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At least 145 records · Page 8Linked to original sources
PubMed2000

Isolation of a new insertion element of Yersinia intermedia closely related to remnants of mobile genetic elements present on Yersinia plasmids harboring the Yop virulon.

A new insertion element present in two alleles, designated IS1635.1 and IS1635.2, was identified on a plasmid of a Yersinia intermedia strain by hybridization with the Yersinia enterocolitica pYV virulence plasmid. IS1635.1 and IS1635.2 are 861 bp long, carry imperfect inverted terminal repeats and possess a single open reading frame encoding a putative transposase of the IS6 family. A truncated IS1635 element is present immediately downstream of element IS1635.2. The capacity of the IS1635 elements to mediate transposition in Yersinia was demonstrated with a R6K-derived suicide vector, where a kanamycin resistance gene had been inserted between IS1635.1 and IS1635.2. Hybridization and sequence alignments showed that remnants of IS1635-like insertion elements harboring large deletions and point mutations are present on the Yop virulon harboring plasmids of pathogenic Yersinia strains. In a few cases, the IS1635 element has also been found on plasmids of apathogenic Yersinia strains.

Bacterial Outer Membrane Proteins↗
PubMed1990

A cryptic 65-kilobase-pair transposonlike element isolated from Bacteroides uniformis has homology with Bacteroides conjugal tetracycline resistance elements.

A 65-kilobase-pair element, XBU4422, which has some transposonlike characteristics but carries no known antibiotic resistance genes, has been isolated from Bacteroides uniformis 0061. XBU4422 was trapped on Bacteroides-Escherichia coli shuttle vectors during experiments in which one of the conjugal Bacteroides tetracycline resistance (Tcr) elements was being used to mobilize the shuttle vectors to Bacteroides recipients. Results of Southern hybridization experiments showed that XBU4422 is normally integrated in the B. uniformis 0061 chromosome and is found only in some strains. Insertion of XBU4422 in the shuttle vectors was site specific and orientation specific. Nonmobilizable vectors that had acquired XBU4422 became transmissible and could be transferred to Bacteroides or E. coli recipients. In B. uniformis transconjugants, the XBU4422 insertion in the vectors was usually intact, but XBU4422 was always lost in matings with E. coli, Bacteroides thetaiotaomicron, or B. ovatus. The loss of XBU4422 did not visibly alter the vector; in the case of E. coli, the loss of the insertion appeared to be RecA dependent. Although XBU4422 carried no antibiotic resistances, it shared regions of homology with six conjugal Bacteroides Tcr elements; this homology was strongest with the ends of XBU4422. Using a strain of B. thetaiotaomicron that contains no XBU4422-hybridizing sequences, we showed that the ends of XBU4422 were probably reacting with the ends of the Tcr elements. These results provide the first direct evidence that the Tcr elements, like XBU4422, are integrated in the chromosome and that insertion of the least some Tcr elements, such as TcrEmr DOT, is relatively site specific.

Bacteroides↗
PubMed2001

A new RNA element located in the coding region of a murine endogenous retrovirus can functionally replace the Rev/Rev-responsive element system in human immunodeficiency virus type 1 Gag expression.

Nuclear export of incompletely spliced RNAs is a prerequisite for retroviral replication. Complex retroviruses like human immunodeficiency virus (HIV) encode a viral transport factor (Rev), which binds to its target sequence on the RNA genome and directs it into the Crm-1-mediated export pathway. Other retroviruses, like Mason-Pfizer monkey virus, contain cis-acting constitutive RNA transport elements (CTE) which achieve nuclear export of intron-containing RNA via cellular transport factors. Here, we describe the identification and characterization of a novel cis-acting orientation-dependent RNA expression element in the coding region of the murine intracisternal A-type particle (IAP) MIA14. This IAP expression element (IAPE) can functionally replace the Rev system in the expression of HIV-1 Gag proteins but functions independently of Crm-1. The presence of this element is needed for the expression of the IAP Gag proteins, indicating its biological significance. The IAPE can be functionally replaced by placing a CTE on the MIA14 RNA, further supporting its role in mRNA export. Northern blot analysis revealed that total RNA, as well as cytoplasmic RNA, was increased when the element was present. The element was mapped to a predicted stem-loop structure in the 3' part of the pol open reading frame. There was no overall homology between the IAPE and the CTE, but there was complete sequence identity between short putative single-stranded loops. Deletion of these loops from the IAPE severely reduced Rev-independent Gag expression.

Animals↗
PubMed2005

Functional characterization of core promoter elements: the downstream core element is recognized by TAF1.

