Biology subjects

Petersen, E.

Publications and source records attributed to Petersen, E..

6 recordsLinked to original sources

bioRxiv2025

Development of a Vibrio natriegens-based plate-clearing assay for rapid screening of PET-hydrolyzing enzymes

Polyethylene terephthalate (PET) is a major contributor to plastic waste. Enzymatic PET degradation offers a sustainable recycling approach, but screening for effective enzymes remains challenging. Herein, we established an experimental plate-clearing assay using Vibrio natriegens, exploiting its protein secretion system to rapidly identify catalytic activity without time-consuming downstream processing. To validate the assays robustness, we tested mutants of Fusarium solani pisi cutinase (FsC) and found that one mutant, T45P, exhibited threefold higher activity and a TPA-to-MHET ratio than the wild-type. As a further test case, we screened an error-prone PCR library of FsC using the assay, obtaining a 25% hit rate after screening 150 colonies. This demonstrates the scalability of the method for screening PET-hydrolytic activity in a large number of enzymes.

biochemistry↗

bioRxiv2024

Method for determining of cytotoxicity based on the release of fluorescent proteins

This paper describes a method for determining the cytotoxicity of chemical compounds based on the detection of fluorescent proteins - in this case, green fluorescent protein (GFP) and red fluorescent protein (RFP), which are released into the medium from dead cells. This method is similar in principle to the lactate dehydrogenase test (LDH test), but it does not require a reaction with a chromogenic substrate. This method also makes it possible to independently determine the viability of different lines when used in cocultures. Experiments were preformed on a classical monolayer, spheroids and 3D cultures in alginate hydrogel. Capecitabine was used as a model cytotoxic agent. We included liver cells (Huh7) in a coculture model and determined changes in the cytotoxicity levels of capecitabine against NCI-H1299 cells. The experimental part also found that there were differences in sensitivity to capecitabine depending on the type of 3D cultures used.

pharmacology and toxicology↗

bioRxiv2024

Multi-species numerical validation of an efficient algorithm for auditory brainstem response hearing threshold estimation

The Auditory Brainstem Response (ABR) can be used to evaluate hearing sensitivity of animals who are unable to respond to behavioral tasks. However, typical data collection methods are time consuming; decreasing the measurement time may save resources or allow researchers to spend more time on other tasks. Here, an adaptive algorithm is proposed for efficient estimation of ABR thresholds. The algorithm relies on the online update of the predicted hearing threshold from a Gaussian process model as ABR data are collected using iteratively optimized stimuli. To validate the algorithm, ABR threshold estimation is simulated by adaptively sub-sampling pre-collected ABR datasets for which the stimuli were systematically varied in frequency and level. The simulated experiment is performed on 5 datasets of Mouse (2 different datasets), Budgerigar, Gerbil, and Guinea Pig ABRs collected by different laboratories, with a total of 27 ears. The original datasets contain between 68 and 106 stimuli conditions, while the adaptive algorithm is run up to a total of 20 stimuli conditions. The adaptive algorithm ABR threshold estimate is compared against human rater estimates who view the full ABR dataset. The adaptive algorithm threshold matches the human estimates within 10 dB, averaged over frequency, for 19 out of 27 ears. The adaptive procedure is able to provide threshold estimates that are comparable to the human rater estimated thresholds while reducing the measurement time by a factor of 3 to 5. The standard deviation of threshold estimates from successive runs is smaller than the inter-human rater differences, indicating adequate test/retest reliability.

bioengineering↗

bioRxiv2022

Biochemical characterization and NMR study of a PET-hydrolyzing cutinase from Fusarium solani pisi

