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At least 73 records · Page 4Linked to original sources
PubMed2006

Sediment reference concentrations of seldom monitored trace elements (Ag, Be, In, Ga, Sb, Tl) in four Swedish boreal lakes--comparison with commonly monitored elements.

This paper presents reference and recent acid-leachable concentrations of some seldom monitored trace elements (SMTE; Ag, Be, Ga, In, Sb and Tl) in sediments from four boreal oligotrophic lakes in a south to north transect in Sweden. For comparison commonly monitored trace elements (As, Cd, Co, Cr, Cu, Ni, Pb and Zn) are included as well as those of relevance for redistribution processes (Al, Ca, Fe, Mg and Mn). Pore water pH and the corresponding solid/solution distribution coefficients (Kd) indicated that redistribution of the elements due to acidification is minor. The depth of impact was defined as the level in the sediment where the mean values became constant on successive exclusion of metal concentrations in overlying strata. Reference concentrations were calculated below the depth of impact. The present concentration changes are estimated by the ratio between the average concentration above the depth of impact and the reference concentration. Reference concentration ranges for the SMT-elements are (mg/kg, dry wt.): Ag 0.16-0.66; Be 1.6-3.7; Ga 2.0-5.1; In 0.05-0.22; Sb 0.05-0.11 and Tl 0.17-0.70. The concentration ratios for these elements ranged in the two most southern lakes from 1.5 to 4.5 and in the two northern ones from 0.6 to 1.6. A high correlation between Kd for the SMT-elements, and iron, except for Sb and Tl, infer that the biogeochemistry of iron is quantitatively important for the accumulation of these elements. The reference concentration ranges for the commonly monitored trace elements are (mg/kg, dry wt.): As 7.0-29.6; Cd 0.33-0.98; Co 5.7-23.8; Cr 15.2-26.1; Cu 27.6-58.4; Ni 5.4-20.8; Pb 44-96. The corresponding concentration ratios were 1.2-18 (second highest 3.9) in the two most southern lakes and 0.8-1.6 in the two northern ones. Declining ratios were found from south to north, most obvious for cobalt and zinc. The copper ratios did not show a regional pattern, partly because of the impact from old mine waste. Increased concentrations of Ag, Be, Ga, In, Sb and Tl in recent sediments up to 4.5 times the reference levels in combination with the geographical pattern infer an elevated loading of these elements.

Environmental Monitoring↗
PubMed1997

Interaction of CArG elements and a GC-rich repressor element in transcriptional regulation of the smooth muscle myosin heavy chain gene in vascular smooth muscle cells.

We have previously shown that maximal expression of the rat smooth muscle myosin heavy chain (SM-MHC) gene in cultured rat aortic smooth muscle cells (SMCs) required the presence of a highly conserved domain (nucleotides -1321 and -1095) that contained two positive-acting serum response factor (SRF) binding elements (CArG boxes 1 and 2) and a negative-acting GC-rich element that was recognized by Sp1 (Madsen, C. S., Hershey, J. C., Hautmann, M. B., White, S. L., and Owens, G. K. (1997) J. Biol. Chem. 272, 6332-6340). In this study, to better understand the functional role of these three cis elements, we created a series of SM-MHC reporter-gene constructs in which each element was mutated either alone or in combination with each other and tested them for activity in transient transfection assays using primary cultured rat aortic SMCs. Results demonstrated that the most proximal SRF binding element (CArG-box1) was active in the absence of CArG-box2, but only upon removal of the GC-rich repressor. In contrast, regardless of sequence context, CArG-box2 was active only when CArG-box1 was present. We further demonstrated using electrophoretic mobility shift assays that Sp1 binding to the GC-rich repressor element did not prevent SRF binding to the adjacent CArG-box2. Thus, unlike other proteins reported to inhibit SRF activity, the repressor activity associated with the GC-rich element does not appear to function through direct inhibition of SRF binding. As a first step toward understanding the importance of these elements in vivo, we performed in vivo footprinting on the intact rat aorta. We demonstrated that both CArG boxes and the GC-rich element were bound by protein within the animal. Additionally, using the rat carotid injury model we showed that Sp1 protein was significantly increased in SMCs located within the myointimal lesion, suggesting that increased expression of this putative repressor factor may contribute to the decreased SM MHC expression within SMCs found in myointimal lesions.

Animals↗
PubMed1997

A competitive mechanism of CArG element regulation by YY1 and SRF: implications for assessment of Phox1/MHox transcription factor interactions at CArG elements.

