Mining sequential patterns for protein fold recognition

Protein data contain discriminative patterns that can be used in many beneficial applications if they are defined correctly. In this work sequential pattern mining (SPM) is utilized for sequence-based fold recognition. Protein classification in terms of fold recognition plays an important role in computational protein analysis, since it can contribute to the determination of the function of a protein whose structure is unknown. Specifically, one of the most efficient SPM algorithms, cSPADE, is employed for the analysis of protein sequence. A classifier uses the extracted sequential patterns to classify proteins in the appropriate fold category. For training and evaluating the proposed method we used the protein sequences from the Protein Data Bank and the annotation of the SCOP database. The method exhibited an overall accuracy of 25% in a classification problem with 36 candidate categories. The classification performance reaches up to 56% when the five most probable protein folds are considered.     

Thrombospondin-2 modulates extracellular matrix remodeling during physiological angiogenesis

Thrombospondin 2 (TSP2) can inhibit angiogenesis in vitro by limiting proliferation and inducing apoptosis of endothelial cells (ECs). TSP2 can also modulate the extracellular levels of gelatinases (matrix metalloproteases, MMPs) and potentially influence the remodeling of the extracellular matrix (ECM). Here, we tested the hypothesis that by regulating MMPs, TSP2 could alter EC-ECM interactions. By using a three-dimensional angiogenesis assay, we show that TSP2, but not TSP1, limited angiogenesis by decreasing gelatinolytic activity in situ. Furthermore, TSP2-null fibroblast-derived ECM, which contains irregular collagen fibrils, was more permissive for EC migration. Investigation of the role of TSP2 in physiological angiogenesis in vivo, using excision of the left femoral artery in both TSP2-null and wild-type mice, revealed that TSP2-null mice displayed accelerated recovery of blood flow. This increase was attributable, in part, to an enhanced arterial network in TSP2-null muscles of the upper limb. Angiogenesis in the lower limb was also increased and was associated with increased MMP-9 deposition and gelatinolytic activity. The observed changes correlated with the temporal expression of TSP2 in the ischemic muscle of wild-type mice. Taken together, our observations implicate the matrix-modulating activity of TSP2 as a mechanism by which physiological angiogenesis is inhibited.     

Paradoxical sleep deprivation potentiates amphetamine-induced behavioural sensitization by increasing its conditioned component

The effects of paradoxical sleep deprivation (PSD-48 h) on the conditioned and unconditioned components of behavioural sensitization to amphetamine (two injections of 2.0 mg/kg, separated by 7 days) were studied using locomotion frequency of mice observed in an open-field as experimental parameter. Behavioural sensitization only occurred in PS deprived mice that were exposed to the open-field after the first amphetamine injection. The possible involvement of PSD in the development of a Pavlovian association between the stimulant effect of amphetamine and environmental as well as interoceptive drug cues is discussed.     

Portal vein thrombosis in children and adolescents: the low prevalence of hereditary thrombophilic disorders

Purpose

The aim of this study was to determine the frequency of thrombophilic disorders in children and adolescents with portal vein thrombosis (PVT) as well as assessing the hereditary character of this disorder.

Methods

A 2-year prospective study was carried out in pediatric PVT patients (n = 14), their parents (n = 25), and an age-matched control group free of liver disease (n = 28). The presence of PVT was assessed by means of Doppler ultrasound scan or angiography. None of the PVT patients presented biochemical or histologic signs of liver disease.

Results

The frequency in PVT patients of protein C (PC), protein S (PS) and antithrombin (AT) deficiency was 42.9% (P < .05 v controls), 21.4% (P > .05) and 7.1% (P > .05), respectively. None of the controls or parents of PVT patients presented hereditary PC, PS, or AT deficiency. One PVT patient and one control (P = .999) presented prothrombin G20210A mutation. Homozygous methylenetetrahydrofolate reductase C677T genotype was observed in 3 of 14 (21.4%) PVT patients and in 5 of 28 (17.9%; P = .356) controls. None of these patients presented factor V G1691A mutation.

