to small size optima have induced repeated convergence upon deeper body and steeper head profile in Centropyge These traits may favour manoeuvrability and visual awareness in these cryptic species living among corals, illustrating that functional demands on small size may be related to habitat specialization and predator avoidance. The absence of shape convergence in large marine angelfishes also suggests that more severe requirements exist for small than for large size optima. © 2017 The Author(s).

Platform Precision Autopilot Overview and Mission Performance

NASA Technical Reports Server (NTRS)

Strovers, Brian K.; Lee, James A.

2009-01-01

The Platform Precision Autopilot is an instrument landing system-interfaced autopilot system, developed to enable an aircraft to repeatedly fly nearly the same trajectory hours, days, or weeks later. The Platform Precision Autopilot uses a novel design to interface with a NASA Gulfstream III jet by imitating the output of an instrument landing system approach. This technique minimizes, as much as possible, modifications to the baseline Gulfstream III jet and retains the safety features of the aircraft autopilot. The Platform Precision Autopilot requirement is to fly within a 5-m (16.4-ft) radius tube for distances to 200 km (108 nmi) in the presence of light turbulence for at least 90 percent of the time. This capability allows precise repeat-pass interferometry for the Unmanned Aerial Vehicle Synthetic Aperture Radar program, whose primary objective is to develop a miniaturized, polarimetric, L-band synthetic aperture radar. Precise navigation is achieved using an accurate differential global positioning system developed by the Jet Propulsion Laboratory. Flight-testing has demonstrated the ability of the Platform Precision Autopilot to control the aircraft within the specified tolerance greater than 90 percent of the time in the presence of aircraft system noise and nonlinearities, constant pilot throttle adjustments, and light turbulence.

Platform Precision Autopilot Overview and Flight Test Results

NASA Technical Reports Server (NTRS)

Lin, V.; Strovers, B.; Lee, J.; Beck, R.

2008-01-01

The Platform Precision Autopilot is an instrument landing system interfaced autopilot system, developed to enable an aircraft to repeatedly fly nearly the same trajectory hours, days, or weeks later. The Platform Precision Autopilot uses a novel design to interface with a NASA Gulfstream III jet by imitating the output of an instrument landing system approach. This technique minimizes, as much as possible, modifications to the baseline Gulfstream III jet and retains the safety features of the aircraft autopilot. The Platform Precision Autopilot requirement is to fly within a 5-m (16.4-ft) radius tube for distances to 200 km (108 nmi) in the presence of light turbulence for at least 90 percent of the time. This capability allows precise repeat-pass interferometry for the Uninhabited Aerial Vehicle Synthetic Aperture Radar program, whose primary objective is to develop a miniaturized, polarimetric, L-band synthetic aperture radar. Precise navigation is achieved using an accurate differential global positioning system developed by the Jet Propulsion Laboratory. Flight-testing has demonstrated the ability of the Platform Precision Autopilot to control the aircraft within the specified tolerance greater than 90 percent of the time in the presence of aircraft system noise and nonlinearities, constant pilot throttle adjustments, and light turbulence.

Hemispheric specialization and the perception of emotion: evidence from right-handers and from inverted and non-inverted left-handers.

PubMed

Reuter-Lorenz, P A; Givis, R P; Moscovitch, M

1983-01-01

Right-handers and inverted and non-inverted left-handers viewed emotional expressions in one hemifield and, simultaneously, a neutral expression of the same poser in the other hemifield. Subjects were required to identify the side containing the affective face. Happy faces with open (i.e. salient) and closed mouth smiles and sad faces were used as stimuli. For right-handers and inverters reaction time was faster to right hemifield presentations for happy faces and to left hemifield presentations for sad faces. Non-inverters showed the reverse pattern. The saliency of the happy expressions had no effect on the magnitude and direction of asymmetry for any group. The data support the hypothesis of differential hemispheric specialization for positive and negative emotion and demonstrate opposite patterns of asymmetry in affect perception for inverted and non-inverted left-handers.

Voltage balanced multilevel voltage source converter system

DOEpatents

Peng, Fang Zheng; Lai, Jih-Sheng

1997-01-01

A voltage balanced multilevel converter for high power AC applications such as adjustable speed motor drives and back-to-back DC intertie of adjacent power systems. This converter provides a multilevel rectifier, a multilevel inverter, and a DC link between the rectifier and the inverter allowing voltage balancing between each of the voltage levels within the multilevel converter. The rectifier is equipped with at least one phase leg and a source input node for each of the phases. The rectifier is further equipped with a plurality of rectifier DC output nodes. The inverter is equipped with at least one phase leg and a load output node for each of the phases. The inverter is further equipped with a plurality of inverter DC input nodes. The DC link is equipped with a plurality of rectifier charging means and a plurality of inverter discharging means. The plurality of rectifier charging means are connected in series with one of the rectifier charging means disposed between and connected in an operable relationship with each adjacent pair of rectifier DC output nodes. The plurality of inverter discharging means are connected in series with one of the inverter discharging means disposed between and connected in an operable relationship with each adjacent pair of inverter DC input nodes. Each of said rectifier DC output nodes are individually electrically connected to the respective inverter DC input nodes. By this means, each of the rectifier DC output nodes and each of the inverter DC input nodes are voltage balanced by the respective charging and discharging of the rectifier charging means and the inverter discharging means.

Voltage balanced multilevel voltage source converter system

DOEpatents

Peng, F.Z.; Lai, J.S.

1997-07-01

Disclosed is a voltage balanced multilevel converter for high power AC applications such as adjustable speed motor drives and back-to-back DC intertie of adjacent power systems. This converter provides a multilevel rectifier, a multilevel inverter, and a DC link between the rectifier and the inverter allowing voltage balancing between each of the voltage levels within the multilevel converter. The rectifier is equipped with at least one phase leg and a source input node for each of the phases. The rectifier is further equipped with a plurality of rectifier DC output nodes. The inverter is equipped with at least one phase leg and a load output node for each of the phases. The inverter is further equipped with a plurality of inverter DC input nodes. The DC link is equipped with a plurality of rectifier charging means and a plurality of inverter discharging means. The plurality of rectifier charging means are connected in series with one of the rectifier charging means disposed between and connected in an operable relationship with each adjacent pair of rectifier DC output nodes. The plurality of inverter discharging means are connected in series with one of the inverter discharging means disposed between and connected in an operable relationship with each adjacent pair of inverter DC input nodes. Each of said rectifier DC output nodes are individually electrically connected to the respective inverter DC input nodes. By this means, each of the rectifier DC output nodes and each of the inverter DC input nodes are voltage balanced by the respective charging and discharging of the rectifier charging means and the inverter discharging means. 15 figs.

Multilevel cascade voltage source inverter with seperate DC sources

DOEpatents

Peng, Fang Zheng; Lai, Jih-Sheng

1997-01-01

A multilevel cascade voltage source inverter having separate DC sources is described herein. This inverter is applicable to high voltage, high power applications such as flexible AC transmission systems (FACTS) including static VAR generation (SVG), power line conditioning, series compensation, phase shifting and voltage balancing and fuel cell and photovoltaic utility interface systems. The M-level inverter consists of at least one phase wherein each phase has a plurality of full bridge inverters equipped with an independent DC source. This inverter develops a near sinusoidal approximation voltage waveform with only one switching per cycle as the number of levels, M, is increased. The inverter may have either single-phase or multi-phase embodiments connected in either wye or delta configurations.

Multilevel cascade voltage source inverter with seperate DC sources

DOEpatents

Peng, Fang Zheng; Lai, Jih-Sheng

2002-01-01

A multilevel cascade voltage source inverter having separate DC sources is described herein. This inverter is applicable to high voltage, high power applications such as flexible AC transmission systems (FACTS) including static VAR generation (SVG), power line conditioning, series compensation, phase shifting and voltage balancing and fuel cell and photovoltaic utility interface systems. The M-level inverter consists of at least one phase wherein each phase has a plurality of full bridge inverters equipped with an independent DC source. This inverter develops a near sinusoidal approximation voltage waveform with only one switching per cycle as the number of levels, M, is increased. The inverter may have either single-phase or multi-phase embodiments connected in either wye or delta configurations.

Multilevel cascade voltage source inverter with seperate DC sources

DOEpatents

Peng, Fang Zheng; Lai, Jih-Sheng

2001-04-03

A multilevel cascade voltage source inverter having separate DC sources is described herein. This inverter is applicable to high voltage, high power applications such as flexible AC transmission systems (FACTS) including static VAR generation (SVG), power line conditioning, series compensation, phase shifting and voltage balancing and fuel cell and photovoltaic utility interface systems. The M-level inverter consists of at least one phase wherein each phase has a plurality of full bridge inverters equipped with an independent DC source. This inverter develops a near sinusoidal approximation voltage waveform with only one switching per cycle as the number of levels, M, is increased. The inverter may have either single-phase or multi-phase embodiments connected in either wye or delta configurations.

Multilevel cascade voltage source inverter with separate DC sources

DOEpatents

Peng, F.Z.; Lai, J.S.

1997-06-24

A multilevel cascade voltage source inverter having separate DC sources is described herein. This inverter is applicable to high voltage, high power applications such as flexible AC transmission systems (FACTS) including static VAR generation (SVG), power line conditioning, series compensation, phase shifting and voltage balancing and fuel cell and photovoltaic utility interface systems. The M-level inverter consists of at least one phase wherein each phase has a plurality of full bridge inverters equipped with an independent DC source. This inverter develops a near sinusoidal approximation voltage waveform with only one switching per cycle as the number of levels, M, is increased. The inverter may have either single-phase or multi-phase embodiments connected in either wye or delta configurations. 15 figs.

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

Stationary and non-stationary occurrences of miniature end plate potentials are well described as stationary and non-stationary Poisson processes in the mollusc Navanax inermis.

