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PubMed1998

Transcription and splicing patterns of M- and O-type P elements in drosophila bifasciata, D. helvetica, and scaptomyza pallida

RT-PCR was applied to analyze the splicing patterns of P-element-derived mRNAs in Drosophila bifasciata, D. helvetica, and Scaptomyza pallida. D. melanogaster was used as a control. The experiments revealed that P elements are transcribed in all species investigated. However, there are differences in the splicing patterns of IVS3, which has to be removed in order to produce transposase mRNA instead of repressor mRNA. These differences are observed among species as well as between the P element subfamilies, the M and the O type, which coexist in the genomes of D. bifasciata and S. pallida. In D. helvetica M-type transposase mRNA was found in the germline and repressor mRNA in the soma, as has been previously described for the canonical (M-type-related) P element of D. melanogaster. In contrast, in S. pallida only repressor mRNA of M-type elements was detected in all tissues. In D. bifasciata, M-type IVS3, although activated both in the soma and the germline, is never completely excised. Instead, two alternative double-spliced variants occur in which two small introns are removed within the IVS3 region. One of these variants codes for a protein 12 aa longer than the regular transposase. Taking these findings together, transposase production and transpositional activity of M-type elements seem to be limited to D. helvetica and D. melanogaster, whereas M-type elements have become immobile in D. bifasciata and S. pallida. Unlike the M type, the splicing of O-type transcripts in D. bifasciata and S. pallida follows the classical rules of tissue-specific P element regulation: transposase mRNA is produced exclusively in the germline whereas repressor mRNA is formed in somatic cells. Thus O-type elements are thought to be still transpositionally active in both species. This finding is in accordance with the postulated recent transfer of O-type elements between the gene pools of D. bifasciata and S. pallida. In addition, we were able to show that the IVS3 double-spliced variants of both P element types are produced regularily in all species of the genus Drosophila investigated so far, but not in S. pallida.

Journal Article↗
PubMed2005

Strategies for the engineered phytoremediation of toxic element pollution: mercury and arsenic.

Plants have many natural properties that make them ideally suited to clean up polluted soil, water, and air, in a process called phytoremediation. We are in the early stages of testing genetic engineering-based phytoremediation strategies for elemental pollutants like mercury and arsenic using the model plant Arabidopsis. The long-term goal is to develop and test vigorous, field-adapted plant species that can prevent elemental pollutants from entering the food-chain by extracting them to aboveground tissues, where they can be managed. To achieve this goal for arsenic and mercury, and pave the way for the remediation of other challenging elemental pollutants like lead or radionucleides, research and development on native hyperaccumulators and engineered model plants needs to proceed in at least eight focus areas: (1) Plant tolerance to toxic elementals is essential if plant roots are to penetrate and extract pollutants efficiently from heterogeneous contaminated soils. Only the roots of mercury- and arsenic-tolerant plants efficiently contact substrates heavily contaminated with these elements. (2) Plants alter their rhizosphere by secreting various enzymes and small molecules, and by adjusting pH in order to enhance extraction of both essential nutrients and toxic elements. Acidification favors greater mobility and uptake of mercury and arsenic. (3) Short distance transport systems for nutrients in roots and root hairs requires numerous endogenous transporters. It is likely that root plasma membrane transporters for iron, copper, zinc, and phosphate take up ionic mercuric ions and arsenate. (4) The electrochemical state and chemical speciation of elemental pollutants can enhance their mobility from roots up to shoots. Initial data suggest that elemental and ionic mercury and the oxyanion arsenate will be the most mobile species of these two toxic elements. (5) The long-distance transport of nutrients requires efficient xylem loading in roots, movement through the xylem up to leaves, and efficient xylem unloading aboveground. These systems can be enhanced for the movement of arsenic and mercury. (6) Aboveground control over the electrochemical state and chemical speciation of elemental pollutants will maximize their storage in leaves, stems, and vascular tissues. Our research suggests ionic Hg(II) and arsenite will be the best chemical species to trap aboveground. (7) Chemical sinks can increase the storage capacity for essential nutrients like iron, zinc, copper, sulfate, and phosphate. Organic acids and thiol-rich chelators are among the important chemical sinks that could trap maximal levels of mercury and arsenic aboveground. (8) Physical sinks such as subcellular vacuoles, epidermal trichome cells, and dead vascular elements have shown the evolutionary capacity to store large quantities of a few toxic pollutants aboveground in various native hyperaccumulators. Specific plant transporters may already recognize gluthione conjugates of Hg(II) or arsenite and pump them into vacuole.

