Biology subjects

Kodvanj, I.

Publications and source records attributed to Kodvanj, I..

7 recordsLinked to original sources

bioRxiv2024

MIROSLAV: A complete open-source hardware and software toolkit for high-throughput circadian activity measurement and analysis in rodents

While conventional behavioural tests offer valuable insight into rodent behaviour in specific paradigms, rodents spend most of their time in a safe, undisturbed environment - their home cage. However, home cage monitoring (HCM) is often impractical at scale over prolonged periods of time without significant loss of data. To achieve this, we developed MIROSLAV, the Multicage InfraRed Open Source Locomotor Activity eValuator, a home cage activity and environmental monitoring device designed to be open, adaptable, and robust. Its transparent and modular design allows the device to be tailored to varying experimental requirements and environmental conditions, while its wireless operation and multiple redundancies minimise loss of data and animal disturbance. Data quality is maintained by a modular software workflow for data preparation (Prepare-a-SLAV) and cleaning (TidySLAV), followed by exploratory (MIROSine - MIRO The Explorer) and statistical (MIROSine - StatistiSLAV) analysis of circadian periodicity. Here, using MIROSLAV, we demonstrate circadian dysrhythmia and a disrupted response to regular stimuli (e.g. behavioural testing, bedding change) in a rat model of sporadic Alzheimers disease, showcasing MIROSLAVs utility in a typical animal study of disease. In accordance with the 3Rs, every rodent study and laboratory performing them can benefit from HCM, provided the existence of transparent and customisable tools which allow robust deployment to tens or hundreds of cages in various conditions. MIROSLAV provides this opportunity to researchers in a cost-effective manner.

animal behavior and cognition↗

bioRxiv2022

Non-alcoholic components of Pelinkovac, a Croatian wormwood-based strong liquor, counteract the inhibitory effect of high ethanol concentration on catalase in vitro

Antioxidant enzyme catalase protects the cells against alcohol-induced oxidative stress by scavenging free radicals and metabolizing alcohol. Concentrations of ethanol present in alcoholic beverages can inhibit catalase and foster oxidative stress and alcohol-induced injury. Non-alcoholic components of pelinkovac counteract the inhibitory effects of high ethanol concentration and acidic pH on catalase in vitro.

pharmacology and toxicology↗

bioRxiv2021

Is galactose a hormetic sugar? Evidence from rat hippocampal redox regulatory network

Galactose is a ubiquitous simple monosaccharide with yet incompletely understood biochemical and physiological role. Most of what we currently know about galactose is based on induction from the research on inherited disorders of galactose metabolism and animal models that exploit galactose-induced oxidative stress to model aging in rodents, however, recent evidence also demonstrates unique properties of galactose to conserve cellular function during the periods of starvation, and prevent and alleviate cognitive deficits in a rat model of sporadic Alzheimers disease. Here, we try to understand the molecular background of both detrimental and beneficial effects of galactose by exploring the acute systemic and hippocampal biochemical changes upon oral administration of galactose solution focusing primarily on the components of the redox regulatory network (RRN). Although orogastric gavage of galactose solution (200 mg/kg) was insufficient to induce systemic RRN disbalance in the first two hours upon administration, analysis of hippocampal RRN revealed a mild pro-oxidative shift accompanied by a paradoxical increase in tissue reductive capacity, suggesting overcompensation of endogenous antioxidant systems in the response to the pro-oxidative stimulus. The more thorough analysis revealed that galactose-induced increment of reductive capacity was accompanied by inflation of the hippocampal pool of nicotinamide adenine dinucleotide phosphates indicating ROS detoxification through disinhibition of the oxidative pentose phosphate pathway flux, reduced neuronal activity, and upregulation of Leloir pathway gatekeeper enzyme galactokinase-1. Based on the observed findings, and in the context of previous work on galactose, we propose a hormetic hypothesis of galactose action suggesting that the protective effects of galactose might be inseparable from its pro-oxidative effects at the biochemical level.

neuroscience↗

bioRxiv2020

Publishing of COVID-19 Preprints in Peer-reviewed Journals, Preprinting Trends, Public Discussion and Quality Issues

