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At least 1,225 records · Page 68Linked to original sources
PubMed2001

Micron, a microsatellite-targeting transposable element in the rice genome.

We have isolated a new family of mobile elements, Micron, which occur within microsatellites dispersed throughout the rice (Oryza sativa) genome. The first of these segments, Micron 001, was found in a microsatellite consisting of a (TA)n sequence upstream of the rice phytochrome A (phyA) gene. PCR analysis of related rice species suggests that Micron 001 integrated into this microsatellite locus prior to the divergence of the two wild species O. rufipogon and O. barthii from a common ancestor. Micron elements are short (393-bp), possess subterminal inverted repeats and the single strands have the potential to form stable secondary structures via several internal repeats. Aside from the absence of terminal inverted repeats, these characteristics resemble those of MITEs (Miniature Inverted-Repeat Transposable Elements). We estimate that 100-200 copies of Micron-related sequences are present in the rice nuclear genome, while the chloroplast and mitochondrial genomes lack this sequence. Nineteen homologs of Micron 001 exhibited extremely high nucleotide sequence conservation (greater than 90%), suggesting a recent spread of Micron elements within the genus Oryza. Surprisingly, nucleotide sequence alignments showed that all of the Micron elements are flanked on both sides by microsatellite sequence consisting mainly of (TA)n. Twenty-three elements were mapped to seven separate chromosomes. Therefore Micron elements form a family of dispersed, highly conserved repeats. This is the first report of a transposable element that targets microsatellite loci.

Amino Acid Sequence↗
PubMed1986

Structural and functional studies of insertion element IS200.

The nucleotide sequence of the insertion element IS200 has been determined partially, including the junctions between the element and the host chromosome at the insertion site. At most, two bases (A-A) are found repeated at the junctions and could be duplications of host sequences generated by the insertion of the element. No obvious sequence repeats, either direct or inverted, have been detected between the sequences just within the two ends of the element. The element is an extremely strong block to host transcription across the insertion site. A sequence similar to known transcription termination signals was found just within the element near the right end. Removal of less than 50 base-pairs at the right end of the element abolishes the transcription block. The putative terminator sequence is located within this 50 base-pair region. Genetic studies suggest that the element contains a promoter located more than 93 base-pairs from its left end. The proposed promoter and terminator are in proper orientation to form an internal transcription unit.

Autoradiography↗
PubMed1980

A chemist's view of the analysis of human hair for trace elements.

With the comparatively recent development of analytical techniques of great power and sensitivity, the significance of the levels of trace elements in human hair has attracted the attention of many disciplines including the environmental sciences. This paper presents the view that an agreed basis for the chemical analysis of trace elements in hair has not been established by the many workers in the field; a chemical basis is proposed here. Levels of 37 trace elements found in human hair are tabulated. Endogenous and exogenous sources of such trace elements are described and discussed. An extended review of the many pre-analysis treatments of hair (for the removal of exogenous elements) is presented. Twenty-four representative treatments are tabulated. Some of these treatments clearly removed significant fractions of endogenous elements along with exogenous elements. It is clear that method of cleaning have frequently been chosen without knowing enough about the basic chemistry and behaviour of the hair shaft. The significance of the results obtained cannot therefore be reliably assessed. A collation of recent literature reports leads to the tentative conclusion that disulphide bonds in the cuticular proteins of hair are major sites both for the deposition of metals during formation of hair and for interaction with exogenous elements. The feasibility of a holistic, no-wash policy for hair analysis is outlined and supported.

Apocrine Glands↗
PubMed1980

DNA rearrangements associated with a transposable element in yeast.

The his4-912 mutation results from insertion of a 6200 bp transposable element into the his4 gene of yeast. In order to clone the his4-912 mutation, the plasmid pBR322 was integrated into the his4 gene by means of yeast transformation, and then the vector sequences and the his4-912 insertion element were excised as a single restriction fragment. This his 4-912 insertion element is homologous to Ty1, a family of repetitive yeast DNA sequences. His+ revertants derived from the his4-912 mutant carry a number of chromosomal aberrations including deletions, translocations, a transposition and an inversion. The majority of His+ revertants result from deletions which have both endpoints within the element and which leave behind only 300 bp of the insertion element. Other derivatives of the his4-912 mutant carry deletions which have one endpoint in the insertion element and one endpoint in the his4 coding sequence. In two His+ revertants carrying reciprocal translocations, the chromosome III translocation breakpoints occur within the his4-912 insertion element. A His+ revertant carrying an inversion of most of the left arm of chromosome III may be an intermediate in transposition of the his4-912 insertion element to a new site on chromosome III.

