Proposal of an ISO/IEEE11073 platform for healthcare telemonitoring: plug-and-play solution with new use cases

Remote patient monitoring in e-Health is everyday closer to be a mature technology / service. However, there is still a lack of development in areas such as standardization of the sensor's communication interface, integration into Electronic Healthcare Record systems or incorporation in ambient-intelligent scenarios. This work identifies a set of use cases involved in the personal monitoring scenario and highlights the related features and functionalities, as well as the integration and implementation difficulties found when these are to be implemented in a system based on the ISO/IEEE11073 (X73) standard. It is part of a cooperative research effort devoted to the development of an end-to-end standards-based telemonitoring solution. Standardization committees are working towards adapting the X73 standard to this emerging personal health devices market and use case identification is essential to direct these revisions.

Complete genome sequences of Maize dwarf mosaic and Sugarcane mosaic virus isolates coinfecting maize in Spain

The genomes of Spanish isolates of Maize dwarf mosaic virus (MDMV-Sp) and Sugarcane mosaic virus (SCMV-Sp) were completely sequenced. Nucleotide sequence identities of SCMV-Sp to those of other SCMV isolates ranged from 79 to 90%. MDMV-Sp shared 85% nucleotide identity with the only other fully sequenced isolate of MDMV. MDMV-Sp and SCMV-Sp differed from each other by 31% in their nucleotide sequences. Phylogenetic analyses showed that SCMV isolates group by host rather than by geographical location. Two significant recombination signals were identified in the NIa and NIb regions of the SCMV-Sp genome.

Expression of Na(+)/K(+)-ATPase alpha-subunit mRNA during embryonic development of the crayfish Astacus leptodactylus

Astacus leptodactylus is a decapod crustacean fully adapted to freshwater where it spends its entire life cycle after hatching under huge osmoconcentration differences between the hemolymph and surrounding freshwater. We investigated the expression of mRNA encoding one ion transport-related protein, Na(+)/K(+)-ATPase alpha-subunit, and one putative housekeeping gene, beta-actin, during crayfish ontogenesis using quantitative real-time PCR. A 216-amino acid part of the open reading frame region of the cDNA coding for the Na(+)/K(+)-ATPase alpha-subunit was sequenced from total embryo, juvenile and adult gill tissues. The predicted amino acid sequence showed a high percentage similarity to those of other invertebrates (up to 95%) and vertebrates (up to 69%). beta-actin expression exhibited modest changes through embryonic development and early post-embryonic stage. The Na(+)/K(+)-ATPase alpha-subunit gene was expressed in all studied stages from metanauplius to juvenile. Two peaks of expression were observed: one in young embryos at 25% of embryonic development (EI=100 mum), and one in embryos just before hatching (at EI=420 mum), continuing in the freshly hatched juveniles. The Na(+)/K(+)-ATPase expression profile during embryonic development is time-correlated with the occurrence of other features, including ontogenesis of excretory antennal glands and differentiation of gill ionocytes linked to hyperosmoregulation processes and therefore involved in freshwater adaptation.

The origin of the Chorthippus parallelus hybrid zone: chromosomal evidence of multiple refugia for Iberian populations

A study of the variation in pattern and frequency of constitutive heterochromatin and nucleolar organizing regions of the X chromosomes of male Chorthippus parallelus grasshoppers in 25 populations within the Iberian peninsula requires us to revise our interpretation of the biogeography and evolutionary history of this species. Hybridization between the subspecies Cp erythropus and Cp parallelus, previously only known from populations in the Pyrenean cols, is shown to extend at least 400 km further into north-west Spain. A novel X-chromosome variant is described that appears to be close to fixation in 18 populations, mainly from the centre and south of Spain. Our findings indicate a possible independent origin for each of three distinct, nonderivative X variants present in Spain: the northern Cp erythropus and Cp parallelus variants, and a central-southern Cp erythropus variant. The first two are distinguished by interstitial and distal C bands, respectively, whereas the central-southern form has neither. This central-southern form is probably the current representative of the ancestral Iberian X variant. The pattern of variation supports the hypotheses of multiple refugia for Iberian populations and that more hybrid zones exist between these chromosomal variants.

