Prediction of allosteric sites and mediating interactions through bond-to-bond propensities.

Allostery is a fundamental mechanism of biological regulation, in which binding of a molecule at a distant location affects the active site of a protein. Allosteric sites provide targets to fine-tune protein activity, yet we lack computational methodologies to predict them. Here we present an efficient graph-theoretical framework to reveal allosteric interactions (atoms and communication pathways strongly coupled to the active site) without a priori information of their location. Using an atomistic graph with energy-weighted covalent and weak bonds, we define a bond-to-bond propensity quantifying the non-local effect of instantaneous bond fluctuations propagating through the protein. Significant interactions are then identified using quantile regression. We exemplify our method with three biologically important proteins: caspase-1, CheY, and h-Ras, correctly predicting key allosteric interactions, whose significance is additionally confirmed against a reference set of 100 proteins. The almost-linear scaling of our method renders it suitable for high-throughput searches for candidate allosteric sites.

First Molecular Identification and Genetic Characterization of Theileria lestoquardi in Sheep of the Maghreb Region.

Theileria lestoquardi is the most prominent Theileria species in small ruminants that causes malignant theileriosis of sheep in Africa and Asia. In the present survey, blood samples and ticks were collected in Kebili (southern Tunisia) from 166 Queue Fine de l'Ouest sheep. Giemsa-stained blood smears, immunofluorescent antibody test (IFAT) and PCR were performed. The DNA was extracted from blood and analysed by PCR targeting 18S rRNA gene of Theileria spp. and then sequenced. A total number of 140 ticks were collected from a total number of 166 sheep during the four seasons. The ticks belonged to two genera and 4 species; the most frequent tick was Hyalomma excavatum 84.3% (118/140) and then Rhipicephalus spp. 15.7% (22/140). Only two animals had positive Giemsa-stained blood smears, and they were also positive by IFAT. The amplicons had 99.3 and 99.6% homology with the BLAST published T. lestoquardi amplicons. To our knowledge, this is the first report of T. lestoquardi in small ruminants within the Maghreb region.

Uncovering allosteric pathways in caspase-1 using Markov transient analysis and multiscale community detection.

Allosteric regulation at distant sites is central to many cellular processes. In particular, allosteric sites in proteins are major targets to increase the range and selectivity of new drugs, and there is a need for methods capable of identifying intra-molecular signalling pathways leading to allosteric effects. Here, we use an atomistic graph-theoretical approach that exploits Markov transients to extract such pathways and exemplify our results in an important allosteric protein, caspase-1. Firstly, we use Markov stability community detection to perform a multiscale analysis of the structure of caspase-1 which reveals that the active conformation has a weaker, less compartmentalised large-scale structure compared to the inactive conformation, resulting in greater intra-protein coherence and signal propagation. We also carry out a full computational point mutagenesis and identify that only a few residues are critical to such structural coherence. Secondly, we characterise explicitly the transients of random walks originating at the active site and predict the location of a known allosteric site in this protein quantifying the contribution of individual bonds to the communication pathway between the active and allosteric sites. Several of the bonds we identify have been shown experimentally to be functionally critical, but we also predict a number of as yet unidentified bonds which may contribute to the pathway. Our approach offers a computationally inexpensive method for the identification of allosteric sites and communication pathways in proteins using a fully atomistic description.

Riboregulators in plant development.