Base Sequence↗
PubMed1980

Terminal repeats of the Drosophila transposable element copia: nucleotide sequence and genomic organization.

We have determined the nucleotide sequence of the terminal regions of two members of the copia sequence family of D. melanogaster. The first 276 bp at one end of a copia element are repeated in direct orientation at its other end. The direct repeats on a single copia element are identical to each other, but they differ by two nucleotide substitutions between the two elements which were examined; this suggests that during transposition only one direct repeat of the parent element is used as a template for both direct repeats of the transposed element. Each direct repeat itself contain a 17 bp imperfectly matched inveted terminal repetition. The ends of copia show significant sequence homology both to the yeast Ty1 element and to the integrated provirus of avian spleen necrosis virus, two other eucaryotic elements known to insert at many different chromosomal locations. Analysis of the genomic organization of the direct repeat sequence demonstrates that it seldom, if ever, occurs unlinked to an entire copia element.

Animals↗
PubMed1982

FB elements are the common basis for the instability of the wDZL and wC Drosophila mutations.

The DNA insertions that cause the highly unstable mutations wC and wDZL share extensive homology with the FB family of transposable elements. FB elements carry long, internally repetitious, inverted terminal repeats and thus differ in structure from other transposable elements. Our results suggest that FB elements may excise and cause chromosomal rearrangements at unusually high frequencies. The wC insertion is a single FB element. The wDZL insertion differs in that it contains two FB elements, one at each terminus. The wC and wDZL insertions contain 4.0 and 6.5 kilobase nonhomologous segments between their terminal repeats. In contrast to the middle repetitive FB elements, the central segment of the wDZL insertion is single-copy and present at a fixed location in the wild-type genome. It has apparently been transposed by the action of flanking FB elements, causing the wDZL mutation at its new location.

Alleles↗
PubMed1984

Analysis of P transposable element functions in Drosophila.

We have made a P-element derivative called Pc[ry], which carries the selectable marker gene rosy, but which acts like a nondefective, intact P element. It transposes autonomously into the germline chromosomes of an M-strain Drosophila embryo and it mobilizes in trans the defective P elements of the singed-weak allele. Frameshift mutations introduced into any of the four major open reading frames of the P sequence were each sufficient to eliminate the transposase activity, but none affected signals required in cis for transposition of the element. Complementation tests between pairs of mutant elements suggest that a single polypeptide comprises the transposase. We have examined transcripts of P elements both from natural P strains and from lines containing only nondefective Pc[ry] elements, and have identified two RNA species that appear to be specific for autonomous elements.

Alleles↗
PubMed2006

Imaging and speciation of trace elements in biological environment.

Mineral elements, often at the trace level, play a considerable role in physiology and pathology of biological systems. Metallogenomics, metalloproteomics, and metallomics are among the emerging disciplines which are critically dependent on spatially resolved concentration maps of trace elements in a cell or tissue, on information on chemical speciation, and on that on metal-binding coordination sites. The mini-review discusses recent progress in analytical techniques for element profiling on the genome scale, biological trace element imaging, and probing, identification and quantification of chemical species in the biological environment. Imaging of the element distribution in cells and tissue sections is becoming possible with sub-micrometer spatial resolution and picogram-level sensitivity owing to advances in laser ablation MS, ion beam and synchrotron radiation X-ray fluorescence microprobes. Progress in nanoflow chromatography and capillary electrophoresis coupled with element specific ICP MS and molecule-specific electrospray MS/MS and MALDI enables speciation of elements in microsamples in a complex biological environment. Laser ablation ICP MS, micro-SXRF, and micro-PIXE allow mapping of trace element distribution in 1D and 2D proteomics gels. The increasing sensitivity of EXAFS and XANES owing to the use of more intense synchrotron beams and efficient focusing optics provide information about oxidation state, fingerprint speciation of metal sites and metal-site structures.

Environmental Pollution↗
PubMed2005

Two novel transposable elements in a cytochrome P450 gene govern anthocyanin biosynthesis of commercial petunias.

