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DEVELOPMENT OF BOTANICAL CONCEPTS THROUGH ELEMENTARY AND SECONDARY EDUCATION
No full textOvim je istraživanjem analizirana usvojenost koncepata botanike kroz osnovnoškolsko i srednjoškolsko obrazovanje te međuodnosi sa stavovima i interesima učenika, studenata i nastavnika za botaniku. Istraživanje je diskontinuirano provođeno tijekom 15 godina, prije i poslije stupanja na snagu novog kurikuluma Prirode i Biologije te prije i poslije online nastave. Pismene provjere provedene su u tiskanom obliku ili online, a anketno istraživanje online. Utvrđeno je da je usvojenost botaničkih koncepata mala, a zbog neprimjerenih nastavnih programa dolazi do stvaranja brojnih miskoncepcija, od kojih neke nastaju i tijekom edukacije studenata nastavničkih profila. Interesi i stavovi učenika najveći su za procese u biljnom organizmu, a učitelja i nastavnika za ekologiju biljaka. Međutim, interesi i stavovi učenika ne mogu se povezati s usvojenošću koncepata botanike, kao ni uspješnost učenika s interesima nastavnika, koji smatraju važnim znanje o biljkama, ali dosadnom školsku botaniku. Na temelju ovog istraživanja identificirane su miskoncepcije i predložen potencijalni novi kurikulum botanike.This research analysed the acquisition of botany concepts through primary and secondary education and the interrelationships with the attitudes and interests of students and teachers in botany. The research was carried out discontinuously over 15 years, before and after the ratification of the new Nature and Biology curriculum and before and after online classes. Written tests were conducted in printed form or online, and polls only online. It has been established that the acquisition of botanical concepts is low, and due to inappropriate teaching programs, numerous misconceptions are created, some of which arise during the education of future teachers. Students' interests and attitudes are greatest for processes in the plant organism, and teachers for plant ecology. However, students' interests and attitudes cannot be linked to the acquisition of botany concepts, nor can students' success with the interests of teachers, who consider plant knowledge important but school botany boring. Based on this research, misconceptions were identified and a potential new botany curriculum was proposed
Quantum chemical calculations and machnie learning in predicting bioactivity of new compounds
No full textMale molekule mogu interagirati s biološkim makromolekulama i tako utjecati na homeostazu organizma. U okviru ovoga doktorskog rada računalno su istraženi odabrani kemijski spojevi kao potencijalni antimikrobni agensi i/ili inhibitori kolinesteraza. Najvažnije interakcije malih molekula s makromolekulama određene su metodama molekularnog dokiranja: 1. novorazvijena metoda tenzorske dekompozicije trajektorija ab initio molekularne dinamike te 2. kvantno-kemijsko Monte Carlo dokiranje unutar aktivnog mjesta enzima. Molekularno dokiranje ab initio molekularnom dinamikom uključuje protokol strojnog učenja za određivanje duljine trajanja simulacija kada su uzorkovani potpuni konfiguracijski prostori. Kvantno-kemijsko Monte Carlo dokiranje podrazumijeva uzorkovanje struktura putem generiranja slučajnih konfiguracija sustava (aktivno mjesto enzima i mala molekula) te kvantno-kemijske proračune energije. Ekstenzivnom primjenom strojnog učenja uspostavljeni su najbolji mogući multivarijatni linearni regresijski modeli koji povezuju biološku aktivnost promatranih spojeva s njihovim teorijski uzorkovanim plohama potencijalne energije. Dobiveni rezultati predstavljat će osnovu za daljnja istraživanja najvažnijih interakcija malih molekula s kolinesterazama i za predviđanje bioaktivnosti te "pametan" dizajn novih bioaktivnih molekula.Small molecules can interact with biological macromolecules and thus affect the organism's homeostasis. Within this doctoral dissertation, selected chemical compounds were theoretically investigated as potential antimicrobial agents and/or cholinesterase inhibitors. The most important interactions of small molecules with macromolecules were determined by molecular docking methods: 1. newly developed method of tensor decomposition of ab initio molecular dynamics trajectories and 2. quantum-chemical Monte Carlo docking within the active site of the enzyme. Molecular docking by ab initio molecular