Downstream elements are a newly appreciated class of core promoter elements of RNA polymerase II-transcribed genes. The downstream core element (DCE) was discovered in the human beta-globin promoter, and its sequence composition is distinct from that of the downstream promoter element (DPE). We show here that the DCE is a bona fide core promoter element present in a large number of promoters and with high incidence in promoters containing a TATA motif. Database analysis indicates that the DCE is found in diverse promoters, supporting its functional relevance in a variety of promoter contexts. The DCE consists of three subelements, and DCE function is recapitulated in a TFIID-dependent manner. Subelement 3 can function independently of the other two and shows a TFIID requirement as well. UV photo-cross-linking results demonstrate that TAF1/TAF(II)250 interacts with the DCE subelement DNA in a sequence-dependent manner. These data show that downstream elements consist of at least two types, those of the DPE class and those of the DCE class; they function via different DNA sequences and interact with different transcription activation factors. Finally, these data argue that TFIID is, in fact, a core promoter recognition complex.

Adenoviridae↗
PubMed2004

Differences in the chromatin structure and cis-element organization of the human and mouse GATA1 loci: implications for cis-element identification.

Cis-element identification is a prerequisite to understand transcriptional regulation of gene loci. From analysis of a limited number of conserved gene loci, sequence comparison has proved a robust and efficient way to locate cis-elements. Human and mouse GATA1 genes encode a critical hematopoietic transcription factor conserved in expression and function. Proper control of GATA1 transcription is critical in regulating myeloid lineage specification and maturation. Here, we compared sequence and systematically mapped position of DNase I hypersensitive sites, acetylation status of histone H3/H4, and in vivo binding of transcription factors over approximately 120 kilobases flanking the human GATA1 gene and the corresponding region in mice. Despite lying in approximately 10 megabase (Mb) conserved syntenic segment, the chromatin structures of the 2 homologous loci are strikingly different. The 2 previously unidentified hematopoietic cis-elements, one in each species, are not conserved in position and sequence and have enhancer activity in erythroid cells. In vivo, they both bind the transcription factors GATA1, SCL, LMO2, and Ldb1. More broadly, there are both species- and regulatory element-specific patterns of transcription factor binding. These findings suggest that some cis-elements regulating human and mouse GATA1 genes differ. More generally, mouse human sequence comparison may fail to identify all cis-elements.

Acetylation↗
PubMed1991

The vitamin D-responsive element in the rat bone Gla protein gene is an imperfect direct repeat that cooperates with other cis-elements in 1,25-dihydroxyvitamin D3- mediated transcriptional activation.

The gene for rat bone gla protein (BGP) was isolated and 1250 basepairs (bp), including 1100 bp of 5' flanking DNA, were placed up-stream of the human GH reporter gene. After transient transfection into the osteoblast-like rat osteosarcoma cell line ROS 17/2.8, the BGP promoter demonstrated a low level of basal activity that was increased approximately 10-fold by the addition of 10(-8) M 1,25-dihydroxyvitamin D3 [1,25-(OH)2D3]. A single 250-bp fragment (-523 to -274) was sufficient to confer hormone inducibility upon both heterologous and homologous promoters. Deletion studies, complemented by evaluation with synthetic oligomers, enabled localization of the 1,25-(OH)2D3 response element to within 19 bp (-456 to -438), containing an element with an imperfect direct repeat [GGTGA(N4)GGACA] and homology to other steroid-responsive elements. Gel retardation assays demonstrated that partially purified chick intestinal 1,25-(OH)2D3 receptor bound specifically and with high affinity to a DNA fragment containing the putative 1,25-(OH)2D3 response element, and this binding was perturbed by monoclonal antibodies to the 1,25-(OH)2D3 receptor. Surprisingly, the 250-bp fragment, when linked in an antisense orientation with respect to the BGP promoter, blocked basal and hormone-dependent gene expression. However, a 246-bp fragment 5' to the 250-bp element (-1100 to -855) restored 20-fold inducibility when linked to the first fragment in the same orientation, suggesting cooperativity between at least two elements to achieve the hormonal regulation observed in this gene.

Animals↗
PubMed1999

Transposable DNA elements and life history traits: II. Transposition of P DNA elements in somatic cells reduces fitness, mating activity, and locomotion of Drosophila melanogaster.

Some transposable DNA elements in higher organisms are active in somatic cells, as well as in germinal cells. What effect does the movement of DNA elements in somatic cells have on life history traits? It has previously been reported that somatically active P and mariner elements in Drosophila induce genetic damage and significantly reduce lifespan. In this study, we report that the movement of P elements in somatic cells also significantly reduces fitness, mating activity, and locomotion of Drosophila melanogaster. If other elements cause similar changes in life history traits, it is doubtful if transposable DNA elements remain active for long in somatic cells in natural populations.

