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PubMed2006

Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes.

BACKGROUND: The human genome contains over one million Alu repeat elements whose distribution is not uniform. While metabolism-related genes were shown to be enriched with Alu, in structural genes Alu elements are under-represented. Such observations led researchers to suggest that Alu elements were involved in gene regulation and were selected to be present in some genes and absent from others. This hypothesis is gaining strength due to findings that indicate involvement of Alu elements in a variety of functions; for example, Alu sequences were found to contain several functional transcription factor (TF) binding sites (BSs). We performed a search for new putative BSs on Alu elements, using a database of Position Specific Score Matrices (PSSMs). We searched consensus Alu sequences as well as specific Alu elements that appear on the 5 Kbp regions upstream to the transcription start site (TSS) of about 14000 genes. RESULTS: We found that the upstream regions of the TSS are enriched with Alu elements, and the Alu consensus sequences contain dozens of putative BSs for TFs. Hence several TFs have Alu-associated BSs upstream of the TSS of many genes. For several TFs most of the putative BSs reside on Alu; a few of these were previously found and their association with Alu was also reported. In four cases the fact that the identified BSs resided on Alu went unnoticed, and we report this association for the first time. We found dozens of new putative BSs. Interestingly, many of the corresponding TFs are associated with early markers of development, even though the upstream regions of development-related genes are Alu-poor, compared with translational and protein biosynthesis related genes, which are Alu-rich. Finally, we found a correlation between the mouse B1 and human Alu densities within the corresponding upstream regions of orthologous genes. CONCLUSION: We propose that evolution used transposable elements to insert TF binding motifs into promoter regions. We observed enrichment of biosynthesis genes with Alu-associated BSs of developmental TFs. Since development and cell proliferation (of which biosynthesis is an essential component) were proposed to be opposing processes, these TFs possibly play inhibitory roles, suppressing proliferation during differentiation.

Alu Elements↗
PubMed2001

A HOX complex, a repressor element and a 50 bp sequence confer regional specificity to a DPP-responsive enhancer.

A central theme during development and homeostasis is the generation of cell type-specific responses to the action of a limited number of extant signaling cascades triggered by extracellular ligands. The molecular mechanisms by which information from such signals are integrated in responding cells in a cell-type specific manner remain poorly understood. We have undertaken a detailed characterization of an enhancer that is regulated by DPP signaling and by the homeotic protein Labial and its partners, Extradenticle and Homothorax. The expression driven by this enhancer (lab550) and numerous deletions and point mutants thereof was studied in wild-type and mutant Drosophila embryos as well as in cultured cells. We find that the lab550 enhancer is composed of two elements, a Homeotic Response Element (HOMRE) and a DPP Response Element (DPPRE) that synergize. None of these two elements can reproduce the expression of lab550, either with regard to expression level or with regard to spatial restriction. The isolated DPPRE of lab550 responds extremely weakly to DPP. Interestingly, we found that the inducibility of this DPPRE is weak because it is tuned down by the action of a repressor element. This repressor element and an additional 50 bp element appear to be crucial for the cooperation of the HOMRE and the DPPRE, and might tightly link the DPP response to the homeotic input. The cooperation between the different elements of the enhancer leads to the segmentally restricted activity of lab550 in the endoderm and provides a mechanism to create specific responses to DPP signaling with the help of a HOX protein complex.

Animals↗
PubMed2001

Age-related changes in the concentrations of major and trace elements in the brain of rats and mice.

Age-related changes in the concentrations of constituent elements in the brains of rats and mice 1 wk to 24 mo old were determined with inductively coupled plasma-mass spectrometry (ICP-MS) and inductively coupled plasma-atomic emission spectrometry (ICP-AES). Seventeen elements could be determined with reasonable accuracy and reproducibility. They were P, K, Na, Mg, Ca, Fe, Zn, Cu, Rb, Al, Mn, Sr, Mo, Co, Pb, Cs, and Cd in order of concentrations in the adult rat brains. In these elements, six major elements (P, K, Na, Fe, Mg, Ca) were determined with ICP-AES and the others with ICP-MS. The concentrations of each element and the pattern of age-related changes were similar between the rat and mouse brains. The elements of which concentrations decreased with aging were K and Rb. On the other hand, the concentrations of some metal elements, including Fe, Cu, Sr, and Co, appeared to increase with growth and aging. The concentrations of other elements were relatively constant throughout the age examined.

