Self-reproduction and doubling time limits of different cellular subsystems.

Ribosomes which can self-replicate themselves practically autonomously in beneficial physicochemical conditions have been recognized as the central organelles of cellular self-reproduction processes. The challenge of cell design is to understand and describe the rates and mechanisms of self-reproduction processes of cells as of coordinated functioning of ribosomes and the enzymatic networks of different functional complexity that support those ribosomes. We show that doubling times of proto-cells (ranging from simplest replicators up to those reaching the size of E.

Protein Turnover in Epithelial Cells and Mucus along the Gastrointestinal Tract Is Coordinated by the Spatial Location and Microbiota.

The gastrointestinal tract is covered by a single layer of epithelial cells that, together with the mucus layers, protect the underlying tissue from microbial invasion. The epithelium has one of the highest turnover rates in the body. Using stable isotope labeling, high-resolution mass spectrometry, and computational analysis, we report a comprehensive dataset of the turnover of more than 3,000 and the expression of more than 5,000 intestinal epithelial cell proteins, analyzed under conventional and germ-free conditions across five different segments in mouse intestine.

Model-based metabolism design: constraints for kinetic and stoichiometric models.

The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization constraints to improve the feasibility of model-based designs of metabolic pathways in organisms.

Comprehensive analysis of proteolysis during 8 months of ripening of high-cooked Old Saare cheese.

We applied capillary electrophoresis, liquid chromatography coupled with tandem mass-spectrometry (MS/MS), and ultra-performance liquid chromatography to determine the composition of water-insoluble and water-soluble proteinaceous fractions of the cheese and to study in detail the degradation of caseins during 8 mo of ripening of Estonian high-temperature cooked hard cheese Old Saare. The application of high-resolution and high-accuracy MS/MS enabled identification of more than 3,000 small peptides, representing a fairly full casein peptidome containing peptides of 4 to 25 AA in length: 1,049 from β-casein (CN), 944 from α-CN, 813 from α-CN, and 234 from κ-CN. The majority of β-CN- and α-CN-derived peptides originated from the N-terminal parts of the molecule, f6-93 and f1-124, respectively; peptides from α-CN arose predominantly from the C-terminal end f100-162.

Step-wise temperature decreasing cultivates a biofilm with high nitrogen removal rates at 9°C in short-term anammox biofilm tests.

The anaerobic ammonium oxidation (anammox) and nitritation-anammox (deammonification) processes are widely used for N-rich wastewater treatment. When deammonification applications move towards low temperature applications (mainstream wastewater has low temperature), temperature effect has to be studied. In current research, in a deammonification moving bed biofilm reactor a maximum total nitrogen removal rate (TNRR) of 1.