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At least 505 records · Page 28Linked to original sources
PubMed2001

Uptake and distribution of rare earth elements in rice seeds cultured in fertilizer solution of rare earth elements.

The uptake behavior of rare earth elements (REEs) under pot conditions using deionized water and a REE fertilizer solution as the culture media as well as the distribution of REEs in rice proteins were studied. The uptake of REEs in rice seeds increased dramatically after a lag period of approximately three days. Roots can accumulate a much higher content of REEs than germs and the resting seeds. The REE content in each water-soluble (albumin) and salt-soluble (globulin) component of the rice seeds accounted for 5-8% and 4-6% of the total REEs, respectively. However, there are less than 1.5% of the total REEs were found in the alcohol-soluble (prolamin) and acetic acid-soluble (glutelin) components. The high performance liquid chromatography (HPLC) in the gel permeation and the reserved-phase were used to monitor changes in the molecular weight distribution changes of the soluble proteins of rice seeds during germination after having been cultured in the same solution for seven days. No changes occurred in the prolamin, while a slight change occurred in the albumin, globulin and glutelin. Fractionation of the albumin of rice seeds cultured in a REE fertilizer solution on the Sephadex G-100 column indicated that REEs, especially Ce, La, Pr and Nd, were associated mainly with biological compounds of a molecular weight between 10,000 and 12,000.

Absorption↗
PubMed1994

1H NMR studies of the high-affinity Rev binding site of the Rev responsive element of HIV-1 mRNA: base pairing in the core binding element.

1H NMR studies of a 30-nucleotide RNA oligonucleotide (RBE3), which contains a high-affinity binding site for Rev of the HIV-1 Rev responsive element (RRE), two derivatives of RBE3 (RBE3AA and RBE3-A), and the complex of RBE3 with peptides derived from the RNA binding domain of HIV-1 Rev, are presented. The high-affinity binding site of the RRE consists of an asymmetric internal loop and surrounding Watson-Crick base pairs. In the wild-type RRE, one of the stems is closed by a loop; this is replaced in REB3 by the stable UUCG tetraloop. NOE data suggest that the internal loop of the free RNA contains structural features that have been predicted on the basis of in vitro selection experiments [Bartel, D.P., et al. (1991) Cell 67, 529-536]. The structural features include a Gsyn.Ganti base pair, a Ganti.Aanti base pair, and a looped out U. When the Rev peptide is bound to the RNA, the base pairs in the internal loop appear to be stabilized, although the RNA chemical shifts indicate that the RNA conformation undergoes some changes when bound by Rev peptide.

Base Composition↗
PubMed2003

Organic and elemental carbon measurements during ACE-Asia suggest a longer atmospheric lifetime for elemental carbon.

During the ACE-Asia intensive field campaign (March 14-April 20, 2001), PM1.0 organic (OC) and elemental carbon (EC) concentrations were measured onboard the NOAA R/V Ronald H. Brown over the Northwest Pacific Ocean using a semi-continuous automated carbon analyzer downstream of a carbon-impregnated filter denuder. This OC and EC measurement achieved a mean time resolution of about 200 min over the Pacific Ocean, substantially lower than that achieved previously (24 h). The semi-continuous measurements, in which the adsorption artifact was substantially reduced using the denuder, showed good agreement with integrated artifact-corrected measurements made without a denuder. Mean particulate OC and EC concentrations were 0.21 and 0.09, 0.70 and 0.29, 1.00 and 0.27, and 2.43 and 0.66 microg of C m(-3) over the background Pacific Ocean, Asian-influenced Pacific Ocean, offshore of Japan, and Sea of Japan, respectively. On April 11, 90-min average OC and EC concentrations peaked at 4.0 and 1.3 microg of C m(-3), respectively, offshore of Korea over the Sea of Japan. The OC/EC ratio of 3.7 over the Sea of Japan and offshore of Japan was substantially higher than that of 2.5 over the Asian-influenced Pacific Ocean, even though backward air mass trajectories put the "Asian-influenced Pacific Ocean" sample downwind. The OC/EC ratio decreased with increasing time since the air mass encountered the source regions of China, Japan, and Korea. This suggests a longer atmospheric residence time for EC than for OC.