Aging↗
PubMed2000

Identification of organically associated trace elements in wood and coal by inductively coupled plasma mass spectrometry.

1-Methyl-2-pyrrolidinone (NMP) was used to extract samples of wood (forest residue) and coal; the extracts were analysed by inductively coupled plasma mass spectrometry (ICP-MS) using two different sample preparation methods, in order to identify trace elements associated with the organic part of the samples. A sample of fly ash was similarly extracted and analysed in order to assess the behaviour of the mineral matter contained within the wood and coal samples. 32% of the biomass was extracted at the higher temperature and 12% at room temperature while only 12% of the coal was extracted at the higher temperature and 3% at room temperature. Less than 2% of the ash dissolved at the higher temperature. Size exclusion chromatograms of the extracts indicated the presence of significant amounts of large molecular mass materials (>1000 mu) in the biomass and coal extracts but not in the ash extract. Trace element analyses were carried out using ICP-MS on the acid digests prepared by 'wet ashing' and microwave extraction. Sixteen elements (As, Ba, Be, Cd, Co, Cr, Cu, Ga, Mn, Mo, Ni, Pb, Sb, Se, V and Zn) were quantified, in the samples before extraction, in the extracts and in the residues. Concentrations of trace elements in the original biomass sample were lower than in the coal sample while the concentrations in the ash sample were the highest. The major trace elements in the NMP extracts were Ba, Cu, Mn and Zn from the forest residue; Ba, Cu, Mn, Pb and Zn from the coal; Cu and Zn from the ash. These elements are believed to be associated with the organic extracts from the forest residue and coal, and also from the ash. Be and Sb were not quantified in the extracts because they were present at too low concentrations; up to 40% of Mn was extracted from the biomass sample at 202 degrees C, while Se was totally extracted from the ash sample. For the forest residue, approximately 7% (at room temperature) and 45% (at 202 degrees C) of the total trace elements studied were in the extract; for the coal, approximately 8% (at room temperature) and 23% (at 202 degrees C) were in the extract. For the ash, only 1.4% of the trace elements were extracted at 202 degrees C, comprising 25% of Cd but less than 1% of Pb.

Biomass↗
PubMed2000

Determination of trace elements by inductively coupled plasma mass spectrometry of biomass and fuel oil reference materials using milligram sample sizes.

Most of the analytical techniques used to quantify elements associated with solid samples suffer from high detection limits and cannot be used for trace elements in biomass samples, particularly when only 20 mg are available for analysis. Inductively coupled plasma mass spectrometry (ICP-MS) can achieve detection limits of parts-per-trillion with liquid sample introduction by solution nebulisation. This technique was therefore tested with two standard biomass reference materials: oriental tobacco leaves and cabbage leaves. Two preparations successfully used on coal standards were used to digest the solid samples: a total digestion method (wet ashing digestion) and a partial leaching (microwave extraction). The concentrations of up to seventeen elements (As, Ba, Be, Cd, Co, Cr, Cu, Ga, Mn, Mo, Ni, Pb, Sb, Se, Sn, V and Zn) were measured after the two preparations. The accuracy and sensitivity of the measurements improved when the dilution factor decreased from 5000 to 1000 and to 500. Since the proportion of mineral matter in biomass samples is small (5%), the microwave digestion extracted elements that are generally not completely extracted from coal samples (e.g. Sb). However, some trace element concentrations were below the limit of quantification after microwave extraction, even with a reduced dilution factor (As, Se and Mo) and could not be quantified. A fuel oil was also digested. The trace element concentrations were very low (between 28 and 0.1 microgram g(-1)) but acceptable results were obtained by applying a dilution factor of 100. Only six elements in the fuel oil (As, Ba, Co, Ni, Se and V) had certified or indicated values. Factors affecting the accuracy and sensitivity of the analyses are discussed. The reproducibility of analysis of the tobacco leaf standard was checked over a period of nine months by both digestion methods. The wet ashing method gave acceptable reproducibility for Ba, Cd, Co, Cu, Ga, Mn, Mo, Ni, Pb, V and Zn but poor precision for Cr, Se and Sn and showed evidence of residual chloride interference for As. The microwave extraction gave good reproducibility for As, Ba, Cd, Co, Cr, Cu, Mo, Ni and Zn but poor precision for Se and low recoveries for Ga, Mn, Sn and V. In spite of the small quantities of material analysed, it proved possible to determine the trace elements at levels down to 0.1 microgram g(-1) in the reference materials.

