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PubMed1983

Some aspects of element turnover in living organism.

The net uptake and loss of any element by a living organism can be described as the quotient of the total amount of the element, present in the organism, and its residence time in the organism. Theoretically it can be derived that the residence time tau i, equals Vi1-b/kappa, in which b, the morphometric coefficient, is related to size and shape of the organism (volume Vi); kappa, the turnover coefficient, is related to its metabolic activity. The net uptake or excretion, phi i, of an element then follows from phi = kappa Ci Vib, Ci being the (average, whole animal) concentration of the element. Residence times, derived from the quotient of body volume (weight) and daily food intake of various animal species of different sizes, show that, independent of animal or element species, the morphometric coefficient and turnover coefficient have values of b = 0.735 and k = 71.4 dm. year-1 respectively. The turnover coefficient may show some variation, related to the metabolic activity of the organism. The value of the morphometric coefficient implies that residence times may vary with body size; in small animals the residence times of the elements may be in the order of several hours, whereas in the largest organisms residence times may be as long as several years. The uptake of Na, Mg, Cl and P calculated from the above equation (phi i = k Ci Vib) corresponds very well with data in the literature on the mineral requirements of domestic animals; for Ca the calculated values were lower, for I higher, but they show the same weight-dependence as predicted from the equation. This suggests that the equation may be used tentatively to assess dietary requirements for elements for which up till now no such information exists. Values derived for the uptake and excretion of various elements by the whole biosphere correspond roughly to those estimated for their oceanic fluxes (from data compiled by Brewer, 1975). This supports the hypothesis that the global turnover of (many) elements is closely related to biological (metabolic) processes.

Animals↗
PubMed1992

Nonautonomous transposable elements in prokaryotes and eukaryotes.

Defective (nonautonomous) copies of transposable elements are relatively common in the genomes of eukaryotes but less common in the genomes of prokaryotes. With regard to transposable elements that exist exclusively in the form of DNA (nonretroviral transposable elements), nonautonomous elements may play a role in the regulation of transposition. In prokaryotes, plasmid-mediated horizontal transmission probably imposes a selection against nonautonomous elements, since nonautonomous elements are incapable of mobilizing themselves. The lower relative frequency of nonautonomous elements in prokaryotes may also reflect the coupling of transcription and translation, which may bias toward the cis activation of transposition. The cis bias we suggest need not be absolute in order to militate against the long-term maintenance of prokaryotic elements unable to transpose on their own. Furthermore, any cis bias in transposition would also decrease the opportunity for trans repression of transposition by nonautonomous elements.

Animals↗
PubMed1992

The population biology and evolutionary significance of Ty elements in Saccharomyces cerevisiae.

The basic structure and properties of Ty elements are considered with special reference to their role as agents of evolutionary change. Ty elements may generate genetic variation for fitness by their action as mutagens, as well as by providing regions of portable homology for recombination. The mutational spectra generated by Ty1 transposition events may, due to their target specificity and gene regulatory capabilities, possess a higher frequency of adaptively favorable mutations than spectra resulting from other types of mutational processes. Laboratory strains contain between 25-35 elements, and in both these and industrial strains the insertions appear quite stable. In contrast, a wide variation in Ty number is seen in wild isolates, with a lower average number/genome. Factors which may determine Ty copy number in populations include transposition rates (dependent on Ty copy number and mating type), and stabilization of Ty elements in the genome as well as selection for and against Ty insertions in the genome. Although the average effect of Ty transpositions are deleterious, populations initiated with a single clone containing a single Ty element steadily accumulated Ty elements over 1,000 generations. Direct evidence that Ty transposition events can be selectively favored is provided by experiments in which populations containing large amounts of variability for Ty1 copy number were maintained for approximately 100 generations in a homogeneous environment. At their termination, the frequency of clones containing 0 Ty elements had decreased to approximately 0.0, and the populations had became dominated by a small number of clones containing > 0 Ty elements. No such reduction in variability was observed in populations maintained in a structured environment, though changes in Ty number were observed. The implications of genetic (mating type and ploidy) changes and environmental fluctuations for the long-term persistence of Ty elements within the S. cerevisiae species group are discussed.