Aerosols↗
PubMed1996

Characterization of cis-acting elements of the gene for macrophage-stimulating protein from the human. The involvement of positive and negative regulatory elements.

To analyze the promotor region of the human macrophage-stimulating protein (MSP) gene, the 5'-flanking region of this gene was cloned. The major initiation site was determined at T located 49 base pairs upstream of the translation initiation site by primer extention with mRNA from HepG2 and Hep3B cells. There was no TATA sequence in this region. Transient transfection assay with 5'-deletion constructs showed that the transcription of this gene was regulated by positive and negative regulatory elements (PRE and NRE). The PRE (-34 to +2) was essential for the maximal transcription of this gene, and the NRE (-141 to -34) appeared to be responsible for the tissue-specific expression of the gene. The PRE contained the CCAAT sequence and a mutation from CCAAT to CTGAT resulted in a significant loss of the transcriptional activity. Electrophoretic mobility shift assay suggested that two different proteins bound to the PRE (MSP-PRE-binding protein-1 (MSP-PREB1) and 2). MSP-PREB1 and 2 were detected in various cell types, and the CCAAT sequence was involved in these bindings. These findings indicate that MSP-PREB1 and 2 are positive regulators. Further characterization also revealed that MSP-PREB2 was identical to CCAAT binding transcription factor, also known as NF-Y.

Base Sequence↗
PubMed2000

The homeodomain protein Arix promotes protein kinase A-dependent activation of the dopamine beta-hydroxylase promoter through multiple elements and interaction with the coactivator cAMP-response element-binding protein-binding protein.

The differentiation and maintenance of a neurotransmitter phenotype is guided by the interaction of exogenous cues with intrinsic genetic machinery. For the noradrenergic phenotype, these influences combine to activate the expression of the catecholaminergic biosynthetic enzymes tyrosine hydroxylase and dopamine beta-hydroxylase (DBH). In this study, we evaluate the molecular mechanisms by which the transcription factor Arix/Phox2a contributes to DBH gene transcription. We have evaluated the contribution of individual homeodomain binding sites in the rat DBH promoter region and find that all are essential for both basal and cAMP-dependent protein kinase A (PKA)-stimulated transcription. Using mammalian one-hybrid and two-hybrid systems, we demonstrate that recruitment of Arix to the positions of homeodomain core recognition sites 1 and 2 at -153 to -166 of the DBH gene restores complete responsiveness of the promoter to PKA in SHSY-5Y neuroblastoma and HepG2 hepatoma cells. Intracellular Arix-Arix interactions are evident and may contribute to the interdependence of homeodomain binding sites. Analysis of functional domains of Arix reveals an N-terminal activation domain and a C-terminal repression domain. The N terminus of Arix contains an amino acid motif similar to a region in Brachyury and Pax9 transcription factors. The N-terminal activation domain of Arix interacts with the transcriptional co-activator, cAMP-response element-binding protein-binding protein, which potentiates transcription from the DBH promoter in a PKA-dependent manner. The present study supports the hypothesis that the paired-like homeodomain protein, Arix, acts as a critical phenotype-specific regulator of the DBH promoter by serving as an integrator of signal-dependent transcription activators within the network of the general transcription machinery.

Animals↗
PubMed2002

Splicing of a myosin phosphatase targeting subunit 1 alternative exon is regulated by intronic cis-elements and a novel bipartite exonic enhancer/silencer element.