Arabidopsis↗
PubMed2005

Multi-elemental EDXRF mapping of polluted soil from former horticultural land.

The distribution of major and trace elements was systematically investigated by use of energy dispersive X-ray fluorescence spectrometry (EDXRF) on a former horticultural soil. The purpose of the study was to combine mapping of soil element concentration levels with multivariate statistics for characterisation of soil metal pollution in relation to previous and present land use. A 1-ha study site was chosen from a former horticulture where a previous preliminary survey indicated increased concentration levels of toxic elements. The soil was sampled from the top 20 cm of the soil surface in a 10 x 10-m grid-like pattern covering the 1-ha study area. In addition, three soil profiles were studied. The elemental composition of the soil samples was investigated by EDXRF while the composition of aqueous soil extracts was determined by total reflection X-ray fluorescence spectrometry (TXRF). Based on mapping and multivariate statistically analysis of the data obtained by EDXRF, most elements were found in almost constant concentration levels in the top soil throughout the investigated site. However, the contents of the toxic elements Zn, Cu, As, and Pb were found to vary significantly within the area. Hence, the samples with high accumulations of As also contained relatively high amounts of Zn, Cu, and Pb, which indicates that toxic-element-containing pesticides have been applied to the soil surface in the area of the former green houses at the study site. The Pb/As mass ratio in the soil indicates that PbHAsO3 was the preferential lead arsenate used for pest management at the investigated site, while Cu as Bordeaux liquid (CuSO4) and Zn were applied to minimize the leaf damaging effect from the former compounds. Calculations indicated that As annually was applied to the soil in the former greenhouses in doses up to 4 kg As/ha while Pb had been annually applied in doses up to 12 kg Pb/ha. The enrichment of Zn, Cu, As and Pb was greatest in the top 20 cm of the soil and no anthropogenic enrichment of these elements occurred below a depth of 50 cm, indicating that the toxic elements are rather immobile in this soil. The results of this investigation suggest that EDXRF used in combination with multivariate statistics is a strong tool for multi-element mapping of elemental contents, sources and mobility in the terrestrial environment.

Agriculture↗
PubMed2006

Discrete functional elements required for initiation activity of the Chinese hamster dihydrofolate reductase origin beta at ectopic chromosomal sites.

The Chinese hamster dihydrofolate reductase (DHFR) DNA replication initiation region, the 5.8 kb ori-beta, can function as a DNA replicator at random ectopic chromosomal sites in hamster cells. We report a detailed genetic analysis of the DiNucleotide Repeat (DNR) element, one of several sequence elements necessary for ectopic ori-beta activity. Deletions within ori-beta identified a 132 bp core region within the DNR element, consisting mainly of dinucleotide repeats, and a downstream region that are required for ori-beta initiation activity at non-specific ectopic sites in hamster cells. Replacement of the DNR element with Xenopus or mouse transcriptional elements from rDNA genes restored full levels of initiation activity, but replacement with a nucleosome positioning element or a viral intron sequence did not. The requirement for the DNR element and three other ori-beta sequence elements was conserved when ori-beta activity was tested at either random sites or at a single specific ectopic chromosomal site in human cells. These results confirm the importance of specific cis-acting elements in directing the initiation of DNA replication in mammalian cells, and provide new evidence that transcriptional elements can functionally substitute for one of these elements in ori-beta.

Animals↗
PubMed2002

Functional studies of potential intrastrand triplex elements in the Escherichia coli genome.

