Species boundaries and phylogenetic relationships within the green algal genus Codium (Bryopsidales) based on plastid DNA sequences

Despite the potential model role of the green algal genus Codium for studies of marine speciation and evolution, there have been difficulties with species delimitation and a molecular phylogenetic framework was lacking. In the present study, 74 evolutionarily significant units (ESUs) are delimited using 227 rbcL exon 1 sequences obtained from specimens collected throughout the genus' range. Several morpho-species were shown to be poorly defined, with some clearly in need of lumping and others containing pseudo-cryptic diversity. A phylogenetic hypothesis of 72 Codium ESUs is inferred from rbcL exon 1 and rps3-rp/16 sequence data using a conventional nucleotide substitution model (GTR + Gamma + I), a codon position model and a covariotide (covarion) model, and the fit of a multitude of substitution models and alignment partitioning strategies to the sequence data is reported. Molecular clock tree rooting was carried out because out-group rooting was probably affected by phylogenetic bias. Several aspects of the evolution of morphological features of Codium are discussed and the inferred phylogenetic hypothesis is used as a framework to study the biogeography of the genus, both at a global scale and within the Indian Ocean. (c) 2007 Elsevier Inc. All rights reserved.

cpDNA-RFLP in Ceramium (Rhodophyta): Intraspecific polymorphism and species-level phylogeny

Restriction fragment length polymorphism (RFLP) analysis of chloroplast (cp) DNA is a powerful tool for the study of microevolutionary processes in land plants, yet has not previously been applied to seaweed populations. We used cpDNA-RFLP, detected on Southern blots using labeled total plastid DNA, to search for intraspecific and intrapopulational cpDNA RFLP polymorphism in two species of the common red algal genus Ceramium in Ireland and Britain. In C. botryocarpum one polymorphism was detected in one individual among 18 from two populations. Twenty-six individuals of C. virgatum from five populations at three locations exhibited a total of four haplotypes. One was frequent (80.8% of individuals); the others were rare (7.7, 7.7 and 4.2%) and were private to particular populations. Polymorphism was observed in two populations. The corrected mean was 2.26 +/- 0.36 haplotypes per population, which was within the typical range determined for higher plants using similar techniques. The spatial distribution of haplotypes was heterogeneous, with highly significant population differentiation (P = 0.00018; Fisher's exact test). Intraspecific polymorphism in C. virgatum had no impact on species-level phylogenetic reconstruction. This is the first unequivocal report of both intraspecific and intrapopulational cpDNA-RFLP polymorphism in algae.

Psychological problems in children with cerebral palsy: A cross-sectional European study

Objectives: To describe psychological symptoms in 8–12-year-old children with cerebral palsy; to investigate predictors of these symptoms and their impact on the child and family.

Design: A cross-sectional multi-centre survey.

Participants: Eight hundred and eighteen children with cerebral palsy, aged 8–12 years, identified from population-based registers of cerebral palsy in eight European regions and from multiple sources in one further region.

Main outcome measures: The Strengths and Difficulties Questionnaire (SDQ)P4-16 and the Total Difficulties Score (TDS) dichotomised into normal/borderline (TDS = 16) versus abnormal (TDS > 16).

Statistical analysis: Multilevel, multivariable logistic regression to relate the presence of psychological symptoms to child and family characteristics.

Results: About a quarter of the children had TDS > 16 indicating significant psychological symptoms, most commonly in the domain Peer Problems. Better gross motor function, poorer intellect, more pain, having a disabled or ill sibling and living in a town were independently associated with TDS > 16. The risk of TDS > 16 was odds ratio (OR) = .2 (95% CI: .1 to .3) comparing children with the most and least severe functional limitations; OR = 3.2 (95%CI: 2.1 to 4.8) comparing children with IQ < 70 and others; OR = 2.7 (95% CI: 1.5 to 4.6) comparing children in severe pain and others; OR = 2.7 (95% CI:1.6 to 4.6) comparing children with another disabled sibling or OR = 1.8 (95%CI: 1.2 to 2.8) no siblings and others; OR = 1.8 (95% CI: 1.1 to 2.8) comparing children resident in a town and others. Among parents who reported their child to have psychological problems, 95% said they had lasted over a year, 37% said they distressed their child and 42% said they burdened the family at least ‘quite a lot’.