In recent years, the drawbacks of plastics have become evident, with plastic pollution becoming a major environmental issue. There is an urgent need to find solutions to efficiently manage plastic waste by using novel recycling methods. Biocatalytic recycling of plastics by using enzyme-catalyzed hydrolysis is one such solution that has gained interest, in particular for recycling polyethylene terephthalate (PET). To provide insights into PET hydrolysis by cutinases, we have here characterized the kinetics of a PET-hydrolyzing cutinase from Fusarium solani pisi (FsC) at different pH values, mapped the interaction between FsC and the PET analog BHET by using NMR spectroscopy, and monitored product release directly and in real time by using time-resolved NMR experiments. We found that primarily aliphatic side chains around the active site participate in the interaction with BHET, and that pH conditions and mutation around the active site (L182A) can be used to tune the relative amounts of degradation products. Moreover, we propose that the low catalytic performance of FsC on PET is caused by poor substrate binding combined with slow MHET hydrolysis. Overall, our results provide insights into obstacles that preclude efficient PET hydrolysis by FsC and suggest future approaches for overcoming these obstacles and generating efficient PET-hydrolyzing enzymes. TOC Graphic (For Table of Contents use only) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/514593v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1f59d35org.highwire.dtl.DTLVardef@242467org.highwire.dtl.DTLVardef@d2198eorg.highwire.dtl.DTLVardef@18bba0d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Brain Network Architecture Constrains Age-related Cortical Thinning

Age-related cortical atrophy, approximated by cortical thickness measurements from magnetic resonance imaging, follows a characteristic pattern over the lifespan. Although its determinants remain unknown, mounting evidence demonstrates correspondence between the connectivity profiles of structural and functional brain networks and cortical atrophy in health and neurological disease. Here, we performed a cross-sectional multimodal neuroimaging analysis of 2633 individuals from a large population-based cohort to characterize the association between age-related differences in cortical thickness and functional as well as structural brain network topology. We identified a widespread pattern of age-related cortical thickness differences including "hotspots" of strong age effects located in brain areas with high centrality (structural network hubs). Regional age-related differences were furthermore strongly correlated within the structurally defined node neighborhood. The overall pattern of thickness differences as well as its change throughout the later lifespan was found to be anchored in the functional network hierarchy as encoded by macroscale functional connectivity gradients. Lastly, the identified difference pattern covaried significantly with cognitive and motor performance. Our findings indicate that connectivity profiles of functional and structural brain networks might act as organizing principles behind age-related cortical thinning as an imaging surrogate of cortical atrophy.

neuroscience↗

bioRxiv2018

A Comprehensive Mathematical Model of Surface Electromyography and Force Generation

The purpose of this article is to provide a unified description of a comprehensive mathematical model of surface electromyographic (EMG) measurements and the corresponding force signal in skeletal muscles. The model comprises motor unit pool organization, recruitment and rate coding, intracellular action potential generation and the resulting EMG measurements, as well as the generated muscular force during voluntary isometric contractions. It consolidates and extends the results of several previous publications that proposed mathematical models for the individual model components. A parameterization of the electrical and mechanical components of the model is proposed that ensures a physiologically meaningful EMG-force relation in the simulated signals. Moreover, a novel nonlinear transformation of the excitation model input is proposed, which ensures that the model force output equals the desired target force. Finally, an alternative analytical formulation of the EMG model is proposed, which renders the physiological meaning of the model more clear and facilitates a mathematical proof that muscle fibers in this model at no point in time represent a net current source or sink.\n\nNeuromuscular physiology is a vibrant research field that has recently seen exciting advances. Many previous publications have focused on thorough analyses of particular aspects of neuromuscular physiology, yet an integration of the various novel findings into a single, comprehensive model is missing. A consistent description of a complete physiological model as presented here, including thorough justification of model component choices, will facilitate the use of these advanced models in future research. Results of a numerical simulation highlight the models capability to reproduce many physiological effects observed in experimental measurements, and to produce realistic synthetic data that are useful for the validation of signal processing algorithms. The model is based on recent advances in the understanding of muscular physiology and hence also applicable for analyzing the influence of various physiological and measurement setup parameters on the measured force and EMG signals.

systems biology↗