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Synergism between two distinct elements of the HTLV-I enhancer during activation by the trans-activator of HTLV-I.

We have conducted functional studies of the enhancer elements of human T-cell leukemia virus type I (HTLV-I) using the human T-cell lines Jurkat and MOLT 4, which are negative for HTLV-I, and MT-2 and TL-Mor, which carry the proviral genome of HTLV-I. Two distinct elements have been implicated in function of the HTLV-I enhancer. One is the 21-base-pair (bp) core element that is responsible for trans-activation by the HTLV-I trans-activator p40tax and that has the ability to bind to cyclic-AMP responsive element binding factor (CREB)-like factor(s). The other is a region interposed between the 21-bp elements. In this study we demonstrate that a subfragment (C26) in the region between the 21-bp elements is involved in trans-activation by p40tax, possibly through binding to an NF-kappa B-like nuclear factor or factors. Formation of the protein-DNA complex with the C26 subfragment was positively affected by p40tax. The C26 element conferred partial responsiveness to p40tax when linked to one copy of the 21-bp element that, by itself, showed little activation in response to p40tax. However, the C26 element alone, even when repeated, could not be activated by p40tax, unlike other NF-kappa B-binding elements. In contrast, the C26 element itself was profoundly activated upon stimulation with 12-O-tetradecanoylphorbol-13-acetate. These findings therefore suggest that the HTLV-I enhancer contains multiple functional elements, including binding sites for at least CREB- and NF-kappa B-like factors, which synergistically cooperate in activation of the HTLV-I enhancer in response to p40tax. Our results also demonstrate that TPA-dependent activation of the HTLV-I enhancer may be mediated through the C26 element.

Base Sequence↗

[Thermosensitive vector derived from RP1 plasmid for detection of transposable elements].

The involvement of the transposable DNA element of E. coli K12 chromosome in integrative recombination of RP1 plasmid was studied. Using temperature sensitive for replication plasmid RP1ts12--the derivative of RP1 which contains mutated transposon Tnl, it was shown that integration of RP1 into host chromosome and Hfr formation may occur according to a mechanism mediated by chromosome IS-elements. Plasmids that are desintegrated from the chromosome of these Hfrs contain discrete DNA segments (IS-elements) and possess elevated frequency of integration into chromosome of rec+ cells. The latter was used for selection of RP1ts12 recombinants carrying chromosome IS. For identification of IS involved in RP1 integration the number of independent RP1ts 12 recombinants was subjected to restriction and heteroduplex analysis. By analysing recombinants integrated into bacterial chromosome with frequency 5 X 10(-3), a new IS-element of E. coli K12 designated IS111 was discovered. IS111-element is about 1500bp of length, contains Smal, Pst1 and BamH1 restriction endonuclease sites and was found in the same position on the plasmid RP1 in two different orientations. IS-elements that have been revealed in a number of other RP1ts12 recombinants were preliminary identified as IS1-like elements. One recombinants plasmid was found to have an IS5-like elements. The activity of IS-elements inserted into RP1ts12 in recA-dependent integrative recombination was estimated. From the data of absolute and relative RP1ts12 integration frequencies mediated by IS111, IS1- and IS5-like elements a conclusion was made about the absence of E. coli K12 chromosome IS-elements in RP1 plasmid. The Hfr-formation and chromosomal gene transfer by recombinant plasmids RP1ts12: IS111 were studied. The possibility to use insertion RP1ts12 derivatives for the estimation of copies number, mapping and definition of orientation of IS-elements in bacterial chromosome and the possibilities for detection of transposable DNA elements using RP1ts12 in a wide range of gram-negative bacteria are discussed.

Bacterial Proteins↗

Elemental fingerprint analysis of barley (Hordeum vulgare) using inductively coupled plasma mass spectrometry, isotope-ratio mass spectrometry, and multivariate statistics.