Isoforms of the smooth muscle myosin phosphatase targeting subunit 1 (MYPT1) are generated by cassette-type alternative splicing of exons. Tissue-specific expression of these isoforms is thought to determine smooth muscle-relaxant properties and unique responses to signaling pathways. We used mini-gene deletion/mutation constructs to identify cis regulators of splicing of the chicken MYPT1 central alternative exon. Comparisons of alternative exon splicing were made between smooth muscle cells of the fast-phasic contractile phenotype (gizzard), in which the central alternative exon is skipped, and slow tonic contractile phenotype (aorta), in which the alternative exon is included. We demonstrate that splicing of the alternative exon requires a cis-enhancer complex in the vicinity of the alternative exon 5'-splice site. This complex consists of two UCUU motifs in an intronic U-rich sequence (putative PTB (polypyrimidine tract binding) or T cell inhibitor of apoptosis-1 binding sites), an intronic 67-nucleotide enhancer that has similarities with the cardiac Troponin T MSE3 enhancer, and a potentially novel exonic splicing enhancer. The exonic enhancer contains the palindromic sequence UCCUACAUCCU present in many other transcripts where alternative splicing of exons occurs, suggesting that it may be more broadly active. The exonic enhancer is adjacent to a potentially novel exonic silencer element that contains a 13-nucleotide imperfect palindromic sequence. This silencer, in conjunction with a distal intronic silencer, is proposed to mediate the silencing of splicing of the MYPT1 central alternative exon in the fast phasic smooth muscle phenotype.

Alternative Splicing↗
PubMedDate not supplied

An edge-element based finite element model of microwave heating in hyperthermia: method and verification.

Hyperthermia has been shown to improve local tumour control of superficial and deep seated lesions when combined with radiotherapy. There remains difficulty in heating larger tumours with conventional applicators, but this is being addressed by several new applicator designs. This paper presents a new numerical model of microwave heating which is designed to aid in the development of new applicators for superficial heating. The model is based on a finite element method which utilises vector valued basis functions instead of the more conventional scalar valued basis functions. These basis functions were chosen since they are inherently suited for the solution of Maxwell's equations due to their vector nature. The model was successfully verified against an analytic solution to the Mie scattering problem as well as against previously published measurements of heating from a modified water bolus attached to a conventional waveguide applicator. An accompanying paper describes an application of this model to the design optimization of this modified bolus.

Biophysical Phenomena↗
PubMedDate not supplied

An edge-element based finite element model of microwave heating in hyperthermia: application to a bolus design.

Heating of superficial tumours with microwave waveguide applicators has been shown in phase III trials to significantly improve the local control of small lesions when combined with radiation therapy. This success has not yet translated to the treatment of larger tumours, due to difficulty in adequately heating the entire tumour region. Several modifications to the water bolus used with external waveguide applicators have been made in the past in order to increase the heating area. One such modification consisted of a large, microwave-absorbing patch placed inside the bolus, which flattens out the beam profile produced by the applicator. Using this bolus instead of a conventional one resulted in a 30% increase in the effective heating volume produced by the BSD MA120 applicator. This paper describes an optimization procedure for this bolus design which utilises a new finite element model of microwave heating described in an accompanying paper. The optimization procedure resulted in a further 28% increase in the effective heating volume.

Adipose Tissue↗
PubMed2004

Long-term field characterization of tapered element oscillating microbalance and modified tapered element oscillating microbalance samplers in urban and rural New York State locations.

Long-term field comparisons of continuous and integrated filter measurements of mass concentrations of particulate matter (PM) with an aerodynamic diameter less than or equal to 2.5 microm (PM2.5) were performed at rural and urban sites in New York State. Two versions of the continuous tapered element oscillating microbalance (TEOM) mass monitor are deployed at each site, in addition to Federal Reference Method filter samplers. Data are grouped into monthly averages to retain and demonstrate seasonal differences. Strong seasonal dependence is observed-the TEOM monitors with the heated sensors are biased systematically low with respect to the Federal Reference Method measurements during the cold season. For the rural site, the average bias for the sample equilibration system (SES)-equipped and standard TEOM monitors is 14 and 24%, respectively. At this location, the TEOM monitor measurements were biased low for all 34 months. For the urban site, the average bias for the SES and standard TEOM monitors is 8 and 18%, respectively. At this location, the TEOM monitor measurements are as likely to be biased high as low during the warm-season months. The hour averaged data from the two versions of the TEOM monitor are also compared, and also indicate that the SES-equipped version of the TEOM monitor captures 7-11% more PM2.5 mass at these locations.