dynamics includes a machine learning protocol for determining the length of simulations where complete configuration spaces are sampled. Quantum-chemical Monte Carlo docking implies sampling of structures through the generation of random system configurations (enzyme active site and small molecule) and quantum-chemical energy calculations. Through the extensive application of machine learning, the best possible multivariate linear regression models that connect the biological activity of the observed compounds with their theoretically sampled potential energy surfaces were established. The obtained results will represent the basis for further research of the most important interactions of small molecules with cholinesterases as well as the prediction of bioactivity and the "smart" design of new bioactive molecule
Macrophyte vegetation of the Odra River and its tributaries
No full textRijeka Odra u potpunosti je ravničarska tekućica, s izvorom i ušćem u nizinama, koja protječe ruralnim i šumovitim predjelom Turopoljske mikroregije. Kao i većina rijeka Europe, i Odra je pod snažnim čovjekovim utjecajem od kojih su najznačajniji kanaliziranje i pad podzemnih voda. Makrofiti ovog područja rijetko su istraživani i ne postoje cjelokupna i sustavna istraživanja ove skupine. Stoga, kako bi se upotpunile spoznaje o makrofitskoj vegetaciji, ali i o čovjekovom utjecaju na ovo područje, provedena su istraživanja tijekom ljeta i jeseni 2022. i 2023. godine na 18 lokaliteta duž Odre i njezinih pritoka. Istraživanjem je utvrđeno kako porječje Odre karakterizira visoka raznolikost i bogatstvo makrofitskih svojti, njih 74 koje pripadaju u pet taksonomskih skupina, a najbrojnije među njima su sjemenjače. Zabilježene vrste horološki spadaju u skupine sa središtima rasprostranjenosti u umjerenom i cirkumpolarnom području. Analizom ekoloških indikatorskih vrijednosti i stanišnih podataka zabilježena je jasna razlika između pritoka i glavnog toka. Ocjenom ekološkog stanja vodotoka utvrđeno je u prosjeku umjereno ekološko stanje, dok se za bolja stanja uglavnom veže više bogatstvo vrsta i pješčani supstrat. Uz invazivne strane vrste, zabilježene su i razne antropogeno izazvane ugroze te relativno dobra ekološka stabilnost uz vodotoke i raznolika morfologija korita duž istraživanog područja.The Odra River is entirely a lowland river with its source and confluence in lowland areas. It flows through the rural and forested areas of the Turopolje microregion. Like many rivers in Europe, the Odra has been significantly affected by human activity, like canalization and the lowering of groundwater levels. There have been few studies related to the macrophytes of this area, and no complete and systematic studies have been conducted. To expand knowledge about macrophyte vegetation and human impact in this area, a survey was conducted in the summer and autumn of 2022 and 2023 at 18 sites along the Odra and its tributaries. The survey revealed that the Odra basin is characterized by a high diverse and richness of macrophyte taxa, totaling 74, which are classified into five taxonomic groups, with spermatophytes being the predominant. The species recorded horologically belong to groups with centers of distribution in temperate and circumpolar regions. Analysis of ecological indicator values and habitat data revealed clear differences between the tributaries and the main stream. The assessment of habitat quality indicated a moderate ecological status, with better conditions associated with greater species richness and sandy substrates. Despite the presence of invasive alien species and various anthropogenic threats along the watercourses, the researched area is considered ecologically stable, with a diverse bed morphology
Targeting the fusion protein RIOX1-dSpCas9 to the promoter region of B4GALT1 for removal of the histone mark H3K4me3