IntroductionCOVID-19-related (vs. non-related) articles appear to be more expeditiously processed and published in peer-reviewed journals. We aimed to evaluate: (i) whether COVID-19-related preprints were favored for publication, (ii) preprinting trends and public discussion of the preprints, and (iii) the relationship between the publication topic (COVID-19-related or not) and quality issues. MethodsManuscripts deposited at bioRxiv and medRxiv between January 1 and September 27 were assessed for the probability of publishing in peer-reviewed journals, and those published were evaluated for submission-to-acceptance time. The extent of public discussion was assessed based on Altmetric and Disqus data. The Retraction Watch Database and PubMed were used to explore the retraction of COVID-19 and non-COVID-19 articles and preprints. ResultsWith adjustment for the preprinting server and number of deposited versions, COVID-19-related preprints were more likely to be published within 120 days since the deposition of the first version (OR=2.04, 95%CI 1.87-2.23) as well as over the entire observed period (OR=1.42, 95%CI 1.33-1.52). Submission-to-acceptance was by 38.67 days (95%CI 34.96-42.39) shorter for COVID-19 articles. Public discussion of preprints was modest and COVID-19 articles were overrepresented in the pool of retracted articles in 2020. ConclusionCurrent data suggest a preference for publication of COVID-19-related preprints over the observed period.

scientific communication and education↗

bioRxiv2020

griPASTA: A hacked kitchen scale for quantification of grip strength in rodents

Assessment of neuromuscular function is critical for understanding pathophysiological changes related to motor system dysfunction in many rodent disease models. Among methods used for quantification of grip performance in rodents, gauge-based grip strength meters provide the most reliable results, however, such instruments are unaffordable by many laboratories. Here we demonstrate how to build a rodent grip strength apparatus from scratch using a digital kitchen scale, an empty cage, and a microcontroller, with both hardware and software being completely open-source to enable maximal modularity and flexibility of the instrument in concordance with the principles of open-source bioinstrumentation. Furthermore, we test the griPASTA system for assessment of increased muscular rigidity in the proof-of-concept experiment in the rat model of Parkinsons disease induced by intrastriatal administration of 6-hydroxydopamine (6-OHDA). Finally, the importance of bioinstrumental customization is demonstrated by utilizing griPASTA for assessment of trial speed from initial-to-maximal deflection time segments and controlling for its potential confounding effects on the grip strength. Significance StatementNeuromuscular function analyzed by grip strength performance tests is an integral part of motor system neuroscience and neurotoxicology. Strain gauge-based grip strength meters provide the most reliable results, however, commercial solutions are unaffordable by many. Consequently, cheap semi-quantitative tests are often used at the expense of precision and reliability. We propose griPASTA - a simple and robust open-source grip strength platform made from an ordinary kitchen scale. griPASTA could improve the quality and reproducibility of grip strength experiments by enabling researchers to obtain quantitative grip strength data in high resolution using a highly customizable platform.

neuroscience↗

bioRxiv2020

Nitrocellulose redox permanganometry: a simple method for reductive capacity assessment

We propose a rapid, simple and robust method for measurement of reductive capacity of liquid and solid biological samples based on potassium permanganate reduction followed by trapping of manganese dioxide precipitate on a nitrocellulose membrane. Moreover, we discuss how nitrocellulose redox permanganometry (NRP) can be used for high-throughput analysis of biological samples and present HistoNRP, its modification used for detailed analysis of reductive capacity spatial distribution in tissue with preserved anatomical relations.

biochemistry↗

bioRxiv2020

Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA

Widely available low-cost electronics encourage the development of open-source tools for neuroscientific research. In recent years, many neuroscientists recognized the open science movement for its potential to stimulate and encourage science that is less focused on money, and more on robustness, validity, questioning and understanding. Here, we wanted to contribute to this global community by creating a research platform based on a common digital kitchen scale. This everyday ordinary kitchen tool is sometimes used in neuroscience research in various ways; however, its use is limited by sampling rate and inability to store and analyze data. To tackle this problem we developed a Platform for Auditory STArtle or PASTA. This robust and simple platform enables users to obtain data from kitchen scale load cells at a high sampling rate, store it and analyze it. Here, we used it to analyze acoustic startle and prepulse inhibition sensorimotor gating in rats treated intracerebroventricularly with streptozotocin, but the system can be easily modified and upgraded for other purposes. In accordance with open science principles, we shared complete hardware design with instructions. Furthermore, we also disclose our software codes written for PASTA data acquisition (C++, Arduino) and acoustic startle experimental protocol (Python) and analysis (R-based Awesome Toolbox for PASTA, ratPASTA R package). To further encourage the development of our PASTA platform we demonstrate its sensitivity by using PASTA-gathered data to extract breathing patterns during rat freezing behavior in our experimental protocol.

neuroscience↗