The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

MOTIVATION: Homology models of proteins are of great interest for planning and analysing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all required tools, programs and databases into a single web-based workspace facilitates access to homology modelling from a computer with web connection without the need of downloading and installing large program packages and databases. RESULTS: SWISS-MODEL workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. A personal working environment is provided for each user where several modelling projects can be carried out in parallel. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. Tools for template selection, model building and structure quality evaluation can be invoked from within the workspace. Workflow and usage of the workspace are illustrated by modelling human Cyclin A1 and human Transmembrane Protease 3. AVAILABILITY: The SWISS-MODEL workspace can be accessed freely at http://swissmodel.expasy.org/workspace/     

Body size and shape evolution in host races of the tick Ixodes uriae

The tick Ixodes uriae is a common ectoparasite of seabirds, and is widely distributed across the circumpolar regions of both hemispheres. Previous work demonstrated the existence of genetically distinct host races of this ectoparasite, occurring across its current range. The objective of the present study was to examine whether these host races have evolved measurable morphological differences. We measured a set of morphological variables on 255 non‐engorged ticks (nymphs and adults) collected from three sympatrically occurring host species in the North Atlantic. Genotyping at eight microsatellite markers enabled us to analyse the relationship between patterns of morphological and neutral genetic variation. Multivariate analyses showed that most morphological variation was associated with size differences among tick individuals. Body size differed among races, but only in adult life stages. A linear discriminant analysis based on shape variation revealed three distinct morphological clusters corresponding to the three tick host races. These results, along with correlated patterns of host‐related genetic variation, suggest that differences among host‐related groups are not simply the result of phenotypic plasticity or drift, but rather reflect host‐associated adaptations. Experimental work and observations across the range of I. uriae will now be required to test the genetic basis and adaptive nature of morphological differences.     

Allogeneic mesenchymal stem cell infusion for the stabilization of focal segmental glomerulosclerosis

Focal segmental glomerulosclerosis (FSGS) is the most frequent acquired renal condition resulting in end stage kidney disease in children. We describe a cell therapy treatment with human allogeneic bone marrow mesenchymal stem cells (MSC) in a 13-year-old patient developing recurrent FSGS after renal transplantation, which was not responding to conventional therapy.This treatment relied on the following measurements:clinical and laboratory evaluation of renal function, proteome array, biopsy, short tandem repeat assay.Before MSC treatment, the patient needed weekly plasmapheresis to achieve proteinuria-to-creatininuria ratio below 5. After three MSC infusions without adverse events, the patient has a stable renal function and the proteinuria target was reached without plasmapheresis. In addition, some circulating inflammatory factors decreased and their levels were still low after one year.This is the first report of an MSC treatment in an FSGS patient. Even though different factors may have contributed to the clinical results, after MSC infusion a stable reduction in the serum level of several inflammatory factors has been registered and the patient does not need anymore plasmapheresis to keep proteinuria under control.In addition, this encouraging single case let us identify some putative efficacy biomarkers that could be of clinical interest in chronic kidney diseases.     

Inventario delle Corallinales del Mar Mediterraneo: considerazioni tassonomiche

Abstract

Inventory of Corallinales of the Mediterranean Sea: taxonomic aspects. - The aim of the present work is the drawing up of a critical inventory of Corallinales of the Mediterranean Sea. This research has been based upon a census of 320 works published since 175 years, upon direct collections and sample exchanges. A census of 88 species of Corallinales (with forms and varieties), made up on the basis of about 5000 records, has been taken. 34 of the 88 species are considered “species dubiae aut rariter inventae”, it has been reported also “species inquirendae” and “species addendae”. From this census it results that there are some taxonomic problems about genera attributions (Lithophyllum, Pseudolithophyllum, Titanoderma, Neogoniolithon, Spongites, Goniolithion, Leptophytum), species attributions of articulated Corallinales (Corallina elongata, C. officinalis e Haliptilon squamatum) and non-articulated Corallinales (Fosliella ischitana, Lithophyllum (Titanoderma) trochanter, Spongites fruticulosus). Definition of these taxonomic attributions might condition not only studies of phytogeographical distribution of these algae but also every successive interpretation.     

The mouse eugenol odorant receptor: structural and functional plasticity of a broadly tuned odorant binding pocket

Molecular interactions of odorants with their olfactory receptors (ORs) are of central importance for the ability of the mammalian olfactory system to detect and discriminate a vast variety of odors with a limited set of receptors. How a particular OR binds and distinguishes different odorant molecules remains largely unknown on a structural basis. Here we investigated this question for the mouse eugenol receptor (mOR-EG). By screening a large odorant library, we discovered a wide range of chemical structures activating the receptor in heterologous mammalian cells. Potent agonists comprise (i) benzene, (ii) cyclohexane, or (iii) polycyclic structures substituted with alcohol, aldehyde, keto, ether, or esterified carboxylic groups. To detect those amino acids within the receptor that are in contact with a particular bound odorant molecule, we investigated how distinct mOR-EG point mutants were activated by the different odorant agonists found for the wild-type receptor. We identified 11 amino acids as a part of the receptor's ligand binding pocket. Molecular modeling predicted 10 of these residues in transmembrane helices TM3-TM6 and one in the extracellular loop between TM2 and TM3. These amino acids participate in odorant binding with variable importance depending on the type of odorant, revealing functional "fingerprints" of ligand-receptor interactions.     

