The effect of VHL gene mutation on the expression levels of mTOR signaling pathway proteins in clear cell renal cell carcinoma

Sporadični svetloćelijski karcinomi bubrega asocirani su sa mutacijama tumor supresorskog gena VHL kod 60-80 % pacijenata. U odsustvu funkcionalnog proteina VHL dolazi do akumulacije faktora indukovanih hipoksijom koji regulišu ekspresiju gena uključenih u procese angiogeneze, eritropoeze, ćelijskog metabolizma i preživljavanja. Pored specifičnog genetičkog profila i povišenog nivoa HIF-2α svetloćelijske karcinome bubrega karakteriše glikolitički metabolički put i povišena aktivnost mTOR signalnog puta. Nepovoljan energetski status i hipoksija blokiraju aktivnost mTOR signalnog puta preko proteina AMPK i REDD1. Ova studija imala je za cilj da utvrdi mogću asocijaciju mutacionog statusa gena VHL sa patohistološkim parametrima, nivoom HIF-2α iRNK i nivoom proteina HIF-2α, mTOR, TSC1, TSC2, eIF4E-BP1, p70S6K1, AMPK, REDD1 i PDK3 u svetloćelijskom karcinomu bubrega. Studija je obuhvatala 47 pacijenata kojima je urađena totalna nefrektomija zbog prisustva svetloćelijskog karcinoma bubrega. Genomska DNK izolovana iz uzoraka venske krvi i somatska DNK izolovana iz uzoraka tumorskog i neizmenjenog tkiva bubrega upotrebljene su za određivanje mutacionog statusa gena VHL i gubitka heterozigotnosti 3p lokusa sekvenciranjem, metodom amplifikacije višestruko ligiranih proba i fragmentnom analizom mikrosatelitnih markera. Metilacioni status promotora gena VHL ispitan je metil specifičnom PCR reakcijom nakon bisulfitne modifikacije DNK. Kvantitativni RT-PCR primenjen je za relativnu kvantifikaciju HIF-2α iRNK u tumorskom i neizmenjenog tkivu bubrega. Kvantitafikacija ekspresije proteina HIF-2α, mTOR, TSC1, eIF4E-BP1, p70S6K1, AMPK, REDD1 i PDK3 utvrđena je Western blot metodom. Semikvantitativna imunohistohemijska analiza korišćena je za utvrđivanje nivoa ekpresije proteina TSC2...Sporadic clear cell renal carcinoma is associated with mutations of the VHL gene in 60-80 % patients. The absence of a functional VHL protein leads to accumulation of hypoxia-inducible factors which regulate expression of genes involved in angiogenesis, erythropoiesis, cell metabolism and survival. Specific genetic background, overexpression of HIF-2α transcription factor as well as glycolytic metabolism and upregulated activity of mTOR pathway are the main characteristics of clear cell renal carcinoma. The lack of energy and hypoxia inhibit mTOR signaling through activity of AMPK and REDD1 proteins. The aim of present study was to determine association of VHL gene mutational status with pathohistological parameters, expression level of mRNA HIF-2α and expression levels of mTOR, TSC1, TSC2, eIF4E-BP1, p70S6K1, AMPK, REDD1 and PDK3 proteins in clear cell renal carcinoma. The study included 47 patients who underwent radical nephrectomy due to unilateral kidney tumor. DNA was extracted from peripheral venous blood, tumorous and corresponding healthy renal tissue. The VHL gene mutational status and loss of heterozigosity of 3p loci were detected using DNA sequencing, MLPA and analysis of microsatellite markers. The VHL gene promoter methylation analysis was examined by MS-PCR after bisulphite modification of DNA. Quantitative real time PCR was performed for relative quantification of HIF-2 alpha mRNA. Expression levels of HIF- 2α, mTOR, TSC1, eIF4E-BP1, p70S6K1, AMPK, REDD1 and PDK3 proteins was determined using Western blot method. Immunohistochemistry was performed for semiquantitative analysis of TSC2 protein. Alteration of VHL gene and/or changes of 3p loci were detected in 37/47 (78.7 %) analysed tumorous samples..

