Traditionally, mass spectrometry has been a powerful analytical method enabling the structural analysis of small molecules, and later on peptides and proteins. With the advent of native mass spectrometry, using a combination of electrospray ionisation and time of flight analysis, mass spectrometry could also be applied to the mass determination of large protein complexes such as ribosomes and whole viruses. More recently, ion mobility has been coupled to mass spectrometry providing a new dimension in the analysis of biomolecules, with ion mobility separating ions according to differences in size and shape. In the context of native mass spectrometry, ion mobility mass spectrometry opens up avenues for the detailed structural analysis of large and heterogeneous protein complexes, providing information on the stoichiometry, topology and cross section of these assemblies and their composite subunits. With these characteristics, ion mobility mass spectrometry offers a complementary tool in the context of structural biology. Here, we critically review the development, instrumentation, approaches and applications of ion mobility in combination with mass spectrometry, focusing on the analysis of larger proteins and protein assemblies (185 references).

Ion mobility mass spectrometry of proteins and protein assemblies.

The Self-Organizing Map (SOM) algorithm has attracted a great deal of interest among researches and practitioners in a wide variety of fields. The SOM has been analyzed extensively, a number of variants have been developed and, perhaps most notably, it has been applied extensively within fields ranging from engineering sciences to medicine, biology, and economics. We have collected a comprehensive list of 5384 scientific papers that use the algorithms, have benefited from them, or contain analyses of them. The list is intended to serve as a source for literature surveys. The present addendum contains 2092 new articles, mainly from the years 1998-2002. We have provided a keyword index to help finding articles of interest, and additionally a modern automatically constructed variant of a thematic index: a WEBSOM interface to the whole article collection of years 1981-2000. The SOM of SOMs is available at http://websom.hut.fi/websom/somref/search.cgi for browsing and searching the collection.

Bibliography of Self-Organizing Map SOM) Papers: 1998-2001 Addendum

Bacterial diversity in agroecosystems

Fermented foods are defined as foods or beverages produced through controlled microbial growth, and the conversion of food components through enzymatic action. In recent years, fermented foods have undergone a surge in popularity, mainly due to their proposed health benefits. The aim of this review is to define and characterise common fermented foods (kefir, kombucha, sauerkraut, tempeh, natto, miso, kimchi, sourdough bread), their mechanisms of action (including impact on the microbiota), and the evidence for effects on gastrointestinal health and disease in humans. Putative mechanisms for the impact of fermented foods on health include the potential probiotic effect of their constituent microorganisms, the fermentation-derived production of bioactive peptides, biogenic amines, and conversion of phenolic compounds to biologically active compounds, as well as the reduction of anti-nutrients. Fermented foods that have been tested in at least one randomised controlled trial (RCT) for their gastrointestinal effects were kefir, sauerkraut, natto, and sourdough bread. Despite extensive in vitro studies, there are no RCTs investigating the impact of kombucha, miso, kimchi or tempeh in gastrointestinal health. The most widely investigated fermented food is kefir, with evidence from at least one RCT suggesting beneficial effects in both lactose malabsorption and Helicobacter pylori eradication. In summary, there is very limited clinical evidence for the effectiveness of most fermented foods in gastrointestinal health and disease. Given the convincing in vitro findings, clinical high-quality trials investigating the health benefits of fermented foods are warranted.

Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease

To increase product yields and to ensure consistent product quality, key issues of industrial fermentations, process optimization and scale up are aimed at maintaining optimum and homogenous reaction conditions minimizing microbial stress exposure and enhancing metabolic accuracy. For each individual product, process and facility, suitable strategies have to be elaborated by a comprehensive and detailed process characterization, identification of the most relevant process parameters influencing product yield and quality and their establishment as scale-up parameters to be kept constant as far as possible. Physical variables, which can only be restrictedly kept constant as single parameters, may be combined with other pertinent parameters to appropriate mathematical groups or dimensionless terms. Process characterization is preferably based on real-time or near real-time data collected by in situ and on-line measurements and may be facilitated by supportive approaches and tools like neural network based chemometric data analysis and modelling, clarification of the mixing and stream conditions through computational fluid dynamics and scale-down simulations. However, as fermentation facilities usually are not strictly designed according to scale-up criteria and the process conditions in the culture vessels thus may differ significantly and since any strategy and model can only insufficiently consider and reflect the highly complex interdependence and mutual interaction of fermentation parameters, successful scale up in most cases is not the result of a conclusive and straight-lined experimental strategy, but rather will be the outcome of a separate process development and optimization on each scale. This article gives an overview on the problems typically coming along with fermentation process optimization and scale up, and presents currently applied scale-up strategies while considering future technologies, with emphasis on Escherichia coli as one of the most commonly fermented organisms.

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Optimization and scale up of industrial fermentation processes

Multivariate modelling of fish freshness index based on ion mobility spectrometry measurements

Actinomycetes were isolated from 10 soil samples, three representing sediments or shoreline of a pulp mill effluent polluted marsh pond and the rest topsoil from Finnish coniferous woodland. After a preliminary screen, 32 isolates exhibiting antifungal, antibacterial or genotoxic activities were obtained. The high incidence of strains with genotoxic properties (12 in this screen) was an unexpected finding. The majority (14) of the 19 antifungal isolates produced antibiotics of polyene type.

Variations in the spectra of biological activities of actinomycetes isolated from different soils

Fiber content of diet affects exhaled breath volatiles in fasting and postprandial state in a pilot crossover study.

Monitoring of yeast fermentation by ion mobility spectrometry measurement and data visualisation with Self-Organizing Maps

Isolation and determination of alizarin in cell cultures of Rubia tinctorum and emodin in Dermocybe sanguinea using solid-phase extraction and high-performance liquid chromatography

Olavi Raatikainen

Papers

Multivariate modelling of fish freshness index based on ion mobility spectrometry measurements

Variations in the spectra of biological activities of actinomycetes isolated from different soils

Fiber content of diet affects exhaled breath volatiles in fasting and postprandial state in a pilot crossover study.

Monitoring of yeast fermentation by ion mobility spectrometry measurement and data visualisation with Self-Organizing Maps

Isolation and determination of alizarin in cell cultures of Rubia tinctorum and emodin in Dermocybe sanguinea using solid-phase extraction and high-performance liquid chromatography