Biological Evolution↗
PubMed1991

Molecular analysis of the Bg-rbg transposable element system of Zea mays L.

The two components of the Bg-rbg transposable element system of maize have been cloned. The Bg element, isolated from the mutable allele wx-m32:: Bg is inserted in the intron of the Waxy (Wx) gene between exons 12 and 13. The length of the element is of 4869 bp. Bg has 5 bp terminal inverted repeats, and generates upon insertion an 8 bp direct duplication of the target sequence. Both ends of the Bg element contain a 76 bp direct repeat adjacent to the terminal inverted repeats. The hexamer motif TATCGGC is here repeated several times in direct or inverse orientation. The rbg element was isolated from the mutable allele o2m(r) where it is located in the promoter region of the Opaque-2 (O2) gene. rbg is approximately 4.5 kb in length, has terminal inverted repeats identical to those of the Bg element, and is also flanked by an 8 bp direct duplication at the target site. Like Bg, rbg carries the 76 bp direct repeats. Restriction enzyme analysis reveals that, compared to Bg, the receptor element is distinguishable by small deletion and insertion events. Sequence data indicate that not more than 75% homology exists at the DNA level between the rbg element and the autonomous Bg element.

Alleles↗
PubMed1989

Structural analysis of Doc transposable elements associated with mutations at the white and suppressor of forked loci of Drosophila melanogaster.

DNA sequences from two spontaneous mutations of Drosophila melanogaster associated with insertion of a Doc transposable element have been cloned. In white-one, the element is inserted in the white locus close to where transcription initiates. In a lethal allele of suppressor of forked, su(f)S2, the element is inserted within the transcription unit in the protein coding region. Four other Doc elements have been cloned from a wild-type strain. Doc is a member of the class of transposable elements known as retroposons, which includes the D. melanogaster F, G, Jockey, and I elements. There is no sequence homology between the ends of the Doc element. The 3' or right end terminates with a polyadenylation signal sequence followed by a stretch of oligo-A. The length of the oligo-A varies between elements, and a duplication of variable size is found as a direct repeat flanking inserted Doc elements. Members of the family are conserved at the 3' end, but may be truncated at the 5' or left end. These structural features suggest a mechanism of transposition via an RNA intermediate.

Alleles↗
PubMed1993

The sex determining region of Chironomus thummi is associated with highly repetitive DNA and transposable elements.

The dominant male sex determiner in chromosome III of the midge Chironomus thummi thummi is closely linked to a large cluster of tandem-repetitive DNA elements, the Cla elements, which are otherwise highly repetitive and distributed over more than 200 sites on all chromosomes. Chromosome III displays a hemizygous cluster of Cla elements in males but not in females. The chromosomal location of this hemizygous Cla element cluster is in the region of the male determiner M as localized by cytogenetic analysis. With Cla elements as hybridization probe, it was possible to clone a large part of the sex determining region. Molecular analysis of the DNA of males and females in this region displayed a number of differences between the two sexes. One striking difference is an unusual transposable element associated with the male sex determining region. The sex determining region also contains several other tandem-repetitive DNA elements in addition to the Cla elements. They are interspersed with single copy DNA. The accumulation of repetitive elements in the sex determining region interpreted as the result of a lack of recombination between the male/female heteromorphic region, although recombination in the other sections of chromosome III occurs.

Animals↗
PubMed1985

Molecular analysis of P element behavior in Drosophila simulans transformants.