PubMed

Cappell, M S; Spray, D C; Bennett, M V

1988-06-28

Protractor muscles in the gastropod mollusc Navanax inermis exhibit typical spontaneous miniature end plate potentials with mean amplitude 1.71 +/- 1.19 (standard deviation) mV. The evoked end plate potential is quantized, with a quantum equal to the miniature end plate potential amplitude. When their rate is stationary, occurrence of miniature end plate potentials is a random, Poisson process. When non-stationary, spontaneous miniature end plate potential occurrence is a non-stationary Poisson process, a Poisson process with the mean frequency changing with time. This extends the random Poisson model for miniature end plate potentials to the frequently observed non-stationary occurrence. Reported deviations from a Poisson process can sometimes be accounted for by the non-stationary Poisson process and more complex models, such as clustered release, are not always needed.

A Spectral Reconstruction Algorithm of Miniature Spectrometer Based on Sparse Optimization and Dictionary Learning.

PubMed

Zhang, Shang; Dong, Yuhan; Fu, Hongyan; Huang, Shao-Lun; Zhang, Lin

2018-02-22

The miniaturization of spectrometer can broaden the application area of spectrometry, which has huge academic and industrial value. Among various miniaturization approaches, filter-based miniaturization is a promising implementation by utilizing broadband filters with distinct transmission functions. Mathematically, filter-based spectral reconstruction can be modeled as solving a system of linear equations. In this paper, we propose an algorithm of spectral reconstruction based on sparse optimization and dictionary learning. To verify the feasibility of the reconstruction algorithm, we design and implement a simple prototype of a filter-based miniature spectrometer. The experimental results demonstrate that sparse optimization is well applicable to spectral reconstruction whether the spectra are directly sparse or not. As for the non-directly sparse spectra, their sparsity can be enhanced by dictionary learning. In conclusion, the proposed approach has a bright application prospect in fabricating a practical miniature spectrometer.

A Spectral Reconstruction Algorithm of Miniature Spectrometer Based on Sparse Optimization and Dictionary Learning

PubMed Central

Zhang, Shang; Fu, Hongyan; Huang, Shao-Lun; Zhang, Lin

2018-01-01

The miniaturization of spectrometer can broaden the application area of spectrometry, which has huge academic and industrial value. Among various miniaturization approaches, filter-based miniaturization is a promising implementation by utilizing broadband filters with distinct transmission functions. Mathematically, filter-based spectral reconstruction can be modeled as solving a system of linear equations. In this paper, we propose an algorithm of spectral reconstruction based on sparse optimization and dictionary learning. To verify the feasibility of the reconstruction algorithm, we design and implement a simple prototype of a filter-based miniature spectrometer. The experimental results demonstrate that sparse optimization is well applicable to spectral reconstruction whether the spectra are directly sparse or not. As for the non-directly sparse spectra, their sparsity can be enhanced by dictionary learning. In conclusion, the proposed approach has a bright application prospect in fabricating a practical miniature spectrometer. PMID:29470406

Impacts of Inverter-Based Advanced Grid Support Functions on Islanding Detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Austin; Hoke, Anderson; Miller, Brian

A long-standing requirement for inverters paired with distributed energy resources is that they are required to disconnect from the electrical power system (EPS) when an electrical island is formed. In recent years, advanced grid support controls have been developed for inverters to provide voltage and frequency support by integrating functions such as voltage and frequency ride-through, volt-VAr control, and frequency-Watt control. With these new capabilities integrated into the inverter, additional examination is needed to determine how voltage and frequency support will impact pre-existing inverter functions like island detection. This paper inspects how advanced inverter functions will impact its ability tomore » detect the formation of an electrical island. Results are presented for the unintentional islanding laboratory tests of three common residential-scale photovoltaic inverters performing various combinations of grid support functions. For the inverters tested, grid support functions prolonged island disconnection times slightly; however, it was found that in all scenarios the inverters disconnected well within two seconds, the limit imposed by IEEE Std 1547-2003.« less

Integral inverter/battery charger for use in electric vehicles

NASA Technical Reports Server (NTRS)

Thimmesch, D.

1983-01-01

The design and test results of a thyristor based inverter/charger are discussed. A battery charger is included integral to the inverter by using a subset of the inverter power circuit components. The resulting charger provides electrical isolation between the vehicle propulsion battery and ac line and is capable of charging a 25 kWh propulsion battery in 8 hours from a 220 volt ac line. The integral charger employs the inverter commutation components at a resonant ac/dc isolated converter rated at 3.6 kW. Charger efficiency and power factor at an output power of 3.6 kW are 86% and 95% respectively. The inverter, when operated with a matching polyphase ac induction motor and nominal 132 volt propulsion battery, can provide a peak shaft power of 34 kW (45 ph) during motoring operation and 45 kW (60 hp) during regeneration. Thyristors are employed for the inverter power switching devices and are arranged in an input-commutated topology. This configuration requires only two thyristors to commutate the six main inverter thyristors. Inverter efficiency during motoring operation at motor shaft speeds above 450 rad/sec (4300 rpm) is 92-94% for output power levels above 11 KW (15 hp). The combined ac inverter/charger package weighs 47 kg (103 lbs).

An Optimal Current Controller Design for a Grid Connected Inverter to Improve Power Quality and Test Commercial PV Inverters.

PubMed

Algaddafi, Ali; Altuwayjiri, Saud A; Ahmed, Oday A; Daho, Ibrahim

2017-01-01

Grid connected inverters play a crucial role in generating energy to be fed to the grid. A filter is commonly used to suppress the switching frequency harmonics produced by the inverter, this being passive, and either an L- or LCL-filter. The latter is smaller in size compared to the L-filter. But choosing the optimal values of the LCL-filter is challenging due to resonance, which can affect stability. This paper presents a simple inverter controller design with an L-filter. The control topology is simple and applied easily using traditional control theory. Fast Fourier Transform analysis is used to compare different grid connected inverter control topologies. The modelled grid connected inverter with the proposed controller complies with the IEEE-1547 standard, and total harmonic distortion of the output current of the modelled inverter has been just 0.25% with an improved output waveform. Experimental work on a commercial PV inverter is then presented, including the effect of strong and weak grid connection. Inverter effects on the resistive load connected at the point of common coupling are presented. Results show that the voltage and current of resistive load, when the grid is interrupted, are increased, which may cause failure or damage for connecting appliances.

An Optimal Current Controller Design for a Grid Connected Inverter to Improve Power Quality and Test Commercial PV Inverters

PubMed Central

Altuwayjiri, Saud A.; Ahmed, Oday A.; Daho, Ibrahim

2017-01-01

Grid connected inverters play a crucial role in generating energy to be fed to the grid. A filter is commonly used to suppress the switching frequency harmonics produced by the inverter, this being passive, and either an L- or LCL-filter. The latter is smaller in size compared to the L-filter. But choosing the optimal values of the LCL-filter is challenging due to resonance, which can affect stability. This paper presents a simple inverter controller design with an L-filter. The control topology is simple and applied easily using traditional control theory. Fast Fourier Transform analysis is used to compare different grid connected inverter control topologies. The modelled grid connected inverter with the proposed controller complies with the IEEE-1547 standard, and total harmonic distortion of the output current of the modelled inverter has been just 0.25% with an improved output waveform. Experimental work on a commercial PV inverter is then presented, including the effect of strong and weak grid connection. Inverter effects on the resistive load connected at the point of common coupling are presented. Results show that the voltage and current of resistive load, when the grid is interrupted, are increased, which may cause failure or damage for connecting appliances. PMID:28540362

Miniaturized GC/MS instrumentation for in situ measurements: micro gas chromatography coupled with miniature quadrupole array and paul ion trap mass spectrometers

NASA Technical Reports Server (NTRS)

Holland, P.; Chutjian, A.; Darrach, M.; Orient, O.

2002-01-01

Miniaturized chemical instrumentation is needed for in situ measurements in planetary exploration and other spaceflight applications where factors such as reduction in payload requirements and enhanced robustness are important. In response to this need, we are 'continuing to develop miniaturized GC/MS instrumentation which combines chemical separations by gas chromatography (GC) with mass spectrometry (MS) to provide positive identification of chemical compounds in complex mixtures of gases, such as those found in the International Space Station's cabin atmosphere. Our design approach utilizes micro gas chromatography components coupled with either a miniature quadrupole mass spectrometer array (QMSA) or compact, high-resolution Paul ion trap.

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.

New type of transformerless high efficiency inverter

NASA Astrophysics Data System (ADS)

Naaijer, G. J.

Inverter architectures are presented which allow economical ac/dc switching for solar cell array and battery power use in domestic and industrial applications. The efficiencies of currently available inverters are examined and compared with a new 2.2 kW transformerless stepped wave inverter. The inverter has low no-load losses, amounting to 200 Wh/24 hr, and features voltage steps occurring 15-30 times/sine wave period. An example is provided for an array/battery/inverter assembly with the inverter control electronics activating or disconnecting the battery subassemblies based on the total number of activated subassemblies in relation to a reference sinewave, and the need to average the battery subassembly discharge rates. A total harmonic distortion of 6 percent was observed, and the system is noted to be usable as a battery charger.

Inverter for Interchangeable Use as Current Source Inverter and Voltage Source Inverter for Interconnecting to Grid

NASA Astrophysics Data System (ADS)

Teruya, Daisuke; Masukawa, Shigeo; Iida, Shoji

We propose a novel inverter that can be operated either as a Current Source Inverter (CSI) or as a Voltage Source Inverter (VSI) by changing only the control signals. It is proper to apply it to the interconnecting system with renewal energy, such as photovoltaic cells or wind generation systems, to a grid. This inverter is usually operated as the CSI connected to the grid. Even if the energy source has a lower voltage than the grid, the energy can be supplied to the grid through the proposed inverter. The power factor can be briefly maintained at almost unity. When power supply from the grid is interrupted, the proposed circuit should be operated as the VSI in the stand-alone operation mode. In this way, the circuit can maintain a constant output voltage to the loads. In this paper, the proposed circuit configuration and the control schemes for both the CSI and the VSI are described. Further, the circuit characteristics for both are discussed experimentally.

