The aim of this study was to check if serum interleukin-18 (IL-18) predicts 2-year cardiovascular mortality in patients at various stages chronic kidney disease (CKD) and history acute myocardial infarction (AMI) within the previous year. Diabetes mellitus one key factors exclusion. It found that an increase concentration IL-18 above cut-off point (1584.5 pg/mL) characterized by 20.63-fold higher risk deaths among studied patients. be superior well-known parameters, like high sensitivity...

ABCG46 of the legume Medicago truncatula is an ABC-type transporter responsible for highly selective translocation phenylpropanoids, 4-coumarate, and liquiritigenin, over plasma membrane. To investigate molecular determinants observed substrate selectivity, we applied a combination phylogenetic biochemical analyses, AlphaFold2 structure prediction, dynamics simulations, mutagenesis. We discovered unusually narrow transient access path to central cavity MtABCG46 that constitutes initial...

Full-size ATP-binding cassette (ABC) transporters belonging to the ABCG subfamily are unique for plants and fungi. There is growing evidence that certain of these proteins play a role in plant defense or signaling systems. As yet, complete set full-size protein genes has been inventoried classified only two plants: Arabidopsis thaliana Oryza sativa. Recently, domain-based clustering analysis predicted presence at least 12 encoding such Lotus japonicus genome. Here, we identify classify 19...

Model development and its analysis is a fundamental step in systems biology. The theory of Petri nets offers tool for such task. Since the rapid computer science, variety tools emerged, offering various analytical algorithms. From this follows problem using different programs to analyse single model. Many file formats representations results make much harder. Especially larger ability visualize proper form provides huge help understanding their significance. We present new called Holmes. Our...

Cholesterol is an essential component of mammalian cells and involved in many fundamental physiological processes; hence, its homeostasis the body tightly controlled, any disturbance has serious consequences. Disruption cellular metabolism cholesterol, accompanied by inflammation oxidative stress, promotes formation atherosclerotic plaques and, consequently, one leading causes death Western world. Therefore, new drugs to regulate disturbed cholesterol are used developed, which help control...

Recent studies have shown that the innate and adaptive immune system, together with low-grade inflammation, may play an important role in essential hypertension. In this work, to verify importance of selected factors for development hypertension, we created a Petri net-based model analyzed it. The analysis was based mainly on t-invariants, knockouts fragments net its simulations. blockade renin-angiotensin (RAA) system revealed most significant effect emergence hypertension has RAA...

The functioning of both normal and pathological tissues depends on an adequate supply oxygen through the blood vessels. A process called angiogenesis, in which new endothelial cells smooth muscles interact with each other, forming vessels either from existing ones or a primary vascular plexus, is particularly important interesting, due to therapeutic possibilities it offers. This multi-step very complex process, so accurate understanding underlying mechanisms significant task, especially...

Interleukin 18 (IL-18) is a proinflammatory and proatherogenic cytokine with pleiotropic properties, which involved in T NK cell maturation the synthesis of other inflammatory cytokines adhesion molecules. It plays significant role orchestrating cascade, accelerates atherosclerosis influences plaque vulnerability. To investigate influence IL-18 on development, stochastic Petri net model was built then analyzed. First, MCT-sets t-clusters were generated, knockout simulation-based analysis...

Atherosclerosis is a multifactorial disease that affects large arteries and causes much morbidity mortality worldwide. Despite ongoing research for several decades, it still global health problem cannot be stopped cured completely. Furthermore, the development of this contributed to by various processes, primarily disturbances in cholesterol metabolism, local low-grade inflammation, oxidative stress, resulting formation atherosclerotic plaques. In work, stochastic Petri net model was...

Sequencing by hybridization allows the reconstruction of DNA string a given length from smaller fragments. These fragments are obtained in experiment which hybridizes to chip. In classical approach, chip consists all oligonucleotides length, with only one type oligonucleotide for each probe this paper, we propose an algorithm solving non-classical case SBH, where probes consist set described some specific pattern. We will present definition such and sequencing problem related Unlike recent...

Virus-like particles (VLPs), due to their nanoscale dimensions, presence of interior cavities, self-organization abilities and responsiveness environmental changes, are interest in the field nanotechnology. Nevertheless, comprehensive knowledge VLP self-assembly principles is incomplete. formation governed by two types interactions: protein–cargo protein–protein. These interactions can be modulated physicochemical properties surroundings. Here, we used brome mosaic virus (BMV) capsid protein...

In many complex systems that can be modeled using Petri nets time a very important factor which should taken into account during creation and analysis of the model. Time data describe starting moments some actions or their duration before immediate effects start to influence other areas system. Places in net often static components system, but they also states. Such state have restrictions, for example, telling how long it elements values describing system may inconsistent incomplete, cause...

Cellular DNA is daily exposed to several damaging agents causing a plethora of lesions. As first aid restore integrity, enzymes got specialized in damage recognition and lesion removal during the process called base excision repair (BER). A large number types different readers nucleic acids lesions BER pathway as well two sub-pathways were considered definition model using Petri net framework. The intuitive graphical representation combination with precise mathematical analysis methods are...

Abstract Motivation The first and necessary step in systems approach to study biological phenomena is building a formal model. One of the possibilities construct model based on Petri nets. They have an intuitive graphical representation one hand, other, can be analyzed using mathematical methods. Finding homologies or conserved processes playing important roles various done by comparing models. ones expressed as nets are especially well-suited for such comparison, but there lack software...