Visual culture in the service of the military of Principality/Kingdom of Serbia 1878-1913

Предмет докторске дисертације су функције и значења која су додељивана визуелној култури у српској војсци у периоду од 1878. до 1913. године. Испитивани су специфично војни захтеви и потребе као фактори који су утицали на уобличавање и пласман одређених дела визуелне културе у војсци. Идентификовани су и политички, економски, друштвени, културни контексти визуелне културе у војсци. Имајући у виду овај делокруг истраживачких проблема, у раду је примењено више метода, разрађених у оквирима студија визуелне културе и тзв. критичке историје уметности, као и нових студија културне историје...The subject of this doctoral dissertation are the functions and meanings assigned to the visual culture in the Serbian military in the period from 1878 to 1913. Specific military requirements and needs were examined as factors that influenced the shaping and placement of certain parts of the visual culture in the military. Political, economic, social and cultural contexts of visual culture in the military were identified. Having in mind this scope of research problems, several methods were applied in this dissertation, elaborated within the framework of visual culture studies and so-called critical art history, as well as recent studies of cultural history..

Phenolic Composition, Antioxidant, Anti-Enzymatic, Antimicrobial and Prebiotic Properties of Prunus spinosa L. Fruits

Blackthorn (Prunus spinosa L.) fruit is bluish-black wild fruit traditionally used in nutrition and medicine. It is recently gaining attention as a functional food and an underutilized source of bioactive compounds for application in the food and pharmaceutical industry. This study aimed to assess the health-promoting potential of blackthorn fruits from Serbia by examining their chemical composition and in vitro biological activities. Phytochemical analysis of the blackthorn fruit extracts was performed using LC-DAD-ESI-MS. The total phenolic (TPC), total flavonoid (TFC), total anthocyanin (TAC) content, antioxidant capacity, and enzyme inhibitory activities were determined spectrophotometrically. The antimicrobial and prebiotic properties were tested using the broth microdilution method. Twenty-seven phenolics belonging to the classes of hydroxybenzoic and hydroxycinnamic acids derivatives, flavonoids, and anthocyanins were identified, with caffeoylquinic acid as the most abundant compound. Blackthorn extracts were characterized by notable TPCs, TFCs, and TACs, and free radical scavenging and reducing ability. The enzyme inhibitory effects (IC50 = 0.43–2.16 mg/mL) were observed towards α-amylase, α-glucosidase, acetylcholinesterase, and tyrosinase. Blackthorn fruit extracts in a concentration-dependent manner (0.3–5 mg/mL) stimulated the growth of several probiotic microorganisms and their mixtures, especially the yeast Saccharomyces boulardii. Obtained results support further evaluation of the functional food potential of blackthorn fruit

Chemical characterization, antioxidant and antimicrobial properties of goji berries cultivated in serbia

Since the fruits of Lycium L. species (Fructus lycii, goji berries) are promoted as a “superfood” with plenty of health benefits, there is extensive research interest in their nutritional and phytochemical composition. In the present study, the nutritional value, minerals, fatty acid composition, and bioactive compounds of L. barbarum L., red, yellow, and black goji berry (L. ruthenicum Murray.) cultivated in Serbia were investigated. Antioxidant and antimicrobial properties of their methanol extracts were assessed. Red goji berry had the highest content of fats, dietary fiber, iron, total carotenoids, and 2-O- -d-glucopyranosyl-l-ascorbic acid (AA-2 G). The yellow goji berry extract showed the highest level of flavonoids and the most prominent antimicrobial (especially against Gram-negative bacteria) properties. The highest total phenolic content and the most potent antioxidant activity were observed for the extract of black goji berry. Therefore, all goji berries could be a valuable source of bioactive compounds in the food and pharmaceutical industry

Combined experimental and theoretical study of Type-II toxin-antitoxin system response to antibiotics