Conclusions

PC deficiency was frequent in pediatric PVT patients and does not seem to be an inherited condition. The hereditary prothrombotic disorders do not seem to play a vital role in thrombosis in children and adolescents with PVT.     

Permanent phenotypic correction of hemophilia B in immunocompetent mice by prenatal gene therapy

Hemophilia B, also known as Christmas disease, arises from mutations in the factor IX (F9) gene. Its treatment in humans, by recombinant protein substitution, is expensive, thus limiting its application to intermittent treatment in bleeding episodes and prophylaxis during surgery; development of inhibitory antibodies is an associated hazard. This study demonstrates permanent therapeutic correction of his disease without development of immune reactions by introduction of an HIV-based lentiviral vector encoding the human factor IX protein into the fetal circulation of immunocompetent hemophiliac and normal outbred mice. Plasma factor IX antigen remained at around 9%, 13%, and 16% of normal in the 3 hemophilia B mice, respectively, until the last measurement at 14 months. Substantial improvement in blood coagulability as measured by coagulation assay was seen in all 3 mice and they rapidly stopped bleeding after venipuncture. No humoral or cellular immunity against the protein, elevation of serum liver enzymes, or vector spread to the germline or maternal circulation were detected.     

Endoscopic nodular gastritis: an endoscopic indicator of high-grade bacterial colonization and severe gastritis in children with Helicobacter pylori

OBJECTIVE: To investigate the significance of endoscopic nodular gastritis associated with Helicobacter pylori infection. METHODS: This prospective study included 185 children (50.8% boys) aged 1 to 12 years (mean, 6.9 +/- 3.0 years) who underwent upper intestinal endoscopy during evaluation of chronic abdominal pain. The authors assessed the endoscopic appearance of the stomach, noting those patients with endoscopic nodular gastritis. Urease activity of gastric mucosal biopsies was measured. With histologic examination, the presence and density of H. pylori organisms, the presence of follicular gastritis, the nature of inflammation, and the gastritis activity grade and overall gastritis score were assessed. RESULTS: H. pylori infection was identified in 50 children (27%). Endoscopic nodular gastritis was significantly associated with active chronic gastritis and follicular gastritis. Nodularity in the stomach showed a high specificity (98.5%) and positive predictive value (91.7%) for the diagnosis of H. pylori infection and was observed in 22 of 50 (44%) H. pylori-positive patients and in 2 of 135 (1.5%) H. pylori-negative patients. A significant association was observed between older age and the prevalence of this finding (P< 0.001). There was a significant increase in endoscopic nodular gastritis with increased H. pylori density and a positive correlation (Pearson coefficient = 0.97) with increased gastritis score on histologic examination. Increase in gastritis score was dependent on increased H. pylori density in patients with gastric nodularity; this finding was independent of age. CONCLUSIONS: Endoscopic findings of antral nodularity in children suggest the presence of H. pylori infection and follicular gastritis and may identify cases of severe gastritis and marked bacterial colonization.     

Matricellular proteins as modulators of wound healing and the foreign body response

Matricellular proteins form a group of extracellular matrix (ECM) proteins that do not subserve a primary structural role, but rather function as modulators of cell-matrix interactions. Members of the group, including thrombospondin (TSP)-1,TSP-2, SPARC, tenascin (TN)-C, and osteopontin (OPN), have been shown to participate in a number of processes related to tissue repair. Specifically, studies in knockout mice have indicated that a deficiency in one or more of these proteins can alter the course of wound healing. More recently, TSP1, TSP2, and SPARC have also been implicated in the foreign body response, an unusual reaction to injury that occurs after the implantation of biomaterials. This review will focus on the roles of these proteins in the response to injury in mice and will show how studies of this pathophysiological process can elucidate some of the intrinsic properties of these matricellular proteins.