Air Pollutants↗
PubMed2000

Major Element, REE, and Other Trace Element Behavior in Amphibolite Weathering under Semiarid Conditions in Southern India.

A body of komatiitic amphibolite, an enclave within the Archean high-grade orthogneisses in southern India, shows mild chemical weathering under semiarid conditions. Along fractures, chemical weathering has advanced (Chemical Index of Alteration &sqbl0;CIA&sqbr0;=53; CIA of fresh rock approximately 26) to the extent that secondary Mg-Fe-Al clay minerals have formed and the rock has turned brownish red, soft, and fine grained. The weathering process has resulted in the mobilization and redistribution of the so-called immobile elements Fe, Al, Ti, and REE effected by the nature of secondary mineral formation (talc vs. aluminous clay minerals) and also possibly by soil microbes. In the initial stages of secondary mineral formation, there is a small loss of Fe, Al, and REE (noticeably Eu). However, in the fracture zone as well as in the incipiently altered zone, there is significant REE enrichment, probably affected by a different precipitation mechanism. Mobilized REE may have come from a minor alteration of clinopyroxene.

Journal Article↗
PubMed1995

Regulation of mouse thymidylate synthase gene expression in growth-stimulated cells: upstream S phase control elements are indistinguishable from the essential promoter elements.

Expression of the mammalian thymidylate synthase (TS) gene in growth-stimulated cells is closely coordinated with entry into S phase. Previous studies with transfected TS minigenes have shown that sequences upstream of the coding region as well as an intron in the transcribed region are both necessary for proper regulation of TS mRNA content in growth-stimulated cells. The goal of the present study was to identify the upstream regulatory elements. Minigenes consisting of TS 5' flanking sequences linked to the TS coding region (interrupted by introns 1 and 2) were stably transfected into mouse 3T6 cells. Deletion and site-directed mutagenesis of the 5' flanking region revealed that there is a close correspondence between the upstream sequences that are necessary for S phase regulation and the 30 nucleotide region that is essential for promoter activity. These observations raised the possibility that regulation of the TS gene occurs at the transcriptional level. However, nuclear run-on assays showed that the rate of transcription of the TS gene changed very little during the G1-S phase transition. Furthermore, when the TS promoter was linked to an intron-less luciferase indicator gene, there was no change in expression following growth-stimulation. Therefore it appears that the TS gene is controlled primarily at the posttranscriptional level, and that the TS essential promoter region is necessary (although not sufficient) for proper S phase regulation.

Animals↗
PubMed1992

A transcriptional regulatory element of the gene encoding the 67,000-M(r) form of human glutamate decarboxylase is similar to a Drosophila regulatory element.

We have isolated the 5' flanking DNA sequences of the human gene encoding the 67,000-M(r) form of glutamate decarboxylase (GAD67), the gamma-aminobutyric acid synthetic enzyme. Transcription begins at a single promoter (P1) in adult brain but at two tandem promoters, P1 and P2, in fetal brain. P1, which is 3' to P2, resembles the promoter regions of many constitutively expressed genes, whereas P2 resembles a tissue-specific promoter. P1 contains a 10-base sequence (dec-1) that closely matches the element I cis-regulatory sequence identified in the promoter region of Drosophila 3,4-dihydroxyphenylalanine decarboxylase. Gel shift and transient expression assays demonstrate that the dec-1 sequence plays a role in the transcription of the human GAD67 gene.

Animals↗
PubMed1992

Finite element stress analysis of a push-out test. Part 1: Fixed interface using stress compatible elements.