Biomass↗
PubMed1979

[Interactions of toxic trace elements with special regard to selenium].

The significance of the trace elements in nutrition is often decisively affected by the interaction of trace elements with other trace elements and of trace elements with other substances. These processes, which include synergistic and antagonistic effects, are of great importance not only to the essentiality, but also to the toxicity of trace elements. There is considerable experience with interactions of essential elements. There is considerable experience with interactions of essential elements or of elements in essential concentrations. On contrast, there is a scarcity of information pertaining to toxic effects that are influenced by synergisms and antagonisms. This situation is illustrated by some examples and especially by the role of selenium. It is shown that these problems deserve closer attention.

Cations↗
PubMed1989

Identification of a fully-functional hobo transposable element and its use for germ-line transformation of Drosophila.

The transposable element hobo can be mobilized to induce a variety of genetic abnormalities within the germ-line of Drosophila melanogaster. Strains containing hobos have 3.0 kb elements and numerous smaller derivatives of the element. By analogy with other transposable element systems, it is likely that only the 3.0 kb elements are capable of inducing hobo mobilization. Here, we report that a cloned 3.0 kb hobo, called HFL1, is able to mediate germ-line transformation and therefore is an autonomous (fully-functional) transposable element. Germ-line transformation was observed when HFL1 and a marked hobo element were co-injected into recipient embryos devoid of endogenous hobos. Integration did not occur in the absence of the 3.0 kb element. A single copy of the marked hobo transposon inserted at each site, and the target sites were widely distributed throughout the genome. Integration occurred at (or very near) the termini of hobo, without internal rearrangement of the hobo or marker gene sequences. The hobo transformation system will allow us to determine the structural and regulatory features of hobo responsible for its mobilization and will provide novel approaches for the molecular and genetic manipulation of the Drosophila genome.

Animals↗
PubMed1989

The ocs-element is a component of the promoters of several T-DNA and plant viral genes.

The ocs-element is an enhancer element first identified in the promoter of the octopine synthase gene (OCS) where it occurs as a 16 bp palindromic sequence. The transcriptional enhancing activity of the ocs-element correlated with in vitro binding of a transcription factor. We have now identified ocs-elements in the promoter regions of six other T-DNA genes involved in opine synthesis and three plant viral promoters including the 35S promoter of cauliflower mosaic virus. These elements bind the ocs transcription factor in vitro and enhance transcription in plant cells. Comparison of the sequences of these 10 elements has defined a 20 bp consensus sequence, TGACG(T/C)AAG(C/G)(G/A)(A/C)T(G/T)ACG(T/C)(A/C)(A/C), which includes the 16 bp palindrome in its central region. We propose the name ocs-element for this class of promoter elements of similar sequence and function.

Base Sequence↗
PubMed2003

Toothbrushing causes elemental release from dental casting alloys over extended intervals.

The release of elements from dental alloys has been linked to alloy biocompatibility. Much of the research measuring elemental release has been done in vitro under passive conditions. The current study supplements a previous report that measured elemental release from dental alloys during and after the equivalent of 1 week of toothbrushing. In the current study, toothbrushing times were extended to the equivalent of 2 years, and elemental release was measured during and after brushing, with and without toothpaste. The results showed that for the major classes of dental alloys, brushing alone caused no significant elemental release during the brushing, and only minor increases after brushing. Brushing with toothpaste caused significant increases in elemental release for all elements of all alloys, but the largest increases were for the two nickel-based alloys. Nickel released during brushing with toothpaste reached 600-800 microg/cm(2) of alloy surface. Both beryllium-containing and non-beryllium-containing nickel-based alloys behaved similarly, refuting claims that non-beryllium alloys are superior in this regard. Thus, brushing with toothpaste under these extended in vitro conditions appears to increase the biological liabilities from elemental release for all alloys, but primarily for nickel-based alloys.

