Hypoxic Regulation of Vascular Endothelial Growth Factor mRNA Stability Requires the Cooperation of Multiple RNA Elements

Vascular endothelial growth factor (VEGF) is a key regulator of developmental, physiological, and tumor angiogenesis. Upregulation of VEGF expression by hypoxia appears to be a critical step in the neovascularization of solid cancers. The VEGF mRNA is intrinsically labile, but in response to hypoxia the mRNA is stabilized. We have systematically analyzed the regions in the VEGF mRNA that are responsible for its lability under normoxic conditions and for stabilization in response to hypoxia. We find that the VEGF mRNA not only contains destabilizing elements in its 3′ untranslated region (3′UTR), but also contains destabilizing elements in the 5′UTR and coding region. Each region can independently promote mRNA degradation, and together they act additively to effect rapid degradation under normoxic conditions. Stabilization of the mRNA in response to hypoxia is completely dependent on the cooperation of elements in each of the 5′UTR, coding region, and 3′UTR. Combinations of any of two of these three regions were completely ineffective in responding to hypoxia, whereas combining all three regions allowed recapitulation of the hypoxic stabilization seen with the endogenous VEGF mRNA. We conclude that multiple regions in the VEGF mRNA cooperate both to ensure the rapid degradation of the mRNA under normoxic conditions and to allow stabilization of the mRNA in response to hypoxia. Our findings highlight the complexity of VEGF gene expression and also reveal a mechanism of gene regulation that could become the target for strategies of therapeutic intervention.

Contaminant bioavailability in soils, sediments, and aquatic environments

The aqueous concentrations of heavy metals in soils, sediments, and aquatic environments frequently are controlled by the dissolution and precipitation of discrete mineral phases. Contaminant uptake by organisms as well as contaminant transport in natural systems typically occurs through the solution phase. Thus, the thermodynamic solubility of contaminant-containing minerals in these environments can directly influence the chemical reactivity, transport, and ecotoxicity of their constituent ions. In many cases, Pb-contaminated soils and sediments contain the minerals anglesite (PbSO4), cerussite (PbCO3), and various lead oxides (e.g., litharge, PbO) as well as Pb2+ adsorbed to Fe and Mn (hydr)oxides. Whereas adsorbed Pb can be comparatively inert, the lead oxides, sulfates, and carbonates are all highly soluble in acidic to circumneutral environments, and soil Pb in these forms can pose a significant environmental risk. In contrast, the lead phosphates [e.g., pyromorphite, Pb5(PO4)3Cl] are much less soluble and geochemically stable over a wide pH range. Application of soluble or solid-phase phosphates (i.e., apatites) to contaminated soils and sediments induces the dissolution of the “native” Pb minerals, the desorption of Pb adsorbed by hydrous metal oxides, and the subsequent formation of pyromorphites in situ. This process results in decreases in the chemical lability and bioavailability of the Pb without its removal from the contaminated media. This and analogous approaches may be useful strategies for remediating contaminated soils and sediments.

d-Ribulose-5-Phosphate 3-Epimerase: Cloning and Heterologous Expression of the Spinach Gene, and Purification and Characterization of the Recombinant Enzyme1

We have achieved, to our knowledge, the first high-level heterologous expression of the gene encoding d-ribulose-5-phosphate 3-epimerase from any source, thereby permitting isolation and characterization of the epimerase as found in photosynthetic organisms. The extremely labile recombinant spinach (Spinacia oleracea L.) enzyme was stabilized by dl-α-glycerophosphate or ethanol and destabilized by d-ribulose-5-phosphate or 2-mercaptoethanol. Despite this lability, the unprecedentedly high specific activity of the purified material indicates that the structural integrity of the enzyme is maintained throughout isolation. Ethylenediaminetetraacetate and divalent metal cations did not affect epimerase activity, thereby excluding a requirement for the latter in catalysis. As deduced from the sequence of the cloned spinach gene and the electrophoretic mobility under denaturing conditions of the purified recombinant enzyme, its 25-kD subunit size was about the same as that of the corresponding epimerases of yeast and mammals. However, in contrast to these other species, the recombinant spinach enzyme was octameric rather than dimeric, as assessed by gel filtration and polyacrylamide gel electrophoresis under nondenaturing conditions. Western-blot analyses with antibodies to the purified recombinant enzyme confirmed that the epimerase extracted from spinach leaves is also octameric.

BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} acts as a phosphate analog in proteins phosphorylated on aspartate: Structure of a BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} complex with phosphoserine phosphatase

Protein phosphoaspartate bonds play a variety of roles. In response regulator proteins of two-component signal transduction systems, phosphorylation of an aspartate residue is coupled to a change from an inactive to an active conformation. In phosphatases and mutases of the haloacid dehalogenase (HAD) superfamily, phosphoaspartate serves as an intermediate in phosphotransfer reactions, and in P-type ATPases, also members of the HAD family, it serves in the conversion of chemical energy to ion gradients. In each case, lability of the phosphoaspartate linkage has hampered a detailed study of the phosphorylated form. For response regulators, this difficulty was recently overcome with a phosphate analog, BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document}, which yields persistent complexes with the active site aspartate of their receiver domains. We now extend the application of this analog to a HAD superfamily member by solving at 1.5-Å resolution the x-ray crystal structure of the complex of BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} with phosphoserine phosphatase (PSP) from Methanococcus jannaschii. The structure is comparable to that of a phosphoenzyme intermediate: BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} is bound to Asp-11 with the tetrahedral geometry of a phosphoryl group, is coordinated to Mg2+, and is bound to residues surrounding the active site that are conserved in the HAD superfamily. Comparison of the active sites of BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document}⋅PSP and BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document}⋅CeY, a receiver domain/response regulator, reveals striking similarities that provide insights into the function not only of PSP but also of P-type ATPases. Our results indicate that use of BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} for structural studies of proteins that form phosphoaspartate linkages will extend well beyond response regulators.

cdc18+ regulates initiation of DNA replication in Schizosaccharomyces pombe.

In the fission yeast Schizosaccharomyces pombe the cdc18'+gene is required both for initiation of DNA replication and for coupling mitosis to the completion of S phase. Cells lacking Cdc18 fail to enter S phase but still undergo nuclear division. Expression of cdc18+ is sufficient to drive a G1-arrested cdc10ts mutant into the S phase of the cell cycle, indicating that cdc18+ represents a critical link between passage through START and the initiation of DNA replication. Here we show that Cdcl8 is a highly unstable protein that is expressed only once per cell cycle at the boundary between GI and S phase. De novo synthesis of Cdc18 is required before, but not after, the initiation of DNA replication, indicating that Cdc18 function is not necessary once the initiation event has occurred. Overproduction of the protein results in an accumulation of cells with DNA content of greater than 2C and delays mitosis, suggesting that Cdc18 is sufficient to cause reinitiation of DNA replication within a given cell cycle. Our data indicate that the synthesis of Cdc18 protein is a critical rate-limiting step in the initiation of DNA replication during each cell cycle. The extreme lability of the protein may contribute to the prevention of reinitiation.

Relationship Maintenance in Couples with a Partner Who Has Attention Deficit Hyperactivity Disorder

The body of research on the relationship functioning of adults with attention deficit hyperactivity disorder (ADHD) is relatively small; the aim of the present study is to advance our understanding of this topic. It has been estimated that three to ten percent of children and one to five percent of adults have impairing symptoms of ADHD, which is a total of 4 million children and 4-5 million adults in the U.S. (Wender, 2000). A recent prevalence study found that approximately 4.4% of adults in the U.S. meet the criteria for a diagnosis of ADHD (Kessler et al., 2006). Children with ADHD show innate temperamental characteristics, usually inattentiveness, distractibility, impulsivity, restlessness, demandingness, hyperreactivity, low tolerance for frustration, temperoutbursts, bossiness and stubbornness, and mood lability, along with an innate proclivity for academic underachievement. It has been estimated that one- to two-thirds of children with ADHD have symptoms that continue into adulthood, and for 40-50% of these adults, these symptoms are serious enough to cause impairment in functioning (Everett & Everett, 1999; Wender, 2000). Research suggests that the majority of cases are transmitted genetically, but some may be due to exposure to environmental toxins such as lead. Consumption of excess sugar or allergies to food may exacerbate or mimic ADHD symptoms in some children, but they are not a cause of ADHD (Wender, 2000). One hypothesized cause of the symptoms associated with ADHD is a deficit in the brain's executive functioning (Barkley & Gordon, 2002). Executive functioning can be conceptualized as the ability to inhibit, organize, and plan behaviors. Barkley and Gordon (2002) define it as the abilityto self-direct and regulate behaviors toward future goals, including social behaviors and goals. Other research suggests that executive functioning consists of inhibition, control of interference, verbal and nonverbal working memory, emotional regulation, attention, verbal fluency, visual scanning, and processing speed. Studies have shown impairments in these areas among adults with ADHD (Barkley & Gordon, 2002; Barkley, Murphy & Kwasnik, 1996; Goldstein, 2002).

