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At least 235 records · Page 13Linked to original sources
PubMed1996

The hermit transposable element of the Australian sheep blowfly, Lucilia cuprina, belongs to the hAT family of transposable elements.

We report the cloning of hermit, a member of the hAT family of transposable elements from the genome of the Australian sheep blowfly, Lucilia cuprina. Hermit is 2716 bp long and is 49% homologous to the autonomous hobo element, HFL1, at the nucleic acid level. Hermit has 15 bp terminal inverted repeats that share 10 bp with the terminal inverted repeats of HFL1. Conceptual translation reveals a 583 residue open reading frame (ORF) that is 64% similar and 42% identical to the HFL1 ORF. However, the sequence of the hermit element contains two frameshifts within the putative ORF, indication that hermit is an inactive element. Analysis of L. cuprina strains from within and outside Australia suggested that hermit is present as a single copy in all the genomes analysed.

Amino Acid Sequence↗
PubMed1995

Variegation patterns caused by excision of the maize transposable element Dissociation (Ds) are autonomously regulated by allele-specific Activator (Ac) elements and are not due to trans-acting modifier genes.

The Ac elements present in the unstable wx-m7 and wx-m9 alleles of maize trigger different patterns of Ds excision in trans. To determine whether this differential regulation is a feature of the Ac alleles themselves or is mediated by genetically distinct factors, maize plants heterozygous for the wx-m7 and wx-m9 alleles were crossed to tester strains homozygous for Ds reporter alleles. Kernels showing the variegation pattern characteristic for the Ac elements carried in the wx-m7 and wx-m9 alleles were found to be present in the ratios expected from the genetic constitution of the strains. The aleurone variegation caused by excision of the Ds reporter element and the endosperm variegation caused by excision of Ac from the wx-m7 and wx-m9 alleles themselves segregated with the original wx-m alleles. In addition, stable Wx and wx derivatives of wx-m9 that have lost Ac no longer exert any trans effect on the wx-m7 allele (and vice versa). Therefore it is concluded that the observed variegation patterns are autonomously determined by specific trans effects of the particular Ac element.

Alleles↗
PubMed1989

Determination of trace elements in human hair. Reference intervals for 28 elements in nonoccupationally exposed adults in the US and effects of hair treatments.

The concentrations of 28 elements in hair of three populations of non-occupationally exposed adults in the US (n = 271) were determined. The 10th, 50th, and 90th percentiles, and geometric means for these data were obtained to define reference intervals for these elements. The effects of various hair treatments, age, and sex on concentrations of 17 selected elements in hair were determined for these populations. Age had little effect on elemental concentrations. Males tended to have higher Cd and Pb levels, but lower Mg and Ti levels than females. Males using dandruff shampoo had significantly higher concentrations of Na, Se, and Ti than those using only regular shampoo and/or conditioners. Ba, Ca, Cu, Mg, Na, and Sr were all elevated in females using permanents or color treatments, compared to those using only dandruff shampoo, regular shampoo, and/or conditioners.

Adult↗
PubMed1997

Intragenomic distribution and stability of transposable elements in euchromatin and heterochromatin of Drosophila melanogaster: elements with inverted repeats Bari 1, hobo, and pogo.

The elements of the Bari 1, hobo, and pogo transposon families that are located in euchromatin, heterochromatin, and on the Y chromosome have been identified, and their stability has been assessed by Southern blot analysis. The fraction of heterochromatic elements appears to be distinctive of all transposon families tested, except for Bari 1. Evidence for instability of heterochromatic elements is described. The analysis of unstable elements in different Drosophila stocks suggests that the host genome contributes to the stability/instability of transposon families.

Animals↗
PubMed2001

The clc element of Pseudomonas sp. strain B13 and other mobile degradative elements employing phage-like integrases.

Genes for metabolic pathways in bacteria that degrade aromatic or aliphatic pollutants have mostly been confined to either plasmid DNAs or to the chromosome. For a few pathways, including classical pathways for chlorocatechol and biphenyl degradation, recent evidence has been obtained for location of the pathway genes on mobile DNA elements which employ phage-like integrases. This enables the DNA elements to integrate into specific sites on the chromosome and yet to excise and transfer to other host bacteria. This mini-review gives an overview of those elements and their relationship to an increasing number of phage-like elements associated with bacterial virulence.

