Rising variance and abrupt shifts of subfossil chironomids due to eutrophication in a deep sub-alpine lake

In response to anthropogenic eutrophication and global warming, deep-water oxygen depletion is expected to have large effects on freshwater lake biogeochemistry and resident communities. In particular, it has been observed that deep-water hypoxia may potentially lead to regime shifts of lake benthic communities. We explored such community shifts by reconstructing a high-resolution subfossil chironomid record from a sediment core collected in the sub-alpine lake Remoray in France. We identified an abrupt shift in chironomid composition triggered by the collapse of the dominant Sergentia coracina-type chironomids around 1980. We found that the collapse of Sergentia coracina type was coupled to a gradual increase in organic matter content in lake sediments caused by eutrophication. We concluded that the most probable cause for the collapse of Sergentia coracina type was a change in oxygen concentrations below the minimal threshold for larval growth. We also analyzed trends in variance and autocorrelation of chironomid dynamics to test whether they can be used as early warnings of the Sergentia collapse. We found that variance rose prior to the collapse, but it was marginally significant (Kendal rank correlation 0.71, p = 0.05), whereas autocorrelation increased but insignificantly and less strongly (Kendal rank correlation 0.23, p = 0.25). By combining reconstructions of ecosystem dynamics and environmental drivers, our approach demonstrates how lake sediments may provide insights into the long-term dynamics of oxygen in lakes and its impact on aquatic fauna.     

A methodology for rapid detection of Salmonella typhimurium using label-free electrochemical impedance spectroscopy

A pathogen detection methodology based on Bayesian decision theory has been developed for rapid and reliable detection of Salmonella typhimurium. The methodology exploits principles from statistical signal processing along with impedance spectroscopy in order to analytically determine the existence of pathogens in the target solution. The proposed technique is validated using a cost-effective and portable immunosensor. This device uses label-free, electrochemical impedance spectroscopy for pathogen detection and has been demonstrated to reliably detect pre-infectious levels of pathogen in sample solutions. The detection process does not entail any pathogen enrichment procedures. The results using the proposed technique indicate a detection time of approximately 6min (5min for data acquisition, 1min for analysis) for pathogen concentrations in the order of 500CFU/ml. The detection methodology presented here has demonstrated high accuracy and can be generalized for the detection of other pathogens with healthcare, food, and environmental implications. Furthermore, the technique has a low computational complexity and uses a minimal data-set (only 30 data-samples) for data analysis. Hence, it is ideal for use in hand-held pathogen detectors.     

A genomic view of yeast membrane transporters.

The yeast membrane transporters play crucial roles in functions as diverse as nutrient uptake, drug resistance, salt tolerance, control of cell volume, efflux of undesirable metabolites and sensing of extracellular nutrients. A significant fraction of the many transporters inventoried after sequencing of the yeast genome has been characterised by classical experimental approaches. Post-genomic analysis has allowed a more extensive characterisation of transporter categories less tractable by genetics, for instance of transporters of intracellular membranes or transporters encoded by multigene families and displaying overlapping substrate specificities. A complete view of the role of membrane transporters in the metabolism of yeast may not be far off.     

Role of salt bridges in homeodomains investigated by structural analyses and molecular dynamics simulations

Homeodomains are a class of helix-turn-helix DNA-binding protein motifs that play an important role in the control of cellular development in eukaryotes. They fold in a three alpha-helix structural module, where the third helix is the recognition helix that fits into the major groove of DNA. Structural analysis of the members of the homeodomain family led to the identification of interactions likely to stabilize the protein domains. Linking the helices pairwise, three salt bridges were found to be well preserved within the family. Also well conserved were two cation-pi interactions between aromatic and positively charged side chains. To analyze the structural role of the salt bridges, molecular dynamics simulations (MD) were carried out on the wild-type homeodomain from the Drosophila paired protein (1fjl) and on three mutants, which lack one or two salt bridges and mimic natural mutations in other homeodomains. Analysis of the trajectories revealed only small structural rearrangements of the three helices in all MD simulations, thereby suggesting that the salt bridges have no essential stabilizing role at room temperature, but rather might be important for improving thermostability. The latter hypothesis is supported by a good correlation between the melting midpoint temperatures of several homeodomains and the number of salt bridges and cation-pi interactions that connect secondary structures.     