Alloys↗
PubMed1987

Identification of an enhancer-like element upstream from a cell cycle dependent human H4 histone gene.

We have identified a segment of DNA in the region 6,500 nucleotides upstream from a cell-cycle-dependent human H4 histone gene (pF0108A) which exhibits properties of an enhancer element. This distal element is not required for cap site initiation from the F0108A H4 histone gene. When the enhancer element is present in the genome as a stable integrated sequence, either in its natural upstream location or in a construct where the element is moved just upstream from the proximal promoter sequences, a 25-fold increase in the level of human H4 histone RNAs is observed. This increased level of mRNA reflects an increase in the rate of transcription. The enhancer effect is also observed when the distal element is inserted in inverse orientation with respect to this gene. In addition, the far upstream element can increase expression of a prokaryotic chloramphenicol acetyl transferase (CAT) gene under control of the simian virus 40 (SV40) early promotor, indicating that the ability to influence transcription is not confined to the gene with which it is normally associated. The ability of the histone gene distal enhancer element to function in both mouse and human cells indicates that transacting regulatory factors encoded by either the human or murine genome are capable of mediating the functional properties of this element, further supporting the cross-species compatibility of regulatory sequences and molecules that influence transcription of human histone genes.

Acetyltransferases↗
PubMed2007

Comparison of diverged Hoxc8 early enhancer activities reveals modification of regulatory interactions at conserved cis-acting elements.

The Hoxc8 early enhancer that controls the initiation and establishment of Hoxc8 expression in the developing mouse embryo is found in different vertebrate lineages including mammals, birds and fish. Mouse and Fugu Hoxc8 early enhancers (200 bp) have diverged in the composition of elements located towards the 3' region. However, they share cis-acting elements A-E located in the 5' region. Mutations at these elements in the context of the mouse Hoxc8 early enhancer affect reporter gene expression in the posterior neural tube, somites and lateral plate mesoderm of day 9.5 mouse embryos. Here, we demonstrate that mutations introduced at the same elements but in the context of the Fugu Hoxc8 early enhancer had different consequences on the reporter gene expression in transgenic mouse embryos. Furthermore, in contrast to the mouse enhancer the Fugu enhancer does not utilize elements D and E in achieving posterior neural tube and somite expression. These results suggest that the diverged sequences prevent regulatory interactions at conserved cis-acting elements. We propose that divergent sequences modify regulatory interactions at conserved elements by providing a "contextual change". Our finding that the enhancer elements do not act in a unitary fashion but function in the context of the surrounding sequence brings a new dimension to the study of cis-regulatory evolution.

Animals↗
PubMed2006

A measuring system for the fast simultaneous isotope ratio and elemental analysis of carbon, hydrogen, nitrogen and sulfur in food commodities and other biological material.

The isotope ratio of each of the light elements preserves individual information on the origin and history of organic natural compounds. Therefore, a multi-element isotope ratio analysis is the most efficient means for the origin and authenticity assignment of food, and also for the solution of various problems in ecology, archaeology and criminology. Due to the extraordinary relative abundances of the elements hydrogen, carbon, nitrogen and sulfur in some biological material and to the need for individual sample preparations for H and S, their isotope ratio determination currently requires at least three independent procedures and approximately 1 h of work. We present here a system for the integrated elemental and isotope ratio analysis of all four elements in one sample within 20 min. The system consists of an elemental analyser coupled to an isotope ratio mass spectrometer with an inlet system for four reference gases (N(2), CO(2), H(2) and SO(2)). The combustion gases are separated by reversible adsorption and determined by a thermoconductivity detector; H(2)O is reduced to H(2). The analyser is able to combust samples with up to 100 mg of organic material, sufficient to analyse samples with even unusual elemental ratios, in one run. A comparison of the isotope ratios of samples of water, fruit juices, cheese and ethanol from wine, analysed by the four-element analyser and by classical methods and systems, respectively, yielded excellent agreements. The sensitivity of the device for the isotope ratio measurement of C and N corresponds to that of other systems. It is less by a factor of four for H and by a factor of two for S, and the error ranges are identical to those of other systems.