No full textŠest epigenetičkih mehanizama simultanim djelovanjem regulira gensku ekspresiju, a njihove su interakcije, zastupljenosti i efekti na transkripcijski status određenog gena specifični u odnosu na kromatinski „okoliš“. Cilj istraživanja bio je ukloniti histonsku oznaku H3K4me3 u promotorskoj regiji gena B4GALT1 pomoću fuzijskog proteina RIOX1-dSpCas9 navođenog na specifičnu regiju sa šest različitih molekula sgRNA (od engl. single guide RNA). Također, cilj je bio dizajnirati testove za analizu stupnja metilacije pirosekvenciranjem ove regije. Metodom kromatinske precipitacije CUT&RUN, nakon koje slijedi qPCR, utvrđeno je da nije došlo do statistički značajnog smanjenja u količini histonske oznake H3K4me3 kao ni do povećanja stupnja metilacije DNA u analiziranoj regiji. Metodom kvantitativnog PCR je utvrđeno da nije došlo do promjene u genskoj ekspresiji. Gen B4GALT1 ima složenu genetičku i epigenetičku regulaciju, a efekt fuzijskog proteina RIOX1-dSpCas9 mogao je ostati nezapažen zbog uskog područja koje je analizirano, ali i zbog već prisutnih epigenetičkih modifikacija i strukture kromatina koji su mogli onemogućiti njegovo vezanje ili katalitičku aktivnost.Gene expression is regulated by six epigenetic mechanisms that work simultaneously. Their interactions as well as their effects on the transcriptional status of a certain gene are specific and depend on chromatin context. The goal of this research was to remove the histone mark H3K4me3 from the promoter region of the B4GALT1 gene using the fusion protein RIOX1-dSpCas9, which was guided to a specific region by six different sgRNA molecules. Also, the goal was to design assays for pyrosequencing in order to analyze DNA methylation level in this region. The CUT&RUN chromatin precipitation method followed with qPCR revealed no statistically significant change in the amount of histone mark H3K4me3 nor in DNA methylation level of the analyzed region. Quantitative PCR showed no change in the the B4GALT1 gene transcriptional activity. The B4GALT1 gene has complex genetic and epigenetic regulation, and the effect of the RIOX1-dSpCas9 fusion protein could have gone unnoticed due to the narrow region in the gene promoter that was analyzed. Also, the already present epigenetic modifications and chromatin structure in the targeted region could have prevent the binding or catalytic activity of RIOX1-dSpCas9
Morphological changes of beaches in Makarska littoral
No full textU razdoblju od 1951. do 2023. godine analizirane su morfološke promjene triju žala: Plišivac, Minerva i Frara na području Makarskog primorja. Analize su temeljene na satelitskim (Google Earth) i ortofoto snimkama (DGU), a načinjene su u ArcGIS Pro i Agisoft softwareu. Analize su pokazale značajne promjene površina žala Plišivac tijekom posljednjih ~70-tak godina, u rasponu od 2 434,54 m2 do 3 958,83 m2 kod žala Plišivac, a od 452,32 m2 do 3 465,85 m2 kod žala Minerva. U istom razdoblju, žalo Frara bilježi samo manje promjene površine, od 825,08 m2 do 1181,1 m2. Razlog različite morfodinamike istraživanih žala je u značajnim antropogenim utjecajima na žalima Plišivac i Minerva gdje je došlo do višekratnih dohranjivanja žala, dok je žalo Frara nedostupno i potpuno prirodno. Osim faza naglog rasta površina žala, što možemo povezati s fazama dohranjivanja, analize pokazuju i epizode erozije koje su slijedile nakon dohranjivanja žala. Zbog dostupnosti velikog broja snimaka s poznatim datumom snimanja Google Earth snimke imale su najveći značaj u analizi promjena površine žala na istraživanom području.In the period from 1951 to 2023, the morphological changes of three beaches: Plišivac, Minerva and Frara were analysed in the Makarska littoral. The analyses are based on satellite (Google Earth) and orthophoto images (State Geodetic Administration) and were made in ArcGIS Pro and Agisoft software. The analyses have shown that the area of Plišivac beach has changed significantly in the last ~ 70 years, from 2,434.54 m2 to 3,958.83 m2 on Plišivac beach and from 452.32 m2 to 3,465.85 m2 on Minerva beach. In the same period, Frara beach showed only minor changes, from 825.08 m2 to 1181.1 m2. The reason for the different morphodynamics of the studied beaches is the significant anthropogenic influence on Plišivac and Minerva beaches, where there have been repeated nourishments, while Frara beach is inaccessible and completely natural. In addition to the phases of sudden growth of the beach surface, which we can associate with phases of nourishments, the analyses also show episodes of beach erosion that followed. Due to the availability of a large number of images with a known date of acquisition, the Google Earth records had the greatest importance in the analysis of morphological changes of beaches in the studied area
The effect of microplastics on oxidative stress appearance and activity of antioxidant enzymes in duckweed (Lemna minor L.)