Animals↗
PubMedDate not supplied

Inductively coupled plasma-mass spectrometry for the determination of elements and elemental species in food: a review.

Inductively coupled plasma-mass spectrometry (ICP-MS) has definitely emerged as a powerful technique for total element determination and as a sensitive and selective detector in hyphenated methods for speciation analyses of elements in foods. In this review, the analytical challenges of elemental analysis of food and agricultural matrixes are discussed and several applications are examined. Selected examples illustrate the analytical approaches being used so far to address specific issues in various areas of food and nutrition research. The applications discussed include studies on dietary intake, element metabolism in man, transfer of elements through the food chain, effects of food processing and domestic preparation, and authenticity and origin assessment. The use of ICP-MS in the field of analytical quality assurance, food control, evaluation of food contact materials, and radionuclide contamination is also examined. Finally, the hyphenated techniques with ICP-MS detection used for elemental speciation in food are reviewed, and an overview of the main applications currently in the literature is presented. Throughout, recent trends and analytical developments likely to have a major impact on food-related areas are highlighted.

Animals↗
PubMed1986

Elemental and trace element distribution in medical samples: analysis by proton-induced X-ray emission.

The analysis of trace elements is performed by proton-induced X-ray emission. The process is most effective if the velocity of the exciting particles--protons--is similar to the velocity of the electron on its orbit in the simple atomic model of Bohr. For K-shell electrons of the elements with 15 less than or equal to z less than or equal to 40 this requires proton energies of a few MeV, available from electrostatic van de Graaf accelerator machines. After knocking out the K-shell electron, the empty place is filled up by electrons jumping from higher orbits with simultaneous emission of characteristic X-rays, which are registered with a cooled Si (Li) detector. By a set of electrodes the beam can be swept across the specimen surface. Therefore this method yields an excellent correlation of trace element distribution within the morphological structure of organic tissue. In the present study the sweep went along a line perpendicular to the arterial wall layers (aortic, renal artery and heart muscle) of normotensive and spontaneously hypertensive rats. Along this line all elements and trace elements are recorded simultaneously. These are P, S, Cl, K, Ca, Fe, Cu, Zn, Br and Sr. The trace element content of the aortic wall and the renal artery, of 22 spontaneously hypertensive and 11 normotensive rats and of human heart muscle was investigated. The results demonstrate that Zn was only detected in the muscle-containing layers of the arteries. There was no different distribution between hypertensive and normotensive rats. However, Ca2+ was mainly detected in the smooth muscle-containing tunica media of hypertensive rats.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1996

An Attempt to Interpret the Spread of Element Concentration in Antarctic Surface Snow: The Same Element in a Given Test Field, Several Elements in Different Sampling Fields

Sampling surface snow on a large test field always leads to a spread of analyte concentration data which partly follows a Gaussian distribution and partly a rectangular one as can be observed from the analysis of literature data. The spread depends on the nonuniformity of the air-snow interface in the field and on the extent of reproducibility of all the procedures used from sampling to analysis. Consequently a sample relevant to a restricted surface might be poorly representative of the surrounding area. Contamination of the sample during the gathering and storing steps is assumed to be the main source of nonrandom results (outliers). Using various statistical tools we were able to evaluate which part of the spread was due to the snow surface nonuniformity in the case of many samples collected in the same test field. In the case of samples gathered in different geographical areas, the possibility of finding correlations among points is greatly enhanced when three or more analytes are considered for each sample. When the same correlation is found for some analytes and a variable tentatively tested, information can be gained about the source of chemical content of snow samples. The use of UV pretreatment of snow samples has been proven to cut down the interference of organics on the electrochemical process in DPASV, allowing one to obtain accurate and reproducible data.

Journal Article↗
PubMed1994

Intracisternal A-type particle elements as genetic markers: detection by repeat element viral element amplified locus-PCR.

We describe a novel, PCR-based technique termed REVEAL-PCR for examining the inheritance of intracisternal A-type particles (IAP). Amplifications use an unlabeled primer to SINE repeats and a radiolabeled primer to the IAP long terminal repeat; labeled products, which can be resolved on sequencing gels, are formed when IAPs lie in proximity to SINEs. With this technique we have identified a total of 124 polymorphisms in the BXH and CXS recombinant inbred strains. We suggest that this method will be equally applicable for examining other gene families present at around a thousand copies per genome.