In this report we describe the successful transformation of Drosophila simulans with an autonomous P element from Drosophila melanogaster without the use of a selectable marker. This result demonstrates that there is no species barrier for P element transposition. Utilizing gel blotting and in situ hybridization techniques, we have monitored the behavior of newly-introduced P elements in several D. simulans transformed lines over twelve generations. In most instances, an overall increase in the number of P elements was observed. An examination of the frequency of P-element-bearing individuals in one line revealed the rapid spread of P elements through the population. Analysis of well-characterized sublines confirmed that P elements increase in number by transposition to new genomic sites. The formation of degenerate elements occurred in at least one case. These observations suggest that P elements may behave similarly in D. melanogaster and D. simulans.

Animals↗
PubMed1990

Isolation and sequence analysis of Caenorhabditis briggsae repetitive elements related to the Caenorhabditis elegans transposon Tc1.

We have identified two repetitive element families in the genome of the nematode Caenorhabditis briggsae with extensive sequence identity to the Caenorhabditis elegans transposable element Tc1. Five members each of the TCb1 (previously known as Barney) and TCb2 families were isolated by hybridization to a Tc1 probe. Tc1-hybridizing repetitive elements were grouped into either the TCb1 or TCb2 family based on cross-hybridization intensities among the C. briggsae elements. The genomic copy number of the TCb1 family is 15 and the TCb2 family copy number is 33 in the C. briggsae strain G16. The two transposable element families show numerous genomic hybridization pattern differences between two C. briggsae strains, suggestive of transpositional activity. Two members of the TCb1 family, TCb1#5 and TCb1#10, were sequenced. Each of these two elements had suffered an independent single large deletion. TCb1#5 had a 627-bp internal deletion and TCb1#10 had lost 316 bp of one end. The two sequenced TCb1 elements were highly conserved over the sequences they shared. A 1616-bp composite TCb1 element was constructed from TCb1#5 and TCb1#10. The composite TCb1 element has 80-bp terminal inverted repeats with three nucleotide mismatches and two open reading frames (ORFs) on opposite strands. TCb1 and the 1610-bp Tc1 share 58% overall nucleotide sequence identity, and the greatest similarity occurs in their ORF1 and inverted repeat termini.

Animals↗
PubMed1990

P-related sequences in Drosophila bifasciata: a molecular clue to the understanding of P-element evolution in the genus Drosophila.

Two P-elements (bif1 and bif2) were isolated from a genomic library of Drosophila bifasciata. Both elements are internally deleted and have lost the coding capacity for a functional transposase. One of the elements (bif2) contains an insert consisting of a repetitive sequence. The terminal inverted repeats and the segments necessary for passive mobility are well conserved. Element bif2 has retained rudiments of the coding sequence of exon 0 and exon 3, but the reading frame is destroyed by insertions and deletions. The comparison of the D. bifasciata P-elements with P-elements of Drosophila melanogaster and Drosophila nebulosa reveals that the two latter sequences are more similar to each other than either of them is to the D. bifasciata elements. This finding contradicts the phylogenetic relationship of the species and can be taken as an indirect but unequivocal evidence for recent horizontal gene transfer from a relative of D. nebulosa to the gene pool of D. melanogaster. The P-elements of D. bifasciata are phylogenetically ancient and have evolved independently for about 50 million years. A higher substitution rate at the third codon position as well as a predominance of conservative replacements at the amino acid level indicates that the P-elements of D. bifasciata have been under selective constraint over a long period and that immunobilization has occurred only recently.

Amino Acid Sequence↗
PubMed1991

Insertion sites of the transposable element mariner are fixed in the genome of Drosophila sechellia.

