Comparative analyses of the vascular flora of the Pčinja river gorges in Serbia and Macedonia

The study’s aim is the comparative chorologic and ecological analysis of the vascular flora of the two gorges of the Pčinja River in Serbia and Macedonia which are 27 km apart. In the two gorges 1564 taxa have been recorded, 1057 being in the upper gorge in Serbia and 1174 in the lower gorge in Macedonia. Common to both gorges are 666 taxa. Chorological spectra show that in both gorges the most abundant are Mediterranean-submediterranean plants, 32.85% being in the upper and 43.97% in the lower gorge. Differences in the studied vegetation result from a diverse participation of other floristic elements such as Central European ones that are more abundant in the upper gorge (17.05%) than in the lower gorge (10.86 %). The life-form spectrum reveals that the flora in both gorges is hemicryptophyte-therophyte in character. Both gorges belong to an enclave of a Mediterranean-submediterranean region, i.e. to its submediterranean Macedonian- Thracian province

Design of peptide and small molecule inhibitors of cyclin dependent kinase 9 / cyclin T1 protein-protein interaction using computational methods

Cilj ove doktorske disertacije je razvoj direktnih inhibitora interakcija u kompleksu CDK9 / ciklin T1. Ciklin zavisna kinaza 9 u kompleksu sa ciklinom T1 čini katalitičko jezgro P-TEFb kompleksa. Inhibicija funkcije P-TEFb kompleksa je od značaja u terapiji više patoloških stanja kod ljudi: nekih tipova maligniteta, HIV-1 infekcije, hipertrofije miokarda, hroničnih inflamatornih bolesti. Postojeći inhibitori P-TEFb funkcije imaju ograničenu selektivnost dejstva, koju je moguće poboljšati primenom direktnih inhibitora CDK9 / ciklin T1 interakcije. U ovom istraživanju urađena je in silico studija P-TEFb kompleksa. Ispitana je struktura, hidratisanost i dinamika vezivnih površina kompleksa. Utvrđene su energetski najznačajnije hot spot aminokiseline u strukturi kompleksa i upotrebljene za dalji dizajn inhibitora. Struktura slobodne CDK9, neophodna za dizajn liganada je, u nedostatku eksperimentalno utvrđene strukture, simulirana klasičnom i ubrzanom molekularnom dinamikom. Ispitana je sposobnost vezivne površine kompleksa da interaguje sa ligandima, kao i postojanje, otvaranje i postojanost privremenih hidrofobnih džepova na vezivnoj površini CDK9, pogodnih za vezivanje liganada. Dobijene informacije o vezivnim površinama kompleksa CDK9 / ciklin T1, upotrebljene su za dizajn peptidnih i nepeptidnih inhibitora interakcije. Peptidni inhibitori su dizajnirani po ugledu na strukturu ciklina T1, ali i de novo dizajnom iz aminokiselina. Peptidne strukture sa najpovoljnijom energijom vezivanja za CDK9, iskorišćene su u razvoju nepeptidnih inhibitora. Predložene su strukture potencijalnih nepeptidnih inhibitora interakcije CDK9 / ciklin T1. U okviru ovog istraživanja urađeno je i ab initio ispitivanje prelaznih stanja intramolekulske Heck-ove ciklizacije alilnih alkohola i predloženo je objašnjenje za eksperimentalno zapaženu regioselektivnost procesa.The goal of this doctoral dissertation is the development of direct inhibitors of CDK9 / cyclin T1 protein-protein interaction. Cyclin dependent kinase 9 in complex with cyclin T1 forms the catalytic core of P-TEFb protein complex. Inhibition of P-TEFb function is of significance in the therapy of several pathological states in humans: some malignancies, HIV-1 infection, cardiac hypertrophy, chronic inflammatory diseases. Existing inhibitors of P-TEFb function have a limited selectivity of action, which could be improved with the direct inhibitors of CDK9 / cyclin T1 interaction. An in silico study of the P-TEFb complex was conducted in this research. The structure, hydration and dynamics of the complex binding surfaces were examined. Energetically most significant amino acids, hot spots, were determined and used in the design of inhibitors. The structure of the free CDK9, needed for the ligand design, was, in absence of an experimentally determined structure, simulated using classical and accelerated molecular dynamics. The ability of complex binding surfaces to interact with ligands was examined, as was the existence, opening and persistence of transient hydrophobic pockets on CDK9 interface surface, suitable for ligand binding. Information obtained of the CDK9 / cyclin T1 complex binding surfaces was used in the design of peptide and small molecule inhibitors of this interaction. Peptide ligands were designed using cyclin T1 as a template structure, as well as using de novo design from amino acids. Peptide structures with the most favourable binding energy to CDK9 were utilised in the design of small molecule inhibitors. Structures of potential small molecule inhibitors of CDK9 / cyclin T1 interaction were proposed. An ab initio study of transition states in an intramolecular Heck cyclisation of allyl alcohols was also conducted in this research. An explanation for the experimentally observed regioselectivity of the process was proposed

