Isolation, Characterisation and Molecular Imaging of a High-Molecular-Weight Insect Biliprotein, a Member of the Hexameric Arylphorin Protein Family

The abundant blue hemolymph protein of the last instar larvae of the moth Cerura vinula was purified and characterized by protein-analytical, spectroscopic and electron microscopic methods. Amino acid sequences obtained from a large number of cleavage peptides revealed a high level of similarity of the blue protein with arylphorins from a number of other moth species. In particular, there is a high abundance of the aromatic amino acids tyrosine and phenylalanine amounting to about 19% of total amino acids and a low content of methionine (0.8%) in the Cerura protein. The mass of the native protein complex was studied by size-exclusion chromatography, analytical ultracentrifugation, dynamic light scattering and scanning transmission electron microscopy and found to be around 500 kDa. Denaturating gel electrophoresis and mass spectrometry suggested the presence of two proteins with masses of about 85 kDa. The native Cerura protein is, therefore, a hexameric complex of two different subunits of similar size, as is known for arylphorins. The protein was further characterized as a weakly acidic (pI ∼ 5.5) glycoprotein containing mannose, glucose and N-acetylglucosamine in an approximate ratio of 10:1:1. The structure proposed for the most abundant oligosaccharide of the Cerura arylphorin was the same as already identified in arylphorins from other moths. The intense blue colour of the Cerura protein is due to non-covalent association with a bilin of novel structure at an estimated protein subunit-to-ligand ratio of 3:1. Transmission electron microscopy of the biliprotein showed single particles of cylindrical shape measuring about 13 nm in diameter and 9 nm in height. A small fraction of particles of the same diameter but half the height was likely a trimeric arylphorin dissociation intermediate. Preliminary three-dimensional reconstruction based on averaged transmission electron microscopy projections of the individual particles revealed a double-trimeric structure for the hexameric Cerura biliprotein complex, suggesting it to be a dimer of trimers.     

Speciation of coagulase negative staphylococci, isolated from indoor air, using SDS PAGE gel bands of expressed proteins followed by MALDI TOF MS and MALDI TOF-TOF MS-MS analysis of tryptic peptides

A group of coagulase negative staphylococcal strains isolated from indoor air of occupied school rooms were the subject of this study. Conventional MALDI TOF MS profiling of cellular extracts and physiological tests (including API STAPH) provided incomplete identification of the set of strains. After separation of a 100 kDa band using 1D gel electrophoresis, profiling of peptides (released with tryptic digestion) using MALDI TOF MS allowed improved bacterial speciation in addition to determination of the identity of the protein of origin (aconitate hydratase). This was performed by Mascot search, empirical observation and computer-generated cross-correlation analysis of environmental isolates versus reference strains. The species studied included some with sequenced genomes and others with un-sequenced genomes. Peptide sequences were confirmed to originate from aconitate hydratase using MALDI TOF-TOF MS-MS analysis of a diverse set of m/z values representing variable and conserved sequences. The methodological approach described here might have widespread application in speciation of environmental isolates of diverse origin and in identification of their expressed proteins.     

小麦全蚀病菌胞外β-1,3-葡聚糖酶的产生和部分特性的研究

本文就小麦全蚀病菌胞外-1,3-葡聚糖酶的产生和部分酶学特性进行了研究。结果表明,小麦全蚀病菌能够产生胞外-1,3-葡聚糖酶。在供试的三种培养基中,最佳产酶培养基为改进的MS培养基。当以改进的MS为基础培养基时,最佳碳源为麦麸皮;最佳氮源为牛肉浸膏;产酶的最适条件为培养基初始pH为6,培养温度为26℃,250ml三角瓶中装培养基量为50ml时接菌量为4块菌饼(直径5mm)。另外,对酶的部分性质的研究结果表明,酶最适作用温度和pH分别为60℃和7.0,在50℃以下以及pH 5.5～7.5范围内稳定。     

Auxin production by plant associated bacteria: impact on endogenous IAA content and growth of Triticum aestivum L.