The abundance of the transposable element mariner differs dramatically in the genomes of the closely related species Drosophila simulans, D. mauritiana, D. sechellia, and D. melanogaster. Natural populations of D. simulans and D. mauritiana have 1-10 and 20-30 copies per diploid genome, respectively, and the insertion sites are polymorphic. The element has not been found in D. melanogaster. In this paper we show that D. sechellia, a species endemic to the Seychelles Islands, contains only two mariner elements that are at fixed sites in the genome. One element, inserted in chromosome 2R at 51A1-2, contains three deletions and is missing much of the 3' end. The other element, inserted in chromosome 3L at 64A10-11, is the full length of 1286 bp. Although the sequence of the full-length element is polymorphic in populations of D. sechellia, at least some of the sequences are closely related to elements from D. simulans and D. mauritiana that are known to be active. However, judging from the progeny of crosses between D. sechellia and D. simulans, the biological activity of the full-length D. sechellia element appears to be low, either because of the nucleotide sequence of the element or because of its position in the genome, or both.

Animals↗
PubMed1991

Influence of nicotine on tissue trace element concentrations and tissue antioxidant defense.

Both altered trace element metabolism and cigarette smoking have been proposed to be risk factors for cardiovascular disease (CVD). Thus, it is important to identify the mechanisms by which cigarette smoke alters trace element metabolism. In the present study, serum trace element concentrations were measured in 19 smokers and 13 nonsmokers. In parallel studies, data from rats treated with 50 mg of nicotine over a 21-d period tested the hypothesis that nicotine induced altered trace element metabolism observed in smokers. Serum Cu and Zn concentrations were significantly higher in smokers than in nonsmokers. Serum nicotine concentrations in rats were comparable to those observed in heavy smokers, but serum trace element concentrations were not significantly altered by nicotine treatment. Tissue trace element concentrations were also not markedly affected by nicotine; however, trace element ratios in liver, kidney, lung, and brain were significantly altered by nicotine treatment. In addition, nicotine-treatment resulted in significantly lower liver glutathione concentrations and higher Cu, Zn superoxide dismutase activity than in controls. These data show that a 50-mg infusion of nicotine over 21 d does not produce in rats the serum trace element abnormalities observed in cigarette smokers. However, nicotine did affect the trace element relationships between tissues as well as components of the free radical defense system.

Adult↗
PubMed2004

The Pal elements in the upstream glucokinase promoter exhibit dyad symmetry and display cell-specific enhancer activity when multimerised.

AIMS/HYPOTHESIS: The upstream glucokinase (betaGK) promoter has previously been shown to contain two 9-bp sequences, termed the Pal motifs, that are conserved in humans, rats and mice. These motifs are necessary for expression of the betaGK promoter in pancreatic beta cell lines and pituitary corticotrope cell lines. DNA probes containing the Pal motifs bind cell-type-specific protein complexes, but these motifs have not been completely characterised. METHODS: Methylation interference and ultraviolet-crosslinking analysis were utilised to characterise, at the single nucleotide level, sites of protein binding within the elements themselves. To determine the function of these elements, mutational analysis of the betaGK promoter and of multimerised GK promoter sequences was performed. RESULTS: Both Pal elements are 14 bp in length and have dyad symmetry. However, while the Pal-1 element is a perfect inverted repeat (GTCACCA-TGGTGAC), the Pal-2 element (GTCACCA-TAGAAAC) is an imperfect repeat. Ultraviolet-crosslinking analysis using nuclear extracts prepared from hamster insulinoma tumour (HIT) cells revealed that the three resolvable complexes that bind to the Pal-1 and Pal-2 elements contain different ratios of three proteins of different size (approximately 90, 110 and 150 M(r)). Mutation of a single nucleotide binding site abrogates betaGK promoter activity. Multimerised repeats of the Pal-1 element augment transcription in HIT cells, but not in baby hamster kidney (BHK) cells. CONCLUSIONS/INTERPRETATION: These results suggest that different combinations of three proteins of different size bind to the Pal elements, probably as homodimers and heterodimers. Together, these results indicate that the betaGK promoter contains two novel 14-bp elements that, when multimerised, exhibit enhancer activity specific to neuroendocrine cells.

Animals↗
PubMed2001

Use of chelating resins and inductively coupled plasma mass spectrometry for simultaneous determination of trace and major elements in small volumes of saline water samples.