We previously used a pattern recognition program for nucleic acids to detect sequences with the potential to form intrastrand triplexes. Potential intrastrand triplex (PIT) element families were found in Escherichia coli, Synechocystis sp. and Haemophilus influenza. We were particularly intrigued with the family found in E. coli, which contained 25 dispersed copies of a particular PIT sequence corresponding to the purine triplex motif. E. coli PIT elements appear to occur exclusively in non-coding regions. We now report biochemical experiments testing the interaction of E. coli PIT elements with polymerases and single-stranded DNA-binding protein (SSB). The elements were also tested in genetic experiments as promoters, transcription terminators, or replication pause sites in E. coli. We show that PIT elements display provocative characteristics in certain biochemical assays. When appropriately oriented, the elements block elongation by Taq DNA polymerase at 72 degrees C, but not elongation by T7 DNA polymerase at 37 degrees C. The G-rich strand of the E. coli PIT sequence folds into a form with reduced affinity for SSB. On the other hand, in vivo studies did not detect replication delays for conjugal transfer of episomes containing PIT elements. These sequences were shown not to act as promoters, but the presence of PIT elements in RNA leaders upstream of a coding region could strongly influence expression of the downstream gene. These effects were shown to be post-transcriptional and were solely dependent on the Watson-Crick stem-loop structure within the PIT element. Thus, although PIT element DNA displays unusual biochemical properties, it remains unknown how these elements arose, and why they persist in the E. coli genome.

Base Sequence↗
PubMed1996

Upstream regulatory elements controlling expression of the Entamoeba histolytica lectin.

Entamoeba histolytica genomic organization and putative promoter elements appear to be distinct from both metazoan and better characterized protozoan organisms. The recent development of DNA-mediated transfection for E. histolytica enabled characterization of cis-acting promoter elements required for gene expression. A deletion and replacement analysis was conducted on the promoter of an E. histolytica gene encoding the heavy subunit of the N-acetyl-beta-D-galactosamine-specific adhesin (hgl5). Deletion of the DNA from -1000 bases to -272 bases upstream from the start of transcription of hgl5 did not decrease reporter gene expression. Subsequent nested deletions and 10-bp replacement mutagenesis identified four positive upstream regulatory elements between bases -219 to -200, -189 to -160, -69 to -60, and -49 to -40. A negative upstream regulatory element between bases -89 to -80 was conserved upstream of three other E. histolytica genes. Mutation of the previously unidentified 'GAAC' element conserved within the putative core promoter decreased reporter gene expression by 75%. Site directed mutagenesis of the putative TATA element decreased reporter gene expression by greater than 50%, while mutation of the putative initiator element resulted in a more modest decrease. This analysis suggests that E. histolytica promoters are unlike other protozoan promoters, with AT-rich upstream regulatory elements, a non-consensus TATA element, the "GAAC' element, and an unusual initiator element.

Animals↗
PubMed2003

Role of an AP-2-like element in transcriptional regulation of mouse mu-opioid receptor gene.

Previously, several important cis-elements and trans-factors have been shown to play a functional role in the proximal promoter of mouse mu-opioid receptor (MOR) gene. In this study, we defined another functional element located the in -450 to -400 bp (translational start site designated as +1) region of the proximal promoter, which is also essential for the full promoter activity. It is designated as the morAP-2-like element for its sequence homologous to the consensus AP-2 element. Surprisingly, electrophoretic mobility shift analysis (EMSA) revealed that Sp1 and Sp3, but not AP-2 proteins, were specifically bound to the morAP-2-like element. Mutation of the morAP-2-like element, resulting in a loss of Sp binding, led to an approximately 35% decrease in activity, further confirming the positive role of the morAP-2-like element in MOR gene expression. Dephosphorylation of Sp proteins with alkaline phosphatase also decreased Sp binding to the morAP-2-like element in EMSA, suggesting phosphorylation of Sp is essential for its binding to this element. However, direct or indirect activation of PKA, a classical G-protein coupled signaling pathway, resulted in no significant change of Sp binding to the morAP-2-like element, nor of the promoter activity the SH-SY5Y cells, MOR expressing cells, suggesting that phosphorylation of Sp does not involve PKA. These results suggest that the binding of different phosphorylated forms of Sp proteins to the morAP-2-like element may contribute to the fine tuning of MOR expression in different cells.

