A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Plastids are small organelles equipped with their own genomes (plastomes). Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (PlasTi-microarray) consisting of 1629 oligonucleotide probes. The oligonucleotides were designed based on the cucumber chloroplast genomic sequence and targeted both strands of the plastome in a non-contiguous arrangement. Up to 4 specific probes were designed for each gene/exon, and the intergenic regions were covered regularly, with 70-nt intervals. We also developed a protocol for direct chemical labeling and hybridization of as little as 2 micrograms of chloroplast RNA. We used this protocol for profiling the expression of the cucumber chloroplast plastome on the PlasTi-microarray. Owing to the high sequence similarity of plant plastomes, the newly constructed microarray can be used to study plants other than cucumber. Comparative hybridization of chloroplast transcriptomes from cucumber, Arabidopsis, tomato and spinach showed that the PlasTi-microarray is highly versatile

Transferrin changes in haemodialysed patients

Transferrin (Tf) is a glycoprotein responsible for iron transport in the human body. Physiologically in reaction with Concanavalin A, Tf occurs in four distinct variants Tf1, Tf2, Tf3 (apo-Tf) and Tf4. It was reported recently that Tf is changing, particularly during acute phase response, taking place among others in end-stage renal disease. In this study, we wanted to find the answer to three main questions: firstly, how Tf is changing in patients treated with maintenance haemodialysis (mHD), secondly, whether there are any Tf changes in the course of mHD treatment, and thirdly, what factors can affect Tf microheterogeneity in these patients. Studies were performed on 80 haemodialysed patients and 21 healthy volunteers. The Tf concentration was determined by the rocket immunoelectrophoresis, and its microheterogeneity was assessed by the ConA crossed immunoaffinity electrophoresis. During the annual observation of the distribution of the Tf variants, we have found both changes of the percentage contents of all Tf variants in the whole Tf concentration and a significant decrease in Tf2, Tf3 and Tf4 serum concentrations. Moreover, we found that decrease in the renal function, duration of mHD, and inflammation may contribute to these above-mentioned changes, which are probably the factors that should be taken into account when explaining the mechanisms of persistence of anaemia in haemodialysed patients

Hepatitis C virus quasispecies in chronically infected children subjected to interferon–ribavirin therapy

Accumulating evidence suggests that certain features of hepatitis C virus (HCV), especially its high genetic variability, might be responsible for the low efficiency of anti-HCV treatment. Here, we present a bioinformatic analysis of HCV-1a populations isolated from 23 children with chronic hepatitis C (CHC) subjected to interferon–ribavirin therapy. The structures of the viral quasispecies were established based on a 132-amino-acid sequence derived from E1/E2 protein, including hypervariable region 1 (HVR1). Two types of HCV populations were identified. The first type, found in non-responders, contained a small number of closely related variants. The second type, characteristic for sustained responders, was composed of a large number of distantly associated equal-rank variants. Comparison of 445 HVR1 sequences showed that a significant number of variants present in non-responding patients are closely related, suggesting that certain, still unidentified properties of the pathogen may be key factors determining the result of CHC treatment

The Role of Macrophage Dynamics in Atherosclerosis Analyzed Using a Petri Net-Based Model

Atherosclerosis, a chronic inflammatory and oxidative stress-mediated disease impacting the arterial system, stands as a primary cause of morbidity and mortality worldwide. The complexity of this disease, driven by numerous factors, requires a thorough investigation of its underlying mechanisms. In our study, we explore the complex interplay between cholesterol homeostasis, macrophage dynamics, and atherosclerosis development using a Petri net-based model anchored in credible, peer-reviewed biological and medical research. Our findings underscore the significant role of macrophage colony-stimulating factor (M-CSF) inhibition in reducing atherosclerotic plaque formation by modulating inflammatory responses and lipid accumulation. Furthermore, our model highlights the therapeutic potential of targeting the C-X-C motif ligand 12 (CXCL12)/ C-X-C motif chemokine receptor type 4 (CXCR4) pathway to hinder hematopoietic stem and progenitor cells’ (HSPCs’) mobilization and plaque development. Based on the results obtained, which are in agreement with current studies, additional strategies are also proposed, such as decreasing M1 macrophage polarization for therapeutic gains, opening the door to future research and novel treatment approaches

Interrelations between Iron and Vitamin A—Studied Using Systems Approach

A deficiency of vitamin A (VAD) and iron is the most common nutritional problem affecting people worldwide. Given the scale of the problem, the interactions between vitamin A and iron levels are widely studied. However, the exact mechanism of the impact of vitamin A on the regulation of iron metabolism remains unclear. An extremely significant issue becomes a better understanding of the nature of the studied biological phenomenon, which is possible by using a systems approach through developing and analyzing a mathematical model based on a Petri net. To study the considered system, the t-cluster analysis, the significance analysis, and the analysis of the average number of transition firings were performed. The used analyses have allowed distinguishing the most important mechanisms (both subprocesses and elementary processes) positively and negatively regulating an expression of hepcidin and allowed to distinguish elementary processes with a higher frequency of occurrence compared to others. The analysis also allowed to resolve doubts about the discrepancy in literature reports, where VAD leads to positive regulation of hepcidin expression or to negative regulation of hepcidin expression. The more detailed analyses have shown that VAD more frequently positively stimulates hepcidin expression and this mechanism is more significant than the mechanism inhibiting hepcidin expression indirectly by VAD

Modelling of the iron participation in the development of atherosclerosis - a systemic approach