Isolation of the melanoma-associated antigen p23 using antibody phage display

The general responsiveness of human melanoma to immunotherapy has been well established, but active immunotherapy of melanoma has been hampered by insufficient information on the immunogenicity of melanoma-associated Ags in patients. In this study, we isolated a recombinant phage-Fab clone (A10-5) from a phage-Fab library derived from the B cells of a melanoma patient in remission after immunotherapy. Purified A10-5 Fab bound at high levels to cultured melanoma cell lines and to tissue sections of metastatic and vertical growth phase primary melanoma, but not to radial growth phase primary melanoma, nevi, or normal skin. A10-5 Fab bound to both the surface and the cytoplasm of cultured melanoma cells, but only to the cytoplasm of cultured fibroblasts. Western blot analysis revealed A10-5 Fab reactivity with a 33- and a 23-kDa glycoprotein under nonreducing conditions, and with a 23-kDa protein only under reducing conditions. A cDNA with an open reading frame predicted to encode a 23-kDa protein was cloned by screening a melanoma cell cDNA library with A10-5 Fab. This protein (p23) is the human homologue of the murine tumor transplantation Ag P198 that interacts with the cytoplasmic domain of ErbB-3 expressed by melanoma cells. Thus, the Ab phage display method has identified a novel, stage-specific melanoma-associated Ag that may have therapeutic and diagnostic value.     

Characterization of the Escherichia coli YedU protein as a molecular chaperone

We have cloned, purified to homogeneity, and characterized as a molecular chaperone the Escherichia coli YedU protein. The purified protein shows a single band at 31 kDa on SDS-polyacrylamide gels and forms dimers in solution. Like other chaperones, YedU interacts with unfolded and denatured proteins. It promotes the functional folding of citrate synthase and alpha-glucosidase after urea denaturation and prevents the aggregation of citrate synthase under heat shock conditions. YedU forms complexes with the permanently unfolded protein, reduced carboxymethyl alpha-lactalbumin. In contrast to DnaK/Hsp70, ATP does not stimulate YedU-dependent citrate synthase renaturation and does not affect the interaction between YedU and unfolded proteins, and YedU does not display any peptide-stimulated ATPase activity. We conclude that YedU is a novel chaperone which functions independently of an ATP/ADP cycle.     

The conserved active site proline determines the reducing power of Staphylococcus aureus thioredoxin

Nature uses thioredoxin-like folds in several disulfide bond oxidoreductases. Each of them has a typical active site Cys-X-X-Cys sequence motif, the hallmark of thioredoxin being Trp-Cys-Gly-Pro-Cys. The intriguing role of the highly conserved proline in the ubiquitous reducing agent thioredoxin was studied by site-specific mutagenesis of Staphylococcus aureus thioredoxin (Sa_Trx). We present X-ray structures, redox potential, pK(a), steady-state kinetic parameters, and thermodynamic stabilities. By replacing the central proline to a threonine/serine, no extra hydrogen bonds with the sulphur of the nucleophilic cysteine are introduced. The only structural difference is that the immediate chemical surrounding of the nucleophilic cysteine becomes more hydrophilic. The pK(a) value of the nucleophilic cysteine decreases with approximately one pH unit and its redox potential increases with 30 mV. Thioredoxin becomes more oxidizing and the efficiency to catalyse substrate reduction (k(cat)/K(M)) decreases sevenfold relative to wild-type Sa_Trx. The oxidized form of wild-type Sa_Trx is far more stable than the reduced form over the whole temperature range. The driving force to reduce substrate proteins is the relative stability of the oxidized versus the reduced form Delta(T(1/2))(ox/red). This driving force is decreased in the Sa_Trx P31T mutant. Delta(T(1/2))(ox/red) drops from 15.5 degrees C (wild-type) to 5.8 degrees C (P31T mutant). In conclusion, the active site proline in thioredoxin determines the driving potential for substrate reduction.     

Temporal and spatial fluctuations in bacterial abundances in four basins of a landfill leachate treatment (Etueffont, France)

The seasonal distribution of bacterial communities was assessed in a landfill leachate station located in Etueffont (Territoire de Belfort, France). Water samples were taken monthly from May 1998 to May 1999 from both the gross leachate and four lagooning basins. Bacterial numbers varied from 0.04x10(6) to 0.35x10(6) cells ml(-1) (m+/-sd=0.13x10(6)+/-0.12x10(6) cells ml(-1)). They decreased from the first to the last basin and were overall lower than those reported in literature for aquatic systems with comparable organic matter content. This may be ascribed to the leachate toxicity on bacteria.     

Validation of a physician global assessment tool for vitiligo extent: Results of an international vitiligo expert meeting

Currently, vitiligo lacks a validated Physician Global Assessment (PGA) for disease extent. This PGA can be used to stratify and interpret the numeric scores obtained by the Vitiligo Extent Score (VES). We investigated the interrater reliability of a 5‐point PGA scale during an international vitiligo workshop. Vitiligo experts from five different continents rated photographs of non‐segmental vitiligo patients with varying degrees of extent with the PGA score. Good interrater agreements (intraclass correlation coefficient >0.6) were observed between the raters overall and within each continent. All hypotheses to evaluate construct validity were confirmed. Median VES values per category were for limited 1.10 [IQR: 0.21–1.67], moderate 3.17 [IQR: 1.75–6.21], extensive 9.58 [IQR: 6.21–13.03] and very extensive 42.67 [IQR: 21.20–42.67]. Defined categories for vitiligo extent can be valuable for inclusion criteria and may impact future reimbursement criteria.