In this first part of a two-part paper, interelement stress compatible finite elements are developed and used to perform the stress analysis of a push-out test with a fixed interface. In the formulation, the required continuity of some of the stresses along either a specific interface or all interelement interfaces is enforced by a penalty procedure. The model is axisymmetric and consists of two cylinders attached to each other through the interface. Various relative material properties and boundary conditions are simulated in order to examine their effects on the interface stresses. Both loadings of axial compression force and axial torque are considered. The predicted results exhibit identical interelement stresses and displacements even when highly dissimilar materials are used. They also exhibit a complex state of interface stresses which depend on the geometry, material arrangement, boundary conditions, and loading. The variation of the shear stress is often highly nonuniform and the radial normal stresses are likely to be large. The present results, therefore, disagree with the common assumptions made in the pull-out tests in the orthopaedic applications. Finally, stress analysis of a number of possible testing configurations could lead to the design of an optimal pull-out test which maximizes the usefulness of the measured results in terms of the interface bond strength and factors affecting it.

Biomechanical Phenomena↗
PubMed2004

Haemophilus ducreyi strain ATCC 27722 contains a genetic element with homology to the vibrio RS1 element that can replicate as a plasmid and confer NAD independence on haemophilus influenzae.

The nucleotide sequence of pNAD1, a plasmid from Haemophilus ducreyi identified on the basis of its ability to confer NAD independence on Actinobacillus pleuropneumoniae and H. influenzae, has been determined. In addition to containing the nadV gene, the plasmid contains homologues of the rstR and rstA genes, genes encoding repressor and replication proteins, respectively, in the Vibrio CTXphi and the Vibrio RS1 element, suggesting a single-stranded bacteriophage origin for pNAD1. Tandem copies of the plasmid are integrated into the H. ducreyi 35000HP genome.

Amino Acid Sequence↗
PubMed1995

HPRS-103 (exogenous avian leukosis virus, subgroup J) has an env gene related to those of endogenous elements EAV-0 and E51 and an E element found previously only in sarcoma viruses.

The avian leukosis and sarcoma virus (ALSV) group comprises eight subgroups based on envelope properties. HPRS-103, an exogenous retrovirus recently isolated from meat-type chicken lines, is similar to the viruses of these subgroups in group antigen but differs from them in envelope properties and has been assigned to a new subgroup, J. HPRS-103 has a wide host range in birds, and unlike other nontransforming ALSVs which cause late-onset B-cell lymphomas, HPRS-103 causes late-onset myelocytomas. Analysis of the sequence of an infectious clone of the complete proviral genome indicates that HPRS-103 is a multiple recombinant of at least five ALSV sequences and one EAV (endogenous avian retroviral) sequence. The HPRS-103 env is most closely related to the env gene of the defective EAV-E51 but divergent from those of other ALSV subgroups. Probing of restriction digests of line 0 chicken genomic DNA has identified a novel group of endogenous sequences (EAV-HP) homologous to that of the HPRS-103 env gene but different from sequences homologous to EAV and E51. Unlike other replication-competent nontransforming ALSVs, HPRS-103 has an E element in its 3' noncoding region, as found in many transforming ALSVs. A deletion found in the HPRS-103 U3 EFII enhancer factor-binding site is also found in all replication-defective transforming ALSVs (including MC29, which causes rapid-onset myelocytomas).

Alpharetrovirus↗
PubMed1994

Two pathways for serum regulation of the c-fos serum response element require specific sequence elements and a minimal domain of serum response factor.

The c-fos serum response element (SRE) is necessary and sufficient for induction of the c-fos gene in response to serum and growth factors. This activation is dependent upon serum response factor (SRF), a transcriptional activator which binds the SRE. A factor, p62TCF, which binds in conjunction with SRF to the SRE and which is activated by mitogen-activated protein kinase, has also been implicated in c-fos regulation. By using a reporter gene system with weak SRE mutations that is dependent upon overexpression of SRF for serum induction, we have found that there are at least two pathways for serum induction that converge on the SRE. Loss of TCF binding by mutations in SRF and the SRE did not reduce serum induction of the reporter genes. We have found a pathway for serum induction that is sensitive to mutations in the A/T-containing central sequence of the SRE and which is independent of TCF. When this pathway was mutated, activation was dependent upon TCF binding, demonstrating that TCF can also function in serum induction. Both of the signalling pathways required a minimal domain of SRF. This domain, spanning SRF's DNA binding domain, was sufficient for serum induction when fused to a heterologous transcriptional activation domain.

