Bio-availability of phosphorus in sediments of the western Dutch Wadden Sea

The purpose of this study was to make a prognosis of the effects of extended purification of terrestrial waste water, reaching the Wadden Sea by the River Rhine and Lake IJssel, on the phosphate concentration in the western Wadden Sea.The quantities of different phosphorus fractions in intertidal and subtidal sediments of the Marsdiep tidal basin (western Dutch Wadden Sea) were measured. Different methods are applied to determine the amount of phosphorus that can be released from these sediments. The direct bioavailability is determined by inoculating sediment suspensions with a natural mixture of precultured micro-organisms from the sampling area. A second approach is the measurement of the phosphate release under different redox conditions. Sequential extraction of sediment samples with different solvents is also applied. Under the present conditions and compared to the nutrient loads from fresh water (Lake IJssel) and from the North Sea, the phosphorus stored in the sediments of the western Dutch Wadden Sea plays a minor role in the total supply to micro-algae and bacteria. The bulk of the biologically available phosphorus in the sediments originates from the metal-associated fraction. Releasable phosphate may contribute to the local annual primary production to an extent of ca 45 to ca 150 g C m^–2 a^–1. The total amount of phosphorus in the sediment (mainly calcite associated) is twice to 6 times the biologically available amount.     

STADEERS: a software package for the statistical design of experiments pertaining to the estimation of parameters in rate expressions that describe enzyme-catalyzed processes

This paper describes a computational algorithm (STADEERS-STAtisticalDesign of Exeriments in Enzyme ReactorS) for the statisticaldesign of biochemical engineering experiments. The type of experimentthat qualifies for this package involves a batch reaction catalyzedby a soluble enzyme where the activity of the enzyme decayswith time. Assuming that both the catalytic action and the deactivationof the enzyme obey known rate expressions, the present codeis helpful in the process of obtaining estimates of the kineticparameters by providing as output the times at which samplesshould be withdrawn from the reacting mixture. Starting D-optimaldesign is used as a basis for the statistical approach. ThisBASIC code is a powerful tool when fitting a rate expressionto data because it increases the effectiveness of experimentationby helping the biochemical kineticist obtain data points withthe largest possible informa tional content.     

Enhanced transformation of tomato co-cultivated with Agrobacterium tumefaciens C58C1Rifr::pGSFR1161 in the presence of acetosyringone

Summary Explants of tomato (Lycopersicon esculentum Mill cv. Ailsa Craig) were co-cultivated with Agrobacterium tumefaciens C58C1Rif^r::pGSFR1161 in the presence of 20 (M acetosyringone). Transformed root clones were selected on kanamycin medium and the presence of the nptII gene in the plant DNA confirmed by the polymerase chain reaction. Root clones derived from acetosyringone treatment grew more vigorously in the presence of kanamycin and synthesized a greater amount of NPT-II enzyme. The conclusion is that acetosyringone treatment enhances the transformation process, possibly by stimulating multiple insertions of the T-DNA into the host genome.Abbreviations AS acetosyringone - CTAB hexadecyltrimethylammonium bromide - EDTA ethylenediaminetetraacetic acid - ELISA enzyme-linked immunosorbant assay - MS Murashige and Skoog (1962) medium - PCR polymerase chain reaction     

COVID-19 plasma proteome reveals novel temporal and cell-specific signatures for disease severity and high-precision disease management

Coronavirus disease 2019 (COVID-19) is a systemic inflammatory condition with high mortality that may benefit from personalized medicine and high-precision approaches. COVID-19 patient plasma was analysed with targeted proteomics of 1161 proteins. Patients were monitored from Days 1 to 10 of their intensive care unit (ICU) stay. Age- and gender-matched COVID-19-negative sepsis ICU patients and healthy subjects were examined as controls. Proteomic data were resolved using both cell-specific annotation and deep-analysis for functional enrichment. COVID-19 caused extensive remodelling of the plasma microenvironment associated with a relative immunosuppressive milieu between ICU Days 3–7, and characterized by extensive organ damage. COVID-19 resulted in (1) reduced antigen presentation and B/T-cell function, (2) increased repurposed neutrophils and M1-type macrophages, (3) relatively immature or disrupted endothelia and fibroblasts with a defined secretome, and (4) reactive myeloid lines. Extracellular matrix changes identified in COVID-19 plasma could represent impaired immune cell homing and programmed cell death. The major functional modules disrupted in COVID-19 were exaggerated in patients with fatal outcome. Taken together, these findings provide systems-level insight into the mechanisms of COVID-19 inflammation and identify potential prognostic biomarkers. Therapeutic strategies could be tailored to the immune response of severely ill patients.     