Inductively coupled plasma mass spectrometry (ICP-MS) and isotope-ratio mass spectrometry (IR-MS) have been used to examine the multi-elemental composition and (15)N/(14)N and (13)C/(12)C isotope ratios of three spring barley (Hordeum vulgare) genotypes (Orthega, Barke, and Bartok) grown in three typical Danish agricultural soils (North Jutland, West Jutland, and East Zealand) differing in soil fertility. The aim of the study was to examine whether it was possible to generate a unique elemental fingerprint of individual barley genotypes irrespective of the elemental imprint plants had received from soils differing in fertility and agricultural practice. Multivariate statistics were used to analyze the elemental fingerprints of the barley genotypes at different times during a full growing season from early tillering to full maturity of the barley grains. Initially, 36 elements were analyzed in the plant samples but this number was subsequently reduced to 15 elements: B, Ba, C, Ca, Cu, Fe, K, Mg, Mn, N, Na, P, S, Sr, and Zn. These elements exceeded the limit of detection ( LOD) for all genotypes, soil types, and plant growth stages and for these elements the accuracy was better than 90% compared with apple leaf certified reference material (CRM). Principal component analysis (PCA) separated multi-elemental data in accordance with soil type when plants of similar physiological age were compared, whereas this separation disappeared if plants of all ages were compared simultaneously. Isotope ratios (delta(15)N) of plants also proved to be a highly accurate property for classification of samples according to soil type. In contrast, the differences in delta(13)C were too small to enable such classification. The differences in delta(15)N among soils were so pronounced that separation of samples according to the physiological age of plants became redundant. However, delta(15)N and the multi-elemental analysis revealed no differences between the three barley genotypes, indicating that the influence of soil chemistry and possibly also climate and agricultural practice was too large to allow an unique elemental fingerprint for the genotypes. This finding was substantiated by analyzing the multi-elemental composition of grain from two additional genotypes (Otira and Barthos) grown at the north and east locations, respectively. PCA showed not only that the elemental fingerprints of these two genotypes were similar to those of the others, but also that the soil in which the plant had been growing could be accurately predicted on the basis of the PCA scores from the genotypes Orthega, Barke, and Bartok. Similar conclusions could be drawn using delta(15)N data.

Agriculture↗

Evidence for enhanced bioavailability of trace elements in the marine ecosystem of Deception Island, a volcano in Antarctica.

This study assessed whether trace elements present at Deception Island, an active submarine volcano in the Antarctic Peninsula, show enhanced biological availability to the local marine community. Using a weak acid extraction method to dissolve organic material and leach associated but not constitutive trace elements of sediments, fifteen elements were measured from seafloor sediment, seawater particulates, and tissues of benthic (bivalves, brittlestars, sea urchins) and pelagic (demersal and pelagic fishes, krill) organisms collected in the flooded caldera. The highest element concentrations were associated with seafloor sediment, the lowest with seawater particulates and organism tissues. In the case of Ag and Se, concentrations were highest in organism tissue, indicating contamination through the food chain and biomagnification of those elements. The elements Al, Fe, Mn, Sr, Ti, and to a lesser extent Zn, were the most concentrated of the trace elements for all sample types. This indicates that the whole ecosystem of Deception Island is contaminated with trace elements from local geothermal activity, which is also reflected in the pattern of element contamination in organisms. Accordingly, element concentrations were higher in organisms collected at Deception Island compared to those from the neighboring non-active volcanic King George Island, suggesting that volcanic activity enhances bioavailability of trace elements to marine organisms. Trace element concentrations were highest in digestive tissue of organisms, suggesting that elements at Deception Island are incorporated into the marine food web mainly through a dietary route.

Analysis of Variance↗

Context-dependent roles of the Entamoeba histolytica core promoter element GAAC in transcriptional activation and protein complex assembly.

Transcriptional control of the hgl5 gene of Entamoeba histolytica is mediated through an unusual core promoter composed of TATA, GAAC and Initiator elements. In the hgl5 promoter the GAAC element (AATGAACT) determines the site and rate of transcription initiation. Here we tested the role of the GAAC element in transcription activation from upstream regulatory elements (UREs) in the hgl5 promoter. We also examined the function of the GAAC element in the ferredoxin (fdx) promoter and characterized the protein binding to the GAAC element. Electrophoretic mobility shift assays (EMSA) demonstrated that the GAAC region is necessary for higher-order nuclear protein complex assembly. The function of the GAAC element in transcription activation mediated by UREs revealed that mutation of the GAAC element did not affect transcription activation mediated by the hgl5 URE4 but abrogated activation by the hgl5 URE3. We compared the role of the GAAC elements in the hgl5 and fdx promoters. Competitive gel shift assays were consistent with the same nuclear protein binding to the GAAC elements in both genes. Mutation of the GAAC element in the fdx gene decreased reporter gene expression, however, in contrast to hgl5 gene, had no effect on the site of transcription initiation. These results support a role for the GAAC element in assembly of nuclear proteins at the core promoter and in transcription activation mediated by URE3. The differing effect on transcription initiation in the hgl5 and fdx genes upon mutation of the GAAC element suggests a context-dependence of the GAAC-binding protein in gene expression.