Amino Acid Sequence↗
PubMed1996

Functional characterization of a non-AUUUA AU-rich element from the c-jun proto-oncogene mRNA: evidence for a novel class of AU-rich elements.

AU-rich RNA-destabilizing elements (AREs) found in the 3' untranslated regions of many labile mRNAs encoding proto-oncoproteins and cytokines generally contain (i) one or more copies of the AUUUA pentanucleotide and (ii) a high content of uridylate and sometimes also adenylate residues. Recently, we have identified a potent ARE from the 3' untranslated region of c-jun proto-oncogene mRNA that does not contain the AUUUA motif. In an attempt to further our understanding of the general principles underlying mechanisms by which AREs direct rapid and selective mRNA degradation, in this study we have characterized the functionally important structural features and properties of this non-AUUUA ARE. Like AUUUA-containing AREs, this non-AUUUA ARE directs rapid shortening of the poly(A) tail as a necessary first step for mRNA degradation. It can be further dissected into three structurally and functionally distinct regions, designated domains I, II, and III. None of three domains alone is able to significantly destabilize the stable beta-globin mRNA. The two unlinked domains, I and III, together are necessary and sufficient for specifying the full destabilizing function of this non-AUUUA ARE. Domain II appears functionally dispensable but can partially substitute for domain I. Domain swaps made between the c-jun non-AUUUA and the c-fos AUUUA-containing AREs reveal that the two AREs, while sharing no sequence homology, appear to contain sequence domains that are structurally distinct but functionally overlapping and exchangeable. These data support the idea that the ultimate destabilizing function of an individual ARE is determined by its own unique combination of structurally distinct and functionally interdependent domains. Our polysome profile studies show tha the destabilizing function of the c-jun non-AUUUA ARE does not require any active transit by ribosomes of the mRNA bearing it, further corroborating that the destabilizing function of AREs is not tightly coupled to ongoing translation by ribosomes. Moreover, unlike AUUUA-containing AREs, the c-jun ARE is insensitive to blockage of its effects by addition of transcription inhibitors. Thus, our data provide further evidence for the existence of a novel class of ARE with unique properties.

3T3 Cells↗
PubMed2004

The Herpesvirus saimiri small nuclear RNAs recruit AU-rich element-binding proteins but do not alter host AU-rich element-containing mRNA levels in virally transformed T cells.

Herpesvirus saimiri (HVS) encodes seven Sm-class small nuclear RNAs, called HSURs (for Herpesvirus saimiri U RNAs), that are abundantly expressed in HVS-transformed, latently infected marmoset T cells but are of unknown function. HSURs 1, 2, and 5 have highly conserved 5'-end sequences containing the AUUUA pentamer characteristic of AU-rich elements (AREs) that regulate the stability of many host mRNAs, including those encoding most proto-oncogenes and cytokines. To test whether the ARE-containing HSURs act to sequester host proteins that regulate the decay of these mRNAs, we demonstrate their in vivo interaction with the ARE-binding proteins hnRNP D and HuR in HVS-transformed T cells using a new cross-linking assay. Comprehensive Northern and microarray analyses revealed, however, that the levels of endogenous ARE-containing mRNAs are not altered in T cells latently infected with HVS mutants lacking HSURs 1 and 2. HSUR 1 binds the destabilizing ARE-binding protein tristetraprolin induced following activation of HVS-transformed T cells, but even in such stimulated cells, the levels of host ARE-containing mRNAs are not altered by deletion of HSURs 1 and 2. Instead, HSUR 1 itself is degraded by an ARE-dependent pathway in HVS-transformed T cells, suggesting that HVS may take advantage of the host ARE-mediated mRNA decay pathway to regulate HSUR expression. This is the first example of posttranscriptional regulation of the expression of an Sm small nuclear RNA.

Animals↗