No full textPlastika je postala neizostavan materijal u svakodnevnom životu čovjeka, s masovnom proizvodnjom koja je i dalje u porastu, a potaknuta je svojstvima poput mekoće, prozirnosti i ekonomske isplativosti. Zbog rastuće proizvodnje i primjene, nepravilno zbrinjavanje plastike i usitnjavanje na manje čestice poput mikroplastike (MPs) predstavlja ozbiljan problem zbog potencijalnog unosa u biljke i životinje, a u konačnici i čovjeka. U ovom radu, ispitan je utjecaj MPs od dvije vrste polimera, polistirena (PS-MPs) i polimetil metakrilata (PMMA-MPs), na pojavu oksidacijskog stresa u vodenoj leći (Lemna minor). Analiziran je sadržaj vodikovog peroksida (H2O2), oštećenja lipida i proteina te promjene u aktivnosti antioksidacijskih enzima i sadržaju neenzimskog antioksidansa prolina. Sadržaj H2O2 je porastao u tretmanu s PS-MPs najviše koncentracije, dok ostali tretmani nisu rezultirali značajnim promjenama u odnosu na kontrolu. Niti u jednom ispitanom tretmanu nisu zabilježena značajna oštećenja lipida i proteina kao ni promjene u aktivnosti antioksidacijskih enzima superoksid dismutaze (SOD) i katalaze (CAT). Iako izlaganje biljaka vodene leće česticama MPs nije rezultiralo povećanjem aktivnosti askorbat (APX) i pirogalol peroksidaze (PPX) u odnosu na kontrolu, pri višim koncentracijama tretmana PS-MPs pokazale su značajno povećanje u usporedbi s PMMA-MPs. S druge strane, povećani sadržaj prolina pri najvećoj ispitanoj koncentraciji zabilježen je samo za PMMA-MPs. Rezultati pokazuju da oba tipa MPs aktiviraju antioksidacijski sustav vodene leće, pri čemu je aktivacija enzima jača s PS-MPs, dok PMMA-MPs imaju veći utjecaj na neenzimski antioksidans prolin.Plastic has become an indispensable material in everyday human life and its mass production continues to increase because of its softness, transparency and economic viability. Due to increasing production and use, improper plastic disposal and fragmentation into smaller particles such as microplastics (MPs) pose a serious problem because of their potential intake by plants and animals, ultimately affecting humans. In this study, the effects of MPs from two types of polymers, polystyrene (PS-MPs) and polymethyl methacrylate (PMMA-MPs), on the occurrence of oxidative stress in duckweed (Lemna minor) were investigated. The content of hydrogen peroxide (H2O2), lipid and protein damage as well as changes in the activities of antioxidant enzymes and the content of the non-enzymatic antioxidant proline were analyzed. The H2O2 content increased in the treatment with the lowest PS-MPs concentration, while other treatments showed no significant changes compared to the control. No significant lipid and protein damage or changes in the activities of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) were recorded in any of the treatments studied. Although duckweed exposure to MPs did not result in increased activity of ascorbate (APX) and pyrogallol peroxidase (PPX) compared to the control, higher concentrations of PS-MPs treatment showed a significant increase compared to PMMA-MPs. On the other hand, increased proline content at the highest examined concentration was only observed in PMMA-MPs. The obtained results indicate that both types of MPs activate the antioxidant system of duckweed, with PS-MPs a stronger enzyme activation, while PMMA-MPs have a greater impact on non-enzymatic antioxidant proline
Oleotourism development potential in Istria County
No full textMaslinarski turizam novi je specifični oblik turizma koji se počinje razvijati u Istarskoj županiji. Bazira se na sudjelovanju posjetitelja u aktivnostima koje se temelje na valorizaciji maslinarske i uljarske baštine te uživanju maslinovog ulja i predstavlja način diversifikacije aktivnosti kojima se bave maslinarska poljoprivredna gospodarstva. Cilj ovog diplomskog rada bila je identifikacija jedinica lokalne samouprave Istarske županije s najvećim potencijalom razvoja maslinarskog turizma na temelju kvantitativne metodologije, i to kroz određivanje varijabli, odnosno statističkih pokazatelja, koje utječu na stupanj razvoja maslinarskog turizma, i izračun