Integration of supercapacitive storage in renewable energy system to compare the response of two level and five level inverter with RL type load

NASA Astrophysics Data System (ADS)

Jana, Suman; Biswas, Pabitra Kumar; Das, Upama

2018-04-01

The analytical and simulation-based study in this presented paper shows a comparative report between two level inverter and five-level inverter with the integration of Supercapacitive storage in Renewable Energy system. Sometime dependent numerical models are used to measure the voltage and current response of two level and five level inverter in MATLAB Simulink based environment. In this study supercapacitive sources, which are fed by solar cells are used as input sources to experiment the response of multilevel inverter with integration of su-percapacitor as a storage device of Renewable Energy System. The RL load is used to compute the time response in MATLABSimulink based environment. With the simulation results a comparative study has been made of two different level types of inverters. Two basic types of inverter are discussed in the study with reference to their electrical behavior. It is also simulated that multilevel inverter can convert stored energy within supercapacitor which is extracted from Renewable Energy System.

Chapter 11.2: Inverters, Power Optimizers, and Microinverters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deline, Christopher A

Inverters span a wide range of sizes, topologies, and connection voltages: from utility-scale megawatt inverters to string inverters. Switch-mode power conversion relies on high frequency chopping of DC signal to periodically charge and discharge energy storage elements, such as inductors and capacitors. Additional circuit components are required to address practical issues in inverters such as voltage ripple and harmonic distortion. Inverters are beginning to incorporate components with a bandgap above should be 3 eV, such as SiC and GaN. Photovoltaic (PV) modules respond dynamically to changing temperature and irradiation conditions. Thus, maximum DC power extraction requires periodic adjustment of themore » PV voltage and current operating point. An inverter's total efficiency is measured by the product of its conversion efficiency and the maximum-power-point tracking (MPPT) efficiency. This chapter lists the primary functions of inverters that include auxiliary capabilities, such as monitoring of DC and AC performance, and other error reporting.« less

The effect of miniaturized body size on skeletal morphology in frogs.

PubMed

Yeh, Jennifer

2002-03-01

Miniaturization has evolved numerous times and reached impressive extremes in the Anura. I compared the skeletons of miniature frog species to those of closely related larger species to assess patterns of morphological change, sampling 129 species from 12 families. Two types of morphological data were examined: (1) qualitative data on bone presence and absence; and (2) thin-plate spline morphometric descriptions of skull structure and bone shape. Phylogenetic comparative methods were used to address the shared history of species. Miniature anurans were more likely to lose skull bones and phalangeal elements of the limbs. Their skulls also showed consistent differences compared to those of their larger relatives, including relatively larger braincases and sensory capsules, verticalization of lateral elements, rostral displacement of the jaw joint, and reduction of some skull elements. These features are explained by functional constraints and by paedomorphosis. Variation among lineages in the morphological response to miniaturization was also explored. Certain lineages appear to be unusually resistant to the morphological trends that characterize miniature frogs as a whole. This study represents the first large-scale examination of morphology and miniaturization across a major, diverse group of organisms conducted in a phylogenetic framework and with statistical rigor.

Development of a Flow Injection Based High Frequency Dual Channel Quartz Crystal Microbalance

PubMed Central

Liang, Jinxing; Zhang, Jing; Zhou, Wenxiang; Ueda, Toshitsugu

2017-01-01

When the quartz crystal microbalance (QCM) is used in liquid for adsorption or desorption monitoring based bio- or chemical sensing applications, the frequency shift is not only determined by the surface mass change, but also by the change of liquid characteristics, such as density and viscosity, which are greatly affected by the liquid environmental temperature. A monolithic dual-channel QCM is designed and fabricated by arranging two QCM resonators on one single chip for cancelling the fluctuation induced by environmental factors. In actual applications, one QCM works as a specific sensor by modifying with functional membranes and the other acts as a reference, only measuring the liquid property. The dual-channel QCM is designed with an inverted-mesa structure, aiming to realize a high frequency miniaturized chip and suppress the frequency interference between the neighbored QCM resonators. The key problem of dual-channel QCMs is the interference between two channels, which is influenced by the distance of adjacent resonators. The diameter of the reference electrode has been designed into several values in order to find the optimal parameter. Experimental results demonstrated that the two QCMs could vibrate individually and the output frequency stability and drift can be greatly improved with the aid of the reference QCM. PMID:28509851

A new type of single-phase five-level inverter

NASA Astrophysics Data System (ADS)

Xu, Zhi; Li, Shengnan; Qin, Risheng; Zhao, Yanhang

2017-11-01

At present, Neutral Point Clamped (NPC) multilevel inverter is widely applied in new energy field. However, it has some disadvantages including low utilization rate of direct current (DC) voltage source and the unbalance of neutral potential. Therefore, a new single-phase five level inverter is proposed in this paper. It has two stage structure, the former stage is equivalent to three level DC/DC converter, and the back stage uses H bridge to realize inverter. Compared with the original central clamp type inverter, the new five level inverter can improve the utilization of DC voltage, and realize the neutral point potential balance with hysteresis comparator.

A study on the impact of high penetration distributed generation inverters on grid operation and stability

NASA Astrophysics Data System (ADS)

Gu, Fei; Brouwer, Jack; Samuelsen, Scott

2013-09-01

Recent advances in inverter technology have enabled ancillary services such as volt/VAR regulation, SCADA communications, and active power filtering. Smart inverters can not only provide real power, but can be controlled to use excess capacity to provide reactive power compensation, power flow control, and active power filtering without supplementary inverter hardware. A transient level inverter model based on the Solectria 7700 inverter is developed and used to assess these control strategies using field data from an existing branch circuit containing two Amonix 68kW CPV-7700 systems installed at the University of California, Irvine.

Nonlinear analysis of a family of LC tuned inverters. [dc to square wave circuits for power conditioning

NASA Technical Reports Server (NTRS)

Lee, F. C. Y.; Wilson, T. G.

1974-01-01

A family of four dc-to-square-wave LC tuned inverters are analyzed using singular point. Limit cycles and waveshape characteristics are given for three modes of oscillation: quasi-harmonic, relaxation, and discontinuous. An inverter in which the avalanche breakdown of the transistor emitter-to-base junction occurs is discussed and the starting characteristics of this family of inverters are presented. The LC tuned inverters are shown to belong to a family of inverters with a common equivalent circuit consisting of only three 'series' elements: a five-segment piecewise-linear current-controlled resistor, linear inductor, and linear capacitor.

DC-DC Type High-Frequency Link DC for Improved Power Quality of Cascaded Multilevel Inverter

NASA Astrophysics Data System (ADS)

Sadikin, Muhammad; Senjyu, Tomonobu; Yona, Atsushi

2013-06-01

Multilevel inverters are emerging as a new breed of power converter options for power system applications. Recent advances in power switching devices enabled the suitability of multilevel inverters for high voltage and high power applications because they are connecting several devices in series without the need of component matching. Usually, a transformerless battery energy storage system, based on a cascaded multilevel inverter, is used as a measure for voltage and frequency deviations. System can be reduced in size, weight, and cost of energy storage system. High-frequency link circuit topology is advantageous in realizing compact and light-weight power converters for uninterruptible power supply systems, new energy systems using photovoltaic-cells, fuel-cells and so on. This paper presents a DC-DC type high-frequency link DC (HFLDC) cascaded multilevel inverter. Each converter cell is implemented a control strategy for two H-bridge inverters that are controlled with the same multicarrier pulse width modulation (PWM) technique. The proposed cascaded multilevel inverter generates lower voltage total harmonic distortion (THD) in comparison with conventional cascaded multilevel inverter. Digital simulations are carried out using PSCAD/EMTDC to validate the performance of the proposed cascaded multilevel inverter.

A Single-Phase Embedded Z-Source DC-AC Inverter

PubMed Central

Kim, Se-Jin; Lim, Young-Cheol

2014-01-01

In the conventional DC-AC inverter consisting of two DC-DC converters with unipolar output capacitors, the output capacitor voltages of the DC-DC converters must be higher than the DC input voltage. To overcome this weakness, this paper proposes a single-phase DC-AC inverter consisting of two embedded Z-source converters with bipolar output capacitors. The proposed inverter is composed of two embedded Z-source converters with a common DC source and output AC load. Though the output capacitor voltages of the converters are relatively low compared to those of a conventional inverter, an equivalent level of AC output voltages can be obtained. Moreover, by controlling the output capacitor voltages asymmetrically, the AC output voltage of the proposed inverter can be higher than the DC input voltage. To verify the validity of the proposed inverter, experiments were performed with a DC source voltage of 38 V. By controlling the output capacitor voltages of the converters symmetrically or asymmetrically, the proposed inverter can produce sinusoidal AC output voltages. The experiments show that efficiencies of up to 95% and 97% can be achieved with the proposed inverter using symmetric and asymmetric control, respectively. PMID:25133241

A single-phase embedded Z-source DC-AC inverter.

PubMed

Kim, Se-Jin; Lim, Young-Cheol

2014-01-01

In the conventional DC-AC inverter consisting of two DC-DC converters with unipolar output capacitors, the output capacitor voltages of the DC-DC converters must be higher than the DC input voltage. To overcome this weakness, this paper proposes a single-phase DC-AC inverter consisting of two embedded Z-source converters with bipolar output capacitors. The proposed inverter is composed of two embedded Z-source converters with a common DC source and output AC load. Though the output capacitor voltages of the converters are relatively low compared to those of a conventional inverter, an equivalent level of AC output voltages can be obtained. Moreover, by controlling the output capacitor voltages asymmetrically, the AC output voltage of the proposed inverter can be higher than the DC input voltage. To verify the validity of the proposed inverter, experiments were performed with a DC source voltage of 38 V. By controlling the output capacitor voltages of the converters symmetrically or asymmetrically, the proposed inverter can produce sinusoidal AC output voltages. The experiments show that efficiencies of up to 95% and 97% can be achieved with the proposed inverter using symmetric and asymmetric control, respectively.

Inverted U-Shaped Dose-Response Curve of the Anxiolytic Effect of Cannabidiol during Public Speaking in Real Life.

