Molecular and immunological characterization of the major outer membrane proteins of Brucella

Abstract Saccharomyces cerevisiae exponentially growing in basic or 0.7 M NaCl medium were isotopically labelled with ³⁵S-methionine, followed by protein separation and quantification by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) combined with computerised image analysis. The electrophoretic separation resolved about 650 proteins of which 13 displayed significant and at least 2-fold changes in rate of synthesis during saline growth. By sequencing of 2D-PAGE resolved proteins, one of the 8 induced spot, p42.9/5.5, was shown to correspond to the full length (containing the N-terminal extension) product of the GPD 1 gene encoding the cytoplasmic glycerol 3-phosphate dehydrogenase. The expression of the TDH 3 gene, glyceraldehyde 3-phosphate dehydrogenase, and the ENO 2 gene, enolase, decreased during growth in NaCl medium, declines hypothesised to have an impact on the flux to glycerol.     

ImShot: An Open-Source Software for Probabilistic Identification of Proteins In Situ and Visualization of Proteomics Data

Imaging mass spectrometry (IMS) has developed into a powerful tool allowing label-free detection of numerous biomolecules in situ. In contrast to shotgun proteomics, proteins/peptides can be detected directly from biological tissues and correlated to its morphology leading to a gain of crucial clinical information. However, direct identification of the detected molecules is currently challenging for MALDI–IMS, thereby compelling researchers to use complementary techniques and resource intensive experimental setups. Despite these strategies, sufficient information could not be extracted because of lack of an optimum data combination strategy/software. Here, we introduce a new open-source software ImShot that aims at identifying peptides obtained in MALDI–IMS. This is achieved by combining information from IMS and shotgun proteomics (LC–MS) measurements of serial sections of the same tissue. The software takes advantage of a two-group comparison to determine the search space of IMS masses after deisotoping the corresponding spectra. Ambiguity in annotations of IMS peptides is eliminated by introduction of a novel scoring system that identifies the most likely parent protein of a detected peptide in the corresponding IMS dataset. Thanks to its modular structure, the software can also handle LC–MS data separately and display interactive enrichment plots and enriched Gene Ontology terms or cellular pathways. The software has been built as a desktop application with a conveniently designed graphic user interface to provide users with a seamless experience in data analysis. ImShot can run on all the three major desktop operating systems and is freely available under Massachusetts Institute of Technology license.     

What Determines Auditory Distraction? On the Roles of Local Auditory Changes and Expectation Violations

Both the acoustic variability of a distractor sequence and the degree to which it violates expectations are important determinants of auditory distraction. In four experiments we examined the relative contribution of local auditory changes on the one hand and expectation violations on the other hand in the disruption of serial recall by irrelevant sound. We present evidence for a greater disruption by auditory sequences ending in unexpected steady state distractor repetitions compared to auditory sequences with expected changing state endings even though the former contained fewer local changes. This effect was demonstrated with piano melodies (Experiment 1) and speech distractors (Experiment 2). Furthermore, it was replicated when the expectation violation occurred after the encoding of the target items (Experiment 3), indicating that the items'' maintenance in short-term memory was disrupted by attentional capture and not their encoding. This seems to be primarily due to the violation of a model of the specific auditory distractor sequences because the effect vanishes and even reverses when the experiment provides no opportunity to build up a specific neural model about the distractor sequence (Experiment 4). Nevertheless, the violation of abstract long-term knowledge about auditory regularities seems to cause a small and transient capture effect: Disruption decreased markedly over the course of the experiments indicating that participants habituated to the unexpected distractor repetitions across trials. The overall pattern of results adds to the growing literature that the degree to which auditory distractors violate situation-specific expectations is a more important determinant of auditory distraction than the degree to which a distractor sequence contains local auditory changes.     