The gene Hf1 plays a key role in the expression of floral color in petunias. Hf1 encodes a flavonoid-3',5'-hydroxylase (F3'5'H). The recessive allele (hf1) in an inbred line of petunia is known to be generated by the insertion of a transposable element (Psl). We isolated a novel Mutator-like transposable element (named dTph9) from the hf1 allele of a commercial petunia with red flowers. Another novel transposable element (named rTph1) was found in hf1 of another red petunia. rTph1 shared features with the copia-like retrotransposable element family. These novel elements were inserted independently in the third exon of the Hf1 gene, at different positions. The hf1 allele harboring dTph9 or rTph1 cannot produce an active F3'5'H enzyme because there are stop codons in the dTph9 and rTph1 sequences. Southern analysis showed that these elements were present in relatively low copy numbers and that mutation of the Hf1 locus was associated with the transposition of both elements. We conclude that a loss-of-function mutation of the petunia Hf1 gene is caused by the insertion of at least two different transposable elements, other than Psl, within the Hf1 gene.

Alleles↗
PubMed2006

Prediction of strength and strain of the proximal femur by a CT-based finite element method.

Hip fractures are the most serious complication of osteoporosis and have been recognized as a major public health problem. In elderly persons, hip fractures occur as a result of increased fragility of the proximal femur due to osteoporosis. It is essential to precisely quantify the strength of the proximal femur in order to estimate the fracture risk and plan preventive interventions. CT-based finite element analysis could possibly achieve precise assessment of the strength of the proximal femur. The purpose of this study was to create a simulation model that could accurately predict the strength and surface strains of the proximal femur using a CT-based finite element method and to verify the accuracy of our model by load testing using fresh frozen cadaver specimens. Eleven right femora were collected. The axial CT scans of the proximal femora were obtained with a calibration phantom, from which the 3D finite element models were constructed. Materially nonlinear finite element analyses were performed. The yield and fracture loads were calculated, while the sites where elements failed and the distributions of the principal strains were determined. The strain gauges were attached to the proximal femoral surfaces. A quasi-static compression test of each femur was conducted. The yield loads, fracture loads and principal strains of the prediction significantly correlated with those measured (r=0.941, 0.979, 0.963). Finite element analysis showed that the solid elements and shell elements in undergoing compressive failure were at the same subcapital region as the experimental fracture site.

Adult↗
PubMed2006

Tetrahedral versus hexahedral finite elements in numerical modelling of the proximal femur.

The objective of this study was to evaluate and compare tetrahedral and hexahedral finite element meshes of simplified and realistic proximal intact femur geometries. Theoretical expressions of stresses and strains were derived for the simplified model of the femur. For the analysis of the realistic geometry of the proximal femur, a CAD model of the third generation composite femur (Pacific Research Labs, Vashion Island, WA) was used and simulations were performed with Hyperworks (Altair Engineering, Inc., Troy, MI) finite element analysis software. Convergence tests with hexahedral (8- and 20-node brick-elements) and tetrahedral (4- and 10-node tetrahedrons) elements were analysed by comparing the periosteal von Mises stresses and principal strains at a selected point of the femur. The numerical periosteal strains were also compared with experimental ones to determine the accuracy of the finite elements. Overall, we concluded, for the simplified femur, that tetrahedral linear element allowed results more closely to theoretical ones, but hexahedral quadratic elements seem to be more stable and less influenced to the degree of refinement (NDOF) of the mesh. It was not possible to correlate these findings with those observed for the realistic proximal femur simulations where no significant differences were seen using refined meshes, with more than NDOF=20,000 for hexahedral elements.

Algorithms↗
PubMed2004

Creation of cis-regulatory elements during sea urchin evolution by co-option and optimization of a repetitive sequence adjacent to the spec2a gene.

The creation, preservation, and degeneration of cis-regulatory elements controlling developmental gene expression are fundamental genome-level evolutionary processes about which little is known. Here, we identify critical differences in cis-regulatory elements controlling the expression of the sea urchin aboral ectoderm-specific spec genes. We found multiple copies of a repetitive sequence element termed RSR in genomes of species within the Strongylocentrotidae family, but RSRs were not detected in genomes of species outside Strongylocentrotidae. spec genes in Strongylocentrotus purpuratus are invariably associated with RSRs, and the spec2a RSR functioned as a transcriptional enhancer and displayed greater activity than did spec1 or spec2c RSRs. Single-base pair differences at two cis-regulatory elements within the spec2a RSR increased the binding affinities of four transcription factors, SpCCAAT-binding factor at one element and SpOtx, SpGoosecoid, and SpGATA-E at another. The cis-regulatory elements to which these four factors bound were recent evolutionary acquisitions that acted to either activate or repress transcription, depending on the cell type. These elements were found in the spec2a RSR ortholog in Strongylocentrotus pallidus but not in RSR orthologs of Strongylocentrotus droebachiensis or Hemicentrotus pulcherrimus. Our results indicated that a dynamic pattern of cis-regulatory element evolution exists for spec genes despite their conserved aboral ectoderm expression.