Early Kinetics of Amyloid Fibril Formation Reveals Conformational Reorganisation of Initial Aggregates

Understanding the initial steps of protein aggregation leading to the formation of amyloid fibrils remains a challenge. Here, the kinetics of such a process is determined for a misfolding protein model, ADA2h. The double nature of the very early kinetics suggests a step model of aggregation, where the denatured polypeptide folds into an aggregated beta-intermediate that subsequently reorganises into a more organised beta-sheet-richer structure that finally results in amyloid fibre formation. To determine the regions of the protein involved in amyloidosis, we have analysed a series of mutants previously made to study ADA2h folding. Using the algorithm TANGO, we have designed mutants that should enhance or decrease aggregation. Experimental analysis of the mutants shows that the C terminus of the molecule (comprising the last and edge beta-strand) is the major contributor to amyloid fibril formation, in good agreement with theoretical predictions. Comparison with proteins with similar topology reveals that family folds do not necessarily share the same principles of protein folding and/or aggregation.

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks

SmartCell has been developed to be a general framework for modelling and simulation of diffusion-reaction networks in a whole-cell context. It supports localisation and diffusion by using a mesoscopic stochastic reaction model. The SmartCell package can handle any cell geometry, considers different cell compartments, allows localisation of species, supports DNA transcription and translation, membrane diffusion and multistep reactions, as well as cell growth. Moreover, different temporal and spatial constraints can be applied to the model. A GUI interface that facilitates model making is also available. In this work we discuss limitations and advantages arising from the approach used in SmartCell and determine the impact of localisation on the behaviour of simple well-defined networks, previously analysed with differential equations. Our results show that this factor might play an important role in the response of networks and cannot be neglected in cell simulations.

Point mutations in protein globular domains: contributions from function, stability and misfolding

Several contrasting hypotheses have been formulated about the influence of functional and conformational properties, like stability and avoidance of misfolding, on the evolution of protein globular domains. Selection at functional sites has been suggested to be detrimental to stability or coupled to it. Avoidance of misfolding may be achieved by discarding misfolding-prone sequences or by maintaining a stable native state and thus destabilizing partially or fully unfolded states from which misfolding can take place. We have performed a hierarchical analysis of a large database of point mutations to dissect the relative contributions of function, stability and misfolding in the evolution of natural sequences. We show that at catalytic sites, selection for function overrules selection for stability but find no evidence for an anticorrelation between function and stability. Selection for stability plays a secondary role at binding sites, but is not fully coupled to selection for function. Remarkably, we did not find a selective pressure against misfolding-prone sequences in globular proteins at the level of individual positions. We suggest that such a selection would compromise native-state stability due to a correlation between the stabilities of native and misfolded states. Stabilization of the native state is the most frequent way in which natural proteins avoid misfolding.

[Telemedicine: science or fiction?]

Telemedicine has been considered to be a scientific discipline midway between medicine and technology. Thus, over the last decade it has been largely influenced by the continuous development of computer and communications technologies. Now that the phase of its laboratory investigation has been completed, it can be considered to be a technique in a mature state. Hence, both from the point of view of technology suppliers and of the users of medicine -patients and professionals- there is a demand for a takeoff in the arena of its implantation, that is to say, the need for new health services based on telemedicine. This article offers an up-to-date view of the state of the art of telemedicine but without entering into an in-depth evaluation and description of the technology and its applications. On the contrary, our aim is to make it known to users and to the different health organisations, including their managers, that the conditions for its development are now available. Thus the success or failure of its implantation is a task for all of the actors involved. What is certain is that in the light of the experience and results of its application during the last decade, both in our surrounding geographical milieu and in the United States, there are unmistakable signs that telemedicine is here to stay.