njihovih vrijednosti iz prikupljenih podataka. Velika količina podataka, odnosno oni koji se odnose na ponudu aktivnosti maslinarskog turizma, način njihove promidžbe te opremljenosti poljoprivrednih gospodarstava, prikupljeni su anketnim istraživanjem. Stupanj razvoja, predstavljen kroz izračunati kompozitni indeks, je kasnije stavljen u odnos s statističkim pokazateljima demografskog, prometnog, turističkog i maslinarskog razvoja provođenjem klaster analize koja je izdvojila pet različitih tipova područja u Istarskoj županiji ovisno o sedam izabranih varijabli.Oleotourism is a new specific type of tourism developing in the Istria County. It is based on the participation of visitors in activities that valorize olive farming and production, as well as olive heritage and the enjoyment of olive oil, and is a way of diversifying the activities of olive farms. The aim of this thesis was to identify the local self-government units of Istria County with the greatest potential for the development of oleotourism based on quantitative methodology, through the determination of variables, i.e. statistical indicators, which influence the level of development of oleotourism, and the calculation of their values from the collected data. A large amount of data, i.e. those related to the offer of olive tourism activities, the way of their promotion and the equipment of olive farms, were collected through survey research. The degree of development, presented through the calculated composite index, was later put into relation with statistical indicators of demographic, traffic, tourism and olive growing development by conducting a cluster analysis that distinguished five different types of areas in the Istria County based on seven selected variables
Mineralogical characteristics of the Miocene deposits near Voćin
No full textNa temelju snimljenog detaljnog geološkog stupa te laboratorijskih analiza uzoraka, utvrđeno je da se osamnaestak metara debeli slijed naslaga na stupu Daljinac-I sastoji od pet različitih litofacija: lapora (F1), biokalkarenita/biokalcirudita (F2), gline (F3), pijeska i pješčenjaka (F4), i pločastog vapnenca (F5). Lapor (F1) iz donjeg dijela profila je bijele boje, masivnog izgleda i bogat mikrofoslinom zajednicom foraminifera, iz središnjeg dijela stupa je sivo ili hrđastosmeđe obojen s jasno izraženom horizontalnom laminacijom i siromašan foraminiferama, dok je lapor iz gornjeg dijela stupa svijetložute ili sive boje, masivnog izgleda i sadrži mikrofosilnu zajednicu ostrakoda. Biokalkareniti/biokalciruditi (F2) se pojavljuju u donjem dijelu profila u obliku slojeva centimetarsko-decimetarskih debljina, a sastoje se fosilnog kršja mekušaca, crvenih algi, mahovnjaka, ježinaca i foraminifera. Facijes glina (F3) debljine je tridesetak centimetara, a pretežito je sastavljen od smektitne gline koja vjerojatno predstavlja alteracijski produkt piroklastičnog materijala. Facijes pijeska i pješčenjaka pojavljuje se u središnjem dijelu stupa u obliku centimetarskih slojeva unutar facijesa lapora. Pješčenjaci su određeni kao grauvake, dok je pijesak loše sortiran i mjestimice koso uslojen. Sastav detritusa ukazuje na porijeklo materijala iz magmatskih i metamofnih stijena jezgre Papuka koje pripadaju podlozi Panonskog bazena. Pločasti vapnenci (F5) iz gornjeg dijela stupa su bijele ili svjetložute boje, sadrže ostatke fosilnih mekušaca i ostrakode koji indiciraju taloženje u litoralnom-sublitoralnom dijelu brakičnog jezera. Litološke značajke, fosilni sadržaj i vertikalni raspored facijesa na stupu Daljinac ukazuje da je taloženje naslaga započelo krajem badena u plitkom marinskom okolišu i bilo je praćeno slabim vulkanizmom. Kontinuirano se nastavilo i tijekom sarmata kada su uvjeti za život marinskih organizama bili znatno nepovoljniji, a završilo u ranom panonu u plitkom boćatom jezerskom okolišu. Svega osamnaest metara debeli slijed naslaga zabilježio je ključne transformacije okoliša u Sjevernohrvatskom bazenu, od plitkog marinskog okoliša Središnjeg Paratethysa u srednjem miocenu do bočatog okoliša Panonskog jezera u kasnom miocenu.Based on the recorded detailed