Animals↗
PubMed2005

Use of minigene systems to dissect alternative splicing elements.

Pre-mRNA splicing is an essential step for gene expression in higher eukaryotes. The splicing efficiency of individual exons is determined by multiple features involving gene architecture, a variety of cis-acting elements within the exons and flanking introns, and interactions with components of the basal splicing machinery (called the spliceosome) and auxiliary regulatory factors which transiently co-assemble with the spliceosome. Both alternative and constitutive exons are recognized by multiple weak protein:RNA interactions and different exons differ in the interactions which are determinative for exon usage. Alternative exons are often regulated according to cell-specific patterns and regulation is mediated by specific sets of cis-acting elements and trans-acting factors. Transient expression of minigenes is a commonly used in vivo assay to identify the intrinsic features of a gene that control exon usage, identify specific cis-acting elements that control usage of constitutive and alternative exons, identify cis-acting elements that control cell-specific usage of alternative exons, and once regulatory elements have been identified, to identify the trans-acting factors that bind to these elements and modulate splicing. This chapter describes approaches and strategies for using minigenes to define the cis-acting elements that determine splice site usage and to identify and characterize the trans-acting factors that bind to these elements and regulate alternative splicing.

Alleles↗
PubMed1998

A secondary ion mass spectroscopic study of the elemental composition pattern in rat incisor dental enamel during different stages of ameloblast differentiation.

In most earlier studies on the elemental composition pattern of dental enamel, a picture is presented which describes a limited region. In this study, estimates of the incorporation of some critical elements into enamel were correlated with the differentiation stages of the ameloblasts through out the whole tooth. Elemental analyses of rat incisor dental enamel during the secretory, transitional and maturation phases were performed using two different modes of secondary ion mass spectrometry (SIMS). The results were presented as ion images and three-dimensional spatial resolution graphs. In the elemental images of 23Na, 26CN, 35Cl and 39K, counts were detected during the secretory and maturation phases of amelogenesis. Variations were interpreted as resulting from secretion of elements during the secretory phase and resorption during the maturation phase. In line scans the ion yield from enamel during different stages of differentiation of the ameloblasts was analysed. The elements investigated were 12C, 19F, 23Na, 31P, 39K and 77CaCl. As seen in the images, most elements exhibited a higher ion yield during the earlier stages of secretion, and lower yields during the maturation-phase resorption. Cl, together with P, increased during the phases of maturation. In the most apical portions of the teeth, corresponding to a presecretory phase, an inverse pattern was seen for most of the elements. If the surface yield was high at the onset of the secretory phase, the presecretory yields were lower, and vice versa.

Amelogenesis↗
PubMed1985

Bound trace element content of bovine retinal disk membranes as determined by particle-induced x-ray emission.

Particle-induced x-ray emission (PIXE) was used to determine the trace element content of bovine retinal disk membranes. PIXE is a multielemental analytical technique capable of the simultaneous detection and quantization of all elements from sodium and above in atomic number. The multielemental capability of PIXE allows the analysis time per element to be very low if a number of elements are detected in each sample. In addition, the multielemental capability of PIXE can be used to determine elemental content with respect to an internal reference. Here the content of detected trace element per rhodopsin was determined without recourse to an external rhodopsin assay. This was accomplished by using the sulfur content of rhodopsin as an internal reference. Detected trace element contents per rhodopsin were 1.58 +/- 0.049 Ca, 0.081 +/- 0.024 Fe, 0.393 +/- 0.200 Cu, and 0.150 +/- 0.031 Zn. Upper limits were placed on the amount of manganese, molybdenum, and nickel per rhodopsin as 0.019, 0.019, and 0.006, respectively. Two proteins known to be present in disk membranes, retinol dehydrogenase and a large protein, approximately 238,000 mol wt, are considered as potential metallo-proteins. No correlation was observed between the content of any detected element and bleaching levels.

Animals↗
PubMed1998

Regulation of the fibronectin EDA exon alternative splicing. Cooperative role of the exonic enhancer element and the 5' splicing site.