First Detection of Wheat dwarf virus in Barley in Spain Associated with an Outbreak of Barley Yellow Dwarf

Severe dwarfing, yellowing, and crop failure were observed on barley in northeastern Spain during March and April of 2003. Leaves from 106 plants collected from 15 barley fields were analyzed using enzyme-linked immunosorbent assay (ELISA) with commercial antisera (Loewe Biochemica, Munich) specific for Barley mild mosaic virus (BaMMV), Barley yellow mosaic virus (BaYMV), the PAV and MAV serotypes of Barley yellow dwarf virus (BYDV), Barley yellow striate mosaic virus (BYSMV), Barley stripe mosaic virus (BSMV), Brome mosaic virus (BMV), Brome streak mosaic virus, (BStMV), Cereal yellow dwarf virus (CYDV), Wheat streak mosaic virus (WSMV), Wheat spindle streak mosaic virus (WSSMV), Soilborne cereal mosaic virus (SBCMV), and Wheat dwarf virus (WDV). In 70 samples, BYDV-PAV was the sole virus detected; in 20 other samples, this virus was detected in association with WDV, WSMV, BaMMV, and/or BaYMV. Mixed infections were further analyzed using reverse transcriptase-polymerase chain reaction (RT-PCR) or PCR with specific primers that amplify 445 bp of BaMMV (3), 433 bp of BaYMV (1), 600 bp of WSMV (primer 1: 5'CGAAACGCAGCG TTATTTC3', primer 2: 5'CATCTGAAG GGCTTGACG3'), and 1,200 bp of WDV (4). Eight samples gave the expected amplicons for WDV, two samples gave the expected amplicon for BaMMV, and one sample gave the BaMMV and BaYMV amplicons. No samples gave the amplicon for WSMV. In addition, 10 samples that were positive with ELISA for BYDV, either as a single or as multiple infections with other viruses, were analyzed with specific primers that amplify 600 bp of the BYDV genome (2) and all gave the expected RT-PCR product. ELISA and RT-PCR results agreed completely for WDV and BYDV samples, but agreed poorly for BaMMV and BaYMV (three of seven ELISA-positive samples). PCR products of WDV were subsequently cloned and sequenced. Sequence analysis confirmed the presence of WDV in these barley samples. This report shows the high occurrence of BYDV in barley fields and its association with BaMMV, BaYMV, and WDV infections that induces barley crop failure. To our knowledge, this is the first detection of WDV in Spain. References: (1) M. A. Achon et al. Plant Dis.87:1004, 2003. (2). E. S. G. Canning et al. J. Virol. Methods 56:191, 1996. (3) D. Hariri et al. Eur. J. Plant Pathol. 106:365, 2000. (4) A. Kvarnheden et al. Arch Virol. 147:206, 2002.

Effects of the insecticide permethrin on three life stages of the grass shrimp, Palaemonetes pugio

Toxicity of the pyrethroid insecticide permethrin was assessed using three life stages of the estuarine grass shrimp, Palaemonetes pugio. Adult and larval shrimp were tested with and without sediment. An aqueous embryo test was also conducted. Cellular stress biomarkers, glutathione, and lipid peroxidation, were assessed. Larval shrimp were the most sensitive life stage with a 96-h lethal concentration (LC(50)) value of 0.05 microg/L, compared to 0.25 microg/L for adults, and 6.4 microg/L for embryos. The presence of sediment significantly decreased toxicity of permethrin to both adult and larval shrimp. Permethrin exposure increased time to hatch in embryos and decreased swimming behavior of larvae. Lipid peroxidation levels were significantly decreased in the adult shrimp, but increased in larval shrimp exposed to permethrin. Low levels of permethrin may negatively affect grass shrimp health and survival. Permethrin use in the coastal zone should be carefully managed to avoid adverse impacts on nontarget estuarine organisms.