PubMed

Zuardi, Antonio W; Rodrigues, Natália P; Silva, Angélica L; Bernardo, Sandra A; Hallak, Jaime E C; Guimarães, Francisco S; Crippa, José A S

2017-01-01

The purpose of this study was to investigate whether the anxiolytic effect of cannabidiol (CBD) in humans follows the same pattern of an inverted U-shaped dose-effect curve observed in many animal studies. Sixty healthy subjects of both sexes aged between 18 and 35 years were randomly assigned to five groups that received placebo, clonazepam (1 mg), and CBD (100, 300, and 900 mg). The subjects were underwent a test of public speaking in a real situation (TPSRS) where each subject had to speak in front of a group formed by the remaining participants. Each subject completed the anxiety and sedation factors of the Visual Analog Mood Scale and had their blood pressure and heart rate recorded. These measures were obtained in five experimental sessions with 12 volunteers each. Each session had four steps at the following times (minutes) after administration of the drug/placebo, as time 0: -5 (baseline), 80 (pre-test), 153 (speech), and 216 (post-speech). Repeated-measures analyses of variance showed that the TPSRS increased the subjective measures of anxiety, heart rate, and blood pressure. Student-Newman-Keuls test comparisons among the groups in each phase showed significant attenuation in anxiety scores relative to the placebo group in the group treated with clonazepam during the speech phase, and in the clonazepam and CBD 300 mg groups in the post-speech phase. Clonazepam was more sedative than CBD 300 and 900 mg and induced a smaller increase in systolic and diastolic blood pressure than CBD 300 mg. The results confirmed that the acute administration of CBD induced anxiolytic effects with a dose-dependent inverted U-shaped curve in healthy subjects, since the subjective anxiety measures were reduced with CBD 300 mg, but not with CBD 100 and 900 mg, in the post-speech phase.

Inverted U-Shaped Dose-Response Curve of the Anxiolytic Effect of Cannabidiol during Public Speaking in Real Life

PubMed Central

Zuardi, Antonio W.; Rodrigues, Natália P.; Silva, Angélica L.; Bernardo, Sandra A.; Hallak, Jaime E. C.; Guimarães, Francisco S.; Crippa, José A. S.

2017-01-01

The purpose of this study was to investigate whether the anxiolytic effect of cannabidiol (CBD) in humans follows the same pattern of an inverted U-shaped dose-effect curve observed in many animal studies. Sixty healthy subjects of both sexes aged between 18 and 35 years were randomly assigned to five groups that received placebo, clonazepam (1 mg), and CBD (100, 300, and 900 mg). The subjects were underwent a test of public speaking in a real situation (TPSRS) where each subject had to speak in front of a group formed by the remaining participants. Each subject completed the anxiety and sedation factors of the Visual Analog Mood Scale and had their blood pressure and heart rate recorded. These measures were obtained in five experimental sessions with 12 volunteers each. Each session had four steps at the following times (minutes) after administration of the drug/placebo, as time 0: -5 (baseline), 80 (pre-test), 153 (speech), and 216 (post-speech). Repeated-measures analyses of variance showed that the TPSRS increased the subjective measures of anxiety, heart rate, and blood pressure. Student-Newman-Keuls test comparisons among the groups in each phase showed significant attenuation in anxiety scores relative to the placebo group in the group treated with clonazepam during the speech phase, and in the clonazepam and CBD 300 mg groups in the post-speech phase. Clonazepam was more sedative than CBD 300 and 900 mg and induced a smaller increase in systolic and diastolic blood pressure than CBD 300 mg. The results confirmed that the acute administration of CBD induced anxiolytic effects with a dose-dependent inverted U-shaped curve in healthy subjects, since the subjective anxiety measures were reduced with CBD 300 mg, but not with CBD 100 and 900 mg, in the post-speech phase. PMID:28553229

Interactions between concentric form-from-structure and face perception revealed by visual masking but not adaptation

PubMed Central

Feczko, Eric; Shulman, Gordon L.; Petersen, Steven E.; Pruett, John R.

2014-01-01

Findings from diverse subfields of vision research suggest a potential link between high-level aspects of face perception and concentric form-from-structure perception. To explore this relationship, typical adults performed two adaptation experiments and two masking experiments to test whether concentric, but not nonconcentric, Glass patterns (a type of form-from-structure stimulus) utilize a processing mechanism shared by face perception. For the adaptation experiments, subjects were presented with an adaptor for 5 or 20 s, prior to discriminating a target. In the masking experiments, subjects saw a mask, then a target, and then a second mask. Measures of discriminability and bias were derived and repeated measures analysis of variance tested for pattern-specific masking and adaptation effects. Results from Experiment 1 show no Glass pattern-specific effect of adaptation to faces; results from Experiment 2 show concentric Glass pattern masking, but not adaptation, may impair upright/inverted face discrimination; results from Experiment 3 show concentric and radial Glass pattern masking impaired subsequent upright/inverted face discrimination more than translational Glass pattern masking; and results from Experiment 4 show concentric and radial Glass pattern masking impaired subsequent face gender discrimination more than translational Glass pattern masking. Taken together, these findings demonstrate interactions between concentric form-from-structure and face processing, suggesting a possible common processing pathway. PMID:24563526

Comprehensive mutagenesis of the fimS promoter regulatory switch reveals novel regulation of type 1 pili in uropathogenic Escherichia coli

PubMed Central

Zhang, Huibin; Susanto, Teodorus T.; Wan, Yue

2016-01-01

Type 1 pili (T1P) are major virulence factors for uropathogenic Escherichia coli (UPEC), which cause both acute and recurrent urinary tract infections. T1P expression therefore is of direct relevance for disease. T1P are phase variable (both piliated and nonpiliated bacteria exist in a clonal population) and are controlled by an invertible DNA switch (fimS), which contains the promoter for the fim operon encoding T1P. Inversion of fimS is stochastic but may be biased by environmental conditions and other signals that ultimately converge at fimS itself. Previous studies of fimS sequences important for T1P phase variation have focused on laboratory-adapted E. coli strains and have been limited in the number of mutations or by alteration of the fimS genomic context. We surmounted these limitations by using saturating genomic mutagenesis of fimS coupled with accurate sequencing to detect both mutations and phase status simultaneously. In addition to the sequences known to be important for biasing fimS inversion, our method also identifies a previously unknown pair of 5′ UTR inverted repeats that act by altering the relative fimA levels to control phase variation. Thus we have uncovered an additional layer of T1P regulation potentially impacting virulence and the coordinate expression of multiple pilus systems. PMID:27035967

Prenatal detection of a de novo terminal inverted duplication 4p in a fetus with the Wolf-Hirschhorn syndrome phenotype.

PubMed

Beaujard, M-P; Jouannic, J-M; Bessières, B; Borie, C; Martin-Luis, I; Fallet-Bianco, C; Portnoï, M-F

2005-06-01

To present the prenatal diagnosis of a de novo terminal inversion duplication of the short arm of chromosome 4 and a review of the literature. An amniocentesis for chromosome analysis was performed at 33 weeks' gestation because ultrasound examination showed a female fetus with multiple abnormalities consisting of severe intrauterine growth retardation, microcephaly, a cleft lip and renal hypoplasia. Cytogenetic analysis and FISH studies of the cultured amniocytes revealed a de novo terminal inversion duplication of the short arm of chromosome 4 characterized by a duplication of 4p14-p16.1 chromosome region concomitant with a terminal deletion 4p16.1-pter. The karyotype was thus: 46,XX, inv dup del (4)(:p14-->p16.1::p16.1-->qter). The parents opted to terminate the pregnancy. Fetopathological examination showed dysmorphic features and abnormalities consistent with a Wolf-Hirschhorn syndrome (WHS) diagnosis, clinical manifestations of partial 4p trisomy being mild. Although relatively rare, inverted duplications have been reported repeatedly in an increasing number of chromosomes. Only two previous cases with de novo inv dup del (4p) and one with tandem dup 4p have been reported, all of them associated with a 4pter deletion. We report the first case diagnosed prenatally. Breakpoints are variable, resulting in different abnormal phenotype. In our case, clinical manifestations resulted in a WHS phenotype.

Study of structural change in volcanic and geothermal areas using seismic tomography

NASA Astrophysics Data System (ADS)

Mhana, Najwa; Foulger, Gillian; Julian, Bruce; peirce, Christine

2014-05-01

Long Valley caldera is a large silicic volcano. It has been in a state of volcanic and seismic unrest since 1978. Farther escalation of this unrest could pose a threat to the 5,000 residents and the tens of thousands of tourists who visit the area. We have studied the crustal structure beneath 28 km X 16 km area using seismic tomography. We performed tomographic inversions for the years 2009 and 2010 with a view to differencing it with the 1997 result to look for structural changes with time and whether repeat tomography is a capable of determining the changes in structure in volcanic and geothermal reservoirs. Thus, it might provide a useful tool to monitoring physical changes in volcanoes and exploited geothermal reservoirs. Up to 600 earthquakes, selected from the best-quality events, were used for the inversion. The inversions were performed using program simulps12 [Thurber, 1983]. Our initial results show that changes in both V p and V s were consistent with the migration of CO2 into the upper 2 km or so. Our ongoing work will also invert pairs of years simultaneously using a new program, tomo4d [Julian and Foulger, 2010]. This program inverts for the differences in structure between two epochs so it can provide a more reliable measure of structural change than simply differencing the results of individual years.

Comprehensive mutagenesis of the fimS promoter regulatory switch reveals novel regulation of type 1 pili in uropathogenic Escherichia coli.

PubMed

Zhang, Huibin; Susanto, Teodorus T; Wan, Yue; Chen, Swaine L

2016-04-12

Type 1 pili (T1P) are major virulence factors for uropathogenic Escherichia coli (UPEC), which cause both acute and recurrent urinary tract infections. T1P expression therefore is of direct relevance for disease. T1P are phase variable (both piliated and nonpiliated bacteria exist in a clonal population) and are controlled by an invertible DNA switch (fimS), which contains the promoter for the fim operon encoding T1P. Inversion of fimS is stochastic but may be biased by environmental conditions and other signals that ultimately converge at fimS itself. Previous studies of fimS sequences important for T1P phase variation have focused on laboratory-adapted E coli strains and have been limited in the number of mutations or by alteration of the fimS genomic context. We surmounted these limitations by using saturating genomic mutagenesis of fimS coupled with accurate sequencing to detect both mutations and phase status simultaneously. In addition to the sequences known to be important for biasing fimS inversion, our method also identifies a previously unknown pair of 5' UTR inverted repeats that act by altering the relative fimA levels to control phase variation. Thus we have uncovered an additional layer of T1P regulation potentially impacting virulence and the coordinate expression of multiple pilus systems.