Animals↗

Beta, a novel repetitive DNA element associated with tRNA genes in the pathogenic yeast Candida albicans.

We have identified a novel 399 bp repetitive DNA element (which we designate beta) 9bp upstream of a seryl-tRNA(CAG) gene in the genome of Candida albicans. There are two copies of the seryl-tRNA(CAG) gene, one on each homologue of chromosome VI, and the beta element is found upstream of one copy of the gene in C. albicans strain 2005E. The beta element is not present upstream of either copy of the seryl-tRNA(CAG) gene in eight other laboratory strains of C. albicans tested, but was detected in this location in several fresh clinical isolates. Southern blot analysis indicated that there are approximately eight copies of the beta element per diploid C. albicans genome and that it is a mobile element, being present on at least two different chromosomes. Three unique genomic DNA clones containing the beta element were isolated from strain 2005E; in each case, a different tRNA gene was found immediately adjacent to the beta element. Three new tRNA genes from C. albicans have thus been identified: tRNA(Asp), tRNA(Ala) and tRNA(Ile). The beta element shows no significant sequence homology to other known prokaryotic or eukaryotic repetitive elements, although an 8 bp repeat at the 3' end of the element is identical to that of the Ty3 retrotransposable element of Saccharomyces cerevisiae. We propose that the beta element is a solo long terminal repeat (LTR) sequence of a Ty3/gypsy-like transposable element in C. albicans that is closely associated with tRNA genes.

Base Sequence↗

Cellular factors binding to a novel cis-acting element mediate steroid hormone responsiveness of mouse mammary tumor virus promoter.

Steroid hormone receptors regulate mouse mammary tumor virus (MMTV) gene expression by binding to hormone response DNA elements present in the long terminal repeat. Tissue-specific expression of MMTV is unlikely to be regulated by steroid hormone-receptor complex alone, and mammary cell-specific factors might play a role in the hormone-induced transcriptional activation. In this report we have investigated the function of a novel cis-acting element designated Kil (-204 to -188) which is located adjacent to the distal glucocorticoid response element, in steroid hormone-induced transcription of MMTV. Electrophoretic mobility shift assays indicate that cellular factors bind to the Kil element, and dexamethasone stimulation results in alterations in the binding pattern of proteins in this region. By transient transfection assays using wild type and deletion mutants of the Kil element, we show that this novel cis-acting element is necessary for hormone-induced transcription of MMTV and functions in mammary tumor cells but not in NIH/3T3 cells. Mutagenesis of the Kil sequence suggests that the entire Kil element functioning as one unit is necessary for hormone-induced transcription of MMTV. When placed in the context of heterologous promoters, neither Kil element nor glucocorticoid response element is able to induce significant hormone-induced transcription of MMTV. The presence of both the DNA elements in tandem results in optimal induction of transcription in the presence of steroid hormones. Our results also indicate that the Kil element functions in human breast carcinoma cell lines such as T47D and MCF-7. These results suggest that Kil element in combination with distal glucocorticoid response element functions as a mammary cell-specific enhancer to regulate MMTV transcription.

3T3 Cells↗

Different composite regulatory elements direct expression of the human alpha subunit gene to pituitary and placenta.