npcRNA (non-protein-coding RNAs) are an emerging class of regulators, so-called riboregulators, and include a large diversity of small RNAs [miRNAs (microRNAs)/siRNAs (small interfering RNAs)] that are involved in various developmental processes in plants and animals. In addition, several other npcRNAs encompassing various transcript sizes (up to several kilobases) have been identified using different genomic approaches. Much less is known about the mechanism of action of these other classes of riboregulators also present in the cell. The organogenesis of nitrogen-fixing nodules in legume plants is initiated in specific root cortical cells that express the npcRNA MtENOD40 (Medicago truncatula early nodulin 40). We have identified a novel RBP (RNA-binding protein), MtRBP1 (M. truncatula RBP 1), which interacts with the MtENOD40 RNA, and is exported into the cytoplasm during legume nodule development in the region expressing MtENOD40. A direct involvement of the MtENOD40 RNA in the relocalization of this RBP into cytoplasmic granules could be demonstrated, revealing a new RNA function in the cell. To extend these results, we searched for npcRNAs in the model plant Arabidopsis thaliana whose genome is completely known. We have identified 86 novel npcRNAs from which 27 corresponded to antisense RNAs of known coding regions. Using a dedicated 'macroarray' containing these npcRNAs and a collection of RBPs, we characterized their regulation in different tissues and plants subjected to environmental stresses. Most of the npcRNAs showed high variations in gene expression in contrast with the RBP genes. Recent large-scale analysis of the sRNA component of the transcriptome revealed an enormous diversity of siRNAs/miRNAs in the Arabidopsis genome. Bioinformatic analysis revealed that 34 large npcRNAs are precursors of siRNAs/miRNAs. npcRNAs, which are a sensitive component of the transcriptome, may reveal novel riboregulatory mechanisms involved in post-transcriptional control of differentiation or environmental responses.

Phenotypic diversity is not determined by independent genetic factors in familial spondylarthropathy.

OBJECTIVE: To analyze the segregation of manifestations belonging to the spectrum of spondylarthropathy (SpA) among patients and unaffected siblings within SpA multiplex families. METHODS: Ninety-five multiplex families have been investigated. The diagnosis of SpA was made according to European Spondylarthropathy Study Group criteria. The prevalence of SpA manifestations was determined in unaffected siblings and compared with their prevalence in patients. RESULTS: We compared 241 SpA patients with 259 unaffected siblings. The prevalence of skeletal and extraarticular features not used as diagnostic criteria, i.e., radiographic sacroiliitis, peripheral enthesitis, uveitis, psoriasis, and inflammatory bowel disease, was significantly increased in patients compared with unaffected siblings. This result was not accounted for by sex or HLA-B27 distribution differences. CONCLUSION: In familial SpA, skeletal and extraarticular manifestations tend to segregate together, implying that all subsets are predominantly determined by a shared component, and that accessory factors must be responsible for phenotype diversity.

What competence does a rheumatologist need?: an international perspective.

OBJECTIVES: To forecast, on the basis of the past and present position of rheumatologists in Europe, the competence needed in the future to secure and promote the specialty within the healthcare network. METHODS: Union Européenne des Médecins Spécialistes/European Board of Rheumatology (UEMS/EBR) questionnaire on (a) training centres in Europe, (b) rheumatologists' skills, (c) UEMS core curriculum. RESULTS: 173 training centres in rheumatology were identified. Reponses to the questionnaire showed both harmony and diversity in the practice of rheumatology. Harmony arises from the need to (a) have an extensive and profound knowledge of, and clinical experience with, all the causes of painful or disabled locomotor apparatus; (b) manage such disorders in the most cost effective way; and (c) promote "shared clinical decision making". The diversity seen both among and within the European countries is due to the different activities of rheumatologists. CONCLUSION: Rheumatological competence must be based on a common core, as described in the UEMS core curriculum, and on deeper and diverse clinical or scientific knowledge covering the entire field of the specialty, to secure its flexibility and resilience in the market place and to promote its scientific development.

The familial form of spondylarthropathy: a clinical study of 115 multiplex families. Groupe Français d'Etude Génétique des Spondylarthropathies.

