Projects

Four ppt lecture files that are part of a UvA course on 'How to design an alien'. They correspond to four lectures given by Hans V. Westerhoff, September - October 2021

The Hippo signalling is a metabolic control pathway of cells proliferation and apoptosis, thus represents an emerging topic in tumour suppression regulation and regenerative medicine. This pathway is activated by anti-proliferative signals which come from the extracellular environment received by membranes proteins. In the cytosol compartment, the pathway is regulated by a phosphorylation cascade of four main proteins with Serin-Treonin kinase activity. At the end-point of this cascade the ...

Testing stuff

testing project to evaluate capabilities of SEEK

Just a test

A project created for demonstration

Test project to see Fairdom capabilities.

Assessing different tools for RDM

to test the api

The placenta remains the key to maternal diseases such as Pre-eclampsia (PE) and Intrauterine growth restriction (IUGR), however the pathophysiology of these disorders remains elusive. The aim of this study is to characterize the key proteomic variations between PE and IUGR, to better understand the pathoetiology of these diseases.Term placentas each were collected from PE, IUGR pregnancies, and age and BMI matched healthy controls. Quadrupole-orbitrap mass spectrometer was used in data dependent ...

To systematically evaluate the general efficacy of nape acupuncture combined with rehabilitation training for the treatment of post-stroke dysphagia and in the recovery of swallowing function.

This project stored supplementary files that we didn't include in the paper ' Exploring the Evolution of the Gene Ontology and itsImpact on Enrichment Analysis'

the Supplementary materials for Journal of Clinical Endocrinology and Metabolism

A chapter on generalized thermodynamics. The chapter is not specifically about biology although it uses many examples in biology due to the richness of the topic. It deals with the first and second law of thermodynamics, catalysts, and engines. This includes heat engines, heat pumps, and protonmotive ATP synthase.

Designing 3D metamaterials

EU FP7 collaborative project TiMet, award number 245143. Funded 2010-2015. "TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity."

generation of a toggle switch based on a non-cooperative network

Investigation 1: An experimental workflow to provide detailed information of the molecular mechanisms of enzymes is described. This workflow will help in the application of enzymes in technical processes by providing crucial parameters needed to plan, model and implement biocatalytic processes more efficiently. These parameters are homogeneity of the enzyme sample (HES), kinetic and thermodynamic parameters of enzyme kinetics and binding of reactants to enzymes. The techniques used to measure ...

A fundamental and enduring challenge for ecosystem managers developing risk and impact assessment tools is to predict the extent of impact that spilled oil can have on the immediate fish populations and on future generations. Modelling approaches are important tools for these assessments, but they currently suffer from two major shortcomings: 1) the failure to acknowledge that effects can be transferred through several generations and 2) the assumption that a small group of toxic compounds, ...

Amino alcohol moieties are found in highly diverse classes of natural products that are of great importance due to their bioactivity, and they function as chiral building blocks for the synthesis of pharmaceuticals and agrochemicals. The chemical synthesis of stereoisomerically pure amino alcohols is difficult and typically requires uneconomical steps for protective group manipulations. Conventional syntheses in the chemical industry often use hazardous substances, consume large amounts of energy ...

Gene interaction networks and models of cation homeostasis in Saccharomyces cerevisiae