Animals↗
PubMed2000

Upstream regulatory elements in chick heme oxygenase-1 promoter: a study in primary cultures of chick embryo liver cells.

Previously, chick heme oxygenase-1 (cHO-1) gene was cloned by us and two regions important for induction by sodium arsenite were identified. These two regions were found to contain consensus sequences of an AP-1 (-1580 to -1573) and a MRE/cMyc complex (-52 to -41). In the current study, the roles of these two elements in mediating the sodium arsenite or cobalt chloride dependent induction of cHO-1 were investigated further. DNA binding studies and site-directed mutagenesis studies indicated that both the AP-1 and MRE/cMyc elements are important for the sodium arsenite induction, while cobalt chloride induction involves only the AP-1 element. Electrophoretic mobility shift assays showed that nuclear protein binding to the AP-1 element was increased by both sodium arsenite or cobalt chloride treatment, whereas the binding of proteins to the MRE/cMyc element showed a high basal expression in untreated cells and the binding activity was only slightly increased by sodium arsenite treatment. Site-directed mutagenesis studies showed that, to completely abolish sodium arsenite induction, both the AP-1 and MRE/cMyc elements must be mutated; mutation of either element alone resulted in only a partial effect. In contrast, a single mutation at AP-1 element was sufficient to reduce the cobalt chloride induction almost completely. The MRE/cMyc complex plays a major role in the basal level expression, and shares some similarities to the upstream stimulatory factor element (USF) identified in the promoter regions of mammalian HO-1 genes and other stress regulated genes. Because sodium arsenite is known to cause oxidative stress and because activation of AP-1 proteins has been shown to be a key step in the oxidative stress response pathway, we also explored the possibility that the induction of the cHO-1 gene by sodium arsenite is mediated through oxidative stress pathway(s) by activation of AP-1 proteins. We found that pretreatment with antioxidants (N-acetyl cysteine or quercetin) reduced the induction of the endogenous cHO-1 message or cHO-1 reporter construct activities induced by sodium arsenite or cobalt chloride. These antioxidants also reduced the protein binding activities to the AP-1 element in the electrophoretic mobility shift assays. In summary, induction of the cHO-1 gene by sodium arsenite or cobalt chloride is mediated by activation of the AP-1 element located at -1,573 to -1,580 of the 5'UTR.

Animals↗
PubMed2000

Chemical characterization of bohrium (element 107)

The arrangement of the chemical elements in the periodic table highlights resemblances in chemical properties, which reflect the elements' electronic structure. For the heaviest elements, however, deviations in the periodicity of chemical properties are expected: electrons in orbitals with a high probability density near the nucleus are accelerated by the large nuclear charges to relativistic velocities, which increase their binding energies and cause orbital contraction. This leads to more efficient screening of the nuclear charge and corresponding destabilization of the outer d and f orbitals: it is these changes that can give rise to unexpected chemical properties. The synthesis of increasingly heavy elements, now including that of elements 114, 116 and 118, allows the investigation of this effect, provided sufficiently long-lived isotopes for chemical characterization are available. In the case of elements 104 and 105, for example, relativistic effects interrupt characteristic trends in the chemical properties of the elements constituting the corresponding columns of the periodic table, whereas element 106 behaves in accordance with the expected periodicity. Here we report the chemical separation and characterization of six atoms of element 107 (bohrium, Bh), in the form of its oxychloride. We find that this compound is less volatile than the oxychlorides of the lighter elements of group VII, thus confirming relativistic calculations that predict the behaviour of bohrium, like that of element 106, to coincide with that expected on the basis of its position in the periodic table.

Journal Article↗
PubMed2006

Patterns of hobo elements and their effects in natural populations of Drosophila melanogaster in Japan.

