A comparison between biotic indices and predictive models in stream water quality assessment based on benthic diatom communities

Diatoms are widely used in stream bioassessment due to their broad distribution, extraordinary variability and the ability to integrate changes in water quality. The indices Specific Polluosensitivity Index (SPI), standardized Biological Diatom Index (BDI), European Economic Community Index (CEC) and Generic Diatom Index (GDI), originally developed in France, are often applied in Portugal to evaluate stream ecological quality based on diatom communities. Alternatively, predictive models resulting from the comparison between the communities of the study site and those of a set of reference sites representing undisturbed or the best available conditions of a given region have been proposed as valuable methods for evaluating the ecological status of streams. In the present study, we applied the four above-mentioned widely used diatom-based indices (SPI, BDI, CEC and GDI) and a predictive model (MoDi) to 54 sites located in central Portugal to assess the sensitivity of the five methods to a range of anthropogenic disturbances cumulatively affecting streams and represented by 27 variables (e.g., organic enrichment, changes in morphology of the channels, integrity of the riparian corridor, land use in the catchment). The results were analyzed comparatively through Spearman correlations, Boxplots and Stepwise Discriminant Analysis. This study confirmed the sensitivity of diatoms to organic and nutrient contamination (showed by the MoDi, BDI, CEC and SPI) and revealed the importance of suspended solids (through the MoDi, GDI, and SPI). The relevance of modifications in land use to diatoms was shown by all methods applied, except for the GDI. The MoDI also revealed the importance of changes in the structure and morphology of the reach and the channel, like the construction of artificial walls or embankments and connectivity; the BDI also related its assessments with the riparian zone integrity; and the SPI was not useful in detecting morphological pressures. The GDI produced the most divergent assessments and was less effective in revealing the anthropogenic disturbances. The use of the predictive model (MoDi) is therefore a good method for the assessment of streams in central Portugal because it expresses a great diversity of quantitative and qualitative changes in freshwater systems reflected in the structure (species richness and abundance) of diatom communities.     

Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design

Background  

In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software. Retrieval and formatting of sequences flanking each SNP, prior to assay design, becomes rate-limiting for more than about ten SNPs, especially if annotated for repetitive regions and adjacent variations. We routinely process up to 50 SNPs at once.     

Exportin-5-mediated nuclear export of eukaryotic elongation factor 1A and tRNA

Transport of proteins and RNA into and out of the cell nucleus is mediated largely by a family of RanGTP-binding transport receptors. Export receptors (exportins) need to bind RanGTP for efficient loading of their export cargo. We have identified eukaryotic elongation factor 1A (eEF1A) and tRNA as RanGTP-dependent binding partners of exportin-5 (Exp5). Exp5 stimulates nuclear export of eEF1A when microinjected into the nucleus of Xenopus laevis oocytes. Surprisingly, the interaction between eEF1A and Exp5 is dependent on tRNA that can interact directly with Exp5 and, if aminoacylated, recruits eEF1A into the export complex. These data suggested to us that Exp5 might support tRNA export. Indeed, not only the canonical tRNA export receptor, exportin-t, but also Exp5 can drive nuclear export of tRNA. Taken together, we show that there exists an alternative tRNA export pathway which can be exploited to keep eEF1A out of the cell nucleus.     

A new experimental setup for studying the formation of phosphate binding iron oxides in marine sediments. Preliminary results

A new laboratory method is introduced to study theformation of phosphate binding iron(III) oxides at theredox boundary in marine sediments. A sediment core isgiven a very well-defined oxic-anoxic interface byplacing a 0.45 µm filter between the sediment andthe overlying water. After a period of 1 months thefilter is covered with a layer of fresh iron oxides,formed by the oxidation of upward diffusing Fe²⁺from the sediment pore water. The formed iron oxidesare investigated by electron probe X-ray microanalysis(EXPMA). With a sediment core from the brackish BalticSea the average molar composition of 788 formedparticles is Fe_1.00±0.13P_0.55±0.06Ca_0.37±0.04 plus unknown amounts of O, H andC. The results show that the particles have a uniformcomposition, and that calcium plays an important rolein the phosphate binding. The laboratory method is auseful supplement to in situ sampling forstudies of iron oxides.     

In vivo aggregation properties of the nuclear poly(A)-binding protein PABPN1

A broad range of degenerative diseases is associated with intracellular inclusions formed by toxic, aggregation-prone mutant proteins. Intranuclear inclusions constitute a pathological hallmark of oculopharyngeal muscular dystrophy (OPMD), a dominantly inherited disease caused by (GCG) repeat expansions in the gene that encodes for nuclear poly(A) binding protein (PABPN1). The mutation results in an extended polyalanine stretch that has been proposed to induce protein aggregation and formation of intranuclear inclusions. Here we show that normal PABPN1 is inherently aggregation-prone when exogenously expressed in either HeLa or myogenic C2 cells. Similar deposits of insoluble PABPN1 are formed by variant forms of the protein containing either a polyalanine expansion or a complete deletion of the polyalanine tract, indicating that the mutation responsible for OPMD is not essential for formation of PABPN1 inclusions. In contrast, interfering with any of the protein domains required for stimulation of poly(A) polymerase prevents the formation of inclusions. Most surprisingly, photobleaching experiments reveal that both normal and expanded PABPN1 molecules are not irreversibly sequestered into aggregates, but rather move rapidly in and out of the inclusions. These findings have important implications for the interpretation of OPMD model systems based on exogenous expression of PABPN1.     

