A computational model for histone mark propagation reproduces the distribution of heterochromatin in different human cell types

Chromatin is a highly compact and dynamic nuclear structure that consists of DNA and associated proteins. The main organizational unit is the nucleosome, which consists of a histone octamer with DNA wrapped around it. Histone proteins are implicated in the regulation of eukaryote genes and they carry numerous reversible post-translational modifications that control DNA-protein interactions and the recruitment of chromatin binding proteins. Heterochromatin, the transcriptionally inactive part of the genome, is densely packed and contains histone H3 that is methylated at Lys 9 (H3K9me). The propagation of H3K9me in nucleosomes along the DNA in chromatin is antagonizing by methylation of H3 Lysine 4 (H3K4me) and acetylations of several lysines, which is related to euchromatin and active genes. We show that the related histone modifications form antagonized domains on a coarse scale. These histone marks are assumed to be initiated within distinct nucleation sites in the DNA and to propagate bi-directionally. We propose a simple computer model that simulates the distribution of heterochromatin in human chromosomes. The simulations are in agreement with previously reported experimental observations from two different human cell lines. We reproduced different types of barriers between heterochromatin and euchromatin providing a unified model for their function. The effect of changes in the nucleation site distribution and of propagation rates were studied. The former occurs mainly with the aim of (de-)activation of single genes or gene groups and the latter has the power of controlling the transcriptional programs of entire chromosomes. Generally, the regulatory program of gene transcription is controlled by the distribution of nucleation sites along the DNA string.Comment: 24 pages,9 figures, 1 table + supplementary materia

Proteomic analysis of the Mycocentrospora acerina-carrot interaction during storage

During post harvest storage, a large proportion of carrots (more than 50%) may have to be discarded due to the development of liquorice rot caused by Mycocentrospora acerina. This fungus is soil borne and brought into the store in to soil adhering to the root. Liquorice rot development is mainly related to physiological or structural resistance of carrot, therefore the control of this storage disease is based on cultural practices and storage conditions. It is believed that carrots at the beginning of storage can resist disease developments due to chemical defence mechanisms involving some proteins, peptides and secondary metabolites. The hypothesis is that proteome changes during storage of carrots are related to the susceptibility to M. acerina. During root-pathogen interactions, several genes have been reported to provide resistance against pathogens but only few proteins have been identified using proteomic approaches. Little is known about proteins involved during M. acerina - carrot interaction. The carrots used in this study are grown under two different agricultural practices (one conventional, one organic) in order to investigate the effect of the cropping system on the susceptibility to liquorice rot. We developed a bioassay for infection studies of M. acerina on conventional and organic carrots in order to determine the important time points of the infection process. Then the proteome is investigated at these different time points. The protocol for extraction of proteins has been improved so that it can be used to obtain an optimal recovery of proteins from both plant and pathogen on their own as well as from infected carrot roots. Proteomes of carrot and of M. acerina are characterized by two dimensional gel electrophoreses and the proteins whose synthesis varies significantly in the course of pathogen infection are identified by mass spectrometry (MALDI TOF-TOF)

The Endogenous and Exogenous Substrate Spectrum of the Human Organic Cation Transporter OCT1 – a Comprehensive Characterization