OBJECTIVE: To investigate the interrelationships among different phenotypes, and their relationship to the HLA-Blocus, in multiplex families with spondylarthropathy (SpA). METHODS: We recruited 115 white French families, each of which had at least 2 members with SpA. Pedigrees were established. Clinical data and pelvic radiographs were collected. The HLA-B27 status of all patients was determined. Analysis was performed to determine the prevalence of SpA manifestations according to sex, disease duration, and HLA-B status, and to examine clustering of specific manifestations in subsets of families. RESULTS: We identified 329 SpA patients. Mean +/-SD age at onset was 24+/-9.4 years. The male:female ratio was 186:143, or 1.3, with few sex differences in disease expression. Axial manifestations and HLA-B27 were each present in 97% of the patients. Inflammatory bowel disease and HLA-B35 were overrepresented in the 7 families containing HLA-B27-negative patients. The frequency of radiographic sacroiliitis increased in parallel with disease duration. Peripheral enthesitis, radiographic sacroiliitis, and psoriasis were evenly distributed in the families. Clustering independent of age was only observed for peripheral arthritis, suggesting that specific factors may predispose individuals to this manifestation. CONCLUSION: Familial SpA appears to be homogeneous, based on the high frequencies of axial skeletal involvement and HLA-B27. The lack of clustering of most manifestations in families suggests that a predominant shared component, including HLA-B27, predisposes individuals to all forms of familial SpA, and that ubiquitous genetic or environmental factors contribute to phenotype diversity.

Concordance between abdominal scintigraphy using technetium-99m hexamethylpropylene amine oxime-labelled leucocytes and ileocolonoscopy in patients with spondyloarthropathies and without clinical evidence of inflammatory bowel disease.

OBJECTIVE: To study the concordance between abdominal scintigraphy using technetium-99m hexamethylpropylene amine oxime (99mTc-HMPAO)-labelled leucocytes (ASTLL) and ileocolonoscopy in patients with spondyloarthropathies (SpA) and without clinical evidence of inflammatory bowel disease (IBD). PATIENTS AND METHODS: Fifteen patients with SpA (European Spondylarthropathy Study Group 1991 criteria) without clinical evidence of IBD were studied prospectively with ASTLL and ileocolonoscopy. RESULTS: This cohort consisted of seven men and eight women aged 31.8+/-10.5 yr (18-47) [mean age +/- S.D. (range)] and with a disease duration of 6.0+/-4.4 yr (0.4-15). ASTLL showed abnormal uptake in four patients. Ileocolonoscopy was abnormal in five patients, showing acute inflammatory lesions in one patient with reactive arthritis, undifferentiated chronic inflammatory lesions in two cases, and features indistinguishable from those of Crohn's disease in two cases. ASTLL was negative in two cases in which ileocolonoscopy showed inflammatory lesions and was positive (terminal ileum) in one case with normal ileocolonoscopy. The concordance between the two examinations was statistically significant (kappa = 0.53; P = 0.008). CONCLUSION: ASTLL may be an interesting tool to detect subclinical gut inflammation in patients with SpA.

Are radiological joint space widths of normal hips asymmetrical?

BACKGROUND: To be certain that the joint space width is abnormal in the case of hip joint pain when compared with the contralateral hip requires knowledge of physiological dissymmetry. AIM OF THE STUDY: To assess interindividual variability and dissymmetry in pelvic radiological joint space width. METHODS: Pelvic radiographs of subjects without hip joint disease. Measurement with a 0.1 mm graduated magnifying glass and 0.5 mm graduated flat ruler at the hip superointermediate site (vertical going through the femoral head centre). After randomisation of the side to measure, analysis of nine groups of 19 plain films by one investigator blind for the result of the contralateral side. RESULTS: The difference between the left and right hip was plotted against the corresponding mean for all 171 normal subjects. This shows the frequency and the limits of the asymmetry at each measurement site. The asymmetry is independent of interindividual variability of the joint space width and greater than the measurement error in most subjects. CONCLUSION: This study confirms the interindividual variability of hip joint space width, shows the frequency of hip joint space asymmetry and defines its limit.

Piroxicam therapy: a double blind, randomized, multicenter study comparing 2 versus 4 week treatment in patients with painful knee osteoarthritis with effusion.

