A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study.

Genomics, transcriptomics, proteomics and fluxomics are powerful omics-technologies that play a major role in today's research. For each of these techniques good sample quality is crucial. Major factors contributing to the quality of a sample is the actual sampling procedure itself and the way the sample is stored directly after sampling.

Metabolic flexibility of D-ribose producer strain of Bacillus pumilus under environmental perturbations.

The metabolic reaction rate vector is a bridge that links gene and protein expression alterations to the phenotypic endpoint. We present a simple approach for the estimation of flux distribution at key branch points in the metabolic network by using substrate uptake, metabolite secretion rate, and biomass growth rate for transketolase (tkt) deficient Bacillus pumilus ATCC 21951. We find that the glucose-6-phosphate (G6P) and pseudo catabolic/anabolic branch points are flexible in the D: -ribose-producing tkt deficient strain of B.

Robust, small-scale cultivation platform for Streptomyces coelicolor.

Background: For fermentation process and strain improvement, where one wants to screen a large number of conditions and strains, robust and scalable high-throughput cultivation systems are crucial. Often, the time lag between bench-scale cultivations to production largely depends on approximate estimation of scalable physiological traits. Microtiter plate (MTP) based screening platforms have lately become an attractive alternative to shake flasks mainly because of the ease of automation.

Role of extracellular protease in nitrogen substrate management during antibiotic fermentation: a process model and experimental validation.

Kinetics of extracellular protease (ECP) production has typically been studied for processes that involve protease as a product. We argue that ECP is equally important in fermentations where protease is not a product of interest. Industrial fermentations typically use complex nitrogen substrates, which are proteolytically hydrolyzed to amino acids (AA) by ECP before assimilation.

Reducing the variability of antibiotic production in Streptomyces by cultivation in 24-square deepwell plates.

Highly reproducible production values of the aminocoumarin antibiotic novobiocin were achieved by cultivation of a heterologous Streptomyces producer strain in commercially available square deepwell plates consisting of 24 wells of 3 ml culture volume each. Between parallel cultivation batches in the deepwell plates, novobiocin accumulation showed standard deviations of 4-9%, compared to 39% in baffled Erlenmeyer flasks. Mycelia used as inoculum could be frozen in the presence of 20% peptone and stored at -70 degrees C, allowing repeated cultivations from the same batch of inoculum over extended periods of time.

Overexpression of a novel endogenous NADH kinase in Aspergillus nidulans enhances growth.

The complete genome sequence of the filamentous fungi Aspergillus nidulans has paved the way for fundamental research on this industrially important species. To the best of our knowledge, this is the first time a gene encoding for ATP-dependent NADH kinase (ATP:NADH 2'-phosphotransferase, EC 2.7.

Detection of phase shifts in batch fermentation via statistical analysis of the online measurements: a case study with rifamycin B fermentation.

Industrial production of antibiotics, biopharmaceuticals and enzymes is typically carried out via a batch or fed-batch fermentation process. These processes go through various phases based on sequential substrate uptake, growth and product formation, which require monitoring due to the potential batch-to-batch variability. The phase shifts can be identified directly by measuring the concentrations of substrates and products or by morphological examinations under microscope.

Sequential utilization of substrates by Pseudomonas putida CSV86: signatures of intermediate metabolites and online measurements.

Pseudomonas putida CSV86 preferentially utilizes aromatics over glucose and co-metabolizes them with organic acids. On aromatics plus glucose, CSV86 utilized aromatics first with concomitant appearance of transient metabolites such as salicylate, benzaldehyde and benzoate. Citrate was the main extracellular metabolite observed during glucose uptake.

Sporulating bacteria prefers predation to cannibalism in mixed cultures.

Predatory behavior, a property associated with ecosystems, is not commonly observed in microorganisms. However, cannibalistic tendencies have been observed in microorganisms under stress. For example, pure culture of Bacillus subtilis exhibits cannibalism under nutrient limitation.

Hierarchical amino acid utilization and its influence on fermentation dynamics: rifamycin B fermentation using Amycolatopsis mediterranei S699, a case study.

Background: Industrial fermentation typically uses complex nitrogen substrates which consist of mixture of amino acids. The uptake of amino acids is known to be mediated by several amino acid transporters with certain preferences. However, models to predict this preferential uptake are not available.

Phase shifts in the stoichiometry of rifamycin B fermentation and correlation with the trends in the parameters measured online.

Antibiotic fermentation processes are raw material cost intensive and the profitability is greatly dependent on the product yield per unit substrate consumed. In order to reduce costs, industrial processes use organic nitrogen substrates (ONS) such as corn steep liquor and yeast extract. Thus, although the stoichiometric analysis is the first logical step in process development, it is often difficult to achieve due to the ill-defined nature of the medium.

A cybernetic model to predict the effect of freely available nitrogen substrate on rifamycin B production in complex media.

It is well-known that secondary metabolite production is repressed by excess nitrogen substrate available in the fermentation media. Although the nitrogen catabolite repression has been known, quantitative process models have not been reported to represent this phenomenon in complex medium. In this paper, we present a cybernetic model for rifamycin B production via Amycolatopsis mediterranei S699 in complex medium, which is typically used in industry.

Structured kinetic model to represent the utilization of multiple substrates in complex media during rifamycin B fermentation.

Industrial fermentations typically use media that are balanced with multiple substitutable substrates including complex carbon and nitrogen source. Yet, much of the modeling effort to date has mainly focused on defined media. Here, we present a structured model that accounts for growth and product formation kinetics of rifamycin B fermentation in a multi-substrate complex medium.

Quantification of metabolically active biomass using Methylene Blue dye Reduction Test (MBRT): measurement of CFU in about 200 s.

Quantification of viable cells is a critical step in almost all biological experiments. Despite its importance, the methods developed so far to differentiate between viable and non-viable cells suffer from major limitations such as being time intensive, inaccurate and expensive. Here, we present a method to quantify viable cells based on reduction of methylene blue dye in cell cultures.

Optimization of rifamycin B fermentation in shake flasks via a machine-learning-based approach.

Rifamycin B is an important polyketide antibiotic used in the treatment of tuberculosis and leprosy. We present results on medium optimization for Rifamycin B production via a barbital insensitive mutant strain of Amycolatopsis mediterranei S699. Machine-learning approaches such as Genetic algorithm (GA), Neighborhood analysis (NA) and Decision Tree technique (DT) were explored for optimizing the medium composition.

An optimized method for Aspergillus niger spore production on natural carrier substrates.

Aspergillus niger spores have wide ranging applications in the fermentation industry as well as in wastewater treatment. We present an optimized method for production of A. niger spores on natural substrates such as rice, split pea, and millet.