An electrogenetic toggle switch model

Synthetic biology uses molecular biology to implement genetic circuits that perform computations. These circuits can process inputs and deliver outputs according to predefined rules that are encoded, often entirely, into genetic parts. However, the field has recently begun to focus on using mechanisms beyond the realm of genetic parts for engineering biological circuits. We analyse the use of electrogenic processes for circuit design and present a model for a merged genetic and electrogenetic toggle switch operating in a biofilm attached to an electrode. Computational simulations explore conditions under which bistability emerges in order to identify the circuit design principles for best switch performance. The results provide a basis for the rational design and implementation of hybrid devices that can be measured and controlled both genetically and electronically.     

Production of pectinases by Aspergillus niger in solid state fermentation at high initial glucose concentrations

Exopectinase (exo-p) and endopectinase (endo-p) production by Aspergillus niger CH4 in solid state culture was studied at initial glucose concentrations of 100, 250, 350 and 450 g/l. The highest activity of exo-p (35 U/g) was produced at 72 and 120 h in the medium containing 100 and 250 g glucose/l, respectively. The maximum endo-p activity (9 U/g) was produced at 72 h in the medium with 250 g glucose/l. The reduction in pectinase production at 350 and 450 g/l initial glucose concentration was due neither to repression of the synthesis of the enzyme nor to the glucose consumption rate of the strain but due to a drastic drop in pH of the medium.S. Solis-Pereyra, E. Favela-Torres, M. Gutiérrez-Rojas, G. Saucedo-Castañeda and G. Viniegra-González are with the Departamento de Biotecnologia, Universidad Autónoma Metropolitana, A.P. 55-535, C.P. 09340, México D.F., México; S. Roussos is with the Laboratoire de Biotechnologie, ORSTOM, B.P. 5045, 34032, Montpellier Cedex, France, and P. Gunasekaran is with the Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625-021, India.     

Manipulating photosynthesis

The levels of individual photosynthetic proteins can be independently decreased by theAgrobacterium-mediated transformation of plants with antisens RNA constructs. Protocols for the introduction of such constructs intoAgrobacterium, theAgrobacterium-mediated transformation of tobacco leaf disks, and the screening and analysis of the transgenic plants produced are described.     

Establishment and characterization of photosynthetic hairy root cultures of Datura stramonium

Twelve different lines of Datura stramonium (normal and hairy) root cultures were subjected to conditions which induce photoautotrophy. Two of the hairy root lines responded to induction, showing clearly a diminished growth rate when compared to heterotrophic cultures, an increase in chlorophyll, a net O₂ evolution, CO₂ fixation, and de novo synthesis of the ribulose 1,5 biphosphate carboxylase enzyme. A time course of growth and tropane alkaloid levels in the tissue and medium, revealed a correlation between the development of the photosynthetic apparatus and the increase in scopolamine. Although normal cultures did not grow photosynthetically, they showed some greening response under the first step of the induction. The correlation between development of photosynthesis and increase in scopolamine synthesis were corroborated with normal root cultures. This experimental model is used for the basic study of the regulatory enzymes involved in the biosynthesis of tropane alkaloids, as well as for the study of their mechanisms of transport.     

Batch culture of Candida utilis in a medium deprived of a phosphorous source

Summary Candida utilis var. major NRRL-Y-1084 was grown in a defined medium without a phosphorous (P) source. During the exponential phase, cells divided according to a specific growth rate of 0.32 h^-1, which is lower than the usual rate for a balanced medium (0.4–0.6 h^-1). The relative P content of the biomass decreased from 2.70% to 0.75% over a period of 6 h, including 2 h of cell division arrest. At the end of this period there was another interruption of cell division. After that, multiplication restarted at a considerably lower rate and it deviated slightly from the exponential pattern. The stationary phase began when biomass P content reached 0.4%–0.5%, slowly decreasing afterwards to 0.25–0.20%. Biomass synthesis was less affected than cell division by the relative decrease of endogenous P, the two processes differing partially in their kinetics. Cell lysis started shortly before the stationary phase and affected about 20% of the population by the end of the assay. RNA and P content of the resulting biomass were 2.4% and 0.25% respecitvely, P being mainly incorporated to RNA.The relationship of biomass production to glucose uptake was very low, probably because the marked P deficiency called for an increase in energy consumption for growth and specially for maintenance. Compared with yeasts grown in a balanced medium, 40% increase in glycogen was observed, whereas no mean changes in the content of cell wall carbohydrates (glucan and mannan) and that of true protein were found.Member of the Scientific Researcher's Career of the Consejo Nacional de Investigaciones Cientificas y Técnicas (CONICET). Agrentina