Conclusions: A significant proportion of children with cerebral palsy have psychological symptoms or social impairment sufficiently severe to warrant referral to specialist services. Care must be taken in the assessment and management of children with cerebral palsy to ensure psychological problems are not overlooked and potentially preventable risk factors like pain are treated effectively. The validity of the SDQ for children with severe disability warrants further assessment.

Electrochemical Oxidation of Hydrogen Sulfide at Platinum Electrodes in Room Temperature Ionic Liquids: Evidence for Significant Accumulation of H2S at the Pt/1-Butyl-3-methylimidazolium Trifluoromethylsulfonate Interface

Electrochemical oxidation of hydrogen sulfide gas (H2S) has been studied at a platinum microelectrode (10 mu m diameter) in five room temperature ionic liquids (RTILs): [C(4)mim][OTf], [C(4)dmim][NTf2], [C(4)mim][PF6],. [C(6)mim][FAP], and [P-14,P-6,P-6,P-6][FAP] (where [C-n mim](+) = 1-alkyl-3-methylimidazolium, [C(n)dmim](+) = 1-alkyl-2,3-dimethylimidazolium, [P-14,P-6,P-6,P-6](+) = tris(p-hexyl)-tetradecylphosphonium, [OTf](-) = trifluoromethlysulfonate, [NTf2](-) = bis(trifluoromethylsulfonyl)imide, [PF6](-) = hexafluorophosphate, and [FAP](-) = trifluorotris(pentafluoroethyl)phosphate). In four of the RTILs ([C(4)dmim][NTf2], [C(4)mim][PF6], [C(6)mim][FAP], and [P-14,P-6,P-6,P-6][FAP]), no clear oxidative signal was observed. In [C(4)mim][OTf], a chemically irreversible oxidation peak was observed on the oxidative sweep with no signal seen on the reverse scan. The oxidative signal showed an adsorptive stripping peak type followed by near steady-state limiting current behavior. Potential step chronoamperometry was carried out on the reductive wave, giving a diffusion coefficient and solubility of 1.6 x 10(-11) m(2) s(-1) and 7 mM, respectively (at 25 degrees C). Using these data, we modeled the oxidation signal kinetically, assuming adsorption preceded oxidation and that adsorption was approximately Langmuirian. The oxidation step was described by an electrochemically fully irreversible Tafel law/Butler-Volmer formalism. Modeling indicated a substantial buildup of H2S in the double layer in excess of the coverage that would be expected for a monolayer of chemisorbed H2S, reflecting high solubility of the gas in [C(4)mim][OTf] and possible attractive interactions with the [OTf](-) anions accumulated at the electrode at potentials positive of the potential of zero charge. Solute enrichment of the double layer in the solution adjacent to the electrode appears a novel feature of RTIL electrochemistry.

sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Background
Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures.

Results
This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies.

Conclusion
The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMap

Proteomic analysis of circulating immune complexes in juvenile idiopathic arthritis reveals disease-associated proteins

Juvenile idiopathic arthritis reflects a group of clinically heterogeneous arthritides hallmarked by elevated concentrations of circulating immune complexes. In this study, the circulating immune complex proteome was examined to elucidate disease-associated proteins that are overexpressed in patients with an aggressive, and at times destructive, disease phenotype. To solve this proteome, circulating immune complexes were isolated from the sera of patients with chronic, erosive or early-onset, aggressive disease and from patients in medical remission or healthy controls subsequent to protein separation by 2-DE. Thirty-seven protein spots were overexpressed in the circulating immune complexes of the aggressive disease groups as compared to controls, 28 of which have been confidently identified to date. Proteolytic fragments of glyceraldehyde-3-phosphate dehydrogenase, serotransferrin, and a-1-antitrypsin have been identified among others. In total, these 28 putative disease-associated proteins most definitely contribute to immune complex formation and likely have a significant role in disease etiology and pathogenesis. Moreover, these proteins represent markers of aggressive disease, which could aid in diagnosis and management strategies, and potential therapeutic targets to prevent or control disease outcome. This is the first in-depth analysis of the circulating immune complex proteome in juvenile idiopathic arthritis.