We studied the dynamics of hobo elements of Drosophila melanogaster in Japan with the goal of better understanding the invasion and evolution of transposons in natural populations. One hundred and twenty-six isofemale lines and 11 older stocks were tested for the presence and genetic phenotype of hobo elements. The oldest H strain, containing complete and deleted hobo elements, is Hikone-H (1957), but Hikone-R (1952) has no hobo-homologous sequences. The findings suggest that the hobo element invaded Japanese populations in the mid-1950s, at about the same time as the P element invasion in Japan. This chronology is consistent with the hypothesis of a recent worldwide hobo element invasion into D. melanogaster in the mid-1950s. In recently collected populations, H degrees strains (low hobo activity and high repression potency) are predominant, whereas H+ strains (high hobo activity and high repression potency) are predominant in the Sakishima Islands, the most southwestern islands of the Japanese archipelago. H' strains (high hobo activity and low repression potency) were first found in limited island populations. Japanese populations have not only full-size hobo elements and 1.5 kb Th elements but also characteristic deletion derivatives (1.6 and 1.8 kb XhoI fragments) that we have named Jh elements. These results are consistent with transgenic experiments with complete hobo elements, in which populations evolved to H+ or H degrees via H', and in which 1.8 kb fragments appeared. We conclude that hobo elements invaded the central region of Japan, spread to the far islands, and that the invasion is currently at an intermediate, nonequilibrium stage.

Animals↗
PubMed1999

Initial versus subsequent release of elements from dental casting alloys.

The release of elements from dental casting alloys is directly related to adverse biological effects they may have. Longer-term (>1 month) studies of elemental release have suggested that release decreases significantly after a higher initial release of elements. The aim of the current study was to measure the release of elements from a variety of clinically relevant dental casting alloys and compare the release at weekly intervals through 4 weeks. The hypothesis was that the release during the initial week should be higher than in subsequent weeks, and that cytotoxicity should decrease as elemental release decreases. Alloy samples were exposed to cell-culture medium which was changed at weekly intervals and assessed for elemental release by means of atomic absorption spectrometry. The cytotoxicity of the medium was also measured. The results showed that for single phase alloys, initial release was often significantly higher in the first weeks than in subsequent weeks, but not for all elements in an alloy. Multiple phase alloys showed steady or increasing release relative to the first week. Cytotoxicity relationships were complex depending on which elements were released and the ratios of elements released. This study suggests that short-term tests (<1 week) may not be appropriate to evaluate longer-term elemental release or cytotoxicity because of changing rates of elemental release.

Animals↗
PubMed1993

Does the ocs-element occur as a functional component of the promoters of plant genes?

The structural requirements of the ocs-element, a promoter element in several genes transferred to the host plant nucleus by Agrobacterium tumefaciens and certain DNA viruses, have been further characterized both in vitro and in vivo. Two adjacent and functionally identical protein-binding sites separated by an exact number of nucleotides are required for in vivo activity of the ocs-element. Plant pathogens have presumably recruited cellular transcription factors that interact with these binding sites to drive the high-level expression of their essential genes. Our functional analyses of the ocs-elements from two pathogen promoters define the structure of a sequence motif that might also be expected to occur in plant nuclear genes, and a search of the plant gene database has identified a number of plant gene promoters that contain sequences that resemble the ocs-element. These sequences were analysed for their ability both to bind the maize nuclear protein OCSTF and to activate transcription of an inactive promoter. A functional ocs-element was identified in only one of the plant genes, the soybean heat-shock gene, Gmhsp26-A. The apparent rarity of the ocs-element in plant genes contrasts with its frequent use by pathogens that transform the plant nucleus. Sequences resembling half of an ocs-element, on the other hand, are common in plant promoters and may form part of multi-element control motifs with a variety of regulatory functions. Plant pathogens may, therefore, have evolved to circumvent tight regulatory control of their promoters by the host by duplicating the half ocs-element promoter motifs to take advantage of the ubiquitous ocs-element-binding transcription factors in plants.

Agrobacterium tumefaciens↗
PubMed1997

Regulatory elements in vivo in the promoter of the abscisic acid responsive gene rab17 from maize.

