Lipidomics: a new window to biomedical frontiers

Lipids are a highly diverse class of molecules with crucial roles in cellular energy storage, structure and signaling. Lipid homeostasis is fundamental to maintain health, and lipid defects are central to the pathogenesis of important and devastating diseases. Newly emerging advances have facilitated the development of so-called lipidomics technologies and offer an opportunity to elucidate the mechanisms leading to disease. Furthermore, these advances also provide the tools to unravel the complexity of the 'allostatic forces' that allow maintenance of normal cellular/tissue phenotypes through the application of bioenergetically inefficient adaptive mechanisms. An alternative strategy is to focus on tissues with limited allostatic capacity, such as the eye, that could be used as readouts of metabolic stress over time. Identification of these allostatic mechanisms and pathological 'scares' might provide a window to unknown pathogenic mechanisms, as well as facilitate identification of early biomarkers of disease.     

Lead soaps formation and biodiversity in a XVIII Century wax seal coloured with minium

A multidisciplinary approach was carried out in order to study the biodeterioration and the associated microbiome of a XVIII Century wax seal coloured with minium. A small wax seal fragment was observed by scanning electron microscopy combined with energy dispersive spectroscopy in non-destructive mode. The same object was analysed by Raman and Fourier-transform infrared spectroscopy. The identification of the microbiota growing on the seal was performed with both a culture-dependent strategy, combined with hydrolytic assays, and high-throughput sequencing using the MinION platform. The whole bacterial 16S rRNA gene and the fungal markers ITS and 28S rRNA were targeted. It was observed that the carnauba wax coloured with lead tetroxide (minium) was covered by a biofilm consisting of a network of filaments and other structures of microbial origin. The culture-dependent and culture-independent investigations showed the presence of a complex microbiota composed mainly by fungal members, which demonstrated interesting properties related to lipids and lead processing. The formation of lead soaps and secondary biogenic minerals was also described.     

Detection of Molecular Paths Associated with Insulitis and Type 1 Diabetes in Non-Obese Diabetic Mouse

Recent clinical evidence suggests important role of lipid and amino acid metabolism in early pre-autoimmune stages of type 1 diabetes pathogenesis. We study the molecular paths associated with the incidence of insulitis and type 1 diabetes in the Non-Obese Diabetic (NOD) mouse model using available gene expression data from the pancreatic tissue from young pre-diabetic mice. We apply a graph-theoretic approach by using a modified color coding algorithm to detect optimal molecular paths associated with specific phenotypes in an integrated biological network encompassing heterogeneous interaction data types. In agreement with our recent clinical findings, we identified a path downregulated in early insulitis involving dihydroxyacetone phosphate acyltransferase (DHAPAT), a key regulator of ether phospholipid synthesis. The pathway involving serine/threonine-protein phosphatase (PP2A), an upstream regulator of lipid metabolism and insulin secretion, was found upregulated in early insulitis. Our findings provide further evidence for an important role of lipid metabolism in early stages of type 1 diabetes pathogenesis, as well as suggest that such dysregulation of lipids and related increased oxidative stress can be tracked to beta cells.     

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system’s electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions. The simulations are performed by employing the open-boundary molecular dynamics method that allows for simulation of open systems that can exchange mass and linear momentum with the environment. In our open-boundary molecular dynamics approach, the computational burden is drastically alleviated by embedding the DNA molecule in a mixed explicit/implicit salt-bathing solution. In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain. Our approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.     

Differential specific mechanical energy as a quality parameter in racing alpine skiing

An important question in alpine skiing is how to determine characteristics of well-performed ski turns, an issue that has become more crucial with the arrival of new carving skis. This article introduces a new method for estimating the quality of skiing at each point of observation based on mechanical energy behavior that can be measured using established motion analysis techniques. It can be used for single or multiple-skier analyses for evaluation of skiing technique as well as racing tactics. An illustration of its use is shown by analyzing 16 top-level racers using a 3-D kinematical system and video recorded during an alpine ski world cup race. Based on energy behavior of several racers, it is demonstrated that the most direct line with shortest radius of turn is not necessarily the most effective strategy in contrast to what some coaches believe.     

MZmine 2: Modular framework for processing,visualizing, and analyzing mass spectrometry-based molecular profile data

Background  

Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2.     

Processing methods for differential analysis of LC/MS profile data

Background  

Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i.e. broad screening of biomolecular components across multiple samples in order to elucidate the observed phenotypes and discover biomarkers. One of the major challenges in this domain remains development of better solutions for processing of LC/MS data.     

National Development Generates National Identities

The purpose of the article is to test the relationship between national identities and modernisation. We test the hypotheses that not all forms of identity are equally compatible with modernisation as measured by Human Development Index. The less developed societies are characterised by strong ascribed national identities based on birth, territory and religion, but also by strong voluntarist identities based on civic features selected and/or achieved by an individual. While the former decreases with further modernisation, the latter may either decrease or remain at high levels and coexist with instrumental supranational identifications, typical for the most developed countries. The results, which are also confirmed by multilevel regression models, thus demonstrate that increasing modernisation in terms of development contributes to the shifts from classical, especially ascribed, identities towards instrumental identifications. These findings are particularly relevant in the turbulent times increasingly dominated by the hardly predictable effects of the recent mass migrations.