Studies

DALEC (Data Assimilation Linked Ecosystem Carbon) represents the C cycle with a simple box model of pools connected via fluxes. There are five pools: C content of foliage (Cf); woody stems and coarse roots (Cw) and fine roots (Cr); and of fresh leaf and fine root litter (Clitter) and soil organic matter (SOM) plus WD (CSOM/WD).  The fluxes among pools are based on the following assumptions: All C fixed during a day is either expended in autotrophic respiration or else allocated to one of three ...

Publication data made available for Biotechnology Reports, supplementary data

edit later

A guidelines for the curation of molecular interactions causal statements.

A repository of causal cellular signalling statement

This study explores how to design an initial rate experiment. It starts with a "zero-round" experiment, which is used to design a "first-round" experiment, which then leads to the design of a "gold-round" experiment.

Since over 40 enzymes will be investigated for their mRNA abundance, processing, and degradation kinetics, the less tedious and more accurate Next Generation Sequencing of the entire mRNA repertoire of the cell is employed. To optimise the proportion of useful sequence, while including RNA fragments that are products of of degradation, rRNA is depleted using the eukaryotic Ribominus kit (Ambion). Two biological replicates are treated with Sinefungin and Actinomycin D to inhibit RNA processing and ...

Determination of essential amino acids for Streptococcus pyogenes M49

Mutant strains which carry deletions of important metabolic enzymes, as well as mutant strains with altered regulation, need to adapt by changing fluxes or gene expression to compensate with the absence/differed concentration of these key enzymes. This may give new insights in the regulation of these pathways/enzymes.

Parasites will be harvested at different growth phases and the total amount of the proteins will be followed by western blot. The absolut concentration will be obtained by comparison with a know amount of the recombinant untagged protein. The thiol redox state of the proteins will be followed by modification of the free cys with methoxy-ethyl-maleinimide poly(ethylenglycol) (Meo-PEG-mal).

We developed a new metabolomics protocol, which involved a comparison of different harvesting techniques, quenching solutions and extraction methods.

Scope: The COVID-19 disease can have gastrointestinal manifestation. The virus replicates in the gut and has potential faecal-oral transmission besides airborne transmission (Lamers et al., 2020). Intestinal organoids are a proven experimental model of the human gut and can help understand the viral infection of the gut without animal models and additional biopsies. Single-cell RNA-seq techniques can distinguish the SARS-CoV-2 replicating cells and thus help to understand how cells respond to the ...

Measure homogeneity of an enzyme sample (Gre2p) with DLS (dynamic light scattering).

Induced fit docking studies of the dinitroaniline parent trifluraline and the newly designed dinitroaniline-etherphospholipid hybrids against different potential binding sites in monomeric and multimeric kinetoplastid tubulin receptors.

Rigid-body docking studies and induced-fit docking studies of pteridine-based compounds to the target proteins TbPTR1, TbDHFR, LmPTR1, LmDHFR and the off-target hDHFR. For both PTR1 variants and human DHFR, conserved structural water sets were considered. Preparations of compound libraries and docking receptors are also covered.

Temperature-sensitive version of Pokhilko 2010 Arabidopsis clock model, from Biomodels BIOMD00273, prepared by Mirela Domijan for the Gould et al. paper on cryptochrome influences on circadian rhythms.    Molecular Systems Biology 9 Article number: 650  doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures Gould, Ugarte, Domijan et al. doi:10.1038/msb.2013.7Originally ...