Animals↗
PubMed1988

Characterization of two divergently transcribed Dictyostelium gene pairs and identification of G-rich sequence element lying between them with the characteristics of a basal promoter element.

The cysteine proteinase 1 (CP1) and cysteine proteinase 2 (CP2) genes of Dictyostelium discoideum encode coordinately expressed mRNA sequences that are inducible by extracellular cAMP. Both genes form part of divergently transcribed gene pairs. The gene proximal to CP1 is coordinately regulated and encodes a protein containing several potential zinc binding domains of the kind found in DNA binding proteins. The gene proximal to CP2 is a constitutively transcribed gene of unknown function. There are multiple, short, G-rich sequence elements between both gene pairs, and deletion of the pair of elements 200 nucleotides upstream from the CP2 gene abolishes cAMP-inducibility. A synthetic oligonucleotide, containing two copies of the G-rich element from the CP1 gene, will reconstitute cAMP-inducibility in the deletion mutant of the CP2 gene. This shows that the elements in the two genes are functionally homologous. Efficient induction requires at least two copies of the CP1 element, but their relative orientation is unimportant. Two copies in an inverted orientation are, however, inactive when moved upstream of their normal position and are incapable of conferring cAMP-inducibility on a heterologous gene. These observations suggest that these sequences are either essential promoter elements, not themselves interacting with the inducer, or that their interaction with a separate class of control sequences is necessary for inducible expression.

Amino Acid Sequence↗
PubMed1990

Three GCN4 responsive elements act synergistically as upstream and as TATA-like elements in the yeast TRP4 promoter.

The yeast TRP4 promoter contains three responsive elements (GCREs) for the 'general control' transcriptional activator GCN4, which are arranged in two upstream elements, UAS1 (GCRE1) and UAS2 (GCRE2 and GCRE3). A point mutation analysis of these elements revealed that all three GCREs are required for GCN4-dependent transcription, but none are involved in basal transcription. Basal transcription and GCN4-dependent transcription use completely different initiator elements in the TRP4 promoter. UAS1 acts synergistically with UAS2 to activate the GCN4-dependent transcription of TRP4. A consensus TATA box can functionally replace the UAS2 element to allow normal GCN4-dependent transcription, suggesting that UAS2 is analogous to the TATA element of other promoters. GCN4 might therefore activate transcription by exhibiting two alternative functions within the natural TRP4 promoter.

Alleles↗
PubMed2001

Fish retroposons related to the Penelope element of Drosophila virilis define a new group of retrotransposable elements.

Poseidon and Neptune are two ancient lineages of retroposons related to the Penelope element from Drosophila virilis. They have been identified in various teleost fish species, including the medakafish (Oryzias latipes), and the pufferfishes Fugu rubripes and Tetraodon nigroviridis, whose genomes are currently being sequenced. Some of these elements are highly reiterated in fish genomes. Penelope-related elements were also identified in blood fluke, shrimp, sea urchin, cichlid fish and frog, showing that they are widespread in animals. Penelope-related retroposons were not detected among sequences from the Drosophila melanogaster and human genome projects, suggesting that they have been lost from certain animal lineages. A sequence encoding a putative Uri (also called GIY-YIG) endonuclease domain was detected downstream from the gene for reverse transcriptase. To the best of our knowledge, this type of endonuclease sequence has previously been identified in group I introns and in genes for prokaryotic excinucleases but not in retrotransposable elements. Penelope-related elements are frequently truncated at their 5' ends and can also be flanked by long terminal repeat-like structures. Phylogenetic analysis of the reverse transcriptase domain failed to assign Penelope-related retroposons to one of the major groups of retroelements. Overall, therefore, the evidence strongly suggests that these sequences represent a new group of retrotransposable elements.

Amino Acid Sequence↗
PubMed2005

Influence of assembly of siRNA elements into RNA-induced silencing complex by fork-siRNA duplex carrying nucleotide mismatches at the 3'- or 5'-end of the sense-stranded siRNA element.

RNA interference (RNAi) is a powerful method for suppressing the expression of a gene of interest, and can be induced by 21-25 nucleotide small interfering RNA (siRNA) duplexes homologous to the silenced gene, which function as sequence-specific RNAi mediators in RNA-induced silencing complexes (RISCs). In the previous study, it was shown that fork-siRNA duplexes, whose sense-stranded siRNA elements carried a few nucleotide mismatches at the 3'-ends against the antisense-stranded siRNA elements, could enhance RNAi activity more than conventional siRNA duplexes in cultured mammalian cells. In this study, we further characterized fork-siRNA duplexes using reporter plasmids carrying target sequences complementary to the sense- or antisense-stranded siRNA elements in the untranslated region of Renilla luciferase. The data presented here suggest that nucleotide mismatches at either the 3'- or 5'-end of the sense-stranded siRNA elements in fork-siRNA duplexes could influence assembly of not only the antisense-stranded siRNA elements but also the sense-stranded elements into RISCs. In addition, we further suggest the possibility that there could be a positional effect of siRNA duplex on RNAi activity.