To identify elements of the human alpha subunit gene necessary for cell-specific expression, we generated an array of block mutations spanning approximately 400 base pairs (bp) of promoter proximal region and examined them using transient transfection analysis in pituitary (alpha T3) and placental (BeWo) cell lines. Comparison of promoter activity in the two cell types revealed both common and unique elements required for transcription in pituitary and placenta. Two strong elements, the cyclic AMP response element (CRE) and the upstream regulatory element (URE), regulate expression of the alpha subunit gene in BeWo cells. In contrast, promoter activity in alpha T3 cells requires an array of weaker elements. These include the CREs, the URE, as well as two previously described elements, pituitary glycoprotein hormone basal element (PGBE) and gonadotrope-specific element (GSE), and two new elements we designated as the alpha basal elements 1 and 2 (alpha BE1 and alpha BE2). These new elements reside between -316 and -302 bp (alpha BE1) and -296 and -285 bp (alpha BE2) of the human alpha subunit promoter and bind distinct proteins designated alpha BP1 and alpha BP2, respectively. Southwestern blot analysis revealed that alpha BE1 specifically binds 54- and 56-kDa proteins. Additional studies disclosed several potential interactions between proteins that bind the CRE and proteins that occupy PGBE, alpha BE1, and alpha BE2, suggesting that gonadotrope-specific expression occurs through a unique composite regulatory element that includes components of the placenta-specific enhancer.

Animals↗

SR2 elements, non-long terminal repeat retrotransposons of the RTE-1 lineage from the human blood fluke Schistosoma mansoni.

As in other eukaryotes, a substantial portion of the genome of the human blood flukes belonging to the genus Schistosoma appears to be composed of mobile genetic elements and other repetitive sequences. The constitutent elements and their relative organization are not well understood, although retroposons (the SM alpha elements) and a family of non-long terminal repeat (LTR) retrotransposons (the SR1 elements) have been reported from the genome of Schistosoma mansoni. Here, we report the presence of a second family of non-LTR retrotransposons from S. mansoni which we have termed the SR2 elements. SR2 elements are members of a recently described lineage of non-LTR retrotransposons typified by the RTE-1 non-LTR retrotransposon of Caenorhabditis elegans. We determined the sequence for approximately 3.9 kb of a consensus full-length SR2 element, which included a long 5' untranslated region (UTR), potential first and second open reading frames (ORFs) of 78 and 1,018 amino acid residues, respectively, a short 3' UTR, and an A-rich 3' terminus. SR2 elements were bound by target site duplications. The putative first and second ORFs did not overlap. The second ORF was homologous to retroviral pol and encoded an apurinic/apyrimidinic endonuclease and a reverse transcriptase. A number of extremely short SR2 elements of less than 0.5 kb, reminiscent of SINEs, were also characterized. These consisted solely of the 5' and 3' UTRs of full-length SR2 elements, having both ORFs deleted. Analysis indicated that these SINE-like SR2 elements were produced by replication of a SINE-like SR2 element, rather than by repeated deletions within larger SR2 elements.

Amino Acid Sequence↗

Elements on the move: How ungulate migration expands Alpine biogeochemical footprints.

Through depositing waste products, animals influence the spatial distribution of elements across landscapes. Yet the relationship between animal movement and element distribution remains poorly characterized. We developed a spatially explicit agent-based model to test how migratory versus resident red deer (Cervus elaphus) influence nitrogen redistribution across an alpine landscape in the Central-Eastern Italian Alps. Specifically, we asked how both local-scale and landscape-scale movement alter the spatial extent and magnitude of nitrogen deposition. We parameterized our model with GPS telemetry from 2021 to 2024 and remotely sensed vegetation data. We simulated four different scenarios which allowed us to disentangle the relative effects of large-scale (migration persisting) and fine-scale (resident behaviour) movement: (i) mixed migratory-resident (300 deer), (ii) fully resident (300 deer), (iii) reduced resident (150 deer) and (iv) reduced migratory (150 deer). The potential for nitrogen intake, assimilation, and excretion occurred hourly across a seasonally dynamic landscape. Across all scenarios, tree cover density and slope consistently emerged as positive predictors of nitrogen transport. Thus, regardless of resident or migratory status, red deer act as mediators of local element transport. Similarly, proximity to roads/trails reduced nitrogen inputs and created closed systems, indicating that barriers constrain both local and landscape-scale element transport. Migration substantially expanded the spatial extent of nitrogen redistribution and enabled the upward movement of elements, both locally upslope and into higher elevation habitats, effectively transporting elements against gravitational forces. Consequently, the loss of migration is likely to weaken these large-scale element linkages and reduce associated ecosystem functions. Our results demonstrate that different animal movement patterns play distinct and complementary roles in connecting element pools across landscapes. While both resident and migrant foraging redistribute elements locally, migratory movements link lowland and alpine habitats, expanding the spatial reach of element redistribution. Thus, loss of migration not only reduces the spatial extent of element distribution but also alters the topographic pathways through which elements are cycled. These findings highlight the broader ecosystem consequences of declining animal movement extent, and migration in particular, and underscore the importance of conserving behavioural diversity to maintain element heterogeneity and ecosystem functioning in mountain systems.

animal ecology↗

Carcinosarcoma of the urinary bladder: expression of epithelial markers and different expression of heat shock proteins between epithelial and sarcomatous elements.