Biodegradation, Environmental↗
PubMed2000

Fast determination of trace elements on aerosol-loaded filters by X-ray fluorescence analysis considering the inhomogeneous elemental distribution.

X-ray fluorescence (XRF) analysis was successfully applied for the determination of Ca, Cu, Fe, Mn, Ni, Pb, V and Zn on aerosol filters with a diameter of 150 mm. Ambient aerosol was collected on quartz-fibre filters by Digitel high-volume samplers. For XRF analysis three small filter pieces with a diameter of 32 mm were cut out of each filter, considering the radial dependence of elemental distribution on the filter. Elemental concentration decreases by 8-10% from the centre to the outer circle for coarse mode elements. Distribution of fine mode elements display only small radial dependence (2-4%). Results of quantitative analysis by XRF were compared with atomic spectrometric methods (GF-AAS, ICP-OES). The good agreement between the methods confirmed the application of XRF spectrometry for routine analysis of filter samples loaded with ambient aerosol.

Aerosols↗
PubMed2004

Creation of EcR isoform-specific mutations in Drosophila melanogaster via local P element transposition, imprecise P element excision, and male recombination.

Collections of single P transposable-element insertion strains that currently inactivate more than 25% of essential Drosophila genes have proven to be a valuable tool for genome research in Drosophila melanogaster. For genes unrepresented in these collections, strategies including local P element transposition and transposase-induced imprecise excision can be used to inactivate or delete the gene of interest. Here we report our use of local P element transposition followed by imprecise P element excision and transposase-induced male recombination to generate two deficiencies specific for the EcR-A isoform of the ecdysone receptor ( EcR) gene, and four larger deficiencies likely to affect multiple EcR functions. We also report here the determination of sequences flanking six EcR-B deficiencies generated in a previous imprecise excision screen. EcR-A encodes one of a family of three related nuclear receptor proteins that, together with the heterodimer partner USP, mediate ecdysone signaling during Drosophila development. Our results delineate sequences required in vivo for EcR-A function, as well as identifying EcR-A intron 1 sequences that are not essential for EcR function.

Animals↗
PubMed1995

The insertion sequence element ISRm2011-2 belongs to the IS630-Tc1 family of transposable elements and is abundant in Rhizobium meliloti.

The insertion sequence (IS) element ISRm2011-2 of Rhizobium meliloti (Rm) is characterized by 19-bp imperfect terminal inverted repeats (three mismatches) and a size of 1053 bp. Upon transposition, ISRm2011-2 generates a putative target duplication of 2 bp. ISRm2011-2 carries two major overlapping open reading frames (ORFA and B) with a coding capacity of 135 and 201 amino acids (aa), respectively. A potential translational frameshifting window (5'-AAAAAAAG) is located in the overlapping region of both ORFs. The putative fusion product of both proteins, which probably represents the mature transposase, has a predicted molecular mass of 35.8 kDa and a pI of 10.5. Comparison of the deduced aa sequence of ORFA with database entries revealed homology to putative transposases of some IS elements of the IS3 family, as well as to eukaryotic transcription factors. The protein encoded by ORFB shows homology to transposases (Tps) of the recently proposed IS630-Tc1 family which includes Tps of both prokaryotic and eukaryotic transposable elements. Analyses of the distribution of ISRm2011-2 in natural Rm populations showed that this IS element is abundant in Rm strains.

Amino Acid Sequence↗
PubMed2006

Identification of a peroxisome proliferator responsive element (PPRE)-like cis-element in mouse plasminogen activator inhibitor-1 gene promoter.