Carbon↗
PubMed1995

A novel group of families of short interspersed repetitive elements (SINEs) in Xenopus: evidence of a specific target site for DNA-mediated transposition of inverted-repeat SINEs.

We have isolated from Xenopus borealis members of a family of short interspersed repetitive elements (SINEs) that we have termed Xbr. Xbr elements are also present in other Xenopus genomes and are typically framed by 46 bp terminal inverted repeats (TIRs). These TIRs and those of two previously described families of inverted-repeat SINEs from X. laevis begin with the sequence TTAAAGGRR. Knowledge of this consensus, termed the T2 motif, allowed us to define four previously uncharacterized families of inverted-repeat SINEs from Xenopus database sequences. We estimate that the group of seven SINE families that possess the T2 motif accounts for about 10% of all X. laevis SINEs. Novel evidence for the transposition of inverted-repeat SINEs is provided: (1) by examples of the presence/absence of T2 elements at corresponding locations in either duplicated genes or pseudotetraploid gene homeologues; and (2) by the existence of contiguous elements from different T2 families that are joined precisely by their TIRs. These examples provide novel evidence for a DNA-mediated mechanism of T2 element transposition. They also show that the tetranucleotide, TTAA, which flanks integrated elements on both sides and is present once at unoccupied sites, is the obligate target site for T2 insertion. The use of a specific sequence as a target site for SINE insertion is unexpected, although such specificity is exhibited by a limited number of larger transposable elements that encode their own transposase. The clear evidence for DNA-mediated transposition provided by T2 elements demonstrates that the evolution and maintenance of SINE families in vertebrate genomes results from two distinctive mechanisms.

Animals↗
PubMed1995

Identification in the human genome of mobile elements spread by DNA-mediated transposition.

We have identified in the human genome two families of mobile elements possessing the sequence characteristics of transposons that move directly from DNA to DNA rather than requiring the reverse transcription of an RNA intermediate. One type of element is closely related to the autonomous transposable element, mariner, and comprises a coding region for a transposase protein flanked by short terminal inverted repeat sequences (TIRs) of 31 or 32 bp. Elements of the second type form a family of short interspersed repetitive elements (SINEs) that are composed simply of two 37 bp TIRs surrounding six unique bps. The TIRs of the human mariner family are identical in all but one position to those of the SINE family, suggesting that the inverted-repeat SINEs represent non-autonomous transposable elements dependent on mariner-type transposase for mobility. Evidence for the mobility of both types of element is provided by examples of their integration into other repeat sequences and by the comparison of orthologous sites in cattle and human genomes. This evidence also shows that these elements have been active in DNA-mediated transposition at some point in the mammalian lineage. Therefore, it appears that the process of DNA-mediated transposition has occurred in mammalian cells and that its maximal cis-requirements are contained in the 80 bp consensus sequence of the human inverted-repeat SINE family.

Amino Acid Sequence↗
PubMed2000

Sequences flanking the cAMP responsive core of the HTLV-I tax response elements influence CREB protease sensitivity.

The human T cell leukemia virus type I (HTLV-I) Tax protein activates transcription from the viral long terminal repeat and select cellular promoters by interacting with cellular DNA-binding proteins. The HTLV-I promoter contains three copies of a Tax-responsive element (TRE-1), each of which possesses a core cAMP response element (CRE). The cAMP response element-binding protein, CREB, binds TRE-1 and mediates Tax association with, and transactivation of, the viral promoter. These activities depend on DNA sequences that flank the core CRE. Although CREs are found in a variety of cellular promoters, cellular CREs vary in sequence from TRE-1, especially in the flanking regions, and are generally not Tax responsive. The molecular basis for differential Tax responsiveness of viral and cellular CREs has not been determined. Here we demonstrate that the conformation of CREB is influenced by the nucleotide sequence of its DNA-binding element. CREB showed altered sensitivity to V8, chymotrypsin, and trypsin proteases when bound to the HTLV-I TRE-1 element as compared to the rat somatostatin CRE element. The phosphorylation state of CREB did not influence its protease sensitivity on either element. Sequences flanking the core CRE-binding site in each element were found to specify protease sensitivity. Since the TRE-1-flanking sequences also modulate Tax association with CREB, and Tax transactivation of CREB-dependent LTR transcription, these results suggest that CREB conformation may determine the ability of Tax to bind CREB.