Can statins prevent or help treat Alzheimer's disease?

Evidence accumulating from biological and epidemiological studies suggests that high levels of serum cholesterol may promote the pathological processes that lead to Alzheimer's disease (AD). Lowering cholesterol in experimental animal models slows the expression of Alzheimer's pathology. These findings raise the possibility that treating humans with cholesterol lowering medications might reduce the risk of developing AD or help treat it. The statins (lovastatin, pravastatin, simvastatin, and others) are powerful cholesterol lowering agents of proven benefit in vascular disease. Several clinical studies comparing the occurrence of AD between users and non-users of statins suggested that risk of AD was substantially reduced among the users. However, because these studies were not randomized trials, they provided insufficient evidence to recommend statin therapy. Cochrane reviews are based on the best available information about healthcare interventions and they focus primarily on randomized controlled trials (RCTs). On the issue of prevention, two randomized trials have been carried out and neither showed any reduction in occurrence of AD in patients treated with statins compared to those given placebo. Statins cannot therefore be recommended for the prevention of AD. Regarding treatment of AD, the large RCTs which have assessed this outcome have not published their results. Initial analysis from the studies available indicate statins have no benefit on the outcome measure ADAS-Cog but have a significant beneficial effect on MMSE as an outcome. We need to await full results from the RCTs before we can be certain. In addition statins were not detrimental to cognition in either systematic review.

Electron-impact excitation of Ni II: Collision strengths and effective collision strengths for low lying fine-structure forbidden transitions

Context. Considerable demand exists for electron excitation data for Ni ii, since lines from this abundant ion are observed in a wide variety of laboratory and astrophysical spectra. The accurate theoretical determination of these data can present a significant challenge however, due to complications arising from the presence of an open 3d-shell in the description of the target ion. Aims. In this work we present collision strengths and Maxwellian averaged effective collision strengths for the electron-impact ex- citation of Ni ii. Attention is concentrated on the 153 forbidden fine-structure transitions between the energetically lowest 18 levels of Ni ii. Effective collision strengths have been evaluated at 27 individual electron temperatures ranging from 30–100 000 K. To our knowledge this is the most extensive theoretical collisional study carried out on this ion to date.Methods. The parallel R-matrix package RMATRX II has recently been extended to allow for the inclusion of relativistic effects. This suite of codes has been utilised in the present work in conjunction with PSTGF to evaluate collision strengths and effective collision strengths for all of the low-lying forbidden fine-structure transitions. The following basis configurations were included in the target model – 3d9 , 3d8 4s, 3d8 4p, 3d7 4s2 and 3d7 4s4p – giving rise to a sophisticated 295 j j-level, 1930 coupled channel scattering problem. Results. Comprehensive comparisons are made between the present collisional data and those obtained from earlier theoretical evaluations. While the effective collision strengths agree well for some transitions, significant discrepancies exist for others.

Electron-impact excitation of Cr II A theoretical calculation of collision and effective collision strengths for forbidden transitions

Context. Absorption or emission lines of Cr II are observed in a wide variety of astrophysical spectra and accurate atomic data are urgently needed to interpret these lines. Many of these data are impossible to measure experimentally and a full theoretical treatment is the only means by which these data can be obtained.

Aims. In this paper, we present collision strengths and effective collision strengths for electron-impact excitation of Cr II for forbidden transitions among the lowest-lying 74 fine-structure levels. Effective collision strengths have been computed for 18 individual electron temperatures of astrophysical importance, ranging from 2000-100 000 K.