Quadcopter altitude estimation using low-cost barometric, infrared, ultrasonic and LIDAR sensors

Cilj ovog istraživanja je procena različitih low-cost senzora za merenje visine leta bespilotne letelice sa više rotora na malim visinama. Primenjene su metode filtriranja podataka i druge metode u cilju optimizacije performansi i tačnosti merenja senzora. Izvšrena su merenja visine leta, a podaci su uskladišteni za kasniju analizu u odnosu na stvarnu visinu leta. Izračunati su stepeni korelacije i srednja kvadratna greška u merenju senzora sa ciljem procene rada senzora. Na osnovu rezultata istraživanja moguće je odrediti izbor adekvatnog senzora za ovu specifičnu primenu. Ovo istraživanje je pokazalo da je u uslovima ovog eksperimenta najbolje rezultate imao lidar senzor Garmin LIDAR-Lite V3HP i senzor Bosch Sensortech BME280 sa mogućnošću istovremenog merenja vlažnosti vazduha, atmosferskog pritiska i temperature.The goal of this research is to assess the different low-cost sensors for flight altitude measuring of a multirotor UAV at low altitude flight. For optimizing the sensor performances and accuracy, data filtering and other methods were applied. The flight altitude data were collected and stored for later analysis with reference to the true altitude. The correlation coefficient and the mean squared error were calculated in order to assess the sensors' performance. On the basis of the results of the study, it was possible to determine the choice of the adequate sensor for this specific use. The study showed that the best characteristics for this experiment conditions had the Garmin LIDAR-Lite V3HP sensor and the Bosch Sensortech BME280 that combined air humidity, atmospheric pressure, and air temperature sensor

Quadcopter altitude estimation using low-cost barometric, infrared, ultrasonic and LIDAR sensors

Cilj ovog istraživanja je procena različitih low-cost senzora za merenje visine leta bespilotne letelice sa više rotora na malim visinama. Primenjene su metode filtriranja podataka i druge metode u cilju optimizacije performansi i tačnosti merenja senzora. Izvšrena su merenja visine leta, a podaci su uskladišteni za kasniju analizu u odnosu na stvarnu visinu leta. Izračunati su stepeni korelacije i srednja kvadratna greška u merenju senzora sa ciljem procene rada senzora. Na osnovu rezultata istraživanja moguće je odrediti izbor adekvatnog senzora za ovu specifičnu primenu. Ovo istraživanje je pokazalo da je u uslovima ovog eksperimenta najbolje rezultate imao lidar senzor Garmin LIDAR-Lite V3HP i senzor Bosch Sensortech BME280 sa mogućnošću istovremenog merenja vlažnosti vazduha, atmosferskog pritiska i temperature.The goal of this research is to assess the different low-cost sensors for flight altitude measuring of a multirotor UAV at low altitude flight. For optimizing the sensor performances and accuracy, data filtering and other methods were applied. The flight altitude data were collected and stored for later analysis with reference to the true altitude. The correlation coefficient and the mean squared error were calculated in order to assess the sensors' performance. On the basis of the results of the study, it was possible to determine the choice of the adequate sensor for this specific use. The study showed that the best characteristics for this experiment conditions had the Garmin LIDAR-Lite V3HP sensor and the Bosch Sensortech BME280 that combined air humidity, atmospheric pressure, and air temperature sensor