Bacterial Type-II toxin-antitoxin (TA) systems, including kacAT in Klebsiella pneumoniae, respond to antibiotics. We investigated kacAT’s regulation relevant to antibiotic persistence, which refers to the survival of antibiotic exposure by dormant bacterial cells. Elevated toxin levels may induce dormancy. KacAT complex binds and represses the kacAT promoter cooperatively, leading to highly non-linear negative feedback. Antibiotics increase transcription of the kacA and kacT genes by inducing KacA degradation and consequently reducing the KacA:KacT ratio. Our model reproduced experimental findings, explaining increased kacAT transcription and reduced [KacA]:[KacT] ratio. Interestingly, KacAT overexpression induces antibiotic stress tolerance, while deleting kacAT has no effect, which our model can also explain. KacAT, therefore, cannot induce spontaneous (in the absence of antibiotics) persister formation. Earlier theoretical models, which predicted spontaneous persistence in Type-II TA systems, assumed the cooperative action of multiple TA systems. Our bioinformatics analysis, however, reveals a limited occurrence of multiple TA instances within clades and that cross-talk between clades is disfavored. These challenges the assumption of cooperativity in TA action, possibly explaining the absence of spontaneous persister generation in kacAT.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Ispitivanje promena na površini nakon dugotrajnog izlaganja vazduhu polazeći od prvih principa-XPS

Within the scope of this paper, a potential impact of noble metal particles on the surface of N-TiO2 and its catalytic properties is observed through correlation with contamination layer thickness. Owing to 'first principle' approach study, without additional experimental measurements or permanent damage to the surface of the samples, it is possible to obtain significant novel information based on a single measurement of the XPS spectra. Presented research demonstrated how the surface contamination layer in the case of samples based on N-TiO2 is related to the nature of two studied noble metals, indicating that Pd might serve as an important co-modifier to suppress surface contamination.Kroz ovaj rad će biti sagledan uticaj čestica plemenitih metala na strukturu površine titanijum dioksida dopiranog azotom i katalitička svojstva kroz uticaj na debljinu sloja nečistoća. U ovakvom pristupu koji polazi od „prvih principa“ je bez dodatnih eksperimentalnih merenja i trajnog oštećenja površine uzoraka moguće dobiti značajne nove informacije korišćenjem rezultata jednom izvedenog merenja rendgenskog fotoelektronskog spektra. Dobijeni rezultati ukazuju na to da promene na površini uzoraka na bazi N-TiO2, do kojih dolazi zbog prisustva Pd, utiču na suzbijanje površinskih organskih nečistoća

Al-ions Charge Storage Ability of the Conductive Polyaniline Emeraldine Salt

Development of new and attractive generation of polymer devices for application in the field of energy storage that meets the requirements of safety and environmental sustainability is an ongoing challenge. The majority of previous scientific results reported that polyaniline-based supercapacitors use only aqueous acid solutions as electrolyte. [1] The aim of this work is to examine the redox activity of polyaniline emeraldine salt (PANI-ES) in an aqueous electrolyte of aluminum salt, that have been studied to a lesser extent and lacking the characterization of charge storage behavior. The advantage of employing aluminum among various post-lithium rechargeable systems has the advantage in the fact that it is the most abundant metal element in the Earth’s crust with one of the highest gravimetrical and volumetric energy densities. By combining experimental (cyclic voltammetry, chronopotentiometry, galvanic charge/discharge, AFM - Atomic Force Microscopy) and theoretical approaches (density functional theory - DFT), the redox mechanism of polyaniline in the aqueous Al-salt solution is explained. [2] Polyaniline has been shown to have higher Coulombic capacitance at the same charge and discharge current in aqueous aluminum nitrate solution (1M Al(NO3)3) than in hydrogen chloride electrolyte solution (1M HCl), which makes it a suitable electrode for supercapacitors. From a practical point of view, a supercapacitor based on polyaniline and an aqueous solution of Al(NO3)3 was constructed and tested in terms of capacitance, cycle time, and self-discharge. The capacitor shows high charge and discharge capacity (≈269 F g-1 at a current density of 10 A g-1) and relatively good capacity retention after 1000 charge and discharge cycles.COIN2022 - Contemporary Batteries and Supercapacitors - International Symposium ; June 1-2, 2022 ; Belgrade, Serbi