A case of carcinosarcoma composed of both adenocarcinoma and sarcomatous elements in the non-trigone region of the urinary bladder is presented. The epithelial element was a well to poorly differentiated adenocarcinoma with focal squamous metaplasia. The sarcomatous elements disclosed spindle cell sarcoma with focal epithelioid pattern and myxoid change in the stroma, together with chondrosarcomatous and rhabdomyosarcomatous elements. By immunohistochemical examination, not only the carcinoma element but also the sarcomatous elements showed a positive immunoreaction for cytokeratin (CK), epithelial membrane antigen (EMA) and carcinoembryonic antigen. Some population of sarcomatous elements expressed smooth muscle actin and muscle specific actin (MSA) and a limited portion of epithelioid area showed a positive immunoreaction for desmin, MSA and myoglobin, indicating leiomyosarcomatous and rhabdomyosarcomatous differentiation, respectively. Unexpectedly, tumor cells in the chondrosarcomatous element revealed a simultaneous positivity of CK and EMA as well as S-100 protein. Both epithelial and sarcomatous elements showed an intensive positive immunoreaction for p53 and heat shock protein (HSP) 70. However, HSP27 and HSP60 were detected in most epithelial elements and only in a small number of tumor cells in the sarcomatous area. These findings indicate that sarcomatous elements, including heterologous elements, may derive from epithelial elements with partial or complete loss of epithelial features, and different factors other than p53 and HSP70 may associate with the morphological alteration of carcinoma.

Biomarkers↗

Natural and synthetic DNA elements with the CArG motif differ in expression and protein-binding properties.

DNA elements with the CC(A/T)6GG, or CArG, motif occur in promoters that are under different regulatory controls. CArG elements from the skeletal actin, c-fos, and myogenin genes were tested for their abilities to confer tissue-specific expression on reporter genes when the individual elements were situated immediately upstream from a TATA element. The c-fos CArG element, also referred to as the serum response element (SRE), conferred basal, constitutive expression on the test promoter. The CArG motif from the myogenin gene was inactive. The skeletal actin CArG motif functioned as a muscle regulatory element (MRE) in that basal expression was detected only in muscle cultures. Muscle-specific expression from the 28-bp MRE and the 2.3-kb skeletal actin promoter was trans repressed by the Fos and Jun proteins. The expression and factor-binding properties of a series of synthetic CArG elements were analyzed. Muscle-specific expression was conferred by perfect 28-bp palindromes on the left and right halves of the skeletal actin MRE. Chimeric elements of the skeletal actin MRE and the c-fos SRE differed in their expression properties. Muscle-specific expression was observed when the left half of the MRE was fused to the right half of the SRE. Constitutive expression was conferred by a chimera with the right half of the MRE fused to the left half of the SRE and by chimeras which exchanged the central CC(A/T)6GG sequences. At least three distinct proteins specifically bound to these CArG elements. The natural and synthetic CArG elements differed in their affinities for these proteins; however, muscle-specific expression could not be attributed to differences in the binding of a single protein. Furthermore, the MRE did not bind MyoD or the myogenin-E12 heterodimer, indicating that muscle-specific expression from this element does not involve a direct interaction with these helix-loop-helix proteins. These data demonstrate that the conserved CArG motifs form the core of a family of functionally different DNA regulatory elements that may contribute to the tissue-specific expression properties of their cognate promoters.

Actins↗

Two distinct osteoblast-specific cis-acting elements control expression of a mouse osteocalcin gene.