In the promoters of many immediate early genes, including c-fos, CArG DNA regulatory elements mediate basal constituitive expression and rapid and transient serum induction. CArG boxes also occur in the promoters of muscle-specific genes, including skeletal alpha-actin, where it confers muscle-specific expression. These elements are regulated, at least in part, by the ubiquitous transcription factors serum response factor (SRF) and YY1. The homeobox transcription factor Phox1/MHox has also been implicated in regulation of the c-fos CArG element and is thought to function by facilitating SRF binding to DNA. Here, we provide in vitro and in vivo evidence that the mechanism of YY1 repression of CArG elements results from competition with SRF for overlapping binding sites. We describe in detail the binding sites of YY1 and SRF through serial point mutations of the skeletal alpha-actin proximal CArG element and identify a mutation that dramatically reduces YY1 binding but retains normal SRF binding. YY1 competes with SRF for binding to wild-type CArG elements, but not to this point mutant in vitro. This mutant is sufficient for muscle-specific expression in vivo but is much less sensitive to repression by YY1 overexpression. We utilized the YY1/SRF competition to address the role of Phox1 at these elements. Phox1 overexpression did not diminish YY1-mediated repression, suggesting that transcriptional activation by Phox1 does not result from enhanced SRF binding to these elements. These methods may prove to be useful for assessing interactions between other CArG element regulatory factors.

Actins↗
PubMed1996

Auxin-sensitive elements from promoters of tobacco GST genes and a consensus as-1-like element differ only in relative strength.

We have investigated the cis-acting potential of several as elements (20-bp as-1/ocs-like sequences) in both yeast and plant cells. These TGACG[N7]TGACG-resembling elements were surprisingly similar with respect to their ability to confer inducibility by auxins and related compounds to a heterologous TATA box in stably transformed plant cells. Both in plant cells and in yeast it was found that differences between as elements were of a quantitative nature. A strong element based on the consensus sequence for as elements conferred the highest level of gene expression. The rather aberrant as elements present in the promoters of auxin-inducible gst genes Nt103 and Nt114 of tobacco were much weaker cis-acting elements. The ability of an element to drive reporter gene expression was found to correlate with the extent to which proteins present in (nuclear) extracts of yeast and plant cells bound to it. The cloned transcription factor TGA1a was shown to be a very good candidate to be the factor that mediates the in vivo regulation of gene expression via as elements. The physiological significance of gene activation by active and inactive auxins is discussed.

2,4-Dichlorophenoxyacetic Acid↗
PubMed1998

Tca1, the retrotransposon-like element of Candida albicans, is a degenerate and inactive element.

Candida albicans is an asexual fungus and as such must rely on mechanisms other than sexual recombination to generate genetic diversity. Retrotransposons are ubiquitous genetic elements known to generate multiple types of genomic alterations. We have further investigated the nature of the retrotransposon-like element Tca1 in C. albicans. Tca1 is present at two loci in strain SC5314. Both loci have now been cloned, and one element was sequenced in its entirety. This element was flanked by alpha elements, or long terminal repeats (LTRs), and contained an intervening region of 5,614 bp. The intervening region was highly degenerate and contained no extended open reading frames, indicating that Tca1 is not a functional element. Partial sequence determination demonstrated that the elements from the two loci were nearly identical. Genetic manipulation of the elements showed that both loci were heterozygous for Tca1, that both were transcriptionally active, and that deletion of both had no effect on growth rate or germ tube formation. Thus, it is unclear why this nonfunctional, highly degenerate element has been maintained in many clinical isolates.

Base Sequence↗
PubMed2001

The X element, a novel LINE transposable element from Drosophila melanogaster.

Whilst analysing the nature of repeated DNA sequences in the transition zone between euchromatin and heterochromatin at the base of the X chromosome of Drosophila melanogaster, we discovered a novel transposable element of the LINE class that we have named the X element. Several apparently complete elements have been cloned and analysed, and one has been sequenced. It is 4740 bp long, with a polyadenylation sequence and a run of A residues at one end. It contains two ORFs: the 5' ORF is related to the retroviral gag gene and encodes a protein with cysteine-rich motifs that are thought to form a "zinc-knuckle" in a nucleic-acid binding protein; the 3' ORF encodes a putative reverse transcriptase that includes the conserved domains found in reverse transcriptases from other LINEs and retroviruses. The DNA sequence and the sequences of the predicted gene products are most similar to other LINEs from D. melanogaster, such as the F, jockey, Doc and BS elements. Southern analysis suggests that there are at least 30 copies in the genome and that some elements are polymorphic between different strains. Analysis of the DNA sequence of the euchromatic arms of the Drosophila genome identified five full-length elements and a similar number of elements that were intact at the 3' end but had variable 5' truncations. Sequences flanking two different insertion sites were used to design PCR primers to assess the occupancy of sites in wild-type flies of different geographical origins. Flies that lacked each of the insertions were found, suggesting that the element is an active transposon.