Postoperative pulmonary hypertensive crisis caused by inverted left atrial appendage after cardiopulmonary bypass surgery for congenital heart disease in a neonate.

PubMed

Zhao, Qifeng; Hu, Xingti

2013-09-01

Postoperative pulmonary hypertensive crisis (PHC) caused by an inverted left atrial appendage (ILAA) is a rare complication following cardiac surgery. We present a case of 23 day-old male infant who developed postoperative PHC attacks after undergoing cardiopulmonary bypass (CPB) surgery for repair of the coactation of aorta. A hyperechogenic left atrial mass was detected via bedside transthoracic echocardiography (TTE), which was identified as an ILAA and corrected following repeat surgery. In this case, both the negative pressure in vent catheter and the long left atrial appendage (LAA) with a narrow base led to an irreversible ILAA. As in this neonate, ILAA had significant influence on the left atrial volume and caused PHC since the ILAA was located on the mitral valve orifice and interfered with the blood flow through the valve. Therefore, we recommend that the vent catheter should be turned off before removing to avoid this potential complication. Additionally, LAA should be carefully inspected after CPB surgery, and intra-operative and post-operative transoesophageal echocardiography (TEE) should be performed to detect ILAA intraoperatively so as to avoid the reoperation. When an ILAA is diagnosed postoperatively, whether conservative treatment or surgery will depend on the balance of benefit and risk for a particular patient. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

Construction and evaluation of photovoltaic power generation and power storage system using SiC field-effect transistor inverter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oku, Takeo, E-mail: oku@mat.usp.ac.jp; Matsumoto, Taisuke; Ohishi, Yuya

A power storage system using spherical silicon (Si) solar cells, maximum power point tracking charge controller, lithium-ion battery and a direct current-alternating current (DC-AC) inverter was constructed. Performance evaluation of the DC-AC inverter was carried out, and the DC-AC conversion efficiencies of the SiC field-effect transistor (FET) inverter was improved compared with those of the ordinary Si-FET based inverter.

Telomerase reverse transcriptase (TERT) promoter mutation analysis of benign, malignant and reactive urothelial lesions reveals a subpopulation of inverted papilloma with immortalizing genetic change.

PubMed

Cheng, Liang; Davidson, Darrell D; Wang, Mingsheng; Lopez-Beltran, Antonio; Montironi, Rodolfo; Wang, Lisha; Tan, Puay-Hoon; MacLennan, Gregory T; Williamson, Sean R; Zhang, Shaobo

2016-07-01

To understand more clearly the genetic ontogeny of inverted papilloma of urinary bladder, we analysed telomerase reverse transcriptase (TERT) promoter mutation status in a group of 26 inverted papillomas in comparison with the mutation status of urothelial carcinoma with inverted growth (26 cases), conventional urothelial carcinoma (36 Ta non-invasive urothelial carcinoma, 35 T2 invasive urothelial carcinoma) and cystitis glandularis (25 cases). TERT promoter mutations in inverted papilloma, urothelial carcinoma with inverted growth, urothelial carcinoma and cystitis glandularis were found in 15% (four of 26), 58% (15 of 26), 63% (45 of 71) and 0% (none of 25), respectively. C228T mutations were the predominant mutations (97%) found in bladder tumours, while C250T aberrations occurred in approximately 3% of bladder tumours. In the inverted papilloma group, TERT mutation occurred predominantly in female patients (P = 0.006). Among urothelial carcinomas, TERT promoter mutation status did not correlate with gender, histological grade or pathological stage. TERT promoter mutations were found in 15% of inverted papillomas. Our data suggest that there is a subpopulation of inverted papilloma that shares a carcinogenetic pathway with urothelial carcinoma with inverted growth and conventional urothelial carcinomas. Caution is warranted in exploring TERT promoter mutation status as a screening or adjunct diagnostic test for bladder cancer. © 2015 John Wiley & Sons Ltd.

Etiological role of human papillomavirus infection for inverted papilloma of the bladder.

PubMed

Shigehara, Kazuyoshi; Sasagawa, Toshiyuki; Doorbar, John; Kawaguchi, Shohei; Kobori, Yoshitomo; Nakashima, Takao; Shimamura, Masayoshi; Maeda, Yuji; Miyagi, Tohru; Kitagawa, Yasuhide; Kadono, Yoshifumi; Konaka, Hiroyuki; Mizokami, Atsushi; Koh, Eitetsu; Namiki, Mikio

2011-02-01

The status of human papillomavirus (HPV) infection in urothelial inverted papilloma was examined in the present study. Formalin-fixed and paraffin-embedded tissues from eight cases of inverted papilloma of the bladder were studied. The presence of HPV-DNA was examined by modified GP5/6+PCR using archival tissue sections by microdissection. HPV genotype was determined with a Hybri-Max HPV genotyping kit. Immunohistochemical analysis for p16-INK4a, mcm7, HPV-E4, and L1, and in situ hybridization for the HPV genome were performed. HPV was detected in seven of eight cases (87.5%) of inverted papilloma. Three cases were diagnosed as inverted papilloma with atypia, while the remaining five were typical cases. HPV-18 was detected in two cases, including one inverted papilloma with atypia, and HPV-16 was detected in four cases, including one inverted papilloma with atypia. Multiple HPV type infection was detected in one typical case and one atypical case. High-risk HPV was present in all HPV-positive cases. Cellular proteins, p16-INK4a and mcm7, which are surrogate markers for HPV-E7 expression, were detected in all HPV-positive cases, and their levels were higher in inverted papilloma with atypia than in typical cases. In contrast, HPV-E4 and L1, which are markers for HPV propagation, were observed in some parts of the typical inverted papilloma tissue. High-risk HPV infection may be one of the causes of urothelial inverted papilloma, and inverted papilloma with atypia may have malignant potential. 2010 Wiley-Liss, Inc.

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.

Flexible and stretchable electrodes for dielectric elastomer actuators

NASA Astrophysics Data System (ADS)

Rosset, Samuel; Shea, Herbert R.

2013-02-01

Dielectric elastomer actuators (DEAs) are flexible lightweight actuators that can generate strains of over 100 %. They are used in applications ranging from haptic feedback (mm-sized devices), to cm-scale soft robots, to meter-long blimps. DEAs consist of an electrode-elastomer-electrode stack, placed on a frame. Applying a voltage between the electrodes electrostatically compresses the elastomer, which deforms in-plane or out-of plane depending on design. Since the electrodes are bonded to the elastomer, they must reliably sustain repeated very large deformations while remaining conductive, and without significantly adding to the stiffness of the soft elastomer. The electrodes are required for electrostatic actuation, but also enable resistive and capacitive sensing of the strain, leading to self-sensing actuators. This review compares the different technologies used to make compliant electrodes for DEAs in terms of: impact on DEA device performance (speed, efficiency, maximum strain), manufacturability, miniaturization, the integration of self-sensing and self-switching, and compatibility with low-voltage operation. While graphite and carbon black have been the most widely used technique in research environments, alternative methods are emerging which combine compliance, conduction at over 100 % strain with better conductivity and/or ease of patternability, including microfabrication-based approaches for compliant metal thin-films, metal-polymer nano-composites, nanoparticle implantation, and reel-to-reel production of μm-scale patterned thin films on elastomers. Such electrodes are key to miniaturization, low-voltage operation, and widespread commercialization of DEAs.

Simplified miniaturized ultrasound-assisted matrix solid phase dispersion extraction and high performance liquid chromatographic determination of seven flavonoids in citrus fruit juice and human fluid samples: hesperetin and naringenin as biomarkers.

PubMed

Barfi, Behruz; Asghari, Alireza; Rajabi, Maryam; Barfi, Azadeh; Saeidi, Iman

2013-10-11

In the present study, for the first time, a simplified miniaturized ultrasound-assisted matrix solid-phase dispersion (SM-USA-MSPD) method with a different application for liquid matrices was developed to extract different flavonoids (hesperidin, diosmin, eriocitrin, narirutin, naringin, hesperetin and naringenin) from citrus fruit juice and human fluid samples prior to their determination using high performance liquid chromatography (HPLC). Different effective parameters were studied and under the optimum conditions (including sample volume: 150μL; solid phase: silica-based C18, 200mg; eluting solvent: methanol, 500μL; pH: 4; and sonication: 6min; at room temperature), limits of detection and limits of quantification were ranged from 23.3 to 46.8ngmL(-1) and 74.8 to 141.5ngmL(-1), respectively. Once optimized, analytical performance of the method was studied in terms of linearity (0.074-198.5μgmL(-1), r(2)>0.991), accuracy (recovery=84.6-101.5%), and precision (repeatability: intra-day precision<5.9%, and inter-day precision<7.2%). At the end, SM-USA-MSPD method was successfully applied to estimate the levels of hesperetin and naringenin in plasma and urinary excretion -after ingestion of orange, grapefruit and lime juices- and the obtained results confirmed that these compounds could be used as good biomarkers of citrus fruit juice intake. Copyright © 2013 Elsevier B.V. All rights reserved.

A high-precision miniaturized rotating coil transducer for magnetic measurements

DOE PAGES

Arpaia, P.; Buzio, M.; De Oliveira, R.; ...

