An ensemble of K-local hyperplanes for predicting protein-protein interactions

Prediction of protein-protein interaction is a difficult and important problem in biology. In this paper, we propose a new method based on an ensemble of K-local hyperplane distance nearest neighbor (HKNN) classifiers, where each HKNN is trained using a different physicochemical property of the amino acids. Moreover, we propose a new encoding technique that combines the amino acid indices together with the 2-Grams amino acid composition. A fusion of HKNN classifiers combined with the 'Sum rule' enables us to obtain an improvement over other state-of-the-art methods. The approach is demonstrated by building a learning system based on experimentally validated protein-protein interactions in human gastric bacterium Helicobacter pylori and in Human dataset.     

Effects of intensive human management on the taxonomic and functional diversity of ground beetles in a planted forest landscape

The rapid expansion of planted forests harms native biodiversity. Few studies report the effects of replacing wetlands with planted forests on ground beetles. We analyze how the taxonomic and functional diversity of ground beetles are affected by intensive management of a planted forest landscape in the Lower Delta of the Parana River. We defined six habitat types (n?=?3, N?=?18): young and mature willow (YW, MW), young and mature poplar without cattle (YP, MP), young and mature silvopastoral poplar (YS, MS). Using pitfall traps (N?=?1728), we recorded 35 species (1896 individuals). YW and MS reached the highest taxonomic diversity and richness. YW with more vertical heterogeneity showed higher species richness than MW. Hydrophilic species were more abundant in YW. Zoophagous species were more abundant in MS. YS, MS, and YW reached the highest functional evenness, which implies that a large part of the functional niches was used. Cattle dung and freshwater canals for livestock offer more resources for ground beetles. The planted tree species, stand age, and presence of cattle affects taxonomic and functional diversity of ground beetles. Willow and silvopastoral planted forests are the most suitable habitats for hosting wetland species. So, we recommend using willow species rather than poplar species when planted forests replace fluvial wetlands, increasing irrigation of poplar planted forests through ditches and canals, conserving or restoring different strata of understory to increase vertical heterogeneity, and maintaining the landscape heterogeneity. These management measures are essential to prevent the loss of wetland species and conserve ground beetle’s diversity.

     

Hospital cluster of HBV infection: molecular evidence of patient-to-patient transmission through lancing device

Introduction

In western countries the transmission of hepatitis B virus (HBV) transmission through multi-patients lancing devices has been inferred since early ‘90s, however no study has ever provided biological evidence which directly link these device with HBV cross-infection. Here we present results of an outbreak investigation which could associate, by molecular techniques, the use of lancing device on multiple patients with HBV transmission in an Italian oncohematology unit.

Methods

The outbreak investigation was designed as a retrospective cohort study to identify all potential cases. All cases identified were eventually confirmed through molecular epidemiology techniques. Audit of personnel including extensive review of infection control measures and reviewing personnel''s tests for HBV was done identify transmission route.

Results

Between 4 May 2006 and 21 February 2007, six incident cases of HBV infection were reported among 162 patients admitted in the oncohematology. The subsequent molecular instigation proved that 3 out 6 incident cases and one prevalent cases (already infected with HBV at the admission) represented a monophyletic cluster of infection. The eventual environmental investigation found that an identical HBV viral strain was present on a multi-patients lancing device in use in the unit and the inferential analysis showed a statistically significant association between undergoing lancing procedures and the infection.

Discussion

This investigation provide molecular evidence to link a HBV infection cluster to multi-patients lancing device and highlights that patients undergoing capillary blood sampling by non-disposable lancing device may face an unacceptable increased risk of HBV infection. Therefore we believe that multi-patients lancing devices should be banned from healthcare settings and replace with disposable safety lancets that permanently retract to prevent the use of the same device on multiple patients. The use of non-disposable lancing devices should be restricted to individual use at patients'' home.     

Antibody Phage Display Assisted Identification of Junction Plakoglobin as a Potential Biomarker for Atherosclerosis

To date, no plaque-derived blood biomarker is available to allow diagnosis, prognosis or monitoring of atherosclerotic vascular diseases. In this study, specimens of thrombendarterectomy material from carotid and iliac arteries were incubated in protein-free medium to obtain plaque and control secretomes for subsequent subtractive phage display. The selection of nine plaque secretome-specific antibodies and the analysis of their immunopurified antigens by mass spectrometry led to the identification of 22 proteins. One of them, junction plakoglobin (JUP-81) and its smaller isoforms (referred to as JUP-63, JUP-55 and JUP-30 by molecular weight) were confirmed by immunohistochemistry and immunoblotting with independent antibodies to be present in atherosclerotic plaques and their secretomes, coronary thrombi of patients with acute coronary syndrome (ACS) and macrophages differentiated from peripheral blood monocytes as well as macrophage-like cells differentiated from THP1 cells. Plasma of patients with stable coronary artery disease (CAD) (n = 15) and ACS (n = 11) contained JUP-81 at more than 2- and 14-fold higher median concentrations, respectively, than plasma of CAD-free individuals (n = 13). In conclusion, this proof of principle study identified and verified JUP isoforms as potential plasma biomarkers for atherosclerosis. Clinical validation studies are needed to determine its diagnostic efficacy and clinical utility as a biomarker for diagnosis, prognosis or monitoring of atherosclerotic vascular diseases.