OBJECTIVE: To compare the efficacy and safety of piroxicam 20 mg once a day for 14 or 28 days in patients with knee osteoarthritis (OA) and synovial effusion. METHODS: We conducted a multicenter, randomized, double blind study in 1905 outpatients. Efficacy was assessed by changes in synovial effusion, pain on a 100 mm visual analog scale (VAS), and impairment using Lequesne's functional index. Patients were classified at Day 28 as improved (defined as VAS and Lequesne index decrease of at least 30% from Day 14), worsened (defined as VAS and Lequesne index increase of at least 30% from Day 14), or unchanged. Safety was assessed on the basis of adverse events reported by the patients. RESULTS: After 14 days, changes in pain, synovial effusion, and functional impairment significantly decreased from baseline within each group (p < 0.001, respectively), but did not differ between the groups. Between 14 and 28 days, outcome measure changes were significantly better in the 28 day group, p = 0.01, 0.0001, and 0.0001, respectively. In the 28 day and 14 day groups, improvement with regard to pain was observed for 339 (52.4%) and 280 (29.4%) patients, respectively, (p < 0.0001), and with regard to functional impairment for 298 (31.5%) and 233 (24.3%) patients (p < 0.0001). Adverse events accounted for 7.5 and 6.7% of withdrawals in the 28 day and 14 day groups, respectively. CONCLUSION: When administration of piroxicam 20 mg is prolonged to 28 days, continuing benefit is observed for some patients with knee OA with painful synovial effusion without a significant difference in safety.

Reiter's syndrome. Diagnosis and clinical features.

After a short review of the history of Reiter's diseases, new definitions of what is now called reactive arthritis are proposed. The best definition is based on a multiple-entry set of criteria validated by other members of the spondyloarthropathy group. This definition needs no reference to origin hypothesis and no exclusion criteria. The epidemiology of Reiter's syndrome is also discussed, and the problems due to previously imprecise definitions are emphasized. Clinical features are described and divided into four syndromes: peripheral arthritis, enthesopathic, pelvic and axial, and extramusculoskeletal syndromes; seven predictive factors of long-term evolution are proposed. Differential diagnosis is discussed within and without the spondyloarthropathy group.

Arthroscopic evaluation of potential structure modifying activity of hyaluronan (Hyalgan) in osteoarthritis of the knee.

OBJECTIVE: Several reported studies suggest that repeated intra-articular injections of hyaluronan result in sustained relief from pain and functional disability in patients with knee osteoarthritis. Several in vivo data suggest that hyaluronan might have a beneficial structural effect in osteoarthritis. The objective of the study was to evaluate the potential structure-modifying effects of Hyalgan (500-730 kDa molecular weight), a highly-purified sodium hyaluronate. DESIGN: Patients with painful knee osteoarthritis (ACR criteria) were enrolled in a prospective, controlled study of 1-year duration. After randomization, either conventional therapy or three cycles (every 3 months) of three intra-articular injections of Hyalgan (once a week during 2 weeks) were given. Clinical outcome was added using pain visual analog score (VAS), functional impairment: Lequesne's index, quality of life: arthritis impact measurement scale (AIMS2) and structural outcome using X-rays: joint space narrowing and arthroscopy: global assessment using VAS, SFA scoring and grading systems. RESULTS: Of the 39 recruited patients, 36 completed the 1-year trial (19 in the Hyalgan group and 17 in the control group). There was no difference between groups at entry. Between-group comparison for changes in clinical parameters reached statistical significance for the quality of life index (AIMS2: -0.4 +/- 0.7 vs 0.2 +/- 0.9 in the Hyalgan and control groups respectively, P < 0.05). Deterioration in the structural parameters was less in the Hyalgan group, with a statistically significant difference for two of the three evaluated parameters (overall assessment of chondropathy: +5.1 +/- 12.7 vs 16.7 +/- 18.3, P = 0.016; SFA scoring system: +3.7 +/- 7.3 vs +9.0 +/- 11.5, P = 0.05) in the Hyalgan and control groups, respectively. CONCLUSIONS: This study supports existing data concerning the favorable symptomatic effect of intra-articular injections of Hyalgan in osteoarthritis of the knee and suggests that repeated intra-articular injections of Hyalgan might delay the structural progression of the disease. Other studies are required to confirm these results and to determine the long-term monitoring of osteoarthritic patients using such local therapy.