2018-02-08

A miniaturized Printed Circuit Board (PCB) sensing coil, jointly developed by CERN and Fermilab for measuring the field of small-gap (less than 10 mm) accelerator magnets, is illustrated. A sensing coil array, with a scheme for compensating the main field when measuring the harmonic error components, hosted on a synthetic sapphire-based transducer, is presented. Key innovating features are (i) very-small size, both for the sensing coil array (thickness of 1.380 mm) and for the transducer (overall diameter of 7.350 mm), (ii) metrological performance, namely accuracy (more than five times better than state of the art), and 1-sigma repeatability (ten timesmore » better on harmonics with amplitude less than 100 ppm), and (iii) manufacturing technology of both the coil array (13 double layers aligned within 10 μm), and the sapphire support (concentricity, the most important uncertainty source for rotating coils, 3 μm of uncertainty, namely one order of magnitude better than fiberglass support). After stating the measurement problem, the design of the transducer and a case study of a two-layer PCB sensor array are also illustrated. Then, the prototyping and quality control of both the sensor and the transducer are discussed. Furthermore, the calibration and the results obtained with a prototype setup at Fermilab are presented. Finally, in the appendix, the theory of the rotating coil, the sensor geometry, and the harmonic compensation are briefly reviewed for the reader easiness.« less

A high-precision miniaturized rotating coil transducer for magnetic measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arpaia, P.; Buzio, M.; De Oliveira, R.

A miniaturized Printed Circuit Board (PCB) sensing coil, jointly developed by CERN and Fermilab for measuring the field of small-gap (less than 10 mm) accelerator magnets, is illustrated. A sensing coil array, with a scheme for compensating the main field when measuring the harmonic error components, hosted on a synthetic sapphire-based transducer, is presented. Key innovating features are (i) very-small size, both for the sensing coil array (thickness of 1.380 mm) and for the transducer (overall diameter of 7.350 mm), (ii) metrological performance, namely accuracy (more than five times better than state of the art), and 1-sigma repeatability (ten timesmore » better on harmonics with amplitude less than 100 ppm), and (iii) manufacturing technology of both the coil array (13 double layers aligned within 10 μm), and the sapphire support (concentricity, the most important uncertainty source for rotating coils, 3 μm of uncertainty, namely one order of magnitude better than fiberglass support). After stating the measurement problem, the design of the transducer and a case study of a two-layer PCB sensor array are also illustrated. Then, the prototyping and quality control of both the sensor and the transducer are discussed. Furthermore, the calibration and the results obtained with a prototype setup at Fermilab are presented. Finally, in the appendix, the theory of the rotating coil, the sensor geometry, and the harmonic compensation are briefly reviewed for the reader easiness.« less

Improved Performance via the Inverted Classroom

ERIC Educational Resources Information Center

Weinstein, Randy D.

2015-01-01

This study examined student performance in an inverted thermodynamics course (lectures provided by video outside of class) compared to a traditional lecture class. Students in the inverted class performed better on their exams. Students in the bottom third of the inverted course showed the greatest improvement. These bottom third students had a C…

Inverting the Linear Algebra Classroom

ERIC Educational Resources Information Center

Talbert, Robert

2014-01-01

The inverted classroom is a course design model in which students' initial contact with new information takes place outside of class meetings, and students spend class time on high-level sense-making activities. The inverted classroom model is so called because it inverts or "flips" the usual classroom design where typically class…

Efficient/reliable dc-to-dc inverter circuit

NASA Technical Reports Server (NTRS)

Pasciutti, E. R.

1970-01-01

Feedback loop, which contains an inductor in series with a saturable reactor, is added to a standard inverter circuit to permit the inverter power transistors to be switched in a controlled and efficient manner. This inverter is applicable where the power source has either high or low impedance properties.

Milliwatt dc/dc Inverter

NASA Technical Reports Server (NTRS)

Mclyman, C. W.

1983-01-01

Compact dc/dc inverter uses single integrated-circuit package containing six inverter gates that generate and amplify 100-kHz square-wave switching signal. Square-wave switching inverts 10-volt local power to isolated voltage at another desired level. Relatively high operating frequency reduces size of filter capacitors required, resulting in small package unit.

75 FR 36119 - In the Matter of Certain Cold Cathode Fluorescent Lamp (“CCFL”) Inverter Circuits and Products...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-24

... Cathode Fluorescent Lamp (``CCFL'') Inverter Circuits and Products Containing the Same; Notice of... States after importation of certain cold cathode fluorescent lamp inverter circuits and products..., and the sale within the United States after importation of CCFL inverter circuits and products...

Experimental Evaluation of PV Inverter Anti-Islanding with Grid Support Functions in Multi-Inverter Island Scenarios

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoke, Anderson; Nelson, Austin; Miller, Brian

As PV and other DER systems are connected to the grid at increased penetration levels, island detection may become more challenging for two reasons: 1.) In islands containing many DERs, active inverter-based anti-islanding methods may have more difficulty detecting islands because each individual inverter's efforts to detect the island may be interfered with by the other inverters in the island. 2.) The increasing numbers of DERs are leading to new requirements that DERs ride through grid disturbances and even actively try to regulate grid voltage and frequency back towards nominal operating conditions. These new grid support requirements may directly ormore » indirectly interfere with anti-islanding controls. This report describes a series of tests designed to examine the impacts of both grid support functions and multi-inverter islands on anti-islanding effectiveness. Crucially, the multi-inverter anti-islanding tests described in this report examine scenarios with multiple inverters connected to multiple different points on the grid. While this so-called 'solar subdivision' scenario has been examined to some extent through simulation, this is the first known work to test it using hardware inverters. This was accomplished through the use of power hardware-in-the-loop (PHIL) simulation, which allows the hardware inverters to be connected to a real-time transient simulation of an electric power system that can be easily reconfigured to test various distribution circuit scenarios. The anti-islanding test design was a modified version of the unintentional islanding test in IEEE Standard 1547.1, which creates a balanced, resonant island with the intent of creating a highly challenging condition for island detection. Three common, commercially available single-phase PV inverters from three different manufacturers were tested. The first part of this work examined each inverter individually using a series of pure hardware resistive-inductive-capacitive (RLC) resonant load based anti-islanding tests to determine the worst-case configuration of grid support functions for each inverter. A grid support function is a function an inverter performs to help stabilize the grid or drive the grid back towards its nominal operating point. The four grid support functions examined here were voltage ride-through, frequency ride-through, Volt-VAr control, and frequency-Watt control. The worst-case grid support configuration was defined as the configuration that led to the maximum island duration (or run-on time, ROT) out of 50 tests of each inverter. For each of the three inverters, it was observed that maximum ROT increased when voltage and frequency ride-through were activated. No conclusive evidence was found that Volt-VAr control or frequency-Watt control increased maximum ROT. Over all single-inverter test cases, the maximum ROT was 711 ms, well below the two-second limit currently imposed by IEEE Standard 1547-2003. A subsequent series of 244 experiments tested all three inverters simultaneously in the same island. These tests again used a procedure based on the IEEE 1547.1 unintentional islanding test to create a difficult-to-detect island condition. For these tests, which used the two worst-case grid support function configurations from the single-inverter tests, the inverters were connected to a variety of island circuit topologies designed to represent the variety of multiple-inverter islands that may occur on real distribution circuits. The interconnecting circuits and the resonant island load itself were represented in the real-time PHIL model. PHIL techniques similar to those employed here have been previously used and validated for anti-islanding tests, and the PHIL resonant load model used in this test was successfully validated by comparing single-inverter PHIL tests to conventional tests using an RLC load bank.« less

Inverter communications using output signal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chapman, Patrick L.

Technologies for communicating information from an inverter configured for the conversion of direct current (DC) power generated from an alternative source to alternating current (AC) power are disclosed. The technologies include determining information to be transmitted from the inverter over a power line cable connected to the inverter and controlling the operation of an output converter of the inverter as a function of the information to be transmitted to cause the output converter to generate an output waveform having the information modulated thereon.

Stabilization and tracking control of X-Z inverted pendulum with sliding-mode control.

PubMed

Wang, Jia-Jun

2012-11-01

X-Z inverted pendulum is a new kind of inverted pendulum which can move with the combination of the vertical and horizontal forces. Through a new transformation, the X-Z inverted pendulum is decomposed into three simple models. Based on the simple models, sliding-mode control is applied to stabilization and tracking control of the inverted pendulum. The performance of the sliding mode control is compared with that of the PID control. Simulation results show that the design scheme of sliding-mode control is effective for the stabilization and tracking control of the X-Z inverted pendulum. Copyright © 2012 ISA. Published by Elsevier Ltd. All rights reserved.

Model Predictive Control of LCL Three-level Photovoltaic Grid-connected Inverter

NASA Astrophysics Data System (ADS)

Liang, Cheng; Tian, Engang; Pang, Baobing; Li, Juan; Yang, Yang

2018-05-01

In this paper, neutral point clamped three-level inverter circuit is analyzed to establish a mathematical model of the three-level inverter in the αβ coordinate system. The causes and harms of the midpoint potential imbalance problem are described. The paper use the method of model predictive control to control the entire inverter circuit[1]. The simulation model of the inverter system is built in Matlab/Simulink software. It is convenient to control the grid-connected current, suppress the unbalance of the midpoint potential and reduce the switching frequency by changing the weight coefficient in the cost function. The superiority of the model predictive control in the control method of the inverter system is verified.

Nanocrystal-based complementary inverters constructed on flexible plastic substrates.

PubMed

Jang, Jaewon; Cho, Kyoungah; Yun, Junggwon; Kim, Sangsig

2013-05-01

We demonstrate a nanocrystal (NC)-based complementary inverter constructed on a flexible plastic substrate. The NC-based complementary inverter consists of n-type HgSe NC- and p-type HgTe NC-based thin-film transistors (TFTs). Solid films on a plastic substrate obtained from HgSe and HgTe nanocrystals by thermal transformation are utilized as the n- and p-channel layers in these TFTs, respectively. The electrical properties of these component TFTs on unstrained and strained substrates are characterized and the performance of the inverter on the flexible substrate is investigated. The inverter on the unstrained substrate exhibits a logic gain of about 8, a logic swing of 90%, and a noise margin of 2.0 V. The characteristics of the inverter are changed under tensile and compressive strains, but not very significantly. Moreover, a comparison of the electrical characteristics of the n- and p-channel TFTs and the inverter is made in this paper.

High-speed all-optical logic inverter based on stimulated Raman scattering in silicon nanocrystal.