Osteoblasts are cells of mesodermal origin that play a pivotal role during bone growth and mineralization. The mechanisms governing osteoblast-specific gene expression are still unknown. To understand these mechanisms, we analyzed the cis-acting elements of mouse osteocalcin gene 2 (mOG2), the best-characterized osteoblast-specific gene, by DNA transfection experiments in osteoblastic and nonosteoblastic cell lines and by DNA-binding assays. 5' deletion analysis of an mOG2 promoter-luciferase chimeric gene showed that a region located between -147 and -34 contained most if not all of the regulatory elements required for osteoblast-specific expression. Three different binding sites, called A, B, and C, for factors present in nuclear extracts of osteoblasts were identified in this short promoter by DNase I footprint assays. In gel retardation assays, the A element, located between bp -64 and -47, bound a factor present only in nuclear extracts of osteoblastic cell lines and nonmineralizing primary osteoblasts. The B element, located between bp -110 and -83, bound a ubiquitously expressed factor. The C element, located between bp -146 and -132, bound a factor present only in nuclear extracts of osteoblastic cell lines and nonmineralizing and mineralizing primary osteoblasts. When cloned upstream of a minimum osteocalcin promoter or a heterologous promoter, multimers of the A element strongly increased the activities of these promoters in osteoblastic cell lines at two different stages of differentiation but in no other cell line; we named this element osteocalcin-specific element 1 (OSE1). Multimers of the C element increased the activities of these promoters predominantly in a differentiated osteoblastic cell line; we named this element OSE2. This study demonstrates that two distinct cis-acting elements are responsible for osteoblast expression of mOG2 and provides for the first time a functional characterization of osteoblast-specific cis-acting elements. We speculate that these two elements may be important at several stages of osteoblast differentiation.

Animals↗

Organization of multiple regulatory elements in the control region of the adenovirus type 2-specific VARNA1 gene: fine mapping with linker-scanning mutants.

The adenovirus type 2-specific virus-associated RNA 1 (VARNA1) gene is transcribed by eucaryotic RNA polymerase III. Previous studies using deletion mutants for transcription have shown that the VARNA1 gene has a large control region which is composed of several regulatory elements. Twenty-five exact linker-scanning mutations in the control region, from -33 to +77, of this gene were used for definition of the number and boundaries of these elements. The effects of these mutations on transcription and competition for transcription factors in human KB cell extracts revealed five positive regulatory elements. The essential element, which coincided with the B block, was absolutely required for both transcription and formation of stable complexes. A second element, which included the A block, was also required for both transcription and formation of stable complexes. Although this element is not as essential as the B-block element, together with the B-block element it may be necessary for formation of the most basal form of transcription machinery. Therefore, these two elements are the promoter elements in this gene. In addition, one possible element in the interblock region and two elements in the 5' flanking region were also required for efficient transcription, but they were moderately required for formation of stable complexes. Transcription of these mutants and the wild-type gene using an extract of 293 cells was stimulated at least threefold over that with the KB cell extract, as expected. Similar regulatory elements of this gene were revealed, however, when the 293 cell extract was used for transcription of these mutants, suggesting that the E1A-mediated specific transcription factors act on the transcription machinery in a sequence-nonspecific manner.

Adenoviruses, Human↗

Regional and species specific bioaccumulation of major and trace elements in Arctic seabirds.

Twenty-five essential and nonessential elements were analyzed in Arctic seabirds to study the influence of phylogeny, tissue, Arctic region, and diet on avian element accumulation and to identify co-occurrence among metals. Muscle and liver concentrations were positively correlated, generally being higher in liver than in muscle, and generally did not differ by sex. Zinc showed the highest absolute concentrations in all samples (mean, 11.2-26.7 microg/g in muscle, depending on species and area), followed by copper (5.2-7.5 microg/g), arsenic (0.5-5.4 microg/g), selenium (1.0-5.8 microg/g), rubidium (1.4-2.2 microg/g), and cadmium (0.04-1.2 microg/g). Mercury levels ranged from 0.05 to 0.8 microg/g in muscle. The concentrations varied among species (dovekie [Alle alle], black guillemot [Cepphus grylle], thick-billed murre [Uria lomvia], black-legged kittiwake [Rissa tridactyla], northern fulmar [Fulmaris glacialis], ivory gull [Pagophila eburnean], Thayer's gull [Larus thayeri], and glaucous gull [Larus hyperboreus]), and between the northern Baffin Bay (Canada) and the Barents Sea, depending on the element. Whereas some elements (e.g., mercury and zinc) increased in absolute and standardized concentrations with trophic level in the northern Baffin Bay, most elements showed no relationship with trophic level or other dietary descriptors. In absolute concentrations, nonessential elements differed between regions, whereas essential elements differed among species but not within a species across the two regions. Standardized concentrations (element pattern) of both essential elements and nonessential elements generally did not differ between regions but was highly species specific and, thus, determined by the phylogenetic element regulation capacity. The usefulness of multivariate ordination in element wildlife studies is illustrated, which provides additional insight regarding element co-occurrence in wildlife, allows inclusion of species with low sample number, and reduces the possibility of type II errors created by low sample size.

