Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system

The microbial degradation of lignocellulose biomass is not only an important biological process but is of increasing industrial significance in the bioenergy sector. The mechanism by which the plant cell wall, an insoluble composite structure, activates the extensive repertoire of microbial hydrolytic enzymes required to catalyze its degradation is poorly understood. Here we have used a transposon mutagenesis strategy to identify a genetic locus, consisting of two genes that modulate the expression of xylan side chain-degrading enzymes in the saprophytic bacterium Cellvibrio japonicus. Significantly, the locus encodes a two-component signaling system, designated AbfS (sensor histidine kinase) and AbfR (response regulator). The AbfR/S two-component system is required to activate the expression of the suite of enzymes that remove the numerous side chains from xylan, but not the xylanases that hydrolyze the beta1,4-linked xylose polymeric backbone of this polysaccharide. Studies on the recombinant sensor domain of AbfS (AbfS(SD)) showed that it bound to decorated xylans and arabinoxylo-oligosaccharides, but not to undecorated xylo-oligosaccharides or other plant structural polysaccharides/oligosaccharides. The crystal structure of AbfS(SD) was determined to a resolution of 2.6A(.) The overall fold of AbfS(SD) is that of a classical Per Arndt Sim domain with a central antiparallel four-stranded beta-sheet flanked by alpha-helices. Our data expand the number of molecules known to bind to the sensor domain of two-component histidine kinases to include complex carbohydrates. The biological rationale for a regulatory system that induces enzymes that remove the side chains of xylan, but not the hydrolases that cleave the backbone of the polysaccharide, is discussed.     

Molecular confirmation of Planktothrix rubescens as the cause of intense,microcystin—Synthesizing cyanobacterial bloom in Lake Ziros,Greece

Cyanobacterial blooms occur increasingly often and raise ecological concerns worldwide. In Mediterranean freshwater ecosystems algal blooms are commonly attributed to Microcystis, Anabaena, and Aphanizomenon genera while Planktothrix is the most common bloom forming cyanobacterium in deep Northern and prealpine European oligotrophic to mesotrophic lakes. In the framework of an undertaken study of cyanobacterial species in lakes of Northwestern Greece we investigated the cyanobacterial diversity in Lake Ziros throughout a 15-month period (January 2006–March 2007) by using molecular methods. Surprisingly, a severe cyanobacterial bloom occurred during the study period, which upon microscopic examination and detailed molecular characterization found to be caused by Planktothrix rubescens species. The appearance of P. rubescens from November 2006 coincided with poor cyanobacterial diversity and resulted in a thick epilimnetic bloom in March 2007 (3.1 × 10⁸ cells/l and microcystin concentration 199 μg/l). Genotype composition of the total cyanobacterial community of the lake was analyzed by using denaturing gradient gel electrophoresis (DGGE) profiling of the intergenic transcribed spacer region of the rnn operon (rRNA-ITS). A P. rubescens strain closely related to Kpr strain from Lake Klinckenberg, The Netherlands, was found to dominate. The importance of this observation is expanded by the fact that microcystin concentrations recorded in Lake Ziros were the highest measured ever in Greek aquatic ecosystems examined so far and also found amongst the highest recorded worldwide.     

Serglycin constitutively secreted by myeloma plasma cells is a potent inhibitor of bone mineralization in vitro

Although the biological significance of proteoglycans (PGs) has previously been highlighted in multiple myeloma (MM), little is known about serglycin, which is a hematopoietic cell granule PG. In this study, we describe the expression and highly constitutive secretion of serglycin in several MM cell lines. Serglycin messenger RNA was detected in six MM cell lines. PGs were purified from conditioned medium of four MM cell lines, and serglycin substituted with 4-sulfated chondroitin sulfate was identified as the predominant PG. Flow cytometry and confocal microscopy showed that serglycin was also present intracellularly and on the cell surface, and attachment to the cell surface was at least in part dependent on intact glycosaminoglycan side chains. Immunohistochemical staining of bone marrow biopsies showed the presence of serglycin both in benign and malignant plasma cells. Immunoblotting in bone marrow aspirates from a limited number of patients with newly diagnosed MM revealed highly increased levels of serglycin in 30% of the cases. Serglycin isolated from myeloma plasma cells was found to influence the bone mineralization process through inhibition of the crystal growth rate of hydroxyapatite. This rate reduction was attributed to adsorption and further blocking of the active growth sites on the crystal surface. The apparent order of the crystallization reaction was found to be n=2, suggesting a surface diffusion-controlled spiral growth mechanism. Our findings suggest that serglycin release is a constitutive process, which may be of fundamental biological importance in the study of MM.     

High sensitivity cardiac troponin T in patients not having an acute coronary syndrome: results from the TRAPID-AMI study

Purpose: To describe the baseline, 1?hr and delta high sensitivity cardiac troponin (hs-cTnT) values in patients with suspected acute myocardial infarction (AMI) but without a final acute coronary syndrome (ACS) diagnosis.