High-throughput screening of novel hydrogen storage materials – ML approach

Hydride formation in metals is a widely studied and applied phenomenon necessary to transition to clean energy solutions and various technological applications. We focus on three perspective applications of these materials, namely near-ambient hydrogen storage, hydrogen storage compressor materials, and alkali metal conversion electrodes, to demonstrate acceleration in the research achieved by utilizing a data-driven approach. Graph neural network was developed using a transfer learning approach from the MEGNet model and data related to the thermodynamics of hydride formation obtained in experimental work. Based on the crystal structure and composition as input features, we apply the MetalHydrideEnth model developed in our previous work to predict hydride formation enthalpy in intermetallic compounds. In this work, we focus on demonstrating how this approach, combined with available crystal information obtained from density functional theory calculations, can be applied for fast and extensive searches of novel metal hydride materials, having in mind the above-listed applications.ICCBIKG 2023 : 2nd International Conference on Chemo and Bioinformatics, 28-29 September 2023, Kragujevac, Serbi

Razvoj materijala za litijum-jonske baterije korišćenjem mašinskog učenja

The development of novel materials is seen as the key approach to improvements in the performance of Li-ion batteries. Recently, conversion-type electrodes have been demonstrated to improve battery capacity and energy density. Metal hydrides are considered promising anode materials, while some hydride materials are also considered solid ionic conductors. In this research, we rely on the machine learning approach to predict the properties of novel anode materials depending on hydride conversion reactions. We limit our search to Mg-containing intermetallic compounds and screen a vast database of optimized crystal structures obtained using density functional theory calculations. The composition and crystal structure of selected metals/intermetallics are input for a graph neural network-based machine learning model to predict hydride formation enthalpy and equilibrium electrode potential vs. Li+ /Li0 . Among 245 intermetallic compounds found to be satisfactory as anode materials, we particularly discuss La-Mg-X intermetallics. The work demonstrates the advantages of combining artificial intelligence tools and theoretical approaches with experimental results for property prediction and fast screening of vast combinatorial space.Brojna istraživanja usmerena su na razvoj novih materijala kao ključnog pristupa u poboljšanju performansi litijum-jonskih baterija. Poslednjih godina posebno se ispituju konverzione elektrode koje omogućavaju veće kapacitete i gustine energija. Posebno, metalni hidridi se ispituju kao pogodni materijali za anode konverzionog tipa, dok se takođe neki hidridi ispituju i kao pogodni jonski provodnici. U ovom radu koristimo modele mašinskog učenja za predviđanje osobina novih anodnih materijala, oslanjajući se na reakcije konverzije hidrida. Pretraga novih intermetalnih jedinjenja ograničana je na one koji sadrže magnezijum, a kao izvor podataka korišćene su dostupne baze kristalnih struktura oprimizovanih proračunima zasnovanim na teoriji funkcionala gustine. Sastav i kristalna struktura odabranih metala/intermetalnih jedinjenja korišćeni su kao ulazni podaci za model mašinskog učenja zasnovan na graf neuronskim mrežama. Na taj način predviđene su entalpije formiranja hidrida i ravnotežni elektrodni potencijali u odnosu na Li+/Li0. Od 245 intermetalnih jedinjenja koja zadovoljavaju uslov za anodni materijal izdvojena su i diskutovana ternarna jedinjenja La-Mg-X. Ovaj rad pokazuje prednost kombinovanja alata veštačke inteligencije i teorijskih pristupa sa eksperimentalnim radom u cilju predviđanja osobina novih materijala i brze pretrage velikog prostora mogućih intermetalnih jedinjenja