Organic carbon and carbohydrates in waters of the Amazon River, Atlantic Ocean, and Tropical Indian Ocean

A method is presented to study carbohydrate composition of marine objects involved into sedimento- and diagenesis (plankton, particulate matter, benthos, and bottom sediments). Analysis of the carbohydrates is based on consecutive separation of their fractions with different solvents (water, alkali, and acid). Ratios of carbohydrate fractions allows to evaluate lability of carbohydrate complexes. They are also usable as an indicators of biogeochemical processes in the ocean, as well of genesis and degree of transformation of organic matter in bottom sediments and nodules. Similarity in monosaccharide composition is shown for dissolved organic matter and aqueous and alkaline fractions of seston and particulate matter.

Organic compounds in surface sediments from the Pakistan continental margin

In order to assess whether the oxygen-minimum zone (OMZ) in the Arabian sea has an effect on the preservation and composition of organic matter in surface sediments we investigated samples from three different transects on the Pakistan continental margin across the OMZ. In addition to determining the total amount of organic carbon (TOC), we analyzed the extractable lipids by gas chromatography, combined gas chromatography/mass spectrometry, and compound-specific stable carbon isotope measurements. The extractable lipids are dominated by marine organic matter as indicated by the abundance of lipids typical of marine biota and by the bulk and molecular isotopic composition. Sediments from within the OMZ are enriched in organic carbon and in several extractable lipids (i.e. phytol, n-alcohols, total sterols, n-C35 alkane) relative to stations above and below this zone. Other lipid concentrations, such as those of total n-fatty acids and total n-alkanes fail to show any relation to the OMZ. Only a weak correlation of TOC with mineral surface area was found in sediments deposited within the OMZ. In contrast, sediments from outside the OMZ do not show any relationship between TOC and surface area. Among the extractable lipids, only the n-alkane concentration is highly correlated with surface area in sediments from the Hab and Makran transects. In sediments from outside the OMZ, the phytol and sterol concentrations are also weakly correlated with mineral surface area. The depositional environment of the Indus Fan offers the best conditions for an enhanced preservation of organic matter. The OMZ, together with the undisturbed sedimentation at moderate rates, seems to be mainly responsible for the high TOC values in this area. Overall, the type of organic matter and its lability toward oxic degradation, the mineral surface area, the mineral composition, and possibly the secondary productivity by (sedimentary) bacteria also appear to have an influence on organic matter accumulation and composition.

Resolution and characterisation of multiple isoforms of bovine kappa-casein by 2-DE following a reversible cysteine-tagging enrichment strategy

Visualisation of multiple isoforms of kappa-casein on 2-D gels is restricted by the abundant alpha- and beta-caseins that not only limit gel loading but also migrate to similar regions as the more acidic kappa-casein isoforms. To overcome this problem, we took advantage of the absence of cysteine residues in alpha(S1)- and beta-casein by devising an affinity enrichment procedure based on reversible biotinylation of cysteine residues. Affinity capture of cysteine-containing proteins on avidin allowed the removal of the vast majority of alpha(S1)- and beta-casein, and on subsequent 2-D gel analysis 16 gel spots were identified as kappa-casein by PMF. Further analysis of the C-terminal tryptic peptide along with structural predictions based on mobility on the 2-D gel allowed us to assign identities to each spot in terms of genetic variant (A or B), phosphorylation status (1, 2 or 3) and glycosylation status (from 0 to 6). Eight isoforms of the A and B variants with the same PTMs were observed. When the casein fraction of milk from a single cow, homozygous for the B variant of kappa-casein, was used as the starting material, 17 isoforms from 13 gel spots were characterised. Analysis of isoforms of low abundance proved challenging due to the low amount of material that could be extracted from the gels as well as the lability of the PTMs during MS analysis. However, we were able to identify a previously unrecognised site, T-166, that could be phosphorylated or glycosylated. Despite many decades of analysis of milk proteins, the reasons for this high level of heterogeneity are still not clear.

