Alkaliphilic Life: Adaptation strategies by Caldalkalibacillus thermarum

Alkaliphiles thrive in environments with a pH of 8.5 or above, while maintaining an internal pH closer to neutral. Thus, alkaliphilic microorganisms have a proton gradient inverted with respect to the normal orientation. Intuitively, this would nullify the potential to generate energy via respiration with regularly oriented respiratory chains...

Alzheimer’s disease, Aging and Centenarians

A remarkable accomplishment of human beings in recent centuries is the extension of their average lifespan, for example by improved living conditions. A downside of this achievement is that aging-related diseases, such as Alzheimer’s disease (AD), have risen, and as a consequence are impacting the lives of an increasing fraction of individuals....

Assessing yeast proteome dynamics using high-resolution mass spectrometry

Mass spectrometry-based cellular proteomics has taken a prominent role in many fields of research, including life sciences, biotechnology and microbial ecology. Still, advanced mass spectrometry-based proteomics methods are not routinely applied to microbes. The cell factory and model organism Saccharomyces cerevisiae, for example, is very well...

Machine learning–based biomarker profile derived from 4210 serially measured proteins predicts clinical outcome of patients with heart failure

Aims Risk assessment tools are needed for timely identification of patients with heart failure (HF) with reduced ejection fraction (HFrEF) who are at high risk of adverse events. In this study, we aim to derive a small set out of 4210 repeatedly measured proteins, which, along with clinical characteristics and established biomarkers, carry...

Aerobic granular sludge phosphate removal using glucose

Enhanced biological phosphate removal and aerobic sludge granulation are commonly studied with fatty acids as substrate. Fermentative substrates such as glucose have received limited attention. In this work, glucose conversion by aerobic granular sludge and its impact on phosphate removal was studied. Long-term stable phosphate removal and...

Quantitative analysis of Saccharomyces cerevisiae's growth and metabolism on sucrose

In recent decades, there has been an increase demand for renewable sources of energy and chemicals in replacement of their fossil-based counterparts to tackle the economic, social, and environmental issues associated with the processing and use of petrochemicals by humanity. Sucrose has proven to be a suitable alternative feedstock to substitute...

Evaluation of FRET X for single-molecule protein fingerprinting

Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands and...

Investigating the chemolithoautotrophic and formate metabolism of nitrospira moscoviensis by constraint-based metabolic modeling and ¹³C-tracer analysis

Nitrite-oxidizing bacteria belonging to the genus Nitrospira mediate a key step in nitrification and play important roles in the biogeochemical nitrogen cycle and wastewater treatment. While these organisms have recently been shown to exhibit metabolic flexibility beyond their chemolithoautotrophic lifestyle, including the use of simple...

Posttranslational control of plsb is sufficient to coordinate membrane synthesis with growth in escherichia coli

Every cell must produce enough membrane to contain itself. However, the mechanisms by which the rate of membrane synthesis is coupled with the rate of cell growth remain unresolved. By comparing substrate and enzyme concentrations of the fatty acid and phospholipid synthesis pathways of Escherichia coli across a 3-fold range of carbon-limited...

Metabolic switches from quiescence to growth in synchronized Saccharomyces cerevisiae

Introduction: The switch from quiescence (G0) into G1 and cell cycle progression critically depends on specific nutrients and metabolic capabilities. Conversely, metabolic networks are regulated by enzyme–metabolite interaction and transcriptional regulation that lead to flux modifications to support cell growth. How cells process and...

Functional expression of a bacterial α-ketoglutarate dehydrogenase in the cytosol of Saccharomyces cerevisiae

Efficient production of fuels and chemicals by metabolically engineered micro-organisms requires availability of precursor molecules for product pathways. In eukaryotic cell factories, heterologous product pathways are usually expressed in the cytosol, which may limit availability of precursors that are generated in other cellular...

Proteomic analysis of methanonatronarchaeum thermophilum AMET1, a representative of a putative new class of euryarchaeota, “methanonatronarchaeia”

The recently discovered Methanonatronarchaeia are extremely halophilic and moderately thermophilic methyl-reducing methanogens representing a novel class-level lineage in the phylum Euryarchaeota related to the class Halobacteria. Here we present a detailed analysis of 1D-nano liquid chromatography–electrospray ionization tandem mass...