Semantic unification and search of bioinformatics databases

Analyzing biological data from various sources offers a comprehensive perspective of a domain, facilitating the identification of patterns that would otherwise be challenging or impossible to observe when focusing solely on individual biological entities. The process of linking data from different databases can present challenges due to inconsistencies in properties and identifiers assigned to the same entity across databases. Although certain databases include a range of identifiers from multiple sources, the search capabilities are restricted to exact property matching, preventing the execution of complex queries involving multiple metadata attributes. We designed a novel data framework that aims to address these challenges by facilitating the linkage and retrieval of information from diverse interconnected biological data sources. To evaluate the effectiveness of the model, we conducted tests and created a knowledge graph using metadata extracted from five separate public datasets: DisProt, HGNC, Tantigen 2.0, IEDB, and DisGeNET. The resulting graph establishes connections between more than 17 million nodes, comprising 2.5 million distinct biological entity objects, and encompasses over 4 million relationships. Additionally, we designed and implemented a general-purpose procedure for extracting new relationships based on semantic similarity from data transformed into the BioGraph data model.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Minerali u ishrani

Minerals in our diet are often divided into two groups: macro- and microelements. Microelements are required in smaller quantities and have different roles in organism: structural role (calcium and magnesium), regulatory role (regulation of acidity and osmotic pressure), catalytic role (enzymes), and different specific roles. Metabolism of minerals differs from metabolism of organic substances: organic molecules are absorbed up to 90%, while minerals only 10 - 40%. The most important alkaline and alkaline earth metals in organism are Ca, Mg, Na and K. Transition metals are usually present as the trace elements in organism (most abundant are Fe, Zn, Cu, Co, Mn, Cr, Ni). In recent years, scientists showed a great interest in nutrition and dietetics and made some new concepts which considered that nutrition does not have an universal character.

Minerali u ishrani

Minerals in our diet are often divided into two groups: macro- and microelements. Microelements are required in smaller quantities and have different roles in organism: structural role (calcium and magnesium), regulatory role (regulation of acidity and osmotic pressure), catalytic role (enzymes), and different specific roles. Metabolism of minerals differs from metabolism of organic substances: organic molecules are absorbed up to 90%, while minerals only 10 - 40%. The most important alkaline and alkaline earth metals in organism are Ca, Mg, Na and K. Transition metals are usually present as the trace elements in organism (most abundant are Fe, Zn, Cu, Co, Mn, Cr, Ni). In recent years, scientists showed a great interest in nutrition and dietetics and made some new concepts which considered that nutrition does not have an universal character.

Increased tumor necrosis factor alpha and interleukin-6 serum levels and their correlation with laboratory parameters in patients with imported malaria

In malaria, blood concentrations of proinflammatory cytokines, such as tumor necrosis factor alpha (TNF-α) and interleukin (IL)-6, are increased. In a study which included 34 patients, TNF-α and IL-6 were examined in two phases, immediately after the admission of patients, and at the end of antimalarial therapy, when the parasitemia was negative. The results show a significant increase of TNF-α and IL-6 in the first phase, before the effects of antimalarial therapy. A very strong correlation between TNF-α and IL-6 is also confirmed, which suggests their coordinated production. Increased TNF-α values were correlated with an older age, the level of parasitemia, the number of platelets and leukocytes, elevated values of procalcitonin, D-dimer and lactate dehydrogenasе, and lower values of serum iron and antithrombin. Increased values of IL-6 were correlated with the level of parasitemia, the number of platelets and leukocytes, and elevated values of D-dimer and lactates

EFFECT OF STORAGE TEMPERATURE AND THERMAL PROCESSING ON CATECHINS, PROCYANIDINS AND TOTAL FLAVONOIDS STABILITY IN COMMERCIALLY AVAILABLE COCOA POWDERS

Storage stability of catechin, epicatechin, procyanidins B1-B4 and total flavonoids in cocoa powder samples was studied over the temperature range 4-35 ºC. Thermal stability of total flavonoids was studied over the temperature range 95-125 ºC. Total flavonoids concentration decreased as a function of time and the degradation was accelerated at higher temperatures: a half-life (t1/2) of total flavonoids was much shorter at room temperature than during cold storage. A first-order kinetic model fitted well to all the data. Temperature dependence of the degradation rate constants, described by the Arrhenius equation, was more pronounced during heating than during storage. In the temperature interval from 4 ºC to 35 ºC, the calculated activation energies (Ea) for catechin, epicatechin and procyanidins B1-B4 were 20.4 kJ/mol, 12.5 kJ/mol, 9.4 kJ/mol, 21.6 kJ/mol, 19.4 kJ/mol, 23.7 kJ/mol, respectively. UTICAJ TEMPERTURE ČUVANJA I ZAGREVANJA NA SADRŽAJ KATEHINA; PROCIJANIDINA I UKUPNIH FENOLA KOMERCIJALNIM UZORCIMA KAKAOA U PRAHUUticaj temperature čuvanja na stabilnost katehina, epikatehina, procijanidina B1-B4 i ukupnih flavonoida u uzorcima kakaoa u prahu praćen je u temperaturnom opsegu od 4 ºC do 35 ºC. Uticaj zagrevanja na sadržaj ukupnih flavonoida je praćen u temperaturnom opsegu od 95 ºC do 125 ºC. U toku skladištenja uzoraka je došlo do smanjenja u sadržaju ukupnih flavonoida. Pomenuta promena je bila izraženija na višim temperaturama: vreme polu-života (t1/2) ukupnih flavonoida u ispitivanom uzorku kakaoa u prahu bilo je kraće kada je on čuvan na sobnoj temperaturi nego kada je čuvan u frižideru. Promene u sadržaju flavonoida u ispitivanim uzorcima prate kinetiku prvog reda. Konstante brzine degradacije, izračunate pomoću Arenijusove jednačine, veće su tokom zagrevanja nego tokom čuvanja ispitivanih uzoraka na nižim temperaturama. Izračunate energije aktivacije (Ea) za katehin, epikatehin i procijanidine B1, B2, B3 i B4 u temperaturnom intevalu od 4 ºC do 35 ºC  bile su: 20,4 kJ/mol, 12,5 kJ/mol, 9,4 kJ/mol, 21,6 kJ/mol, 19,4 kJ/mol i 23,7 kJ/mol. HIGHLIGHTS Storage stability of (epi)catechin, procyanidins B1-B4 and total flavonoids in cocoa powder samples was studied(temperature range 4-35 °C)The stability of the total flavonoids was studied over the temperature range 95-125 °CThe degradation of the total flavonoids was significantly accelerated at higher temperaturesTemperature dependence of the degradation rate constants was more pronounced during heating than during storag