Animals↗
PubMed1992

A non-LTR retrotransposon from the Hawaiian Drosophila: the LOA element.

An interspersed sequence has been isolated from the genome of D. silvestris, a species endemic to the Hawaiian Islands. The LOA element is 7.7 kb long and its 3' end consists of (TAA)n tandem repeats. Five different LOA elements were isolated, of which three were truncated at their 5' ends. Large deletions within the elements were frequent. A consensus sequence of the LOA element has been constructed using the nucleotide sequence of three elements. Two overlapping open reading frames (ORF) are present in the LOA element. In ORF1 two 'cys' motifs characteristic for gag proteins are found. The protein translated from ORF2 has similarities with retroviral pol genes. A protein databank search revealed 22% to 25% identity with the reverse transcriptase domains of retrotransposons. This region also shows the pattern of invariant amino acid residues which are most conserved in retroviral reverse transcriptases. In ORF2 an integrase specific 'cys' motif and a conserved sequence of retroviral proteases were identified. Structural similarities with LINE-like elements suggest that the LOA element represents a new non-LTR retrotransposon.

Amino Acid Sequence↗
PubMed1992

Evolution of the transposable element Uhu in five species of Hawaiian Drosophila.

The complete DNA sequence of three independent isolates of Uhu, a member of the Tc1-like class of transposable elements from D. heteroneura (Uhu-1, Uhu-3, and Uhu-4), has been determined. These isolates have between 95 and 96.4% nucleotide sequence identity indicating that Uhu is well conserved within this species. A comparison of the DNA sequences of Uhu and the D. melanogaster Hb1 transposable element shows that the nucleotide substitution rate for Uhu is comparable to the synonymous rate for the Adh gene in these species. Uhu has been identified in four other species of endemic Hawaiian Drosophila, D. silvestris, D. differens, D. planitibia and D. picticornis, and nine Uhu elements were isolated from genomic libraries of these four species. A 444 base pair region from within the coding region of the Uhu element, with well conserved ends, was amplified by the polymerase chain reaction and used for sequence comparison of elements from different species. The analysis of the sequence similarities between the elements within and between the species shows a grouping of the two pairs of most closely related species (D. heteroneura and D. silvestris, and D. differens and D. planitibia), but shows a much larger variation within the most recently diverged species (D. heteroneura and D. silvestris) than expected. There are extensive nucleotide substitutions and deletions in the Uhu elements from D. picticornis showing that they are degenerating and being lost in this species. These observations indicate that the Uhu element has been transmitted vertically and that transposition may have been activated at the time of formation of each species as it colonized the newly formed islands of the Hawaiian archipelago.

Amino Acid Sequence↗
PubMed1992

Evolution of the transposable element mariner in the Drosophila melanogaster species group.

The population biology and molecular evolution of the transposable element mariner has been studied in the eight species of the melanogaster subgroup of the Drosophila subgenus Sophophora. The element occurs in D. simulans, D. mauritiana, D. sechellia, D. teissieri, and D. yakuba, but is not found in D. melanogaster, D. erecta, or D. orena. Sequence comparisons suggest that the mariner element was present in the ancestor of the species subgroup and was lost in some of the lineages. Most species contain both active and inactive mariner elements. A deletion of most of the 3' end characterizes many elements in D. teissieri, but in other species the inactive elements differ from active ones only by simple nucleotide substitutions or small additions/deletions. Active mariner elements from all species are quite similar in nucleotide sequence, although there are some species-specific differences. Many, but not all, of the inactive elements are also quite closely related. The genome of D. mauritiana contains 20-30 copies of mariner, that of D. simulans 0-10, and that of D. sechellia only two copies (at fixed positions in the genome). The mariner situation in D. sechellia may reflect a reduced effective population size owing to the restricted geographical range of this species and its ecological specialization to the fruit of Morinda citrifolia.

Alleles↗