Aims:  The aim of this study was to investigate the potential of bacterial strains of Bacillus, Pseudomonas, Escherichia, Micrococcus and Staphylococcus genera associated with wild herbaceous flora to enhance endogenous indole-3-acetic acid (IAA) content and growth of Triticum aestivum var. Inqalab-91.
Methods and Results:  Gas chromatography and mass spectrometric (GC–MS) analysis revealed that bacterial strains produced 0·6–8·22 μg IAA ml⁻¹ in the presence of L-tryptophan. Plant microbe experiments showed a significant positive correlation between auxin production by bacterial strains and endogenous IAA content of T. aestivum for GC–MS ( r  = 0·618; P  = 0.05) and colorimetric analysis ( r  = 0·693; P  = 0.01). Similarly, highly significant positive correlation for shoot length ( r  = 0·627; P  = 0.01) and shoot fresh weight ( r  = 0·626; P  = 0.01) was observed with auxin production under axenic conditions. Bacterial inoculations also enhanced shoot length (up to 29·16%), number of tillers (up to 97·35%), spike length (up to 25·20%) and seed weight (up to 13·70%) at final harvest.
Conclusions:  Bacterial strains have the ability to increase the endogenous IAA content and growth of T. aestivum var. Inqalab-91.
Significance and Impact of the Study:  Microbial strains of wild herbaceous flora can be effectively used to enhance the growth and yield of agronomically important crops.     

Evaluation of serum proteome from Indian psoriasis patients

Psoriasis is a polygenic chronic skin condition, associated with many systemic disorders. Though it is most studied dermatological condition, molecular mechanism leading to its pathogenesis is still unclear. An insight into its proteome may help unrevealing some biomarkers and therapeutic targets. In this study, we carried out mass spectrometry based quantitative proteomic analysis of serum from psoriasis patients by employing Tandem Mass Tags (TMT) approach. We identified 861,887 MS/MS spectra corresponding to 493 proteins. These dysregulated proteins were further classified by Gene Ontology and protein-protein interaction of dys-regulated proteins revealed networks in psoriasis patients.     

Evolution of organic matter in a full-scale composting plant for the treatment of sewage sludge and biowaste by respiration techniques and pyrolysis-GC/MS

A full-scale composting plant treating in two parallel lines sewage sludge and the source-selected organic fraction of municipal solid waste (OFMSW or biowaste) has been completely monitored. Chemical routine analysis proved not to be suitable for an adequate plant monitoring in terms of stabilization and characterization of the process and final compost properties. However, the dynamic respiration index demonstrated to be the most feasible tool to determine the progression of the degradation and stabilization of organic matter for both sewage sludge and OFMSW lines. Both lines exhibited an important degree of stabilization of organic matter using rapid and cumulative respiration indices. Pyrolysis-GC/MS was applied to the most important inputs, outputs, and intermediate points of the plant. It proved to be a powerful tool for the qualitative characterization of molecular composition of organic matter present in solid samples. A full characterization of the samples considered is also presented.     

Reproducibility in urine peptidome profiling using MALDI‐TOF

MALDI‐TOF profiling of low molecular weight peptides (peptidome) usage is limited due to the lack of reproducibility from the confounding inferences of sample preparation, data acquisition, and processing. We applied MALDI‐TOF analysis to profile urine peptidome with the aims to: (i) compare centrifugal ultrafiltration and dialysis pretreatments, (ii) determine whether using signal LOD (sLOD), together with data normalization, may reduce MALDI‐TOF variability. We also investigated the influence of peaks detection on reproducibility. Dialysis allowed to obtain better MALDI‐TOF spectra than ultrafiltration. Within the 1000–4000 m/z range, we identified 120 and 129 peaks in intra‐ and interassay studies, respectively. To estimate the sLOD, serial dilution of pooled urines up to 1/256 were analyzed in triplicate. Six data normalization strategies were investigated–the mean, median, internal standard, relative intensity, TIC, and linear rescaling normalization. Normalization methods alone performed poorly in reducing features variability while when combined to sLOD adjustment showed an overall reduction in features CVs. Applying a feedback signal processing approach, after median normalization and sLOD adjustment, CVs were reduced from 103 to 26% and 113 to 25% for the intra‐ and interassay, respectively, and spectra became more comparable in terms of data dispersion.     

Quantitative Proteomics Identified TTC4 as a TBK1 Interactor and a Positive Regulator of SeV‐Induced Innate Immunity

TBK1, STING, and MDA5 are important players within the antiviral innate immune response network. We mapped the interactome of endogenous TBK1, STING, and MDA5 by affinity enrichment MS in virally infected or uninfected THP‐1 cells. Based on quantitative data of more than 2000 proteins and stringent statistical analysis, 58 proteins were identified as high‐confidence interactors for at least one of three bait proteins. Our data indicated that TBK1 and MDA5 mostly interacted within preexisting protein networks, while STING interacted with different proteins with different viral infections. Functional analysis was performed on 17 interactors, and six were found to have functions in innate immune responses. We identified TTC4 as a TBK1 interactor and positive regulator of sendai virus‐induced innate immunity.