The rab17 gene from maize is transcribed in late embryonic development and is responsive to abscisic acid and water stress in embryo and vegetative tissues. In vivo footprinting and transient transformation of rab17 were performed in embryos and vegetative tissues to characterize the cis-elements involved in regulation of the gene. By in vivo footprinting, protein binding was observed to nine elements in the promoter, which correspond to five putative ABREs (abscisic acid responsive elements) and four other sequences. The footprints indicated that distinct proteins interact with these elements in the two developmental stages. In transient transformation, six of the elements were important for high level expression of the rab17 promoter in embryos, whereas only three elements were important in leaves. The cis-acting sequences can be divided in embryo-specific, ABA-specific and leaf-specific elements on the basis of protein binding and the ability to confer expression of rab17. We found one positive, new element, called GRA, with the sequence CACTGGCCGCCC. This element was important for transcription in leaves but not in embryos. Two other non-ABRE elements that stimulated transcription from the rab17 promoter resemble previously described abscisic acid and drought-inducible elements. There were differences in protein binding and function of the five ABREs in the rab17 promoter. The possible reasons for these differences are discussed. The in vivo data obtained suggest that an embryo-specific pathway regulates transcription of the rab genes during development, whereas another pathway is responsible for induction in response to ABA and drought in vegetative tissues.

Abscisic Acid↗
PubMed1997

Four P-like elements are required for optimal transcription of the mouse IL-4 gene: involvement of a distinct set of nuclear factor of activated T cells and activator protein-1 family proteins.

We previously identified the P sequence as a critical regulatory element of the human IL-4 promoter. In the mouse IL-4 promoter, there are five elements homologous to the human P sequence designated conserved lymphokine element 0 (CLE0), P, P2, P3 and P4. To characterize the role of these P-like elements and their binding factors in the native promoter, we did transient transfection and electrophoretic mobility shift assays (EMSA). Transfection of EL-4 cells with the IL-4 promoter-reporter constructs carrying mutated P-like elements showed that four P-like elements, CLE0, P, P2 and P4, but not P3, were required for optimal activation of the IL-4 promoter. EMSA showed that both constitutive and inducible complexes bound to CLE0, P, P2 and P4, whereas only a constitutive complex bound to P3. In competition and antibody supershift assays in EMSA, complexes formed with P or P2 proved to contain nuclear factor of activated T cells (NFAT) family proteins as major components. Activator protein (AP)-1 family proteins interacted with CLE0, P, P2 and P4. NFAT/AP-1 complex formed only with P and P2. Cross-competition assays among the P-like elements revealed element-specific and common complexes. Six tandem repeats of the P element linked to the SV40 promoter responded to phorbol 12-myristate 13-acetate, while that of other elements did not. It would thus appear that components of each P-like element-binding complexes are not identical and may coordinately contribute to transcriptional activity.

Animals↗
PubMed1992

A combination of upstream and proximal elements is required for efficient expression of the mouse renin promoter in cultured cells.

Renin, a key enzyme controlling blood pressure, is produced mainly in the kidney. To identify the transcriptional regulatory elements of the mouse Ren-1c gene, the promoter regions were fused to the CAT reporter gene and transfected into embryonic kidney-derived 293 cells and four extrarenal cell lines, HeLa, HepG2, HT1080 and NIH3T3 cells. Transient transfection assay showed that sequences from -365 to +16 of the renin gene could direct transcription of the CAT hybrid gene only in 293 cells. Deletion analysis identified two transcriptionally active regions; the renin upstream-promoter element (RU-1 element; position -224 to -138) and the renin proximal-promoter element (RP-2 element; position -75 to -47). Although the RU-1 element functioned as an activator, depending on its orientation, it failed to trans-activate the renin promoter when the RP-2 element was deleted. By contrast, the proximal element alone exhibited a weak trans-activator property. Gel shift assay identified RU-1 element-binding factors in both 293 and HeLa cells, whereas 293 cell-dominant factors were shown to bind only to RP-2 element. Therefore, both RU-1 and RP-2 elements were found to be necessary for efficient CAT expression from the renin promoter in 293 cells, suggesting that activation of the Ren-1c promoter requires combined action between cell type-dominant and ubiquitous nuclear factors.

Animals↗
PubMed2001

Mode of DNA-protein interaction between the C-terminal domain of Escherichia coli RNA polymerase alpha subunit and T7D promoter UP element.