Animals↗
PubMed1989

Drosophila P element transposase recognizes internal P element DNA sequences.

Drosophila P transposable elements encode an 87 kd trans-acting protein, transposase, that is required to catalyze P element transposition and excision. We show here that purified transposase is a site-specific DNA binding protein. P element transposase does not interact with the terminal 31 bp inverted repeats but instead interacts specifically with an internal 10 bp consensus sequence present at both the 5' and 3' ends of P element DNA. These binding sites lie within sequences known to be important for transposition in vivo. Transposase also displays an unusually high nonspecific affinity for DNA. The transposase binding site at the 5' and overlaps sequences we show to be essential for transcription from the P element promoter in vitro, which raises the possibility that either transposase or the related 66 kd P element protein may affect P element transcription. From these and other observations, we suggest that the P element transposition reaction probably requires the binding of additional Drosophila protein factors to the terminal DNA sequences.

Animals↗
PubMed2006

Detection of a mariner-like element and a miniature inverted-repeat transposable element (MITE) associated with the heterochromatin from ants of the genus Messor and their possible involvement for satellite DNA evolution.

The satellite DNA of ants Messor bouvieri, M. barbarus and M. structor, studied in a previous paper, is organized as tandemly repeated 79-bp monomers in the three species showing high sequence similarity. In the present paper, a mariner-like element (Mboumar) and a new MITE (miniature inverted-repeat transposable element) called IRE-130, inserted into satellite DNA from M. bouvieri, are analyzed. The study of Mboumar element, of its transcription and the putative transposase that it would encode, suggests that it could be an active element. Mboumar elements inserted into IRE-130 elements have also been detected. It is the first time, to our knowledge, that a MITE has been described in Hymenoptera and it is also the first time that a mariner-like element inserted into a MITE has been detected. A mariner-like element, inserted into satellite DNA from M. structor and in M. barbarus, also has been found. The results seem to indicate that transposition events have participated in the satellite DNA mobilization and evolution.

Amino Acid Sequence↗
PubMed2004

Repetitive elements in the major histocompatibility complex (MHC) class I region of a teleost, medaka: identification of novel transposable elements.

The repetitive elements of medaka (Oryzias latipes) are poorly characterized in spite of recent rapid progress in the medaka genome analysis. Here we report the characterization of the repetitive elements in the major histocompatibility complex (MHC) class I region, which spans about 400 kb and is one of the best characterized regions of the medaka genome. Microsatellite, low complexity regions, transposable elements, and other repeats occupied 0.68, 0.98, 7.0 and 2.9%, respectively, of the MHC class I region. Eleven transposable elements, three LTR-type, six LINE-type and two DNA-type, including several novel ones, were identified. Genomic Southern hybridization analysis indicated that these LINE-type and DNA-type elements have many copies in the medaka genome, whereas the LTR-type elements have only several copies. The comparison of the medaka MHC class I region with those of zebrafish and fugu shows the presence of three medaka lineage-specific tandem duplications of the PSMB (proteasome beta-type subunit) 8 and class Ia genes. Since eight of the 11 transposable elements were located in this region, these elements may have played a role in the medaka-specific DNA rearrangement.

Animals↗
PubMedDate not supplied

Apparent absence of transposable elements related to the P elements of D. melanogaster in other species of Drosophila.

P elements are transposable elements found in P strain, but usually not in M strain, Drosophila melanogaster, and are responsible for the hybrid dysgenesis that occurs when male D. melanogaster of the P strain mate with females of the M strain (ref. 1 and references therein). Several P elements, which vary in length and genetic effects, have now been cloned. To investigate the evolutionary origin of P elements, we have used a cloned copy of a D. melanogaster P element to look for related sequences in the genomes of six other Drosophila species. We report here that, unlike many other transposable elements found in D. melanogaster, which seem also to be present in other Drosophila species, we have found no sequences closely enough related to P elements to be detected by DNA hybridization in any other Drosophila species. This result supports the hypothesis that P elements have recently invaded D. melanogaster by horizontal transmission.