The correlation of metal content in medicinal plants and their water extracts

The quality of some medicinal plants and their water extracts from South East Serbia is determined on the basis of metal content using atomic absorption spectrometry. The two methods were used for the preparation of water extracts, to examine the impact of the preparation on the content of metals in them. Content of investigated metals in both water extracts is markedly lower then in medicinal plants, but were higher in water extract prepared by method (I), with exception of lead content. The coefficients of extraction for the observed metal can be represented in the following order: Zn > Mn > Pb > Cu > Fe. Correlation coefficients between the metal concentration in the extract and total metal content in plant material vary in the range from 0.6369 to 0.9956. This indicates need the plants to be collected and grown in the unpolluted area and to examine the metal content. The content of heavy metals in the investigated medicinal plants and their water extracts is below the maximum allowable values, so they are safe to use

Phytogeographical characteristics and endemism of the flora of Rogozna Mt. (SW Serbia)

Based on presence of area types and area groups, the phytogeographical analysis show that Rogozna Mt. is area with eurasian-submediterranean-centraleuropean-pontic characteristics. Eurasian area type is dominant in the flora of Rogozna Mt. Detailed analysis of the Eurasian area type showed a numerous presence of the species with Central European-Mediterranean (73) and Central European-Mediterranean-Pontic (73) types of distribution. The influence of the Mediterranean region is especially pronounced. There are 117 species with Mediterranean-Submediterranean type of distribution, many of which are endemics or subendemics. Typical Pontic elements of flora are present in very low percent (1.27%), but taxa with Mediterranean-Pontic (14.7%) and Central-European-Mediterranean-Pontic (9.38%) are numerous. The presence of an imposing number of endemic taxa (51) has a great significance from the aspect of biodiversity and conservation of the area

Phylogeny, karyotype evolution and taxonomy of Crocus ser. Verni (Iridaceae)

The taxonomically complicated Crocus series Verni is characterized by high intra-and interspecific variability of karyotypes (2n = 8-23). With the aim to get more insights into complex karyotype evolution and to clarify the taxonomy of this group, we combined morphological (twelve characters), molecular (chloroplast DNA: trnL-trnF, ndhF; nuclear DNA: ITS, pCOSAt103) and karyological analyses. Samples of different populations of C. etruscus, C. ilvensis, C. kosaninii, C. tommasinianus, C. vernus sensu lato and C. longiflorus (series Longiflori) were analyzed. Quantitative karyotype parameters were calculated for all taxa involved based on the available literature. For the taxon traditionally known as C. vernus, the analyses suggest that it should be split in five species: C. heuffelianus, C. neapolitanus, C. neglectus sp. nov., C. siculus and C. vernus. The comparison of genome total haploid lengths suggests that in the evolution of the group polyploidization only played a role within the C. vernus species complex, where we also detected two hybridization events. In all other taxa, chromosome evolution is probably characterized by chromosome fusions and fissions, sometimes affecting the entire haploid chromosome set. Comparative cytogenetics of the group indicates that series Verni is subject to a peculiar type of unequal change in chromosome size, i.e., that not both chromosome arms gain or lose equally in DNA content. As a taxonomic consequence of our study, series Verni is newly circumscribed, now including the autumn-flowering C. longiflorus and excluding C. baytopiorum

Diterpenes from Achillea clypeolata

The isolation of 16 alpha,17-epoxy-ent-kaurane (a known compound), 3 alpha-acetoxy-16 alpha,17-epoxy-ent-kaurane and 19-acetoxy-16 alpha,17-epoxy-ent-kaurane from roots of Achillea clypeolata is reported. Copyright (C) 1996 Elsevier Science Lt