PAI-1 is expressed and secreted by adipose tissue which may mediate the pathogenesis of obesity-associated cardiovascular complications. Evidence is presented in this report that PAI-1 is not expressed by preadipocyte, but significantly induced during 3T3-L1 adipocyte differentiation and the PAI-1 expression correlates with the induction of peroxisome proliferator-activated receptor gamma (PPARgamma). A peroxisome proliferator responsive element (PPRE)-like cis-element (-206TCCCCCATGCCCT-194) is identified in the mouse PAI-1 gene promoter by electrophoretic mobility shift assay (EMSA) combined with transient transfection experiments; the PPRE-like cis-element forms a specific DNA-protein complex only with adipocyte nuclear extracts, not with preadipocyte nuclear extracts; the DNA-protein complex can be totally competed away by non-labeled consensus PPRE, and can be supershifted with PPARgamma antibody. Mutation of this PPRE-like cis-element can abolish the transactivation of mouse PAI-1 promoter mediated by PPARgamma. Specific PPARgamma ligand Pioglitazone can significantly induce the PAI-1 expression, and stimulate the secretion of PAI-1 into medium.

3T3-L1 Cells↗
PubMed2002

Multi-element analysis of trace element levels in human autopsy tissues by using inductively coupled atomic emission spectrometry technique (ICP-AES).

Autopsy tissue samples from the brain front lobe, cerebellum, heart, kidney (cortex and medulla), liver, pancreas, spleen and ovary were analysed for AL, B, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, Se, Sr and Zn in 30 (17 women and 13 men) subjects ranging in age from 17 to 96 years at Haukeland University Hospital in Norway. The tissues were selected from macroscopically normal organs and samples were handled according to guidelines recommended to avoid contamination in the pre-analytical phase. Concentration of the trace elements were determined by the inductively coupled plasma atomic emission spectrometry technique (ICP-AES). In most tissues the concentrations of the essential trace elements followed the order Fe> Zn> Cu> Mn> Se> Cr> Co except in the ovary where Se was higher than Mn. The liver was the major site of deposition for Co, Cu and Mn as well as the spleen for Co, brain front lobe for Cu and pancreas for Mn. Ba, Sr and Ni built up in the ovary foLLowed by the kidney. Older subjects accumulated Ba and Sr in most tissues, whereas Al accumulated in the kidney cortex and Cd in the brain cerebellum. Generally males had higher concentrations of trace elements in the different tissue sampLes than females with the exception of Mn in the brain front lobe and heart and Sr in the liver. ICP-AES is a useful method to assess the concentration and the profiLe of trace elements in human autopsy tissues.

Adolescent↗
PubMed2003

Total-diet study: dietary intakes of macro elements and trace elements in Italy.

The present study provides the dietary intakes of macro elements (Ca, Mg, Na, K, P) and trace elements (Fe, Zn, Cu, Se) from the Italian total diet. The contribution of the most representative food groups of the total diet (cereals and cereal products, vegetables, fruit, milk and dairy products, meat and meat products, fish) to the daily intakes of these nutrients was also evaluated. The Italian total diet was formulated following the 'market-basket' approach. Cereals represented the primary sources of Cu (35 %), Fe (30 %) and Mg (27 %). About 89 % of the total daily intake of Fe was derived from plant foods. The vegetables food group was the main source of dietary K (27 %). Most of the Ca (59 %) and P (27 %) was derived from the milk-and-dairy food group. Of the dietary Zn, 41 % was provided by meat, which, together with the fish food group, was the primary source of Se (20 %). The adequacy of the Italian total diet with respect to nutritional elements was assessed by comparing the daily intakes with the average requirement values of the Italian recommended dietary allowances. The present findings indicated that the dietary patterns of the Italian total diet were generally consistent with current Italian dietary recommendations for both macro and trace elements. The major concern was for Ca, for which daily intake was 76 % of the average recommendation for the Italian population. It should not be ruled out that there could be a potential risk of inadequate Fe intake in some segments of the population.

Adolescent↗
PubMed2005

Representation of bioelectric current sources using Whitney elements in the finite element method.

