Fast proteomics with dia-PASEF and analytical flow-rate chromatography.

Increased throughput in proteomic experiments can improve accessibility of proteomic platforms, reduce costs, and facilitate new approaches in systems biology and biomedical research. Here we propose combination of analytical flow rate chromatography with ion mobility separation of peptide ions, data-independent acquisition, and data analysis with the DIA-NN software suite, to achieve high-quality proteomic experiments from limited sample amounts, at a throughput of up to 400 samples per day. For instance, when benchmarking our workflow using a 500-μL/min flow rate and 3-min chromatographic gradients, we report the quantification of 5211 proteins from 2 μg of a mammalian cell-line standard at high quantitative accuracy and precision.

The Impact of Acute Nutritional Interventions on the Plasma Proteome.

Context: Humans respond profoundly to changes in diet, while nutrition and environment have a great impact on population health. It is therefore important to deeply characterize the human nutritional responses.

Objective: Endocrine parameters and the metabolome of human plasma are rapidly responding to acute nutritional interventions such as caloric restriction or a glucose challenge.

Reduced Mass and Diversity of the Colonic Microbiome in Patients with Multiple Sclerosis and Their Improvement with Ketogenic Diet.

Colonic microbiome is thought to be involved in auto-immune multiple sclerosis (MS). Interactions between diet and the colonic microbiome in MS are unknown. We compared the composition of the colonic microbiota quantitatively in 25 MS patients and 14 healthy controls.

Impact of humic acids on the colonic microbiome in healthy volunteers.

Aim: To test the effects of humic acids on innate microbial communities of the colon.

Methods: We followed the effects of oral supplementation with humic acids (Activomin) on concentrations and composition of colonic microbiome in 14 healthy volunteers for 45 d. 3 × 800 mg Activomin were taken orally for 10 d followed by 3 × 400 mg for 35 d.

Noninvasive Oxygen Monitoring in Three-Dimensional Tissue Cultures Under Static and Dynamic Culture Conditions.

We present a new method for noninvasive real-time oxygen measurement inside three-dimensional tissue-engineered cell constructs in static and dynamic culture settings in a laminar flow bioreactor. The OPAL system (optical oxygen measurement system) determines the oxygen-dependent phosphorescence lifetime of spherical microprobes and uses a two-frequency phase-modulation technique, which fades out the interference of background fluorescence from the cell carrier and culture medium. Higher cell densities in the centrum of the scaffolds correlated with lower values of oxygen concentration obtained with the OPAL system.

Three-Dimensional Modelling inside a Differential Pressure Laminar Flow Bioreactor Filled with Porous Media.

A three-dimensional computational fluid dynamics- (CFD-) model based on a differential pressure laminar flow bioreactor prototype was developed to further examine performance under changing culture conditions. Cell growth inside scaffolds was simulated by decreasing intrinsic permeability values and led to pressure build-up in the upper culture chamber. Pressure release by an integrated bypass system allowed continuation of culture.

Alignment-Annotator web server: rendering and annotating sequence alignments.

Unlabelled: Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers.

Sequence alignment visualization in HTML5 without Java.

Motivation: Java has been extensively used for the visualization of biological data in the web. However, the Java runtime environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for some tasks may render Java unnecessary.

A differential pressure laminar flow reactor supports osteogenic differentiation and extracellular matrix formation from adipose mesenchymal stem cells in a macroporous ceramic scaffold.

We present a laminar flow reactor for bone tissue engineering that was developed based on a computational fluid dynamics model. The bioreactor design permits a laminar flow field through its specific internal shape. An integrated bypass system that prevents pressure build-up through bypass openings for pressure release allows for a constant pressure environment during the changing of permeability values that are caused by cellular growth within a porous scaffold.

Metannogen: annotation of biological reaction networks.

Motivation: Semantic annotations of the biochemical entities constituting a biological reaction network are indispensable to create biologically meaningful networks. They further heighten efficient exchange, reuse and merging of existing models which concern present-day systems biology research more often. Two types of tools for the reconstruction of biological networks currently exist: (i) several sophisticated programs support graphical network editing and visualization.

FASIMU: flexible software for flux-balance computation series in large metabolic networks.

Background: Flux-balance analysis based on linear optimization is widely used to compute metabolic fluxes in large metabolic networks and gains increasingly importance in network curation and structural analysis. Thus, a computational tool flexible enough to realize a wide variety of FBA algorithms and able to handle batch series of flux-balance optimizations is of great benefit.

Results: We present FASIMU, a command line oriented software for the computation of flux distributions using a variety of the most common FBA algorithms, including the first available implementation of (i) weighted flux minimization, (ii) fitness maximization for partially inhibited enzymes, and (iii) of the concentration-based thermodynamic feasibility constraint.

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology.

We present HepatoNet1, the first reconstruction of a comprehensive metabolic network of the human hepatocyte that is shown to accomplish a large canon of known metabolic liver functions. The network comprises 777 metabolites in six intracellular and two extracellular compartments and 2539 reactions, including 1466 transport reactions. It is based on the manual evaluation of >1500 original scientific research publications to warrant a high-quality evidence-based model.