For some saline environments (e.g. deeply percolating groundwater, interstitial water in marine sediments, water sample collected after several steps of fractionation) the volume of water sample available is limited. A technique is presented which enables simultaneous determination of major and trace elements after preconcentration of only 60 mL sample on chelating resins. Chelex-100 and Chelamine were used for the preconcentration of trace elements (Cd, Cu, Pb, Zn, Sc) and rare earth elements (La, Ce, Nd, Yb) from saline water before their measurement by inductively coupled plasma mass spectrometry. Retention of the major elements (Na, Ca, Mg) by the Chelamine resin was lower than by Chelex; this enabled their direct measurement in the solution after passage through the resin column. For trace metal recoveries both resins yield the same mass balance. Only Chelex resin enabled the quantitative recovery of rare earth elements. The major elements, trace metals and rare earth elements cannot be measured after passage through one resin only. The protocol proposes the initial use of Chelamine for measurement of trace and major elements and then passage the same sample through the Chelex resin for determination of the rare earth elements. The detection limit ranged from 1 to 12 pg mL(-1). At concentrations of 1 ng mL(-1) of trace metals and REE spiked in coastal water the precision for 10 replicates was in the range of 0.3-3.4% (RSD). The accuracy of the method was demonstrated by analyzing two standard reference waters, SLRS-3 and CASS-3.

Buffers↗
PubMed2003

Pearl, a novel family of putative transposable elements in bivalve mollusks.

While genome sequencing projects have discovered numerous types of transposable elements in diverse eukaryotes, there are many taxa of ecological and evolutionary significance that have received little attention, such as the molluscan class Bivalvia. Examination of a 0.7-MB genomic sequence database from the cupped oyster Crassostrea virginica revealed the presence of a common interspersed element, CvA. CvA possesses subterminal inverted repeats, a tandemly repeated core element, a tetranucleotide microsatellite region, and the ability to form stable secondary structures. Three other less abundant repetitive elements with a similar structure but little sequence similarity were also found in C. virginica. Ana-1, a repetitive element with similar features, was discovered in the blood ark Anadara trapezia by probing a genomic library with a dimeric repeat element contained in intron 2 of a minor globin gene in that species. All of these elements are flanked by the dinucleotide AA, a putative target-site duplication. They exhibit structural similarity to the sea urchin Tsp family and Drosophila SGM insertion sequences; in addition, they possess regions of sequence similarity to satellite DNA from several bivalve species. We suggest that the Crassostrea repetitive elements and Ana-1 are members of a new MITE-like family of nonautonomous transposable elements, named pearl. Pearl is the first putative nonautonomous DNA transposon to be identified in the phylum Mollusca.

Animals↗
PubMed2005

Why are young and old repetitive elements distributed differently in the human genome?

Alu elements are not distributed homogeneously throughout the human genome: old elements are preferentially found in the GC-rich parts of the genome, while young Alus are more often found in the GC-poor parts of the genome. The process giving rise to this differential distribution remains poorly understood. Here we investigate whether this pattern could be due to a preferential degradation of Alu elements integrated in GC-poor regions by small indel mutations. We aligned 5.1 Mb of human and chimpanzee sequences and examined whether the rate of insertion and deletion inside Alu elements differed according to the base composition surrounding them. We found that Alu elements are not preferentially degraded in GC-poor regions by indel events. We also looked at whether very young L1 elements show the same change in distribution compared to older ones. This analysis indicated that L1 elements also show a shift in their distribution, although we could not assess it as precisely as for Alu elements. We propose that the differential distribution of Alu elements is likely to be due to a change in their pattern of insertion or their probability of fixation through evolutionary time.

Alu Elements↗
PubMed2001

The occurrence and distribution of selected trace elements in the Upper Rio Grande and tributaries in Colorado and northern New Mexico.