PubMed

Sen, Mrinal; Das, Mukul K

2015-11-01

In this paper, we propose a new device architecture for an all-optical logic inverter (NOT gate), which is cascadable with a similar device. The inverter is based on stimulated Raman scattering in silicon nanocrystal waveguides, which are embedded in a silicon photonic crystal structure. The Raman response function of silicon nanocrystal is evaluated to explore the transfer characteristic of the inverter. A maximum product criterion for the noise margin is taken to analyze the cascadability of the inverter. The time domain response of the inverter, which explores successful inversion operation at 100 Gb/s, is analyzed. Propagation delay of the inverter is on the order of 5 ps, which is less than the delay in most of the electronic logic families as of today. Overall dimension of the device is around 755  μm ×15  μm, which ensures integration compatibility with the matured silicon industry.

Control method for peak power delivery with limited DC-bus voltage

DOEpatents

Edwards, John; Xu, Longya; Bhargava, Brij B.

2006-09-05

A method for driving a neutral point-clamped multi-level voltage source inverter supplying a synchronous motor is provided. A DC current is received at a neutral point-clamped multi-level voltage source inverter. The inverter has first, second, and third output nodes. The inverter also has a plurality of switches. A desired speed of a synchronous motor connected to the inverter by the first second and third nodes is received by the inverter. The synchronous motor has a rotor and the speed of the motor is defined by the rotational rate of the rotor. A position of the rotor is sensed, current flowing to the motor out of at least two of the first, second, and third output nodes is sensed, and predetermined switches are automatically activated by the inverter responsive to the sensed rotor position, the sensed current, and the desired speed.

Mobile Inverted Constructivism: Education of Interaction Technology in Social Media

ERIC Educational Resources Information Center

Chai, Jia-Xiang; Fan, Kuo-Kuang

2016-01-01

The combination of social media and invert teaching is a new path to inverting interation technology education and reconstructing the curriculum of context. In this paper, based on the theory of constructivism learning, a model named Mobile Inverted Constructivism (MIC) is provided. Moreover, in view of the functional quality of social media in…

21 CFR 184.1859 - Invert sugar.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Invert sugar. 184.1859 Section 184.1859 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1859 Invert sugar. (a) Invert sugar (CAS Reg. No. 8013-17-0) is an aqueous...

21 CFR 184.1859 - Invert sugar.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Invert sugar. 184.1859 Section 184.1859 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1859 Invert sugar. (a) Invert sugar (CAS Reg. No. 8013-17-0) is an aqueous...

21 CFR 184.1859 - Invert sugar.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Invert sugar. 184.1859 Section 184.1859 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1859 Invert sugar. (a) Invert sugar (CAS Reg. No. 8013-17-0) is an aqueous...

21 CFR 184.1859 - Invert sugar.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Invert sugar. 184.1859 Section 184.1859 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN... Substances Affirmed as GRAS § 184.1859 Invert sugar. (a) Invert sugar (CAS Reg. No. 8013-17-0) is an aqueous...

DC-to-AC inverter ratio failure detector

NASA Technical Reports Server (NTRS)

Ebersole, T. J.; Andrews, R. E.

1975-01-01

Failure detection technique is based upon input-output ratios, which is independent of inverter loading. Since inverter has fixed relationship between V-in/V-out and I-in/I-out, failure detection criteria are based on this ratio, which is simply inverter transformer turns ratio, K, equal to primary turns divided by secondary turns.

A SiC MOSFET Based Inverter for Wireless Power Transfer Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Onar, Omer C; Chinthavali, Madhu Sudhan; Campbell, Steven L

2014-01-01

In a wireless power transfer (WPT) system, efficiency of the power conversion stages is crucial so that the WPT technology can compete with the conventional conductive charging systems. Since there are 5 or 6 power conversion stages, each stage needs to be as efficient as possible. SiC inverters are crucial in this case; they can handle high frequency operation and they can operate at relatively higher temperatures resulting in reduces cost and size for the cooling components. This study presents the detailed power module design, development, and fabrication of a SiC inverter. The proposed inverter has been tested at threemore » center frequencies that are considered for the WPT standardization. Performance of the inverter at the same target power transfer level is analyzed along with the other system components. In addition, another SiC inverter has been built in authors laboratory by using the ORNL designed and developed SiC modules. It is shown that the inverter with ORNL packaged SiC modules performs simular to that of the inverter having commercially available SiC modules.« less

Stability Assessment of a System Comprising a Single Machine and Inverter with Scalable Ratings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Brian B; Lin, Yashen; Gevorgian, Vahan

From the inception of power systems, synchronous machines have acted as the foundation of large-scale electrical infrastructures and their physical properties have formed the cornerstone of system operations. However, power electronics interfaces are playing a growing role as they are the primary interface for several types of renewable energy sources and storage technologies. As the role of power electronics in systems continues to grow, it is crucial to investigate the properties of bulk power systems in low inertia settings. In this paper, we assess the properties of coupled machine-inverter systems by studying an elementary system comprised of a synchronous generator,more » three-phase inverter, and a load. Furthermore, the inverter model is formulated such that its power rating can be scaled continuously across power levels while preserving its closed-loop response. Accordingly, the properties of the machine-inverter system can be assessed for varying ratios of machine-to-inverter power ratings and, hence, differing levels of inertia. After linearizing the model and assessing its eigenvalues, we show that system stability is highly dependent on the interaction between the inverter current controller and machine exciter, thus uncovering a key concern with mixed machine-inverter systems and motivating the need for next-generation grid-stabilizing inverter controls.« less

Actively stabilized optical fiber interferometry technique for online/in-process surface measurement.

PubMed

Wang, Kaiwei; Martin, Haydn; Jiang, Xiangqian

2008-02-01

In this paper, we report the recent progress in optical-beam scanning fiber interferometry for potential online nanoscale surface measurement based on the previous research. It attempts to generate a robust and miniature measurement device for future development into a multiprobe array measurement system. In this research, both fiber-optic-interferometry and the wavelength-division-multiplexing techniques have been used, so that the optical probe and the optical interferometer are well spaced and fast surface scanning can be carried out, allowing flexibility for online measurement. In addition, this system provides a self-reference signal to stabilize the optical detection with high common-mode noise suppression by adopting an active phase tracking and stabilization technique. Low-frequency noise was significantly reduced compared with unstabilized result. The measurement of a sample surface shows an attained repeatability of 3.3 nm.

Inverted stream channels in the Western Desert of Egypt: Synergistic remote, field observations and laboratory analysis on Earth with applications to Mars

NASA Astrophysics Data System (ADS)

Zaki, Abdallah S.; Pain, Colin F.; Edgett, Kenneth S.; Giegengack, Robert

2018-07-01

Inverted relief landforms occur in numerous regions on Mars, ranging in age from Noachian to more recent Amazonian periods (<3.0 Ga). A better understanding of the conditions in which inverted fluvial channel features on Earth form, and the geologic records they preserve in arid settings, can yield insights into the development of inverted landforms on Mars. Inverted channel landforms in the Western Desert of Egypt are well represented across an area of ∼27,000 km2. We investigated inverted channel features at seven sites using remotely-sensed data, field observations, and lab analysis. Inverted channel features in the Western Desert record fluvial environments of differing scales and ages. They developed mainly via inversion of cemented valley floor sediment, but there is a possibility that inverted fluvial landforms in the Dakhla Depression might have been buried, lithified, and exhumed. A few examples, in the southeastern part of the Western Desert, record, instead, a resistance to erosion caused by surface armouring of uncemented valley floor sediment. We show that the grain-size distribution for investigated and reviewed inverted channels is highly variable, with boulders that are commonly 0.35 - 1 m in size; large particles provide high porosity that influences the cementation mechanism. The studied inverted channel sediments are mainly cemented with ferricrete, calcrete, gypcrete, and silcrete. Inverted channels are valuable for the reconstruction of paleoclimate cycles or episodes on Earth and Mars; observations from the Western Desert, when offered as analogs, add to the growing list of Earth examples that provide suites of observables relevant to reconstruction of paleoenvironmental conditions on Mars.

The complete chloroplast genome sequence of Actinidia arguta using the PacBio RS II platform

PubMed Central

Lin, Miaomiao; Qi, Xiujuan; Chen, Jinyong; Sun, Leiming; Zhong, Yunpeng; Fang, Jinbao; Hu, Chungen

2018-01-01

Actinidia arguta is the most basal species in a phylogenetically and economically important genus in the family Actinidiaceae. To better understand the molecular basis of the Actinidia arguta chloroplast (cp), we sequenced the complete cp genome from A. arguta using Illumina and PacBio RS II sequencing technologies. The cp genome from A. arguta was 157,611 bp in length and composed of a pair of 24,232 bp inverted repeats (IRs) separated by a 20,463 bp small single copy region (SSC) and an 88,684 bp large single copy region (LSC). Overall, the cp genome contained 113 unique genes. The cp genomes from A. arguta and three other Actinidia species from GenBank were subjected to a comparative analysis. Indel mutation events and high frequencies of base substitution were identified, and the accD and ycf2 genes showed a high degree of variation within Actinidia. Forty-seven simple sequence repeats (SSRs) and 155 repetitive structures were identified, further demonstrating the rapid evolution in Actinidia. The cp genome analysis and the identification of variable loci provide vital information for understanding the evolution and function of the chloroplast and for characterizing Actinidia population genetics. PMID:29795601

Revisiting the Plastid Phylogenomics of Pinaceae with Two Complete Plastomes of Pseudolarix and Tsuga

PubMed Central

Sudianto, Edi; Wu, Chung-Shien; Lin, Ching-Ping; Chaw, Shu-Miaw

2016-01-01

Phylogeny of the ten Pinaceous genera has long been contentious. Plastid genomes (plastomes) provide an opportunity to resolve this problem because they contain rich evolutionary information. To comprehend the plastid phylogenomics of all ten Pinaceous genera, we sequenced the plastomes of two previously unavailable genera, Pseudolarix amabilis (122,234 bp) and Tsuga chinensis (120,859 bp). Both plastomes share similar gene repertoire and order. Here for the first time we report a unique insertion of tandem repeats in accD of T. chinensis. From the 65 plastid protein-coding genes common to all Pinaceous genera, we re-examined the phylogenetic relationship among all Pinaceous genera. Our two phylogenetic trees are congruent in an identical tree topology, with the five genera of the Abietoideae subfamily constituting a monophyletic clade separate from the other three subfamilies: Pinoideae, Piceoideae, and Laricoideae. The five genera of Abietoideae were grouped into two sister clades consisting of (1) Cedrus alone and (2) two sister subclades of Pseudolarix—Tsuga and Abies—Keteleeria, with the former uniquely losing the gene psaM and the latter specifically excluding the 3 psbA from the residual inverted repeat. PMID:27352945

Segmented and "equivalent" representation of the cable equation.