Computational analysis of protein-protein interactions in metabolic networks of Escherichia coli and yeast.

Protein-protein interactions are operative at almost every level of cell function. In the recent years high-throughput methods have been increasingly used to uncover protein-protein interactions at genome scale resulting in interaction maps for entire organisms. However, biochemical implications of high-throughput interactions are not always obvious.

Superimpose: a 3D structural superposition server.

The Superimposé webserver performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e.g.

Computer aided optimization of carbon atom labeling for tracer experiments.

Isotopomer tracer experiments are indispensable for the determination of flux rates in already known pathways as well as for the identification of new pathways. The information gained from such experiments depends on the labeling of the feed tracer metabolite, i.e.

A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling.

Protein-protein interactions are operative at almost every level of cell structure and function as, for example, formation of sub-cellular organelles, packaging of chromatin, muscle contraction, signal transduction, and regulation of gene expression. Public databases of reported protein-protein interactions comprise hundreds of thousands interactions, and this number is steadily growing. Elucidating the implications of protein-protein interactions for the regulation of the underlying cellular or extra-cellular reaction network remains a great challenge for computational biochemistry.

METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks.

Background: One central goal of computational systems biology is the mathematical modelling of complex metabolic reaction networks. The first and most time-consuming step in the development of such models consists in the stoichiometric reconstruction of the network, i. e.

Plasmodia express two threonine-peptidase complexes during asexual development.

Threonine-peptidases of the T1-family are multi-subunit complexes with broad substrate specificity. In eukaryotes, at least 14 genes encode subunits of the prototypic T1 threonine-peptidase, the proteasome. The proteasome determines the turnover of most proteins and thereby plays a fundamental role in diverse processes such as protein quality control, signal transduction, and cell cycle regulation.

HotSwap for bioinformatics: a STRAP tutorial.

Background: Bioinformatics applications are now routinely used to analyze large amounts of data. Application development often requires many cycles of optimization, compiling, and testing. Repeatedly loading large datasets can significantly slow down the development process.

A fibrillin-1-fragment containing the elastin-binding-protein GxxPG consensus sequence upregulates matrix metalloproteinase-1: biochemical and computational analysis.

Mutations in the gene for fibrillin-1 cause Marfan syndrome (MFS), a common hereditary disorder of connective tissue. Recent findings suggest that proteolysis, increased matrix metalloproteinase activity, and fragmentation of fibrillin-rich microfibrils in tissues of persons with MFS contribute to the complex pathogenesis of this disorder. In this study we show that a fibrillin-1 fragment containing a EGFEPG sequence that conforms to a putative GxxPG elastin-binding protein (EBP) consensus sequence upregulates the expression and production of matrix metalloproteinase (MMP)-1 by up to ninefold in a cell culture system.

Combining bioinformatics resources for the structural modelling of eukaryotic metabolic networks.

The architecture of the cellular metabolic network is almost completely available from several databases. This has paved the way for computational analyses. Whereas kinetic modelling is still restrained to small metabolic sub-systems for which enzyme-kinetic details are known, so-called structural modelling techniques can be applied to complete metabolic networks even if the kinetics and regulation of the underlying enzymes is still unknown.

Structural interpretation of mutations and SNPs using STRAP-NT.

Visualization of residue positions in protein alignments and mapping onto suitable structural models is an important first step in the interpretation of mutations or polymorphisms in terms of protein function, interaction, and thermodynamic stability. Selecting and highlighting large numbers of residue positions in a protein structure can be time-consuming and tedious with currently available software. Previously, a series of tasks and analyses had to be performed one-by-one to map mutations onto 3D protein structures; STRAP-NT is an extension of STRAP that automates these tasks so that users can quickly and conveniently map mutations onto 3D protein structures.

KISS for STRAP: user extensions for a protein alignment editor.

Summary: The Structural Alignment Program STRAP is a comfortable comprehensive editor and analyzing tool for protein alignments. A wide range of functions related to protein sequences and protein structures are accessible with an intuitive graphical interface. Recent features include mapping of mutations and polymorphisms onto structures and production of high quality figures for publication.

Accelerating screening of 3D protein data with a graph theoretical approach.

Motivation: The Dictionary of Interfaces in Proteins (DIP) is a database collecting the 3D structure of interacting parts of proteins that are called patches. It serves as a repository, in which patches similar to given query patches can be found. The computation of the similarity of two patches is time consuming and traversing the entire DIP requires some hours.

Online tool for the discrimination of equi-distributions.

Background: For many applications one wishes to decide whether a certain set of numbers originates from an equiprobability distribution or whether they are unequally distributed. Distributions of relative frequencies may deviate significantly from the corresponding probability distributions due to finite sample effects. Hence, it is not trivial to discriminate between an equiprobability distribution and non-equally distributed probabilities when knowing only frequencies.