Materials and methods: hs-cTnT assay for RAPID rule out of acute myocardial infarction (TRAPID-AMI) was a prospective diagnostic trial that enrolled emergency department (ED) patients with suspected AMI. Final patient diagnoses were adjudicated by a clinical events committee and subjects placed in different clinical groups: AMI, unstable angina, non-ACS cardiac, non-cardiac and unknown origin. The baseline, 1?hr and delta hs-cTnT values were analysed in the 902 non-ACS patients.

Results: Amongst the 1282 studied the patient groups were 213 (17%) AMI, 167 (13%) unstable angina, 113 (9%) non-ACS cardiac, 288 (22%) non-cardiac and 501 (39%) unknown origin. The hs-cTnT values in the non-cardiac and unknown origin groups were combined. The median hs-cTnT values (ng/L) were higher (p?<?0.001) in the non-ACS cardiac compared to the non-cardiac/unknown origin group at baseline (11.8,?<5) and 1?hr (12.3,?<5). Their negative predictive values were 0.955 (baseline) and 0.954 (1?hr) for predicting non-ACS cardiac versus non-cardiac/unknown origin diagnoses.

Conclusions: Hs-cTnT may help predict whether non-ACS ED patients have a final non-ACS cardiac or non-cardiac/unknown origin diagnoses.     

Spatial management of the Mediterranean bottom-trawl fisheries: the case of the southern Aegean Sea

A time series of survey abundance indices for commercially important demersal fish and cephalopod species, inhabiting the narrow continental shelf of the southern Aegean Sea, is analyzed in relation to the topography of the area in order to evaluate the impact of different spatial fishery bans on the bottom-trawl fishery. With reference to the current situation, results suggested that implementation of the 1967/2006 EC Regulation, which bans bottom-trawl activities within 1.5 NM off the coast, will significantly increase (20–80%, depending on the species) the proportion of the populations that are inaccessible to the bottom-trawl fishery. It might also result in shifting of fishing activities toward deeper waters, adding fishing pressure onto slope resources inhabiting the slope. As depth determines, to a large extent, the distribution pattern of the species, it constitutes a variable of crucial importance for the spatial management of marine fisheries and should be taken into account when adopting relevant management regimes.     

Ubiquitination and proteasomal degradation of ATG12 regulates its proapoptotic activity

During macroautophagy, conjugation of ATG12 to ATG5 is essential for LC3 lipidation and autophagosome formation. Additionally, ATG12 has ATG5-independent functions in diverse processes including mitochondrial fusion and mitochondrial-dependent apoptosis. In this study, we investigated the regulation of free ATG12. In stark contrast to the stable ATG12–ATG5 conjugate, we find that free ATG12 is highly unstable and rapidly degraded in a proteasome-dependent manner. Surprisingly, ATG12, itself a ubiquitin-like protein, is directly ubiquitinated and this promotes its proteasomal degradation. As a functional consequence of its turnover, accumulation of free ATG12 contributes to proteasome inhibitor-mediated apoptosis, a finding that may be clinically important given the use of proteasome inhibitors as anticancer agents. Collectively, our results reveal a novel interconnection between autophagy, proteasome activity, and cell death mediated by the ubiquitin-like properties of ATG12.     

Structure-revealing data fusion

Background

Analysis of data from multiple sources has the potential to enhance knowledge discovery by capturing underlying structures, which are, otherwise, difficult to extract. Fusing data from multiple sources has already proved useful in many applications in social network analysis, signal processing and bioinformatics. However, data fusion is challenging since data from multiple sources are often (i) heterogeneous (i.e., in the form of higher-order tensors and matrices), (ii) incomplete, and (iii) have both shared and unshared components. In order to address these challenges, in this paper, we introduce a novel unsupervised data fusion model based on joint factorization of matrices and higher-order tensors.

Results

While the traditional formulation of coupled matrix and tensor factorizations modeling only shared factors fails to capture the underlying structures in the presence of both shared and unshared factors, the proposed data fusion model has the potential to automatically reveal shared and unshared components through modeling constraints. Using numerical experiments, we demonstrate the effectiveness of the proposed approach in terms of identifying shared and unshared components. Furthermore, we measure a set of mixtures with known chemical composition using both LC-MS (Liquid Chromatography - Mass Spectrometry) and NMR (Nuclear Magnetic Resonance) and demonstrate that the structure-revealing data fusion model can (i) successfully capture the chemicals in the mixtures and extract the relative concentrations of the chemicals accurately, (ii) provide promising results in terms of identifying shared and unshared chemicals, and (iii) reveal the relevant patterns in LC-MS by coupling with the diffusion NMR data.

Conclusions

We have proposed a structure-revealing data fusion model that can jointly analyze heterogeneous, incomplete data sets with shared and unshared components and demonstrated its promising performance as well as potential limitations on both simulated and real data.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-239) contains supplementary material, which is available to authorized users.