The organic cation transporter 1 (OCT1) is most extensively expressed in the human liver. OCT1 is involved in the hepatic uptake of several drugs and endogenous compounds, which then undergo bioactivation, recycling, metabolism, or elimination. The aim of this work was to extend the knowledge about OCT1 substrates and non-substrates of endogenous and exogenous origin. Establishing an in vitro model for studying uptake and subsequent metabolism was an additional goal, as well as finding an endogenous biomarker for OCT1 activity. These studies should contribute to our basic understanding of the biological role of this transporter and to the understanding of the role of OCT1 in pharmacology and toxicology. Influx transport of 18 psychostimulant or hallucinogenic compounds, which all meet the conventional physicochemical criteria of OCT1 substrates, was investigated for OCT1 and related transporters. Mescaline was newly identified as a substrate of OCT1. To more systematically and comprehensively search for additional substrates, a machine learning-based model was used. This approach exploited existing knowledge about OCT1 substrates. Machine learning-aided prediction of new substrates was highly reliable as subsequent in vitro validation showed. The in silico prediction, which was based on two-dimensional structures, did not include three-dimensional information, which is important for enantiomers. Therefore, stereoselectivity of OCT1 transport was investigated in vitro. It revealed a surprisingly stereoselective cell uptake for some substrates, e.g. fenoterol, but not all, e.g. salbutamol. For the purpose of in vitro-to-in vivo translation in more complex biological systems, a cell model was developed, which allowed the chromosomal integration of two genes of interest in a targeted manner, to investigate uptake and metabolism in a more holistic fashion. Both genes can be transfected simultaneously and are expressed with equal strength. As a first proof of the value, the sequential uptake of proguanil and subsequent CYP-dependent activation to cycloguanil resembled indeed the uptake and metabolism in primary hepatocytes. Several European and American investigators have already expressed their interest to adopt the system for their research. Thiamine (Vitamin B1) had been proposed as a biomarker for in vivo OCT1 activity. Although thiamine was a substrate of OCT1 in vitro, thiamine was rejected as a suitable biomarker for OCT1 activity through a human clinical trial. After the intake of a large thiamine dose, neither thiamine trough concentrations nor maximum concentrations showed any correlation with individual OCT1 activity according to genotype. Results suggested that other transporters play the central role in thiamine uptake into the liver and other organs. In total, I could add more than 20 previously unknown substrates to the list of well characterized OCT1 substrates. I could show that OCT1 transport can be quite different depending on subtle structural differences between enantiomers. Moreover, the developed cell model may serve as an interesting tool to mimic the complex interplay between hepatic uptake and metabolism, and human pharmacokinetics of thiamine is not dependent on OCT1 - at least not in a quantitatively relevant fashion. Together, these findings may contribute to a gradually improving understanding of OCT1 functionality and biomedical relevance.2021-07-2

Distractor inhibition by alpha oscillations is controlled by an indirect mechanism governed by goal-relevant information

The role of alpha oscillations (8–13 Hz) in cognition is intensively investigated. While intracranial animal recordings demonstrate that alpha oscillations are associated with decreased neuronal excitability, it is been questioned whether alpha oscillations are under direct control from frontoparietal areas to suppress visual distractors. We here point to a revised mechanism in which alpha oscillations are controlled by an indirect mechanism governed by the load of goal-relevant information – a view compatible with perceptual load theory. We will outline how this framework can be further tested and discuss the consequences for network dynamics and resource allocation in the working brain

Reform and backlash to reform : economic effects of ageing and retirement policy

Using a stochastic general equilibrium model with overlapping generations, this paper studies (i) the effects on both extensive and intensive labor supply responses to changes in fertility rates, and (ii) the potential of a retirement reform to mitigate the effects of fertility changes on labor supply. In order to neutralize the effects on effective labor supply of a fertility decline, a retirement reform, designed to increase labor supply at the extensive margin, is found to simultaneously reduce labor supply at the intensive margin. This backlash to retirement reform requires the statutory retirement age to increase more than proportionally to fertility changes in order to compensate for endogenous responses of the intensity of labor supply. The robustness of this result is checked against alternative model specifications and calibrations relevant to an economic region such as Europe.Labor Policies,Labor Markets,Pensions&Retirement Systems,Economic Theory&Research,Population Policies

Labour supply and retirement policy in an overlapping generations model with stochastic fertility

Using a stochastic general equilibrium model with overlapping generations, this paper studies a policy rule for the retirement age aiming at offsetting the effects on the supply of labour following fertility changes. We find that the retirement age should increase more than proportionally to the direct fall in the labour supply caused by a fall in fertility. The robustness of this result is checked against alternative model specifications and parameter values. The efficacy of the policy rule depends crucially on the link between the preference for leisure and the response of the intensive margin of labour supply to changes in the statutory retirement age.Labour supply; fertility; retirement age; overlapping generations; method of undetermined coefficients