Hipotezę zakładającą, że wyższe stężenie żelaza w surowicy odgrywa ważną rolę w rozwoju chorób układu sercowo-naczyniowego zaproponował w 1981 r. J.L. Sullivan. Dziś, wyniki coraz liczniejszych badań potwierdzają istotne znaczenie żelaza w rozwoju miażdżycy. Zasadniczą rolę przypisuje się katalizowanej przez jony tego pierwiastka reakcji Fentona, w następstwie której powstaje silnie toksyczny rodnik hydroksylowy, biorący udział w peroksydacji lipidów. W następstwie wspomnianego procesu powstają zmienione cząsteczki lipidowe, które w sposób nieograniczony wyłapywane są przez komórki jednojądrzaste i stają się komórkami piankowatymi, a potem ciałkami apoptotycznymi tworzącymi blaszkę miażdżycową. W pracy tej przedstawiono systemowe podejście do badania prezentowanego zagadnienia. W tym celu został zbudowany model dotyczący udziału żelaza w powstawaniu miażdżycy oparty na sieciach Petriego. Analiza tego modelu pozwoliła na wyciągnięcie wniosków, iż bez reakcji Fentona, którą katalizuje żelazo, blaszka miażdżycowa nie może powstać.The hypothesis that higher serum iron concentration plays an important role in the development of diseases of the cardiovascular system has been proposed in 1981 by J.L. Sullivan. Nowadays, more and more research results confirm importance of iron in the development of atherosclerosis. The essential role plays Fenton reaction catalyzed by ions of this chemical element, which produces highly toxic hydroxyl radical involved in lipids peroxidation. As a result of this process, modified lipid molecules are produced and phagocytosed in unlimited way by mononuclear cells to become foam cells and then apoptotic bodies that form atherosclerotic plaque. In this paper, a systemic approach to the study of these issue is presented. For this purpose, a model based on Petri nets of the iron participation in the development of atherosclerosis has been built. The analysis of this model allowed us to draw the conclusion that without the Fenton reaction, which is catalyzed by iron, atherosclerotic plaque cannot actually arise

Chronic Kidney Disease as a Cardiovascular Disorder—Tonometry Data Analyses

Tonometry is commonly used to provide efficient and good diagnostics for cardiovascular disease (CVD). There are many advantages of this method, including low cost, non-invasiveness and little time to perform. In this study, the effort was undertaken to check whether tonometry data hides valuable information associated with different stages of chronic kidney disease (CKD) and end-stage renal disease (ESRD) treatment. For this purpose, six groups containing patients at different stages of CKD following different ways of dialysis treatment, as well as patients without CKD but with CVD and healthy volunteers were assessed. It was revealed that each of the studied groups had a unique profile. Only the type of dialysis was indistinguishable a from tonometric perspective (hemodialysis vs. peritoneal dialysis). Several techniques were used to build profiles that independently gave the same outcome: analysis of variance, network correlation structure analysis, multinomial logistic regression, and discrimination analysis. Moreover, to evaluate the classification potential of the discriminatory model, all mentioned techniques were later compared and treated as feature selection methods. Although the results are promising, it could be difficult to express differences as simple mathematical relations. This study shows that artificial intelligence can differentiate between different stages of CKD and patients without CKD. Potential future machine learning models will be able to determine kidney health with high accuracy and thereby classify patients. ClinicalTrials.gov Identifier: NCT05214872

Applications of Petri nets for modeling of biological processes

Rapid growth of the amount of available biological data made it clear that an analysis of complex biological processes can be made only with the support of mathematics and computer sciences. It is especially important nowadays when the systems biology approach is becoming more and more widely used in biological science. This new way of investigation of biological phenomena allows, at least in principle, to observe complex relationships between different parts of the analyzed system. These interactions may be crucial for the system's nature and behavior, so observing them may lead to important biological discoveries. Probably the most important part of this process consists in building of a formal model of the biological process. One of the promising methods of such an analysis is based on the theory of Petri nets. Models expressed in the language of this theory are very precise on the one hand, and on the other, they are intuitive, which makes their analysis easier in comparison, for example, to models based on ordinary differential equations. In this paper, a brief introduction to the theory of Petri nets is given and its applications for modeling of some exemplary biological processes are shortly discussed. Moreover, some extensions of the classical Petri nets and their biological applications are also presented

Theoretical Studies on the Engagement of Interleukin 18 in the Immuno-Inflammatory Processes Underlying Atherosclerosis

Interleukin 18 (IL-18) is one of the pro-inflammatory cytokines expressed by macrophages, suggesting that it plays important physiological and immunological functions, among the others: stimulation of natural killers (NKs) and T cells to interferon gamma (IFN- γ ) synthesis. IL-18 was originally identified as interferon gamma inducing factor and now it is recognized as multifunctional cytokine, which has a role in regulation of innate and adaptive immune responses. Therefore, in order to investigate IL-18 contribution to the immuno-inflammatory processes underlying atherosclerosis, a systems approach has been used in our studies. For this purpose, a model of the studied phenomenon, including selected pathways, based on the Petri-net theory, has been created and then analyzed. Two pathways of IL-18 synthesis have been distinguished: caspase 1-dependent pathway and caspase 1-independent pathway. The analysis based on t-invariants allowed for determining interesting dependencies between IL-18 and different types of macrophages: M1 are involved in positive regulation of IL-18, while M2 are involved in negative regulation of IL-18. Moreover, the obtained results showed that IL-18 is produced more often via caspase 1-independent pathway than caspase 1-dependent pathway. Furthermore, we found that this last pathway may be associated with caspase 8 action