Two sampling trips were undertaken in 1994 to determine the distribution of trace elements in the Upper Rio Grande and several of its tributaries. Water discharges decreased in the main stem of the Rio Grande from June to September, whereas dissolved concentrations of trace elements generally increased. This is attributed to dilution of base flow from snowmelt runoff in the June samples. Of the three major mining districts (Creede, Summitville, and Red River) in the Upper Rio Grande drainage basin, only the Creede District appears to impact the Rio Grande in a significant manner, with both waters and sediments having elevated concentrations of some trace elements considerably downriver. For example, dissolved zinc concentrations upriver of Willow Creek, which primarily drains the Creede District, were about 2-3 microg/L; immediately downstream of the Willow Creek confluence, concentrations were above 20 microg/L; and elevated concentrations occurred in the Rio Grande for the next 100 km. The Red River District does not significantly impact the Upper Rio Grande for most trace elements. Because of current water management practices, it is difficult to assess the impact of the Summitville District on the Upper Rio Grande. There are, however, large increases in many dissolved trace element concentrations as the Rio Grande passes through the San Luis Valley, coincident with elevated concentrations of those same trace elements in tributaries. Among these elements are As, B, Cr, Li, Mn, Mo, Ni, Sr, U, and V. None of the trace elements exceeded U.S. EPA primary drinking water standards in either survey, with the exception of cadmium in Willow Creek. Secondary drinking water standards were frequently violated, especially in tributaries draining areas where mining has occurred. Dissolved zinc (in Willow Creek in both June and September) was the only element that exceeded the EPA Water Quality Criteria for aquatic life of 120 microg/L.

Animals↗
PubMed1997

Biogeographic analysis of the Uhu and LOA elements in the Hawaiian Drosophila.

Two transposable elements have been isolated from the Hawaiian Drosophila, the Uhu and LOA elements. The Uhu element has been shown to be present in a group of closely related species, the planitibia subgroup of the picture-winged Drosophila. This study examines the distribution of the Uhu element in several other subgroups of the picture-winged Drosophila, as well as the modified-mouthparts and antopocerus groups of the Hawaiian Drosophila. The LOA element has a much more limited distribution, having only been found in representatives of the planitibia and grimshawi subgroups of the picture-winged Drosophila. For both the Uhu and LOA elements there is an inverse correlation between the copy number of the element and the age of the island on which the species is endemic, i.e., species endemic to the Island of Hawaii, the youngest island, have the highest copy number, while species endemic to Kauai, the oldest island, have the lowest copy number of the element. The correlation suggests there is a relationship between speciation and the activity of transposable elements.

Animals↗
PubMed2002

A transcriptionally active maize MuDR-like transposable element in rice and its relatives.

Two Mu-like transposable elements were cloned from a rice genomic library using a partial cDNA clone that exhibits high homology to the mudrA gene of the maize element MuDR. Database searches led to the identification of six other sequences that carried highly homologous terminal inverted repeats (TIRs). All the rice elements possessed approximately 200-bp TIRs, and four were flanked by 9-bp target-site duplications (TSDs). The longer of the two cloned elements, OsMu4-2, could potentially encode a protein colinear with a MURA-like transposase, but it had stop codons in the coding region indicating that it is a pseudogene. All the other elements had large internal deletions. Direct dinucleotide repeats were found in two elements at positions flanking the deleted regions, suggesting that the deletions arose via the interrupted-gap-repair mechanism. Sequences related to empty sites of insertion were found in OsMu4-2 and one of the elements identified in the databases. These results provide evidence that the rice OsMu element was active and transposed in the past. Analysis of OsMu4-2 cDNAs revealed two types of transcripts produced by alternative splicing. Genomic Southern analysis suggested that OsMu4-2 was conserved in rice species with the A genome, but a deleted version was unique to japonica subspecies. Some wild rice species harbored paralogous copies of the OsMu element.

Amino Acid Sequence↗