Neuromuscular electrical stimulation training induces atypical adaptations of the human skeletal muscle phenotype: a functional and proteomic analysis

The aim of the present study was to define the chronic effects of neuromuscular electrical stimulation (NMES) on the neuromuscular properties of human skeletal muscle. Eight young healthy male subjects were subjected to 25 sessions of isometric NMES of the quadriceps muscle over an 8-wk period. Needle biopsies were taken from the vastus lateralis muscle before and after training. The training status, myosin heavy chain (MHC) isoform distribution, and global protein pattern, as assessed by proteomic analysis, widely varied among subjects at baseline and prompted the identification of two subgroups: an "active" (ACT) group, which performed regular exercise and had a slower MHC profile, and a sedentary (SED) group, which did not perform any exercise and had a faster MHC profile. Maximum voluntary force and neural activation significantly increased after NMES in both groups (+～30% and +～10%, respectively). Both type 1 and 2 fibers showed significant muscle hypertrophy. After NMES, both groups showed a significant shift from MHC-2X toward MHC-2A and MHC-1, i.e., a fast-to-slow transition. Proteomic maps showing ～500 spots were obtained before and after training in both groups. Differentially expressed proteins were identified and grouped into functional categories. The most relevant changes regarded 1) myofibrillar proteins, whose changes were consistent with a fast-to-slow phenotype shift and with a strengthening of the cytoskeleton; 2) energy production systems, whose changes indicated a glycolytic-to-oxidative shift in the metabolic profile; and 3) antioxidant defense systems, whose changes indicated an enhancement of intracellular defenses against reactive oxygen species. The adaptations in the protein pattern of the ACT and SED groups were different but were, in both groups, typical of both resistance (i.e., strength gains and hypertrophy) and endurance (i.e., a fast-to-slow shift in MHC and metabolic profile) training. These training-induced adaptations can be ascribed to the peculiar motor unit recruitment pattern associated with NMES.     

Ceruloplasmin and oxidative stress in severe eosinophilic asthma patients treated with Mepolizumab and Benralizumab

IntroductionSevere eosinophilic asthma has been associated with Th2 airway inflammation and elevated proinflammatory cytokines and chemokines, such as IL-5. Precision therapies have recently been shown to improve asthma symptoms with a steroid-sparing effect. Two such therapies, Benralizumab and Mepolizumab, humanized IgG antibodies directed against the IL-5 receptor and IL-5, have been approved for severe eosinophilic asthma.MethodsHere we used a differential proteomic approach to analyse serum from patients with severe eosinophilic asthma treated with Benralizumab and Mepolizumab in a search for differential molecular modifications responsible of their effects. Enrichment analysis of differential proteins was performed for the two treatments.Results and discussionAfter one month of Benralizumab treatment we detected up-regulation of certain protein species of the antioxidant ceruloplasmin. To investigate oxidative stress, we performed redox proteomics which detected lower oxidative burst after one month of Benralizumab treatment than in the pre-treatment phase or after one month of Mepolizumab therapy.     

Serum Reference Values for Leptin in Healthy Infants

ObjectiveReports on leptin concentrations in pediatric populations lack reference values for infants in the first months of life. Our study was conducted on healthy full-term infants between 2002 and 2012 to determine serum leptin reference values in subjects less than 18 months old.MethodsRoutine outpatient blood tests for serum leptin were performed on 317 infants using a radioimmunoassay method. The median and 10^th–90^th percentiles were calculated to obtain reference values using quantile regression. Values established in this study were compared with another independent cohort of 110 infants.ResultsThe median (IQR) serum leptin concentration in the infants was 2.37 (3.26) ng/ml (n = 317). The median leptin concentration was 2.81 (3.49) ng/ml (n = 202) in infants younger than 6 months of age, 1.44 (2.27) ng/ml (n = 59) in infants between 6–12 months of age and 1.77 (2.05) ng/ml (n = 56) in infants between 12–18 months of age. We obtained leptin reference values based on age by estimating the lower and upper percentiles. In the entire cohort, the median (IQR) leptin concentration was 2.22 (3.11) ng/ml in males (n = 168) and 2.60 (3.32) ng/ml in females (n = 149). According to the type of feeding median serum leptin concentration was higher in breast-fed infants (n = 188) than in formula-fed infants (n = 129) (2.63 (3.34) ng/ml vs. 2.12 (2.77) ng/ml; p<0.05).ConclusionsOur data revealed no gender difference in leptin concentration in early infancy. After 6 months of life, leptin concentrations decreased slightly. We used a large cohort to confirm that breast-fed infants had significantly higher serum leptin levels than formula-fed infants during the first 6 months of life, although this difference disappeared later in life. In this study, we defined the leptin reference range in healthy infants in the first 18 months of life according to the Clinical and Laboratory Standards Institute (CLSI).     

Proteomic Analysis of Lymphoblastoid Cells from Nasu-Hakola Patients: A Step Forward in Our Understanding of This Neurodegenerative Disorder

Nasu-Hakola disease (NHD) is a recessively inherited rare disorder characterized by a combination of neuropsychiatric and bone symptoms which, while being unique to this disease, do not provide a rationale for the unambiguous identification of patients. These individuals, in fact, are likely to go unrecognized either because they are considered to be affected by other kinds of dementia or by fibrous dysplasia of bone. Given that dementia in NHD has much in common with Alzheimer’s disease and other neurodegenerative disorders, it cannot be expected to achieve the differential diagnosis of this disease without performing a genetic analysis. Under this scenario, the availability of protein biomarkers would indeed provide a novel context to facilitate interpretation of symptoms and to make the precise identification of this disease possible. The work here reported was designed to generate, for the first time, protein profiles of lymphoblastoid cells from NHD patients. Two-dimensional electrophoresis (2-DE) and nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) have been applied to all components of an Italian family (seven subjects) and to five healthy subjects included as controls. Comparative analyses revealed differences in the expression profile of 21 proteins involved in glucose metabolism and information pathways as well as in stress responses.