Purification and mass spectrometry based characterization of a pediocin produced by Pediococcus acidilactici 13

Bacteriocins are antimicrobial peptides produced by several bacterial species. Among the bacteriocins pediocin-like bacteriocins have a significant inhibitory activity on the foodborne pathogens especially on Listeria monocytogenes. This study aims to select a simple and usable purification method to purify/concentrate the antimicrobial peptide and characterization of the bacteriocin produced by Pediococcus acidilactici 13 by using proteomic approaches which is a recent omic technology. For purification dialysis, ultrafiltration method was used, and as a result of this study the bacteriocin activity reached 819,200 AU/mL from 102,400 AU/mL initially. Two dimensional gel electrophoresis and then matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS) analysis were carried out to identify the current bacteriocin and related proteins. Obtained data revealed similarity to pediocin PA-1 transport/processing ATP-binding protein PedD (accession number: P36497), pediocin operon PedC (accession number: Q68GC4) and bacteriocin pediocin PA-1 (accession number: P29430) from UniProtKB/Swiss-Prot databank, thus the bacteriocin produced by P. acidilactici 13 is considered similar to pediocin PA-1.     

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.     

A novel DAD type and folic acid conjugated fluorescent monomer as a targeting probe for imaging of folate receptor overexpressed cells

We describe a modification and post‐functionalization technique for a donor–acceptor–donor type monomer; 6‐(4,7‐bis(2,3‐dihydrothieno[3,4‐b][1,4]dioxin‐5‐yl)‐2H‐benzo[d][1,2, 3]triazol‐2‐yl)hexan‐1‐amine. Folic acid was attached to the fluorescent structure. The conjugation was confirmed via NMR and Fourier transform infrared analyses. Cytotoxicity was investigated and the comparison of association of targeted monomeric structures in tumor cells was monitored via fluorescence microscopy. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:952–959, 2014     

Homology in Trivaline Complex Formation with dsDNA and ssRNA

Abstract

It has been shown by the equilibrium dialysis that at a polyU concentration above the “critical” one, the complete polymer saturation with trivaline reaches approximately 0.7 trivaline molecules per one phosphate group. i.e. at these conditions peptide dimer occupies on polyU a site of three bases (phosphates) in length. The trivaline complex with polyU at a concentration lower than the “critical” one does not reveal any noticeable fluorescence, but has rather significant positive linear dichroism at 265 and 330 nm. The trivaline-nucleic acids complex has a significant fluorescence at any dsDNA concentration while with polyU it is only so at a concentration above the “critical” one. Electron microscopy has shown that at a rather high concentration of dsDNA molecules in solution a “biduplex” structure undergoes an additional stage of compaction, during which the extended particles more than 30 nm in diameter are formed.

Schematic models for the trivaline complexes and compact structures with dsDNA and ssRNA are propose     

iASPP protects the heart from ischemia injury by inhibiting p53 expression and cardiomyocyte apoptosis

Currently, there remains a great need to elucidate the molecular mechanism of acute myocardial infarction in order to facilitate the development of novel therapy. Inhibitor of apoptosis-stimulating protein of p53 (iASPP) is a member of the ASPP family proteins and an evolutionarily preserved inhibitor of p53 that is involved in many cellular processes, including apoptosis of cancer cells. The purpose of this study was to investigate the possible role of iASPP in acute myocardial infarction. The protein level of iASPP was markedly reduced in the ischemic hearts in vivo and hydrogen peroxide-exposed cardiomyocytes in vitro. Overexpression of iASPP reduced the infarct size and cardiomyocyte apoptosis of mice subjected to 24 h of coronary artery ligation. Echocardiography showed that cardiac function was improved as indicated by the increase in ejection fraction and fractional shortening. In contrast, knockdown of iASPP exacerbated cardiac injury as manifested by impaired cardiac function, increased infarct size, and apoptosis rate. Mechanistically, overexpression of iASPP inhibited, while knockdown of iASPP increased the expressions of p53 and Bax, the key regulators of apoptosis. Taken together, our results suggested that iASPP is an important regulator of cardiomyocyte apoptosis, which represents a potential target in the therapy of myocardial infarction.     

Novel,potent, selective,and metabolically stable stearoyl-CoA desaturase (SCD) inhibitors

We identified a series of structurally novel SCD (Δ9 desaturase) inhibitors via high-throughput screening and follow-up SAR studies. Modification of the central bicyclic scaffold has proven key to our potency optimization effort. The most potent analog (8g) had IC₅₀ value of 50 pM in a HEPG2 SCD assay and has been shown to be metabolically stable and selective against Δ5 and Δ6 desaturases.     

Dendroclimatological potential of three juniper species from the Turkestan range,northwestern Pamir-Alay Mountains,Uzbekistan

Key message

Intensity and magnitude of the growth-climate relationship depends on juniper species and sites. Juniperus seravschanica at low elevations shows highest potential for April–September drought reconstruction in the Turkestan range (Pamir-Alay), Uzbekistan.

Abstract

We present a detailed dendroclimatological study of three juniper species, Juniperus seravschanica Kom., Juniperus semiglobosa Regel and Juniperus turkistanica Kom., sampled at six sites of different elevation (2100–2700 m a.s.l.), exposition (west and south) and steepness (10°–30°) in the Zaamin National Park, Turkestan range, Pamir-Alay mountain system in eastern Uzbekistan. Simple correlation statistics and redundancy analyses were applied to detect species- and site-specific climate responses during the twentieth century, which were additionally investigated in the high-frequency domain by identifying extreme growth years. Our results show that tree-ring formation of J. seravschanica at our low-elevation site is strongly limited by April to September drought conditions, while J. semiglobosa inherits a weak and variable climate response with respect to elevation. J. turkistanica growth at high altitudes is positively associated with warm spring and summer temperatures. Species-specific growth extremes are triggered by incoming air masses from the Atlantic and Arctic, highlighting the connection of synoptic climate regimes across Eurasia. From a dendroclimatic perspective, J. seravschanica exhibits a high potential for reconstructing past drought and pluvials, but under sustained temperature rise also J. semiglobosa will likely increase its sensitivity to drought. Moreover, J. turkistanica at its distribution limit at the tree line is a suitable proxy of summer temperature. Our findings clearly demonstrate that a careful selection of the site, overall topography and elevation as well as the different juniper species are important for successfully reconstructing past climate in Uzbekistan.