Alternatively spliced exons generally contain weak splicing sites, and exonic and/or intronic regulatory elements recognised by trans-acting auxiliary splicing factors. The EDA exon of the fibronectin gene is a typical example of an exon bearing a purine-rich exon splicing enhancer (ESE) element recognised by members of the SR phosphoprotein family. The regulatory region that governs splicing in the human EDA exon also contains an exon splicing silencer (ESS) element. We have cloned the mouse EDA genomic region, and we show that the ESE and the ESS elements, although they have base differences, can be replaced by the human elements without significant change in the exon inclusion/exclusion ratio. This fact suggests a common splicing regulatory mechanism across species. We demonstrate in vivo the functional activity of the mouse ESE element in splicing. We also show that the trans-acting factors recognising this element cooperate with the 5' splicing site of the EDA exon to facilitate proper exon recognition. Indeed, a strong 5' splicing site overrides the ESE function in exon recognition. However, the presence of a strong 3' splicing site is not sufficient to compensate for the absence of the splicing enhancer. Our data provide in vivo evidence of the interplay between the exonic splicing regulatory elements and the splicing sites, leading finally to subtle regulation of alternative splicing.

3T3 Cells↗
PubMed1998

Absence of cyclic adenosine 3':5' monophosphate responsive element modulator expression at the spermatocyte arrest stage.

OBJECTIVE: To test the hypotheses that variations in the expression of adenosine 3':5' monophosphate (cAMP) responsive element modulator are found in human seminiferous epithelium in men with impaired testicular function and subsequent infertility and that variations in apoptosis frequency are associated with differential cAMP responsive element modulator expression in male infertility states. DESIGN: Standard immunohistochemical staining using a rabbit polyclonal antibody against the tau isoform of the cAMP responsive element modulator protein was performed on 5-microM sections of Bouin's fixed, paraffin-embedded testicular tissue obtained from azoospermic or severely oligozoospermic men for routine clinical purposes. Histologic diagnosis was confirmed with computerized image analysis of Feulgen-stained sections. SETTING: Tertiary male infertility referral center at a medical school. PATIENT(S): Forty-eight testis biopsies were performed in 38 azoospermic or severely oligozoospermic males. INTERVENTION(S): Rabbit polyclonal cAMP responsive element modulator tau antibody was applied to the paraffin-embedded testis sections. MAIN OUTCOME MEASURE(S): Testis immunoreactivity to polyclonal cAMP responsive element modulator tau antibody and apoptotic indices. RESULT(S): Although cAMP responsive element modulator immunoreactivity was present in the round spermatid stage of meiosis in testis biopsy specimens showing normal spermatogenesis, spermatid maturation arrest, and hypospermatogenesis, there was complete absence of expression in biopsy specimens from patients with Sertoli cell only and spermatocyte maturation arrest states. In addition, significantly increased apoptotic indices were observed in the spermatocyte maturation arrest state in comparison with normal spermatogenesis and Sertoli cell only pattern. CONCLUSION(S): These data suggest that cAMP responsive element modulator may be important for spermatid development and a stage-specific regulator of human spermatogenesis. Absence of cAMP responsive element modulator may be a cause of testicular failure in various types of male infertility.

Adult↗
PubMed2000

Determination of 14 elements in Taiwanese bones.

The objective of this study was to measure the concentration of 14 elements in human bone and investigate the affecting factors. This study aims to establish a database of elements in Taiwanese bone. Seventy-seven bone samples were taken from 70 subjects who were undertaking various bone surgeries from a medical center in central Taiwan. Bone samples were pretreated using microwave digestion and then, after determining the optimal conditions for analysis, fourteen elements were analyzed using Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES). Results showed that Ca had the highest concentration, followed by Mg and Zn. The lowest concentrations were of Mn, followed by Cd and Co. There was a positive correlation between the frequency of seafood intake and presence of all the 14 elements in human bone. There were several elements that had positive inter-correlation: As with Co; Al, Ag and Ca; Ni with Co, Mn and Al; Co with Al, Ag and Ca; Mn with Cr and Cu; Cr with Cu; Mg with Ca; Al with Ag and Ca; Ag with Ca; and also Zn with Mg. There were no significant differences found between concentrations of elements and etiology of bone disease and age. The authors suggest that further studies be conducted to establish a normal value of elements in human bone in Taiwan. This will greatly benefit the understanding of the relationship between disease pattern and elements in human bone.

Adult↗