Clustering and classification of SARS-COV-2 isolates using RSCU

The existence of a large number of sequenced SARS-COV-2 isolates provides an opportunity to observe genomic variability in a massive sample. The goal of our research was to use data mining techniques to study possible correlation between codon usage and classification by WHO-labels in a certain period of time. The material includes 745,533 isolates with 12,236,672 coding sequences (proteins) from NCBI (10.08.2022.). RSCU was used as a measure of codon usage. Samples are associated with WHO-labels (based on Pango_Id) and time intervals. Inconsistency of WHO-labels with periods in which the respective strains were actually present was observed. The isolates with the observed discrepancy were excluded from the sample. Isolates without assigned WHO-labels were also excluded. In addition, individual coding sequences containing ambiguous nucleotide codes were eliminated. Clustering was performed for each of the 12 common types of coding sequences (proteins), with multiple methods and a different number of clusters. Neural clustering gave the best results. For different protein types, different degrees of RSCU variability are observed. In the case of proteins with a small variation in nucleotide contents, over 95% of the material belongs to a single cluster, while the other clusters are of negligible size. In the case of proteins with more variations, a higher number of pure clusters (by WHO-labels) is obtained, with a small number of heterogeneous clusters (about 10% of the material). In those heterogeneous clusters, there are isolates with different WHOlabels that were present in parallel at some point, as a kind of transitional forms between two strains. Different classification models were created on the same sample. Models based on protein types with higher diversity between coding sequences are highly accurate (96- 100%). Using the classification models, the corresponding WHO-labels were associated with isolates without previously assigned WHO-labels.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Progesterone exerts protective effects in rat permanent bilateral common carotid artery occlusion model

Introduction: Cerebral hypoperfusion (CH), a reduced cerebral blood flow, characteristic for aging and neurodegenerative disorders, might be associated with a pro-oxidative state in the brain due to the generation of reactive oxygen species (ROS) that cause neuronal damage. These overgenerated pro-oxidants might be reduced, disabled and neutralized by the endogenous antioxidant enzymes, including superoxide dismutase (SOD) and catalase (CAT). A sex steroid hormone, progesterone, in several experimental models of neuronal injury exerts anti-oxidative properties upregulating anti-oxidative molecules and thus promoting neuroprotection. However, its efficacy in the state of CH is still unknown and it is necessary to better understand the mechanism underlying this hormone’s neuroprotective effects. Aim: We investigated whether progesterone is able to modulate CH-induced pro-oxidative/anti-oxidative imbalance, as well as SOD and CAT activities, in the prefrontal cortex of three-month-old male Wistar rats subjected to permanent bilateral common carotid artery occlusion (2VO). Methods: The appropriate actions were undertaken to reduce the distress of the animals in agreement with the European Community Council Directive of 86/609/EEC and 010/63/EU for animal experiments. All experimental procedures were allowed by the Ethical Committee for the Use of Laboratory Animals of VINČA Institute of Nuclear Sciences - National Institute of thе Republic of Serbia, University of Belgrade, Belgrade, Republic of Serbia (protocol authorization numbers 02/11 and 323-07-04253/2016-05). Following chloral hydrate anaesthesia, 8 rats randomly assigned in 2VO groups were double occluded with 5–0 silk suture, while 4 animals from sham operated group were subjected to the same surgical procedure but without actual ligation of carotid arteries. Four hours following the surgical procedure animals from sham operated group, used as controls, were subcutaneously treated with vehicle (commercial flax oil, 1 mg/kg/day, S + V), while animals in 2VO groups were subjected to either progesterone (1.7 mg/kg/day, 2VO + P) or vehicle (commercial flax oil, 1 mg/kg/day, 2VO + V). Following 7 days lasting treatments, pro-oxidative/anti-oxidative balance was assessed according to the method of Alamdari et al. [1]; while activities of anti-oxidative enzymes were determined as described in the study by Tatalović et al. [2]. One-way analysis of variance (ANOVA) test followed by Tukey’s post hoc test was employed to analyse data. The values of p < 0.05 or less were considered statistically significant. Results: Obtained results demonstrate that compared to controls, 2VO and vehicle treatment induced a significant increase of pro-oxidants levels (p < 0.01) as well as the activities of both investigated anti-oxidative enzymes, although only the CAT activity was significantly increased (p < 0.05). Following progesterone treatment, pro-oxidants levels were lowered to the control level which caused the difference between the 2VO groups (p < 0.05). In parallel, no statistically significant change in SOD activity was observed, while CAT was upregulated (p < 0.05). Conclusion: Presented results suggest that in the prefrontal cortex in the state of CH, progesterone, by modulating the CAT activity, downregulates overgenerated reactive species, reduces CH-induced oxidative stress and exerts anti-oxidative outcomes