Animals↗
PubMed1996

Genetic evidence for repression of somatic P element movements in Drosophila melanogaster consistent with a role for the KP element.

The P family of transposable elements in Drosophila melanogaster has, since its introduction into D. melanogaster populations in this century, diversified into a number of internally deleted forms. One of these, the KP element, is abundant in the genomes of flies from populations from Asia, Europe and Africa. There is some evidence that this sequence can act as a repressor of transposition. We have studied a mutation, signed(very weak) (snVW), in which a KP element is one of two P elements inserted into the 5' exon of the X-linked singed gene. These elements can be mobilized by a trans-acting dominant mutation, Mo, with a maternal effect, on the second chromosome. The rate of somatic reversion of snvw induced by Mo is reduced threefold if the mother herself possesses snvw on her X chromosomes. This implies that snvw may be responsible for a form of repression of P element movement. The cause of this effect may be related to transcription of the KP element in snvw. However, an effect of other genomic P elements in the repression of somatic reversion of snvw cannot be entirely excluded.

Animals↗
PubMed1991

Capture of flanking DNA by a P element in Drosophila melanogaster: creation of a transposable element.

A 6.1-kilobase insertion into the rudimentary (r) gene was cloned and partially sequenced. The insertion consists of a 703-base-pair (bp) P element next to a 5.4-kilobase single-copy sequence. The normal position of the single-copy sequence is near the tip of the X chromosome. Upon insertion into the r gene, this chimeric element generated an 8-bp target-site duplication, characteristic of P elements. At the non-P-element end of the insertion, the first 8 bp are identical to the first 8 bp of the inverted terminal repeats of the P element. Thus, this element has inverted terminal repeats of 8 bp. This large element can excise from the r gene under conditions of hybrid dysgenesis, which indicates that it behaves like a normal P element. These data support the conclusion that a normally stable single-copy sequence has now become unstable and duplicated within the genome.

Animals↗
PubMed1994

Local transposition of P elements in Drosophila melanogaster and recombination between duplicated elements using a site-specific recombinase.

The transposase source delta 2-3(99B) was used to mobilize a P element located at sites on chromosomes X, 2 and 3. The transposition event most frequently recovered was a chromosome with two copies of the P element at or near the original site of insertion. These were easily recognized because the P element carried a hypomorphic white gene with a dosage dependent phenotype; flies with two copies of the gene have darker eyes than flies with one copy. The P element also carried direct repeats of the recombination target (FRT) for the FLP site-specific recombinase. The synthesis of FLP in these flies caused excision of the FRT-flanked white gene. Because the two white copies excised independently, patches of eye tissue with different levels of pigmentation were produced. Thus, the presence of two copies of the FRT-flanked white gene could be verified. When the P elements lay in the same orientation, FLP-mediated recombination between the FRTs on separated elements produced deficiencies and duplications of the flanked region. When P elements were inverted, the predominant consequence of FLP-catalyzed recombination between the inverted elements was the formation of dicentric chromosomes and acentric fragments as a result of unequal sister chromatid exchange.

Animals↗
PubMed1996

P-element-induced recombination in Drosophila melanogaster: hybrid element insertion.

It has previously been shown that the combination of two deleted P elements in trans, one containing the left functional end and the second element the right functional end, can lead to high levels of male recombination. This finding strongly suggests that P-element ends from different chromosomes can become associated, followed by "pseudo-excision". We show that two different processes are involved in resolving the pseudo-excision event: (1) the excised P-element ends continue to function as a single unit (Hybrid Element) and insert at a nearby site in the chromosome or into the element itself [Hybrid Element Insertion (HEI)] and (2) free ends that do not contain P elements repair and rejoin [(Hybrid Excision and Repair (HER)]. Both types of resolution can lead to recombination, and this paper concentrates on the HEI class. One type of HEI event predicts the exact reverse complementary duplication of an 8-bp target site, and we have confirmed the existence of such a structure in six independently derived recombinant chromosomes. There is also a high tendency for insertion events to occur within a few bases of the original 8-bp target site, including six apparent cases of insertion into the exact site.

Animals↗
PubMed1998

Repression of hybrid dysgenesis in Drosophila melanogaster by combinations of telomeric P-element reporters and naturally occurring P elements.