Sediment phosphate composition in relation to emergent macrophytes in the Doñana Marshes (SW Spain)

We have studied the effect of the presence of emergent macrophytes on the sediment phosphate composition of a eutrophic shallow marsh on the NE margin of Doñana (SW Spain). Top sediment and water samples were collected from both the open-water and the vegetated sites at three areas covered by different plant species: Scirpus maritimus, Juncus subulatus and Phragmites australis. The concentration of organic matter was significantly higher in the top sediment of sites covered by vegetation than in their adjacent open-water sites at the three vegetation areas. The P-fractional composition showed that the sediment was dominated by the inorganic P-fractions in all cases, reaching the highest concentration in the Ca-bound P-fraction (281-372 microg g(-1) d.w.). The sum of all P-fractions was significantly higher in the top sediment of the sites covered by J. subulatus and S. maritimus than in their adjacent open-water sites, and so were the org-P fraction extracted by hot NaOH and the concentration of phytate within this fraction. Deposition of plant material on the top sediment of areas vegetated by J. subulatus and S. maritimus explains these differences. The P-fractional composition of the seeds from J. subulatus showed that they contained a large proportion of organic P-fractions, particularly of the fraction extracted by hot NaOH (1868 microg g(-1) d.w., 85% of which was phytate). The presence of emergent macrophytes, therefore, influenced the distribution of P-fractions in the sediment depending on plant species. The P-bioavailability of shallow aquatic systems must be fully understood if wetlands are to be protected from further eutrophication.

Solvation in protein folding analysis: combination of theoretical and experimental approaches

An effort to combine theoretical analyses and protein engineering methods has been made to probe the folding mechanism of SH3 by using Energy Landscape Theory and a phi-value analysis. Particular emphasis was given to core residues and the effect of desolvation during the folding event by replacing the core valines with isosteric threonines. These mutations have the advantage of keeping the core structurally invariant while affecting core stability relative to the unfolded state. Although the valines that form the core appear spatially invariant, the folding kinetics of their threonine mutants varies, indicating their different extent of solvation in the transition-state ensemble. Theoretical studies predicted the distribution of folding kinetics of threonine mutants without previous knowledge of the measured rates. This initial success encourages further investigations of the molecular details behind these macroscopic phenomena and of the role of solvation in the folding mechanism.

SERTRALINE FOR THE PREVENTION OF RELAPSE IN DETOXICATED ALCOHOL DEPENDENT PATIENTS WITH A COMORBID DEPRESSIVE DISORDER: A RANDOMIZED CONTROLLED TRIAL

AIMS

We performed a double-blind, placebo-controlled randomized trial of sertraline in recently detoxified alcohol-dependent patients with current depressive symptoms. The objectives of the study were to evaluate the efficacy of sertraline at achieving stable abstinence, at ameliorating depressive symptoms and at improving quality of life in these patients.

METHODS

The study included 83 patients, who received either sertraline (50-150 mg/day) or placebo for 24 weeks. The primary outcome criteria were the rate of relapse into alcohol consumption and the rate of response on the Montgomery and Asberg Depression Rating Scale (MADRS).

RESULTS

At the end of the treatment period, relapse rates were 23.1% in the placebo group and 31.8% in the sertraline group. Responder rates for depression were 38.5% for the placebo group and 44.2% for the sertraline group. There was no significant difference between treatment groups with either variable. However, when patients were stratified into severe (MADRS score >or=26) and moderate (MADRS score <26) depression at inclusion, a significant treatment benefit with sertraline was observed in the former group. Quality of life, determined by the SF-36, improved in both groups, with more benefit observed for the sertraline group on mental health items. Sertraline was well tolerated, and the incidence of adverse events was similar in the two treatment groups.

CONCLUSIONS

The explanation for the overall good outcome in both treatment groups and for the inability to demonstrate a clear treatment effect may reside in the clinical features of the patients included.