Bioelectric current sources of magneto- and electroencephalograms (MEG, EEG) are usually modelled with discrete delta-function type current dipoles, despite the fact that the currents in the brain are naturally continuous throughout the neuronal tissue. In this study, we represent bioelectric current sources in terms of Whitney-type elements in the finite element method (FEM) using a tetrahedral mesh. The aim is to study how well the Whitney elements can reproduce the potential and magnetic field patterns generated by a point current dipole in a homogeneous conducting sphere. The electric potential is solved for a unit sphere model with isotropic conductivity and magnetic fields are calculated for points located on a cap outside the sphere. The computed potential and magnetic field are compared with analytical solutions for a current dipole. Relative difference measures between the FEM and analytical solutions are less than 1%, suggesting that Whitney elements as bioelectric current sources are able to produce the same potential and magnetic field patterns as the point dipole sources.

Algorithms↗
PubMed1999

Origination of Ds elements from Ac elements in maize: evidence for rare repair synthesis at the site of Ac excision.

Although it has been known for some time that the maize transposon Ac can mutate to Ds by undergoing internal deletions, the mechanism by which these mutations arise has remained conjectural. To gain further insight into this mechanism in maize we have studied a series of Ds elements that originated de novo from Ac elements at known locations in the genome. We present evidence that new, internally deleted Ds elements can arise at the Ac donor site when Ac transposes to another site in the genome. However, internal deletions are rare relative to Ac excision footprints, the predominant products of Ac transposition. We have characterized the deletion junctions in five new Ds elements. Short direct repeats of variable length occur adjacent to the deletion junction in three of the five Ds derivatives. In the remaining two, extra sequences or filler DNA is inserted at the junction. The filler DNAs are identical to sequences found close to the junction in the Ac DNA, where they are flanked by the same sequences that flank the filler DNA in the deletion. These findings are explained most simply by a mechanism involving error-prone DNA replication as an occasional alternative to end-joining in the repair of Ac-generated double-strand breaks.

DNA Repair↗
PubMed2003

Genome-wide analysis of mariner-like transposable elements in rice reveals complex relationships with stowaway miniature inverted repeat transposable elements (MITEs).

Stowaway is a superfamily of miniature inverted repeat transposable elements (MITEs) that is widespread and abundant in plant genomes. Like other MITEs, however, its origin and mode of amplification are poorly understood. Several lines of evidence point to plant mariner-like elements (MLEs) as the autonomous partners of the nonautonomous Stowaway MITEs. To better understand this relationship, we have taken advantage of the nearly complete genome sequences of two rice subspecies to generate the first inventory of virtually all MLEs and Stowaway families coexisting in a single plant species. Thirty-four different MLEs were found to group into three major clades and 25 families. More than 22,000 Stowaway MITEs were identified and classified into 36 families. On the basis of detailed sequence comparisons, MLEs were confirmed to be the best candidate autonomous elements for Stowaway MITEs. Surprisingly, however, sequence similarity between MLE and Stowaway families was restricted to the terminal inverted repeats (TIRs) and, in a few cases, to adjacent subterminal sequences. These data suggest a model whereby most of the Stowaway MITEs in rice were cross-mobilized by MLE transposases encoded by distantly related elements.

Base Sequence↗
PubMed1987

Characterization of xenobiotic responsive elements upstream from the drug-metabolizing cytochrome P-450c gene: a similarity to glucocorticoid regulatory elements.

The DNA element governing the inducible expression of drug-metabolizing P-450c gene by xenobiotic treatments was investigated by gene transfer methods. A variety of dissected fragments from -844 to -1140bp region which was essential for the inducibility of P-450c gene were placed on the heterologous SV40 promoter for testing the inducibility. Mapping studies in combination with gel retardation assay defined the presence of the two xenobiotic responsive elements (XRE, XRE1, -1007 - -1021bp; XRE2, -1088 - -1092bp) composed of about 15 nucleotides which expressed the enhancer activity in response to xenobiotic inducers. The two XREs share 10 nucleotides in common out of 15 as expressed in the sequence CG/CTG/CC/TTG/CTCACGCT/AA and are arranged in the inverse orientation. They are different from DREs (drug responsive element) proposed previously (Sogawa, K. et al. Proc. Natl. Acad. Sci. 83, 8044-8048 (1986] and expressed a strong enhancer activity in response to 3-methylcholanthrene. The XRE shows a significant homology with glucocorticoid regulatory elements and apparently needs normal functions of a putative xenobiotic receptor for the inducible enhancer activity.