Animals↗

Prioritizing selection of new elements: bottom-up versus top-down control.

Watson and Humphreys (1997) have proposed that prioritized selection of new over old elements occurs because observers can apply top-down inhibition to the locations of the old elements by a mechanism they refer to as visual marking. However, recent evidence has suggested that the top-down mechanism is questionable (Donk & Theeuwes, 2001). In the present study, we investigated whether prioritized selection of new over old elements occurs in a bottom-up or a top-down fashion. Observers were presented with displays containing one set of elements (old elements) followed, after a certain time interval, by a second set of elements (new elements). The observers were instructed to search for the presence of a target that was presented with equal probability among the old and the new elements (Experiments 1 and 2) or twice as often among the old elements than among the new elements (Experiment 3). The results show that new elements were prioritized for selection over old ones even though the observers had no incentive to do so. The results suggest that prioritized selection of new over old elements is not mediated by a top-down inhibition process, as was proposed by Watson and Humphreys (1997). Instead, prioritization of new elements appears to be a bottom-up process. The implications of these results are discussed in terms of models of attentional control.

Adolescent↗

Prioritizing new elements with a brief preview period: evidence against visual marking.

Watson and Humphreys (1997) have proposed that the ability to prioritize new elements over old elements involves a time-consuming process (of at least 400 msec) of active inhibition of the locations of the old elements, which they referred to as visual marking. Recently, Donk and Theeuwes (2001) have suggested that prioritized selection of new over old elements is an instantaneous process related to the luminance change accompanying the appearance of the new elements. The aim of the present study was to test these two alternatives by investigating whether prioritized selection of new over old elements could be achieved with a very short preview of the old elements (50 msec). The results indicated that participants were able to prioritize selection of new over old elements when the new elements were presented with luminance onset whereas the old elements were not. New elements could not be prioritized if both the old and the new elements appeared with luminance onset. The results indicated that prioritization of new elements is based on an instantaneous process, rather than on a time-consuming process.

Adult↗

Active Alu element "A-tails": size does matter.

Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly understood. The data presented in this paper indicate that the length of Alu "A-tails" is one of the principal factors in determining the retropositional capability of an Alu element. The A stretches of the Alu subfamilies analyzed, both old (Alu S and J) and young (Ya5), had a Poisson distribution of A-tail lengths with a mean size of 21 and 26, respectively. In contrast, the A-tails of very recent Alu insertions (disease causing) were all between 40 and 97 bp in length. The L1 elements analyzed displayed a similar tendency, in which the "disease"-associated elements have much longer A-tails (mean of 77) than do the elements even from the young Ta subfamily (mean of 41). Analysis of the draft sequence of the human genome showed that only about 1000 of the over one million Alu elements have tails of 40 or more adenosine residues in length. The presence of these long A stretches shows a strong bias toward the actively amplifying subfamilies, consistent with their playing a major role in the amplification process. Evaluation of the 19 Alu elements retrieved from the draft sequence of the human genome that are identical to the Alu Ya5a2 insert in the NF1 gene showed that only five have tails with 40 or more adenosine residues. Sequence analysis of the loci with the Alu elements containing the longest A-tails (7 of the 19) from the genomes of the NF1 patient and the father revealed that there are at least two loci with A-tails long enough to serve as source elements within our model. Analysis of the A-tail lengths of 12 Ya5a2 elements in diverse human population groups showed substantial variability in both the Alu A-tail length and sequence homogeneity. On the basis of these observations, a model is presented for the role of A-tail length in determining which Alu elements are active.

3' Flanking Region↗