Delta(13)C and tree-ring width reflect different drought responses in Quercus ilex and Pinus halepensis

Holm oak (Quercus ilexL.) and Aleppo pine (Pinus halepensisMill) are representative of two different functional types of trees extensively found in the Mediterranean: evergreen sclerophyllous and drought-adapted conifers. The former is considered a partially drought-tolerant species, whereas the latter is a typically drought-avoiding, water-saving species. We postulated that contrasting strategies in response to water deficits in Q. ilex and P. halepensis would lead to a differential sensitivity to changes in water availability. To test this hypothesis, we compared the response of both species in growth rate (measured as radial increments) and intrinsic water use efficiency WUE(i), as inferred from carbon isotope discrimination (Delta(13)C) in wood samples] among sites from different provenance regions in NE Spain. We found significant differences in Delta(13)C and growth among provenance regions, partly explained by contrasting water availability. Wood Delta(13)C was positively related with precipitation and the ratio between precipitation and potential evapotranspiration (P/ E). However, these relationships were stronger in P. halepensis (for P / E, r(2)=0.67, P <0.001) than in Q. ilex ( r(2)=0.42, P <0.01). In addition, radial growth was positively related with precipitation and Delta(13)C in P. halepensis ( r(2)=0.32 and r(2)=0.35, respectively, P <0.01), but not in Q. ilex. We concluded that P. halepensis was more sensitive than Q. ilex to water availability, showing faster increase in WUE(i) in response to water stress. We also found that the effect of north/south aspect on Delta(13)C and growth was site-specific, and unrelated to climatic variables.

Identification of peptides that neutralize bacterial endotoxins using beta-hairpin conformationally restricted libraries

Bacterial endotoxins are the major mediator of septic shock; therefore, endotoxin-neutralizing molecules could have biomedical applications. The septic shock cascade relies in a series of molecular recognition processes. The large contact-surface described for the interacting macromolecules, in most cases, prevents the identification of small molecules that could modulate such recognition events. Here we report on a beta-hairpin conformationally restricted combinatorial library that has been generated and screened towards the identification of new peptides that neutralize bacterial endotoxins. Starting with a de novo designed linear peptide that shows a beta-hairpin structure population of around 30%, (Ramirez-Alvarado, M., Blanco, F. J. and Serrano, L. Nat. Struc. Biol., 7, 604-612 (1996)), we selected four positions to build up a combinatorial library of 20(4) sequences. Deconvolution of the library reduced such a sequence complexity to 8 defined sequences. The newly identified peptides have a biological activity equivalent to that reported for peptides derived from natural endotoxin-binding proteins.

Towards the design and computational characterization of a membrane protein

The design of a transmembrane four-helix bundle is described. We start with an idealized four-helix bundle geometry, then use statistical information to build a plausible transmembrane bundle. Appropriate residues are chosen using database knowledge on the sequences of membrane helices and loops, then the packing of the bundle core is optimized, and favorable side chain rotamers from rotamer libraries are selected. Next, we use explicit physical knowledge from biomolecular simulation force fields and molecular dynamics simulations to test whether the designed structure is physically possible. These procedures test whether the designed protein will indeed be alpha-helical, well packed and stable over a time scale of several nanoseconds in a realistic lipid bilayer environment. We then test a modeling approach that does not include sophisticated database knowledge about proteins, but rather relies on applying our knowledge of the physics that governs protein motions. This independent validation of the design is based on simulated annealing and restrained molecular dynamics simulation in vacuo, comparable to procedures used to refine NMR and X-ray structures.