geological column and laboratory analysis of samples, it has been determined that the sequence of layers, about eighteen meters thick in the Daljinac-I column, consists of five different lithofacies: limestone (F1), biocalcarenite/biocalcirudite (F2), clay (F3), sandstone (F4), and platy limestone (F5). The limestone (F1) from the lower part of the profile is white, massive in appearance, and rich in a microfossil community of foraminifera. In the central part of the column, it is gray or rust-brown with well-defined horizontal lamination and poor in foraminifera, while the limestone from the upper part of the column is light yellow or gray, massive in appearance, and contains a microfossil community of ostracods. Biocalcarenites/biocalcirudites (F2) appear in the lower part of the profile as layers of centimeter-to-decimeter thickness and consist of fossilized fragments of mollusks, red algae, bryozoans, echinoids, and foraminifera. The clay facies (F3) is about thirty centimeters thick and consists mainly of smectitic clay, which likely represents an alteration product of pyroclastic material. The sandstone facies (F4) appears in the central part of the column as centimeter-thick layers within the limestone facies. The sandstones are identified as graywackes, while the sand is poorly sorted and occasionally cross-bedded. The detrital composition suggests a provenance from the magmatic and metamorphic rocks of the Papuk core belonging to the basement of the Pannonian Basin. The platy limestones (F5) from the upper part of the column are white or light yellow and contain remains of fossilized mollusks and ostracods, indicating deposition in the littoral-sublittoral part of a brackish lake. The lithological features, fossil content, and vertical arrangement of facies in the Daljinac column indicate that sedimentation of the layers began in the late Badenian in a shallow marine environment and was accompanied by weak volcanism. It continued continuously during the Sarmatian when the conditions for marine life were significantly unfavorable, and ended in the early Pannonian in a shallow, lagoon-like lake environment. The eighteen-meter-thick sequence of layers recorded key environmental transformations in the North Croatian Basin, from the shallow marine environment of the Central Paratethys in the middle Miocene to the lagoon environment of the Pannonian Lake in the late Miocene
The role of aminoacyl-tRNA synthetases in cellular oxidative stress response
No full textAminoacil-tRNA-sintetaze (AARS) su enzimi koji kataliziraju nastanak kovalentne veze između pripadne aminokiseline i tRNA pri čemu nastaje aminoacil-tRNA, supstrat u procesu translacije. Citosolne AARS zbog redukcijskog okoliša inače nemaju disulfidnu vezu, no pronađena je u kristalnoj strukturi citosolne seril-tRNA-sintetaze (SerRS) iz biljke Arabidopsis thaliana. U ovom radu dizajnirane su jednostruko (SerRS_C213S, SerRS_C244S) i dvostruko mutirane inačice (SerRS_C213S/C244S) i pokazano je da dolazi do reverzibilnog nastajanja disulfidne veze što omogućuje enzimu nepromijenjenu aktivnost u oksidacijskom stresu. Također je istražen utjecaj mistranslacije uzrokovane ugradnjom valina (Val) ili norvalina (Nva) umjesto izoleucina na odgovor na oksidacijski stres. U tu svrhu korišteni su sojevi bakterije Escherichia coli koji eksprimiraju izoleucil-tRNA-sintetazu s inaktiviranom domenom za popravak pogreške (PS7066 i ED-). Rezultati su pokazali da prethodni uzgoj stanica u mistranslatirajućim uvjetima do stacionarne faze uzrokuje bolje preživljenje i rast u oksidacijskom stresu u odnosu na stanice koje nisu rasle u mistranslatirajućim uvjetima. Nadalje, uočeno je da uzgoj stanica s inaktiviranim RpoS-om u mediju s višim koncentracijama valina ili norvalina izaziva adaptaciju na oksidacijski stres koja je neovisna o RpoS-u, dok stanice uzgojene pri nižim koncentracijama valina ili norvalina ne preživljavaju u uvjetima oksidacijskog stresa.Aminoacyl-tRNA synthetases (AARS) are enzymes that catalyze covalent bond formation between cognate amino acid and tRNA to produce aminoacyl-tRNA - substrate in the translation