3' Flanking Region↗
PubMed2006

The 3'-UTR of the glutamine-synthetase gene interacts specifically with upstream regulatory elements, contains mRNA-instability elements and is involved in glutamine sensing.

Glutamine synthetase (GS) is expressed at various levels in a wide range of tissues, suggesting that a complex network of modules regulates its expression. We explored the interactions between the upstream enhancer, regulatory regions in the first intron, and the 3'-untranslated region and immediate downstream genomic sequences of the GS gene (the GS "tail"), and compared the results with those obtained previously in conjunction with the bovine growth hormone (bGH) tail. The statistical analysis of these interactions revealed that the GS tail was required for full enhancer activity of the combination of the upstream enhancer and either the middle or the 3'-intron element. The GS tail also prevented a productive interaction between the upstream enhancer and the 5'-intron element, whereas the bGH tail did not, suggesting that the 5'-intron element is a regulatory element that needs to be silenced for full GS expression. Using the CMV promoter/enhancer and transfection experiments, we established that the 2.8 kb GS mRNA polyadenylation signal is approximately 10-fold more efficient than the 1.4 kb mRNA signal. Because the steady-state levels of both mRNAs are similar, the intervening conserved elements destabilize the long mRNA. Indeed, one but not all constructs containing these elements had a shorter half life in FTO-2B cells. A construct containing only 300 bases before and 100 bases after the 2.8 kb mRNA polyadenylation site sufficed for maximal expression. A stretch of 21 adenines inside this fragment conferred, in conjunction with the upstream enhancer and the 3'-part of the first intron, sensitivity of GS expression to ambient glutamine.

3' Untranslated Regions↗
PubMed2002

Characterization of elemental pollution and its variations in sediments and suspended particulate matter from the River Elbe via multi-element analysis combined with chemometric data evaluation.

Sediments and suspended particulate matter taken from about 100 sampling sites along the River Elbe from the source to the mouth during the period 1992 and 1998 have been analyzed for the concentrations of more than 60 elements in each sample. The analytical data were subsequently processed by means of multivariate statistics in order to characterize the charge of the River Elbe with inorganic pollutants to elucidate pollution trends. Using factor analysis 18 elements were found to be enriched by human activities. By means of cluster analysis--using the 18 anthropogenically influenced elements as variables--the sampling sites were aggregated into groups having similar element distributions. Thus, the entire stretch of the River Elbe was divided into three sections of characteristic elemental pollution. Finally, the trends in anthropogenic pollution within the characteristic regions since the early nineties were assessed. It turned out that most of the anthropogenically influenced elements showed a decrease in the upper and middle parts of the river, whereas no decrease could be verified in the estuary region.

Environmental Monitoring↗
PubMed2006

Sequential element extraction of soils from abandoned farms: an investigation of the partitioning of anthropogenic element inputs from historic land use.

Enhanced soil element concentrations may serve as indicators not only of modern pollution, but also of former historic and/or pre-historic human activity. However, there is little consensus over the most appropriate means of extraction for identifying chemical signatures of modern and archaeological pollution. This study addressed this question by using a 5-step sequential extraction to examine the partitioning of elements within the soil. Samples were taken from known functional areas (hearth, house, byre, arable, and grazing areas) on a 19th century abandoned croft (small farm). A hot nitric acid digest and five-stage sequential extraction method were used to examine the partitioning of elements in soil and identify the current elemental distribution of anthropogenic contamination. The results indicate that although a significant proportion of Ca tends to be bound with exchangeable and weak acid soluble fractions, in the hearth and house areas there is also a significant proportion held within the recalcitrant residue. Pb concentrations tend to be associated with organic matter, ammonium oxalate extractable fractions and the residue, whilst Zn generally has a more even partitioning between the six soil fractions. The implications of this for extraction methodology are element and soil specific. However, the presence of a significant proportion of anthropogenically significant elements (including Ca, Pb, Zn, Sr, and Ba) within the resistant residue suggests the use of only a weak acid or an exchangeable fraction extraction would result in the loss of information from contamination resulting from former human activity. Hence, a total or pseudo-total extraction method is recommended for this type of study.

Agriculture↗