The C-terminal domain (CTD) downstream from residue 235 of Escherichia coli RNA polymerase alpha subunit is involved in recognition of the promoter UP element. Here we have demonstrated, by DNase I and hydroxyl radical mapping, the presence of two UP element subsites on the promoter D of phage T7, each located half and one-and-a-half helix turns, respectively, upstream from the promoter -35 element. This non-typical UP element retained its alphaCTD-binding capability when transferred into the genetic environment of the rrnBP1 basic promoter, leading to transcription stimulation as high as the typical rrnBP1 UP element. Chemical protease FeBABE conjugated to alphaCTD S309C efficiently attacked the T7D UP element but not the rrnBP1 UP element. After alanine scanning, most of the amino acid residues that were involved in rrnBP1 interaction were also found to be involved in T7D UP element recognition, but alanine substitution at three residues had the opposite effect on the transcription activation between rrnBP1 and T7D promoters. Mutation E286A stimulated T7D transcription but inhibited rrnBP1 RNA synthesis, while L290A and K304A stimulated transcription from rrnBP1 but not the T7D promoter. Taken together, we conclude that although the overall sets of amino acid residues responsible for interaction with the two UP elements overlap, the mode of alphaCTD interaction with T7D UP element is different from that with rrnBP1 UP element, involving different residues on helices III and IV.

Amino Acids↗
PubMed1997

A single lineage of r2 retrotransposable elements is an active, evolutionarily stable component of the Drosophila rDNA locus.

R2 elements are non-long-terminal-repeat (non-LTR) retrotransposons that insert specifically in the 28S rRNA genes of many insects. Previous reports concerning this element in the genus Drosophila have suggested that R2 elements are absent from many species of this genus, particularly those species from the subgenus Drosophila. In this report, we present an extensive study of the distribution and evolution of R2 elements in Drosophila. A PCR survey of 59 species from 23 species groups of the two major Drosophila subgenera found that R2 elements are present in all but two species of the melanogaster species subgroup. Phylogenetic analysis based on partial nucleotide sequences of R2 elements from 23 species demonstrates that the relationships of R2 elements are congruent with those of the Drosophila species phylogeny, suggesting that these elements have been vertically inherited since the divergence of this genus some 60 MYA. Sequence variation between different copies of R2 elements within each species was less than 0.16%, indicating that these elements are undergoing concerted evolution similar to that of the 28S genes. Several properties of the R2 sequences suggest that these elements depend on retrotransposition in addition to simple recombination to remain within the rDNA locus: the rates of synonymous substitutions averaged 4.8 times the rate of replacement substitutions, 82 of 83 R2 copies partially sequenced contained intact open reading frames, and, finally, length variation associated with the poly(A) 3' tails indicated that many R2 copies are the direct result of retrotransposition.

Animals↗
PubMed2003

Diagnostic tissue elements in melanocytic skin tumors in automated image analysis.

In tissue counter analysis, digital images are divided into subregions (elements), and the digital information in each element is used for statistical analysis. In this study, we assessed the morphologic details of tissue elements that have turned out to be of diagnostic significance in the discrimination of benign common nevi and malignant melanoma. After creation of a data set based on a total of 12,000 cellular elements obtained from 100 benign common nevi and 100 malignant melanomas, classification and regression tree (CART) analysis was performed to differentiate between cellular elements of nevi and melanoma. In a second step, the slides were re-evaluated by the decision tree; cellular elements suggestive either for benign common nevi or for malignant melanoma were highlighted on zoomed images of the whole sections, and the individual elements were displayed in galleries. Eight groups of elements (so-called terminal nodes) seemed to indicate benign common nevi, whereas seven terminal nodes were suggestive for malignant melanoma. The elements of nodes suggestive for benign nevi largely contained nevus cells with amphiphilic cytoplasm intermingled with fibrillary material, whereas the elements of the nodes suggestive for malignant lesions often showed hyperchromatism, perinuclear halos, heavy pigmentation, or a lymphohistiocytic infiltrate. Tissue counter analysis automatically detects tissue elements that are in accordance with morphologic criteria used in conventional histopathology for diagnostic discrimination.

Biopsy↗