NMR and SAXS characterization of the denatured state of the chemotactic protein CheY: implications for protein folding initiation

The denatured state of a double mutant of the chemotactic protein CheY (F14N/V83T) has been analyzed in the presence of 5 M urea, using small angle X-ray scattering (SAXS) and heteronuclear magnetic resonance. SAXS studies show that the denatured protein follows a wormlike chain model. Its backbone can be described as a chain composed of rigid elements connected by flexible links. A comparison of the contour length obtained for the chain at 5 M urea with the one expected for a fully expanded chain suggests that approximately 25% of the residues are involved in residual structures. Conformational shifts of the alpha-protons, heteronuclear (15)N-[(1)H] NOEs and (15)N relaxation properties have been used to identify some regions in the protein that deviate from a random coil behavior. According to these NMR data, the protein can be divided into two subdomains, which largely coincide with the two folding subunits identified in a previous kinetic study of the folding of the protein. The first of these subdomains, spanning residues 1-70, is shown here to exhibit a restricted mobility as compared to the rest of the protein. Two regions, one in each subdomain, were identified as deviating from the random coil chemical shifts. Peptides corresponding to these sequences were characterized by NMR and their backbone (1)H chemical shifts were compared to those in the intact protein under identical denaturing conditions. For the region located in the first subdomain, this comparison shows that the observed deviation from random coil parameters is caused by interactions with the rest of the molecule. The restricted flexibility of the first subdomain and the transient collapse detected in that subunit are consistent with the conclusions obtained by applying the protein engineering method to the characterization of the folding reaction transition state.

Computer-assisted re-design of spectrin SH3 residue clusters

We have developed a protein design computer program, called Perla, which performs searches in sequence space to uncover optimal amino acid sequences for desired protein three-dimensional structures. Optimal sequences are localised at the minima of a sequence-structure energy landscape defined using a complex scoring function (an all-atom molecular mechanics force field plus statistical terms including entropy and solvation) measured with respect to a reference state simulating a denatured protein. Sequence choices eventually optimise side chain packing, secondary structure propensities, and hydrogen bonding and electrostatics interactions. Perla was used to re-design clusters of residues of the SH3 domain of alpha-spectrin. Several mutant proteins were produced and characterised. Some of our designed proteins have significantly higher stabilities (stability enhancements about 0.25, 0.70 and 1.0 kcal mol(-1)) than the wild-type protein. These successful protein re-designs, and similar examples found in the literature, establish the quality of the structure-based computational approach to protein design.

Computer-aided design of beta-sheet peptides

The design of beta-sheet proteins is still a challenge in the field of de novo protein design. Here, we have tested the validity of automatic design methods to create and/or improve beta-sheet peptides and proteins. We chose Betanova, a three-stranded beta-sheet peptide, as target system, and, as an automatic design tool, a protein design algorithm called PERLA (protein engineering rotamer library algorithm). PERLA was used to define both stabilising and destabilising single- and multiple-residue mutations of Betanova. Conformational analysis by NMR spectroscopy and far-UV circular dichroism (CD) allowed us to evaluate population differences among the set of designed peptides. Some of the new mutants are approximately 1 kcal/mol more stable than the wild-type peptide. Comparison of the scale of predicted and observed stabilities demonstrates that they are in good agreement for most peptides studied. Our results show that automatic design algorithms can be successfully applied to the design of beta-sheet peptides.

Bergerac-SH3: "frustation" induced by stabilizing the folding nucleus

The influence of an inserted exogenous independent folding element on the thermodynamics and folding properties of SH3 domain from alpha-spectrin has been investigated by creating a fused form between this small all-beta domain and a stable beta-hairpin (BH19). NMR analysis of synthetic peptides shows that insertion of BH19 nucleates formation of the original natural beta-hairpin (distal loop) that is part of the SH3 folding nucleus. The resulting protein (Bergerac-SHH) is more stable, folds faster and contains an elongated hairpin protruding from the globular domain as determined by 2D-NMR. "Protein engineering" analysis of the inserted region shows that it is folded in the transition state. Interestingly, stabilisation by insertion of the distal loop region results in the appearance of a compact intermediate revealed by a curved chevron plot at low denaturant concentration. This effect is eliminated at low salt concentrations by a single mutation of a hydrophobic residue within BH19 sequence, which is most probably involved in non-native interactions. Local stabilisation by enlargement and reinforcement of the folding nucleus, global compaction by the addition of salt and non-native interactions are shown to contribute to the observed deviation from the two-state behaviour.