Ice‐‐bacteria as antagonists in biological frost protection

Investigated was the efficacy of 4 ice nucleation‐inactive (ice^‐) bacterial strains (A506, GSPB 1147, 1181, 2357) at 4 ice nucleation active (ice⁺) strains (553, 554, GSPB 1139, 2035) on the surface of 4 culture crops (corn, tomato, bush‐ and field bean). Examinated was the reduction of frost damage at the used culture crops by inoculation with ice⁺ and ice^‐ strains at 4 different variants (A‐D) under laboratory conditions. The ice nucleation activity was determined by the tube‐freezing‐assay. An effective reduction of ice⁺ bacteria was possible, when plant surfaces were preinoculated (3days) with ice^‐bacteria before ice⁺ bacterial strains colonized the surfaces of plants. A statistical comparison of mean values of obtained results showed, the ice crystallization (INT) by inoculation started at ‐3°C and in mean (MNT) below ‐5°C independent of the used ice⁺ and ice^‐ strains. Obtained differences were not significant. As untreated as colonized plants with antagonists started to freeze at ‐5 and ‐6°C and in average at ‐7°C. However, the preinoculation resulted in 1.38 K differences for the temperatures, at which 50% of leaves were frozen (PROZ 50) in favour of preinoculated plants. This difference in freeze temperatures by preinoculation with ice^‐ bacteria was discussed as a possible method of frost protection.     

We are devo-evo

Workshop: Novartis Foundation Symposium No. 222: Homology, London, UK, 21–23 July 1998. Followed by an Open Meeting: Homology, Welcome Trust, London, UK, 24 July 1998.     

Flavin Mononucleotide-Based Fluorescent Proteins Function in Mammalian Cells without Oxygen Requirement

Usage of the enhanced green fluorescent protein (eGFP) in living mammalian cells is limited to aerobic conditions due to requirement of oxygen during chromophore formation. Since many diseases or disease models are associated with acute or chronic hypoxia, eGFP-labeling of structures of interest in experimental studies might be unreliable leading to biased results. Thus, a chromophore yielding a stable fluorescence under hypoxic conditions is desirable. The fluorescence of flavin mononucleotide (FMN)-based fluorescent proteins (FbFPs) does not require molecular oxygen. Recently, the advantages of FbFPs for several bacterial strains and yeasts were described, specifically, their usage as a real time fluorescence marker in bacterial expression studies and their ability of chromophore formation under anaerobic conditions. Our objective was to verify if FbFPs also function in mammalian cells in order to potentially broaden the repertoire of chromophores with ones that can reliably be used in mammalian studies under hypoxic conditions. In the present study, we demonstrate for the first time, that FbFPs can be expressed in different mammalian cells, among them murine neural stem cells during proliferative and differentiated stages. Fluorescence intensities were comparable to eGFP. In contrast to eGFP, the FbFP fluorescence did not decrease when cells were exposed to defined hypoxic conditions neither in proliferating nor in differentiated cells. Thus, FbFPs can be regarded as an alternative to eGFP in studies that target cellular structures which are exposed to hypoxic conditions.     

Conservation genetics: Linking science with practice

Conservation genetics is a well‐established scientific field. However, limited information transfer between science and practice continues to hamper successful implementation of scientific knowledge in conservation practice and management. To mitigate this challenge, we have established a conservation genetics community, which entails an international exchange‐and‐skills platform related to genetic methods and approaches in conservation management. First, it allows for scientific exchange between researchers during annual conferences. Second, personal contact between conservation professionals and scientists is fostered by organising workshops and by popularising knowledge on conservation genetics methods and approaches in professional journals in national languages. Third, basic information on conservation genetics has been made accessible by publishing an easy‐to‐read handbook on conservation genetics for practitioners. Fourth, joint projects enabled practitioners and scientists to work closely together from the start of a project in order to establish a tight link between applied questions and scientific background. Fifth, standardised workflows simplifying the implementation of genetic tools in conservation management have been developed. By establishing common language and trust between scientists and practitioners, all these measures help conservation genetics to play a more prominent role in future conservation planning and management.