In Drosophila melanogaster, hybrid dysgenesis occurs in the germline of flies produced by crosses between females lacking P elements and males carrying 25-55 P elements. We have previously shown that a complete maternally inherited repression of P transposition in the germline (P cytotype) can be elicited by only two autonomous P elements located at the X chromosome telomere (cytological site 1A). We have tested whether P transgenes at 1A, unable to code for a P-repressor, may contribute to the repression of P elements. Females carrying a P-lacZ transgene at 1A ["P-lacZ(1A)"], crossed with P males, do not repress dysgenic sterility in their progeny. However, these P-lacZ(1A) insertions, maternally or paternally inherited, contribute to P-element repression when they are combined with other regulatory P elements. This combination effect is not seen when the P-lacZ transgene is located in pericentromeric heterochromatin or in euchromatin; however a P-w,ry transgene located at the 3R chromosome telomere exhibits the combination effect. The combination effect with the P-lacZ(1A) transgene is impaired by a mutant Su(var)205 allele known to impair the repression ability of the autonomous P elements at 1A. We hypothesized that the combination effect is due to modification of the chromatin structure or nuclear location of genomic P elements.

Animals↗
PubMed1991

Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains.

Most strains of the Mycobacterium tuberculosis complex carry multiple copies of an IS3-like element, and these strains are highly polymorphic with regard to the site of integration in the chromosome. In contrast, Mycobacterium bovis BCG contains a single copy of the insertion element, and in all strains this copy is integrated at the same site in the chromosome. In this study, we determined the sequence of the single-copy insertion element from M. bovis BCG, IS987, and its flanking regions. The analysis of IS987 revealed that this element was virtually identical to the sequence of IS986 from M. tuberculosis. IS987 is located in a region containing direct repeats (DRs). The cloned flanking regions contained 20 virtually identical DRs of 36 bp, each separated by 35 to 41 bp of spacer DNA. Analysis of chromosomal DNA by the polymerase chain reaction revealed the presence of a cluster of 49 DRs, and IS987 is inserted in the 30th DR. Furthermore, the DR sequences were found to occur only in species of the M. tuberculosis complex and not in nine other mycobacterial species tested. Analysis of 14 M. tuberculosis strains revealed the presence of one insertion sequence element in the DR-containing region of eight strains, two insertion sequence elements were located in the DR region of five strains, and one strain did not contain an insertion sequence element in this region. Additionally, the DR-containing regions of these 14 M. tuberculosis strains were polymorphic in length and composition. We conclude that the DR cluster is a specific, hot-spot region for integration of insertion elements in the chromosome of M. tuberculosis complex strains.

Amino Acid Sequence↗
PubMed1997

Bone mineral density and survival of elements and element portions in the bones of the Crow Creek massacre victims.

The interpretation of archaeologically-derived skeletal series is dependent on the elements and portions of elements preserved for examination. Bone and bone portion survival is affected by factors, both intrinsic and extrinsic to the elements themselves, that influence deterioration and preservation. Among the intrinsic variables, the density of the element and element portion are particularly important with respect to the degree of preservation. Recently reported bone mineral density values from a contemporary human sample are compared to the survival of prehistoric limb bones of the Crow Creek specimens, a fourteenth-century massacre skeletal series. The contemporary density values are positively correlated with Crow Creek element and element portion survival. Two calculations of bone mineral density, however, are more closely related to preservation than a third. Such density information has implications for assessing minimum number of elements and individuals and documenting taphonomic processes.

Adolescent↗
PubMed2005

A rapid decrease in number of the complete ninja element and concomitant increase of the defective element in a strain of Drosophila simulans.

The ninja element, originally isolated from an unstable white mutant strain white-milky (w(mky)) of Drosophila simulans, is a member of the retrotransposon family with long terminal repeats (LTRs). We show that ninja is present in high copy numbers in the w(mky)-derivative sublines white-chocolate (w(cho)) and white-persimmonl (w(psm1)), in a low copy number in another derivative subline white-milky 3 (w(mky3)), and in only a few copies in a wild type strain. We have cloned the ninja elements from these sublines and examined their structures. Most of the elements cloned (38 out of 41 independent clones) from w(cho) were full length. In contrast, only 9 of 23 independent clones from w(mky3) were full length. We hypothesize that ninja elements were integrated and lost frequently in the w(mky) strain and its derivative genomes, and that a rapid decrease in numbers of the ninja element was caused not by an increased rate of loss but by a reduction of integration of full length ninja elements in w(mky3). Each defective element had a unique deletion and/or an insertion except for the three from w(mky3), which had exactly the same 81-bp deletion in each of the 5' and 3' LTRs. The 5' and 3' ends of the deletion appeared to represent sequences similar to those of Drosophila consensussplicing sites. Ectopic splicing may have produced these defective ninja elements.

Animals↗