Animals↗
PubMed1989

Ty4, a novel low-copy number element in Saccharomyces cerevisiae: one copy is located in a cluster of Ty elements and tRNA genes.

We have identified a composite element, Ty4, in S. cerevisiae that is ca 6.3 kb in length and contains two tau sequences as long terminal repeats. According to hybridization analyses, Ty4 occurs in low but varying copy number (one to four copies) in different yeast strains. By several criteria, Ty4 is a novel type of retroelement which is similar but not related to the other Ty elements in yeast. Two cosmid clones from strain C836 (c90 and c476) carrying individual copies of Ty4 were isolated. By restriction analysis and nucleotide sequence we show that c476 derives from the 'transposition right arm hot spot' of chromosome III [1]. The analysis of c476 revealed that an initiator tRNA(Met) gene is present at this locus and that an unusual concentration of different Ty elements has occurred: in addition to the Ty4, a Ty1 and a Ty2 element were detected in this region, confirming its highly polymorphic character.

Base Sequence↗
PubMed1992

Identification of an internal cis-element essential for the human L1 transcription and a nuclear factor(s) binding to the element.

L1 (LINE-1) is a long interspersed repetitive sequence derived from a retrotransposon. Transfection studies using the CAT gene as a reporter demonstrated that the first 155bp in the human L1 sequence contains an element(s) responsible for the promoter activity in HeLa cells. The transcription was shown to initiate at the first nucleotide of the L1 sequence in the transgene. Three prominent nuclear protein binding sites were found in the 5' region of the L1 sequence by DNaseI footprint analysis. One of the binding sites, designated as site A located at +3 to +26, was shown to be essential for the L1 transcription because the mutation at the site A caused almost complete loss of the promoter activity. A sequence AAGATGGCC at +11 to +19 in the site A was defined as a target core element for the protein binding. The site A-binding protein (designated TFL1-A) was found in various types of cells including an embryonic teratocarcinoma cell line. These results indicate that an internal short element located at the very 5' terminal of L1 sequence and the nuclear factor binding to the element play a crucial role in the transcription of human L1.

Amino Acid Sequence↗
PubMed1998

Multiple DNA elements for sterol regulatory element-binding protein and NF-Y are responsible for sterol-regulated transcription of the genes for human 3-hydroxy-3-methylglutaryl coenzyme A synthase and squalene synthase.

The expression of the human SREBP-2 gene is transcriptionally regulated in a cooperative manner by sterol regulatory element-binding proteins (SREBPs) and the general transcription factor NF-Y [Sato, R., Inoue, J., Kawabe, Y., Kodama, T., Takano, T., and Maeda, M. (1996) J. Biol. Chem. 271, 26461-26464]. To understand the sterol-dependent transcriptional regulation by these factors in detail, we have examined the regulation of the 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) synthase and squalene synthase genes, whose promoters have multiple potential sterol regulatory elements (SRE, SREBP binding site) and NF-Y binding sites. The promoter of the human HMG CoA synthase gene was cloned, sequenced, and functionally characterized by means of reporter gene assays. The results indicate that an inverted CCAAT box, two SRE motifs and two Sp1 sites localized in a 90-bp region coordinately regulate the transcription. In the case of the human squalene synthase promoter, two SRE motifs and an inverted CCAAT box between the motifs localized in a 51-bp region are responsible for the sterol-regulated transcription of the gene. Gel mobility shift assay reveals that these two inverted CCAAT boxes are recognized by NF-Y. The involvement of multiple responsive elements in the transcription of HMG CoA synthase and squalene synthase seems to induce a higher level of sterol-dependent regulation (3.5 to 5. 8-fold) compared with that of the SREBP-2 promoter, which contains a single pair of SRE motif and CCAAT box (1.8 to 2.6-fold). Reporter gene assays using constructs containing various nucleotide spacing lengths between the SRE motif and the CCAAT box demonstrate that the 16 to 20-bp spacing range is required for maximal transcriptional regulation. These results agree with the findings that the distances between the two motifs in the known sterol responsive elements in several genes, including the human HMG CoA synthase and squalene synthase genes, are in this range.

Base Sequence↗