Methods. The parallel suite of R-matrix packages, RMATRX II, which has recently been extended to allow for the inclusion of relativistic effects, has been used in the present work to compute the collision strengths and effective collision strengths for electron-impact excitation of Cr II. We concentrate in this publication on low-lying forbidden lines among the lowest 74 jj fine-structure levels with configurations 3d(5) and 3d(4)4s, although atomic data has been evaluated for all 39 060 transitions among the 280 jj levels of configurations 3d(5), 3d(4)4s and 3d(4)4p. This work constitutes the largest evaluation ever performed for this ion involving 1932 coupled channels.

Results. Collision and effective collision strengths are presented for all transitions among the lowest 74 J pi states of Cr II and comparisons made with the work of Bautista et al. (2009). While the effective collision strengths agree well for some transitions, significant discrepancies exist for others. We believe that the present atomic data represents the most accurate, most sophisticated and most complete data set for electron-impact excitation of Cr II and we would recommend them to astrophysicists and plasma physicists in their application work. We would expect that the effective collision strengths presented for the important low-lying forbidden lines are accurate to within 15%.

Rhodopsin and the Others: A Historical Perspective on Structural Studies of G Protein-Coupled Receptors

The role of rhodopsin as a structural prototype for the study of the whole superfamily of G protein-coupled receptors (GPCRs) is reviewed in an historical perspective. Discovered at the end of the nineteenth century, fully sequenced since the early 1980s, and with direct three-dimensional information available since the 1990s, rhodopsin has served as a platform to gather indirect information on the structure of the other superfamily members. Recent breakthroughs have elicited the solution of the structures of additional receptors, namely the beta 1- and beta 2-adrenergic receptors and the A(2A) adenosine receptor, now providing an opportunity to gauge the accuracy of homology modeling and molecular docking techniques and to perfect the computational protocol. Notably, in coordination with the solution of the structure of the A(2A) adenosine receptor, the first "critical assessment of GPCR structural modeling and docking" has been organized, the results of which highlighted that the construction of accurate models, although challenging, is certainly achievable. The docking of the ligands and the scoring of the poses clearly emerged as the most difficult components. A further goal in the field is certainly to derive the structure of receptors in their signaling state, possibly in complex with agonists. These advances, coupled with the introduction of more sophisticated modeling algorithms and the increase in computer power, raise the expectation for a substantial boost of the robustness and accuracy of computer-aided drug discovery techniques in the coming years.

delta C-13 and delta N-15 reveal significant differences in the coastal foodwebs of the seas surrounding Trinidad and Tobago

This study assessed nearshore, marine ecosystem function around Trinidad and Tobago (TT). The coastline of TT is highly complex, bordered by the Atlantic Ocean, the Caribbean Sea, the Gulf of Paria and the Columbus Channel, and subject to local terrestrial runoff and regional riverine inputs (e.g. the Orinoco and Amazon rivers). Coastal organisms can assimilate energy from allochthonous and autochthonous Sources, We assessed whether stable isotopes delta C-13 and delta N-15 Could be used to provide a rapid assessment of trophic interactions in primary consumers around the islands. Filter-feeding (bivalves and barnacles) and grazing organisms (gastropods and chitons) were collected from 40 marine sites during the wet season. The flesh of organisms was analysed for delta C-13 and delta N-15. Results indicate significant variation in primary consumers (by feeding guild and sampling zone). This variation was linked to different energy Sources being assimilated by consumers. Results suggest that offshore production is fuelling intertidal foodwebs; for example, a depleted delta C-13 signature in grazers from the Gulf of Paria, Columbus Channel and the Caribbean and Atlantic coastline of 9 Tobago indicates that carbon with an offshore origin (e.g. phytoplankton and dissolved organic matter) is more important than benthic or littoral algae (luring the wet season. Results also confirm findings from other studies indicating that much of the coastline is subject to Cultural eutrophication. This Study revealed that ecosystem function is spatially variable around the coastline of TT, This has clear implications for marine resource management, as a single management approach is unlikely to be successful at a national level.