Fossilization and degradation of archaeal intact polar tetraether lipids in ODP Site 201-1229 sediments

Glycerol dibiphytanyl glycerol tetraether (GDGT) lipids are part of the cellular membranes of Thaumarchaeota, an archaeal phylum composed of aerobic ammonia oxidizers, and are used in the paleotemperature proxy TEX86. GDGTs in live cells possess polar head groups and are called intact polar lipids (IPL-GDGTs). Their transformation to core lipids (CL) by cleavage of the head group was assumed to proceed rapidly after cell death but it has been suggested that some of these IPL-GDGTs can, just like the CL-GDGTs, be preserved over geological timescales. Here, we examined IPL-GDGTs in deeply buried (0.2-186 mbsf, ~2.5 Myr) sediments from the Peru Margin. Direct measurements of the most abundant IPL-GDGT, IPL-crenarchaeol, specific for Thaumarchaeota, revealed depth profiles which differed per head group. Shallow sediments (<1 mbsf) contained IPL-crenarchaeol with both glycosidic- and phosphate headgroups, as also observed in thaumarchaeal enrichment cultures, marine suspended particulate matter and marine surface sediments. However, hexose, phosphohexose-crenarchaeol is not detected anymore below 6 mbsf (~7 kyr), suggesting a high lability. In contrast, IPL-crenarchaeol with glycosidic head groups is preserved over time scales of Myr. This agrees with previous analyses of deeply buried (>1 m) marine sediments, which only reported glycosidic and no phosphate-containing IPL-GDGTs. TEX86 values of CL-GDGTs did not markedly change with depth, and the TEX86 of IPL-derived GDGTs decreased only when the proportions of monohexose- to dihexose-GDGTs changed, likely due to the enhanced preservation of the monohexose GDGTs. Our results support the hypothesis that in situ GDGT production and differential IPL degradation in sediments is not substantially affecting TEX86 paleotemperature estimations based on CL GDGTs and indicate that likely only a small amount of IPL-GDGTs present in deeply buried sediments is part of cell membranes of active Archaea. The amount of archaeal biomass in the deep biosphere based on these IPLs may have been substantially overestimated.

Affective Instability, Childhood Trauma and Major Affective Disorders

Background and Aims Affective instability (AI), childhood trauma, and mental illness are linked, but evidence in affective disorders is limited, despite both AI and childhood trauma being associated with poorer outcomes. Aims were to compare AI levels in bipolar disorder I (BPI) and II (BPII), and major depressive disorder recurrent (MDDR), and to examine the association of AI and childhood trauma within each diagnostic group. Methods AI, measured using the Affective Lability Scale (ALS), was compared between people with DSM-IV BPI (n = 923), BPII (n = 363) and MDDR (n = 207) accounting for confounders and current mood. Regression modelling was used to examine the association between AI and childhood traumas in each diagnostic group. Results ALS scores in descending order were BPII, BPI, MDDR, and differences between groups were significant (p < 0.05). Within the BPI group any childhood abuse (p = 0.021), childhood physical abuse (p = 0.003) and the death of a close friend in childhood (p = 0.002) were significantly associated with higher ALS score but no association was found between childhood trauma and AI in BPII and MDDR. Conclusions AI is an important dimension in bipolar disorder independent of current mood state. There is a strong link between childhood traumatic events and AI levels in BPI and this may be one way in which exposure and disorder are linked. Clinical interventions targeting AI in people who have suffered significant childhood trauma could potentially change the clinical course of bipolar disorder.

