Integrative meta-omics in Galaxy and beyond.

Background: 'Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as "meta-omics", they enhance the understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize environmental nutrients. Here we present three integrative meta-omics workflows, developed in Galaxy, for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with our newly developed web-application, ViMO (Visualizer for Meta-Omics) to analyse metabolisms in complex microbial communities.

Chromatographic analysis of oxidized cello-oligomers generated by lytic polysaccharide monooxygenases using dual electrolytic eluent generation.

Research on oligosaccharides, including the complicated product mixtures generated by lytic polysaccharide monooxygenases (LPMOs), is growing at a rapid pace. LPMOs are gaining major interest, and the ability to efficiently and accurately separate and quantify their native and oxidized products chromatographically is essential in furthering our understanding of these oxidative enzymes. Here we present a novel set of methods based on dual electrolytic eluent generation, where the conventional sodium acetate/sodium hydroxide (NaOAc/NaOH) eluents in high-performance anion-exchange chromatography (HPAEC) are replaced by electrolytically-generated potassium methane sulfonate/potassium hydroxide (KMSA/KOH).

Alginate Degradation: Insights Obtained through Characterization of a Thermophilic Exolytic Alginate Lyase.

Enzymatic depolymerization of seaweed polysaccharides is gaining interest for the production of functional oligosaccharides and fermentable sugars. Herein, we describe a thermostable alginate lyase that belongs to polysaccharide lyase family 17 (PL17) and was derived from an Arctic Mid-Ocean Ridge (AMOR) metagenomics data set. This enzyme, AMOR_PL17A, is a thermostable exolytic oligoalginate lyase (EC 4.

Quantitative comparison of the biomass-degrading enzyme repertoires of five filamentous fungi.

The efficiency of microorganisms to degrade lignified plants is of great importance in the Earth's carbon cycle, but also in industrial biorefinery processes, such as for biofuel production. Here, we present a large-scale proteomics approach to investigate and compare the enzymatic response of five filamentous fungi when grown on five very different substrates: grass (sugarcane bagasse), hardwood (birch), softwood (spruce), cellulose and glucose. The five fungi included the ascomycetes Aspergillus terreus, Trichoderma reesei, Myceliophthora thermophila, Neurospora crassa and the white-rot basidiomycete Phanerochaete chrysosporium, all expressing a diverse repertoire of enzymes.

Metaproteomics: Sample Preparation and Methodological Considerations.

Meta-omic techniques have progressed rapidly in the past decade and are frequently used in microbial ecology to study microorganisms in their natural ecosystems independent from culture restrictions. Metaproteomics, in combination with metagenomics, enables quantitative assessment of expressed proteins and pathways from individual members of the consortium. Together, metaproteomics and metagenomics can provide a detailed understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize nutrients, and these insights can be obtained directly from environmental samples.

Proteomic Detection of Carbohydrate-Active Enzymes (CAZymes) in Microbial Secretomes.

Secretomes from microorganisms growing on biomass contain carbohydrate-active enzymes (CAZymes) of potential biotechnological interest. By analyzing such secretomes, we may discover key enzymes involved in degradation processes and potentially infer the mode-of-action of biomass conversion. Some of these enzymes may have predicted functions in carbohydrate degradation, while others may not, while yet exhibiting a similar expression pattern; these latter enzymes constitute potential novel enzymes involved in the degradation process and provide a basis for further biochemical exploration.

Cell death proteomics database: consolidating proteomics data on cell death.

Programmed cell death is a ubiquitous process of utmost importance for the development and maintenance of multicellular organisms. More than 10 different types of programmed cell death forms have been discovered. Several proteomics analyses have been performed to gain insight in proteins involved in the different forms of programmed cell death.

Quantitative proteome analysis using isobaric peptide termini labeling (IPTL).

The quantitative comparison of proteome level changes across biological samples has become an essential feature in proteomics that remains challenging. We have recently introduced isobaric peptide termini labeling (IPTL), a novel strategy for isobaric quantification based on the derivatization of peptide termini with complementary isotopically labeled reagents. Unlike non-isobaric quantification methods, sample complexity at the MS level is not increased, providing improved sensitivity and protein coverage.

The association between maternal education and postneonatal mortality. Trends in Norway, 1968-1991.

Background: This study examines whether the association between maternal educational level and postneonatal death has changed over time.

Methods: All single survivors of the neonatal period in Norway in three periods, 1968-1971, 1978-1981 and 1989-1991 were studied. There were 582 046 births and 1717 postneonatal deaths.

Marital status as a risk factor for fetal and infant mortality.

In order to study pregnancy outcome for married versus unmarried mothers when controlling statistically for maternal age, educational level, socioeconomic status and income, a total of 93,800 firstborn singleton births in 1978-1982 were examined. The unmarried mothers were younger, less well educated and had a lower socioeconomic status than the married mothers. The stillbirth, neonatal, and postneonatal mortality rates were higher among offspring of unmarried mothers.

Is the higher postneonatal mortality in lower social status groups due to SIDS?

In order to study the influence of sociodemographic factors, postneonatal mortality of all live births surviving the neonatal period registered in the Norwegian Medical Birth Registry in 1978-1982 were examined (n = 209,030). Postneonatal deaths (n = 634) were divided into two categories; deaths due to the sudden infant death syndrome (SIDS) (n = 359) and deaths due to other causes (non-SIDS) (n = 275). SIDS and non-SIDS deaths showed different relationships to sociodemographic factors, and the associations appeared to be different for first-born and later born children.

Different effects of maternal and paternal education on early mortality in Norway.

In order to separate the effects of maternal and paternal education on pregnancy outcome, a total population of 97,526 single, firstborn infants and their parents was studied. Census information from 1980 was linked to the Medical Birth Registry for 1978-82. Children of parents with high education (> 12 years) were the most likely to survive the first year of life.

No correlation in post-neonatal deaths for twins. A study of the early mortality of twins based on the Norwegian Medical Birth Registry.

The records of 10,204 pairs of twins born in Norway 1967-84 in the Norwegian Birth Registry were examined. The probabilities of stillbirth, neonatal death and post-neonatal death, conditional on the fate of the cotwin, were calculated. The neonatal death rate was four times increased when the cotwin was stillborn.