Gene regulatory divergence among species estimated by altered developmental patterns in interspecific hybrids

Disturbances in the schedules of gene expression in developing interspecific fish hybrids have been used to draw inferences about the extent of gene regulatory divergence between species and about the degree to which this gene regulatory divergence is correlated with structural gene divergence, as estimated by genetic distance. Sperm from each of 10 different species representing six genera within the family Centrarchidae was used to fertilize eggs of the Florida largemouth bass (Micropterus salmoides floridanus). The genetic distances (D; Nei 1978) between the parental species used to form the hybrids ranged from 0.133 to 0.974. The developmental success and temporal patterns of gene expression of each of the hybrids were compared with those of the Florida largemouth bass. As the genetic distance between the paternal species and the Florida largemouth bass increased, there was a general decline in developmental success in the hybrid embryos as demonstrated by the observed reductions in the percentage of hatching and by progressively earlier and more extensive morphological abnormalities. Concomitantly, progressively more marked alterations in developmental schedules of expression of 15 enzyme loci occurred in the hybrids as the genetic distance between parental species increased. However, observed deviations from this trend for a few species may represent an uncoupling of the rates and modes of evolution of structural genes from those for genes regulating developmental processes.      

A case of spontaneous coronary artery disease regression

Coronary angiographic trials have demonstrated that lowering cholesterol can slow the progression of atherosclerosis, limit the formation of new lesions and enhance atherosclerotic regression together with reducing the incidence of clinical events (Waters D, 1996). Spontaneous regression of coronary atherosclerotic lesions is rare. We report the case of a patient with a severe within-stent restenotic lesion whose coronary disease spontaneously regressed 12 months after initial diagnosis, allowing for medical treatment of symptoms rather than repeated intervention. (Int J Cardiovasc Interventions 1999; 2: 121-123)     

Physicochemical study of floranol, its copper(II) and iron(III) complexes, and their inhibitory effect on LDL oxidation

The antioxidant activity of floranol (3,5,7,2'-tetrahydroxy-6-methoxy-8-prenylflavanone), a new flavonoid isolated from the roots of Dioclea grandiflora, was evaluated by the inhibition of human low-density lipoprotein (LDL) oxidation. Floranol increased its oxidation lag-phase significantly in a dose-dependent manner. As the antioxidant mechanism may involve metal coordination, we have undertaken a detailed study of floranol interactions with Cu(II) and Fe(III) by combination of UV-visible (UV-Vis) and mass spectrometries and cyclic voltammetry. The acidity constants of the ligand as well as the stability constants of the metal complexes were calculated. The pKa values of 6.58, 11.97 and 13.87 were determined and the following acidity order is proposed 7-OH>5-OH>2'-OH. The best fit between experimental and calculated spectra was obtained assuming the formation of two Cu(II) complexes: [CuL] logbeta=19.34+/-0.05 and [CuL(2)](2-) logbeta=26.4+/-0.10 and three Fe(III) complexes: [FeL(3)](3-) logbeta=44.72+/-0.09, [FeL(2)](-) logbeta=35.32+/-0.08 and [FeL](+) logbeta=19.51+/-0.04. In addition, copper and iron reduction is less favorable in the presence of floranol. These results indicate that floranol can efficiently bind Cu(II) and Fe(III) ions thus preventing their effect on LDL oxidation.     

VEGF and VEGFR-2 (KDR) internalization is required for endothelial recovery during wound healing

Vascular endothelial growth factor (VEGF) receptor activation regulates endothelial cell (EC) survival, migration and proliferation. Recently, it was suggested the cross-talk between the VEGF receptors-1 (FLT-1) and -2 (KDR) modulated several of these functions, but the detailed molecular basis for such interactions remained unexplained. Here we demonstrate for the first time that VEGF stimulation of EC monolayers induced a rapid FLT-1-mediated internalization of KDR to the nucleus, via microtubules and the endocytic pathway, internalization which required the activation of PI 3-kinase/AKT. KDR deletion mutants were generated in several tyrosine residues; in these, VEGF-induced KDR internalization was impaired, demonstrating this process required activation (phosphorylation) of the receptor. Furthermore, we demonstrate that in vitro wounding of EC monolayers leads to a rapid and transient internalization of VEGF+KDR to the nucleus, which is essential for monolayer recovery. Notably, FLT-1 blockade impedes VEGF and KDR activation and internalization, blocking endothelial monolayer recovery. Our data reveal a previously unrecognized mechanism induced by VEGF on EC, which regulates EC recovery following wounding, and as such indicate novel targets for therapeutic intervention.