Development of a new analytical approach based on cellulose membrane and chelator for differentiation of labile and inert metal species in aquatic systems

A new procedure was developed in this study, based on a system equipped with a cellulose membrane and a tetraethylenepentamine hexaacetate chelator (MD-TEPHA) for in situ characterization of the lability of metal species in aquatic systems. To this end, the DM-TEPHA system was prepared by adding TEPHA chelator to cellulose bags pre-purified with 1.0 mol L-1 of HCl and NaOH solutions. After the MD-TEPHA system was sealed, it was examined in the laboratory to evaluate the influence of complexation time (0-24 h), pH (3.0, 4.0, 5.0, 6.0 and 7.0), metal ions (Cu, Cd, Fe, Mn and Ni) and concentration of organic matter (15, 30 and 60 mg L-1) on the relative lability of metal species by TEPHA chelator. The results showed that Fe and Cu metals were complexed more slowly by TEPHA chelator in the MD-TEPHA system than were Cd, Ni and Mn in all pH used. It was also found that the pH strongly influences the process of metal complexation by the MD-TEPHA system. At all the pH levels, Cd, Mn and Ni showed greater complexation with TEPHA chelator (recovery of about 95-75%) than did Cu and Fe metals. Time also affects the lability of metal species complexed by aquatic humic substances (AHS); while Cd, Ni and Mn showed a faster kinetics, reaching equilibrium after about 100 min, and Cu and Fe approached equilibrium after 400 min. Increasing the AHS concentration decreases the lability of metal species by shifting the equilibrium to AHS-metal complexes. Our results indicate that the system under study offers an interesting alternative that can be applied to in situ experiments for differentiation of labile and inert metal species in aquatic systems. (c) 2006 Elsevier B.V. All rights reserved.

Estudo da labilidade de Cu(II), Cd(II), Mn(II) e Ni(II) em substâncias húmicas aquáticas utilizando-se membranas celulósicas organomodificadas

In this work commercial filters papers were organomodified with tetraethylorthosilicate (TEOS) and 3-aminopropyltriethoxysilane (3-APTS), aiming at the development of a new analytical procedure for in-situ speciation of labile and inert metal species in aquatic systems. Parameters that exert influence on the metal lability such as pH, chelating time, concentration and characteristics of the organic matter were studied in the laboratory using tests for metal recuperation. The results showed slower kinetics for Cu ion than for Ni, Mn and Cd in the absence of aquatic humic substances (AHS). The relative lability observed for complexed metals in aquatic humic substances using organomodified filter papers was Cu>>Cd>Ni>Mn. The pH values, structural characteristics and concentration of AHS exert strong influence on the lability of the metals. The results obtained showed that the utilization of organomodified filter papers can be an interesting and promising alternative for in situ characterization of metal lability in aquatic systems.

In situ differentiation of labile/inert metal species in Brazilian tropical rivers by means of a time-controlled batch-procedure based on TEPHA resin

The present study deals with a new analytical procedure based on a cellulose diffusion membrane and immobilised tetraethylene-pentamine-hexaacetate chelator (DM-TEPHA) for an in situ differentiation of labile and inert metal species in aquatic systems. The DM-TEPHA system was prepared by placing TEPHA chelator in pre-purified cellulose bags and in situ applied immersing the system in two Brazilian rivers to study the relative lability of metal species (Cu, Pb, Fe, Mn and Ni) as a function of the time and the quantity of exchanger, respectively. The procedure is simple and enables a new perspective for understanding the complexation, transport, stability and lability of metal species in aquatic systems rich in organic matter.

Dynamics and Heterogeneity of Pb(II) Binding by SiO2 Nanoparticles in an Aqueous Dispersion

Pb(II) binding by SiO2 nanoparticles in an aqueous dispersion was investigated under conditions where the concentrations of Pb2+ ions and nanoparticles are of similar magnitude. Conditional stability constants (log K) obtained at different values of pH and ionic strength varied from 4.4 at pH 5.5 and I = 0.1 M to 6.4 at pH 6.5 and I = 0.0015 M. In the range of metal to nanoparticle ratios from 1.6 to 0.3, log K strongly increases, which is shown to be due to heterogeneity in Pb(II) binding. For an ionic strength of 0.1 M the Pb2+/SiO2 nanoparticle system is labile, whereas for lower ionic strengths there is loss of lability with increasing pH and decreasing ionic strength. Theoretical calculations on the basis of Eigen-type complex formation kinetics seem to support the loss of lability. This is related to the nanoparticulate nature of the system, where complexation rate constants become increasingly diffusion controlled. The ion binding heterogeneity and chemodynamics of oxidic nanoparticles clearly need further detailed research.