PubMed

Andrietti, F; Bernardini, G

1984-11-01

The linear cable theory has been applied to a modular structure consisting of n repeating units each composed of two subunits with different values of resistance and capacitance. For n going to infinity, i.e., for infinite cables, we have derived analytically the Laplace transform of the solution by making use of a difference method and we have inverted it by means of a numerical procedure. The results have been compared with those obtained by the direct application of the cable equation to a simplified nonmodular model with "equivalent" electrical parameters. The implication of our work in the analysis of the time and space course of the potential of real fibers has been discussed. In particular, we have shown that the simplified ("equivalent") model is a very good representation of the segmented model for the nodal regions of myelinated fibers in a steady situation and in every condition for muscle fibers. An approximate solution for the steady potential of myelinated fibers has been derived for both nodal and internodal regions. The applications of our work to other cases dealing with repeating structures, such as earthworm giant fibers, have been discussed and our results have been compared with other attempts to solve similar problems.

The complete chloroplast genome of Capsicum annuum var. glabriusculum using Illumina sequencing.

PubMed

Raveendar, Sebastin; Na, Young-Wang; Lee, Jung-Ro; Shim, Donghwan; Ma, Kyung-Ho; Lee, Sok-Young; Chung, Jong-Wook

2015-07-20

Chloroplast (cp) genome sequences provide a valuable source for DNA barcoding. Molecular phylogenetic studies have concentrated on DNA sequencing of conserved gene loci. However, this approach is time consuming and more difficult to implement when gene organization differs among species. Here we report the complete re-sequencing of the cp genome of Capsicum pepper (Capsicum annuum var. glabriusculum) using the Illumina platform. The total length of the cp genome is 156,817 bp with a 37.7% overall GC content. A pair of inverted repeats (IRs) of 50,284 bp were separated by a small single copy (SSC; 18,948 bp) and a large single copy (LSC; 87,446 bp). The number of cp genes in C. annuum var. glabriusculum is the same as that in other Capsicum species. Variations in the lengths of LSC; SSC and IR regions were the main contributors to the size variation in the cp genome of this species. A total of 125 simple sequence repeat (SSR) and 48 insertions or deletions variants were found by sequence alignment of Capsicum cp genome. These findings provide a foundation for further investigation of cp genome evolution in Capsicum and other higher plants.

Molecular Characterization of Herpes Simplex Virus 2 Strains by Analysis of Microsatellite Polymorphism

PubMed Central

Ait-Arkoub, Zaïna; Voujon, Delphine; Deback, Claire; Abrao, Emiliana P.; Agut, Henri; Boutolleau, David

2013-01-01

The complete 154-kbp linear double-stranded genomic DNA sequence of herpes simplex virus 2 (HSV-2), consisting of two extended regions of unique sequences bounded by a pair of inverted repeat elements, was published in 1998 and since then has been widely employed in a wide range of studies. Throughout the HSV-2 genome are scattered 150 microsatellites (also referred to as short tandem repeats) of 1- to 6-nucleotide motifs, mainly distributed in noncoding regions. Microsatellites are considered reliable markers for genetic mapping to differentiate herpesvirus strains, as shown for cytomegalovirus and HSV-1. The aim of this work was to characterize 12 polymorphic microsatellites within the HSV-2 genome by use of 3 multiplex PCR assays in combination with length polymorphism analysis for the rapid genetic differentiation of 56 HSV-2 clinical isolates and 2 HSV-2 laboratory strains (gHSV-2 and MS). This new system was applied to a specific new HSV-2 variant recently identified in HIV-1-infected patients originating from West Africa. Our results confirm that microsatellite polymorphism analysis is an accurate tool for studying the epidemiology of HSV-2 infections. PMID:23966512

Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae.

PubMed

Häring, Monika; Peng, Xu; Brügger, Kim; Rachel, Reinhard; Stetter, Karl O; Garrett, Roger A; Prangishvili, David

2004-06-01

A novel virus, termed Pyrobaculum spherical virus (PSV), is described that infects anaerobic hyperthermophilic archaea of the genera Pyrobaculum and Thermoproteus. Spherical enveloped virions, about 100 nm in diameter, contain a major multimeric 33-kDa protein and host-derived lipids. A viral envelope encases a superhelical nucleoprotein core containing linear double-stranded DNA. The PSV infection cycle does not cause lysis of host cells. The viral genome was sequenced and contains 28337 bp. The genome is unique for known archaeal viruses in that none of the genes, including that encoding the major structural protein, show any significant sequence matches to genes in public sequence databases. Exceptionally for an archaeal double-stranded DNA virus, almost all the recognizable genes are located on one DNA strand. The ends of the genome consist of 190-bp inverted repeats that contain multiple copies of short direct repeats. The two DNA strands are probably covalently linked at their termini. On the basis of the unusual morphological and genomic properties of this DNA virus, we propose to assign PSV to a new viral family, the Globuloviridae.

Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome.

PubMed

Aljohi, Hasan Awad; Liu, Wanfei; Lin, Qiang; Zhao, Yuhui; Zeng, Jingyao; Alamer, Ali; Alanazi, Ibrahim O; Alawad, Abdullah O; Al-Sadi, Abdullah M; Hu, Songnian; Yu, Jun

2016-01-01

Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5.07% of the total assembly length, including 13 proteins, 2 pseudogenes, and 11 tRNAs. The mt genome has a relatively large fraction of repeat content (17.26%), including both forward (tandem) and inverted (palindromic) repeats. Sequence variation analysis shows that the Ti/Tv ratio of the mt genome is lower as compared to that of the nuclear genome and neutral expectation. By combining public RNA-Seq data for coconut, we identify 734 RNA editing sites supported by at least two datasets. In summary, our data provides the second complete mt genome sequence in the family Arecaceae, essential for further investigations on mitochondrial biology of seed plants.

Number word structure in first and second language influences arithmetic skills

PubMed Central

Prior, Anat; Katz, Michal; Mahajna, Islam; Rubinsten, Orly

2015-01-01

Languages differ in how they represent numerical information, and specifically whether the verbal notation of numbers follows the same order as the symbolic notation (in non-inverted languages, e.g., Hebrew, “25, twenty-five”) or whether the two notations diverge (in inverted languages, e.g., Arabic, “25, five-and-twenty”). We examined how the structure of number–words affects how arithmetic operations are processed by bilingual speakers of an inverted and a non-inverted language. We examined Arabic–Hebrew bilinguals’ performance in the first language, L1 (inverted) and in the second language, L2 (non-inverted). Their performance was compared to that of Hebrew L1 speakers, who do not speak an inverted language. Participants judged the accuracy of addition problems presented aurally in L1, aurally in L2 or in visual symbolic notation. Problems were presented such that they matched or did not match the structure of number words in the language. Arabic–Hebrew bilinguals demonstrated both flexibility in processing and adaptation to the language of aural–verbal presentation – they were more accurate for the inverted order of presentation in Arabic, but more accurate for non-inverted order of presentation in Hebrew, thus exhibiting the same pattern found for native Hebrew speakers. In addition, whereas native Hebrew speakers preferred the non-inverted order in visual symbolic presentation as well, the Arabic–Hebrew bilinguals showed enhanced flexibility, without a significant preference for one order over the other, in either speed or accuracy. These findings suggest that arithmetic processing is sensitive to the linguistic representations of number words. Moreover, bilinguals exposed to inverted and non-inverted languages showed influence of both systems, and enhanced flexibility in processing. Thus, the L1 does not seem to have exclusive power in shaping numerical mental representations, but rather the system remains open to influences from a later learned L2. PMID:25852591

Evidence that human papillomavirus causes inverted papilloma is sparse.

PubMed

Justice, Jeb M; Davis, Kern M; Saenz, Daniel A; Lanza, Donald C

2014-12-01

Controversy exists regarding the pathogenesis of inverted papilloma as it relates to the involvement of human papillomavirus (HPV). The purpose of this report is to describe the prevalence of HPV in nondysplastic, "early inverted papilloma" and to summarize HPV detection rates in the general population and in other HPV related neoplasia. This case series report characterizes consecutive inverted papilloma patients from January 2005 to August 2012 with regard to smoking history, dysplasia, and HPV detection rates. Presence or absence of low/high risk HPV was determined by standardized in situ hybridization DNA probes. Medline literature review was performed to determine the prevalence of HPV in inverted papilloma without moderate or severe dysplasia. Thirty-six consecutive patients were identified with an average age of 63.6 (range, 40-84) years; gender: 23 men, 13 women. More than half (55%) were active or former smokers (14% active and 41% former). High/low risk HPV was present in 1 in 36 (2.7%) patients and 1 in 36 (2.7%) had mild dysplasia. In the literature review: (1) HPV was detected in 16.4% of inverted papilloma without dysplasia; (2) oral cavity HPV detection was 4.2% to 11.4% in the normal population; and (3) HPV was normally detected in 85% to 95% of HPV-related neoplasia. Given histological features of inverted papilloma and comparatively low detection rates of HPV in inverted papilloma without dysplasia (2.7%), as well as the summary of the world literature, HPV is not related to the initial pathogenesis of inverted papilloma or inverted papilloma's tendency to persist or recur. It is postulated that since inverted papilloma is more an inflammatory polyp, it is susceptible to secondary HPV infection because of its metaplasia. Tobacco and other causes of respiratory epithelium remodeling are more plausible explanations for the initial tissue transformation to inverted papilloma. © 2014 ARS-AAOA, LLC.