process. Due to the reductive environment, cytosolic AARSs do not have disulfide bonds, however, one was found in the crystal structure of cytosolic seryl-tRNA synthetase (SerRS) from the plant Arabidopsis thaliana. In this study, point (SerRS_C213S, SerRS_C244S) and double mutants (SerRS_C213S/C244S) were designed and it was shown that the reversible disulfide bond formation allows unchanged enzyme activity under oxidative stress. Also, the effect of isoleucine-to-valine (Val) or norvaline (Nva) mistranslation on oxidative stress response was investigated. For this purpose, Escherichia coli strains expressing isoleucyl-tRNA synthetase with a mutation in the editing domain were used (PS7066 and ED-). The results show that prior cell growth in mistranslating conditions to stationary phase leads to higher survival and growth rates under oxidative stress compared to cells that were not grown in mistranslating conditions. Furthermore, it was shown that prior growth of cells with inactivated RpoS in media with higher concentrations of Val or Nva leads to adaptation to oxidative stress that is RpoS- independent, while the cells grown with lower concentrations of Val or Nva do not survive in oxidative stress conditions
Thermodynamic and structural characterization of cyclopeptide complexes with colorimetric and fluorescent anionic dyes
No full textU ovom su radu ispitana spektroskopska i strukturna svojstva te termodinamička stabilnost kompleksa homociklopentapeptida s kolorimetrijskim i fluorescentnim anionskim bojama u acetonitrilu pomoću spektrofluorimetrijskih i spektrofotometrijskih titracija i simulacija molekulske dinamike. Kao ciklopeptidi korišteni su ciklopentafenilalanin, ciklopentaleucin i derivat ciklopentalizina čije su amino skupine na bočnim ograncima zaštićene BOC skupinama. Kao reprezentativni anioni sulfonatnih fluorescentnih boja korišteni su 8-anilino-1-naftalensulfonska kiselina i alizarin crveno S, a kao reprezentativni anion sulfonatnih kolorimetrijskih boja korišten je metiloranž. Kao reprezentativni anioni karboksilatnih fluorescentnih boja korištene su N-acetilirane aromatske amino kiseline triptofan i fenilalanin. Rezultati upućuju na stvaranje stabilnih kompleksa između ciklopepentaleucina i derivata ciklopentalizina sa sulfonatnim i karboksilatnim fluorescentnim i kolorimetrijskim bojama, dok je u slučaju ciklopentafenilalanina afinitet prema fluorescentnim karboksilatnim bojama nešto viši. Kod nastalih kompleksa ciklopeptida s fluorescentnim sulfonatnim i karboksilatnim bojama u većini slučajeva opažena je značajna razlika u molarnim spektrima kompleksa, dok ta razlika nije uočena kod kompleksa s kolorimetrijskom sulfonatnom bojom. Također, rezultati provedenih MD simulacija u otapalu upućuju na koordinaciju aniona preko amidnih protona ciklopeptida.In this work, spectroscopic and structural properties, as well as thermodynamic stability of homocyclopentapeptide complexes with colorimetric and fluorescent anionic dyes in acetonitrile were examined by means of spectrofluorimetric and spectrophotometric titrations and molecular dynamics simulations. As cyclopeptides, cyclopentaphenylalanine, cyclopentaleucine and cyclopentalysine derivative with BOC protected amino group side chains were used. 8-anilino-1-naftalenesulfonic acid and alizarin red S were used as sulfonic fluorescent dyes representatives, while methyl orange was used as sulfonic colorimetric dye representative. N-acetylated aromatic amino acids tryptophan and phenylalanine were used as carboxylic fluorescent dyes representatives. The results indicate that both of cyclic peptides form stabile complexes with fluorescent and colorimetric sulfonic and carboxylic dyes, while the affinity of cyclopentaphenylalanine towards fluorescent carboxylic dyes is somewhat higher. In most cases a significant difference in molar spectra of fluorescent dye complexes with both peptides were observed. That significant difference was not observed with colorimetric anion dye complexes. Also, the results obtained by MD simulations indicate that the anions are coordinated by the amide protons of the peptide