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Međudjelovanje električno pobudljivih stanica i fotokondenzatora
No full textThis thesis investigates the interaction between electrically excitable cells and organic electrolytic photocapacitor (OEPC) devices, with the goal of enhancing photocapacitive stimulation for neurostimulation applications. The study takes a multidisciplinary approach, combining materials science, biophysics, and computational modeling to refine OEPC design and better understand the mechanisms underlying their interaction with biological tissues. The original research contributions include improvements in OEPC device design and geometry, optimization of organic semiconductor layer thickness, and the incorporation of advanced return electrode materials such as PEDOT:PSS. This thesis presents a key discovery: 2D structuring and the adoption of an "inverted" OEPC geometry can enhance electric field strength by up to 20 times, enabling precise single-cell stimulation with high spatial resolution. A comprehensive numerical model was developed to simulate extracellular stimulation of excitable cells, incorporating three subunits: the device model, the electrode-electrolyte interface model, and the target cell model. Finite element simulations demonstrate that capacitive microelectrodes exhibit lower stimulation thresholds than Faradaic electrodes when in close proximity to the target cell. The model also validates that photocapacitive devices can effectively stimulate neurons under sufficiently high illumination intensities, provided the cells are tightly attached to the device surface. This research concludes that OEPCs, especially those with inverted geometries and PEDOT:PSS coatings, significantly enhance spatial resolution and stimulation efficiency, highlighting their potential for wireless, minimally invasive neurostimulation applications.Cilj ovog doktorskog rada je detaljno istražiti međudjelovanje fotokondenzatorskih uređaja i električki pobudljivih stanice poput neurona. Ovoj temi pristupamo korištenjem različitih pristupa, od optimizacije samog uređaja u vidu dizajna, geometrije i odabira materijala, biofizičkim modeliranjem stanica radi boljeg razumijevanja praga aktivacije potrebnog za učinkovitu stimulaciju, modeliranjem sučelja između elektrode i stanice kako bi se osiguralo djelotvorno prenošenje podražaja te u konačnici i izradom samih uređaja. Kako bi se svi ovi aspekti mogli u potpunosti istražiti, nužno je usvojiti multidisciplinarni pristup koji uključuje stručnost iz područja biofizike, znanosti o materijalima i medicin
Petrographic and sedimentological characteristics of gravel on artificial Ploče beach (Rijeka)
No full textProvedeno je istraživanje petrografskih i sedimentoloških karakteristika šljunka umjetne plaže Ploče. Sedimentološka analiza provedena je direktnim mjerenjem prikupljenih 105 valutica uz pomoć pomičnog digitalnog mjerila. Utvrđene su tri granulometrijske frakcije: 16-32 mm (1 %), 32-64 mm (94 %) te 64-128 mm (5 %) te se odabrani materijal karakterizira kao vrlo krupni šljunak koji je dobro sortiran i simetrične krivulje. Petrografskom analizom, koja je provedena mikroskopskim i makroskopskim promatranjima valutica i njihovih izrađenih preparata, utvrđeno je da se odabrane nekarbonatne valutice mogu svrstati kao metagranitne valutice i valutice efuzivnih stijena koje potječu iz dravskih terasa te kao takve, ne pripadaju originalnom materijalu plaže Ploče.A study was conducted on the petrographic and sedimentological characteristics of the gravel from the artificial Ploče Beach. The sedimentological analysis was performed by directly measuring 105 collected pebbles using a digital caliper. Three grain size fractions were identified: 16–32 mm (1%), 32–64 mm (94 %), and 64–128 mm (5%). The selected material is classified as very coarse gravel, which is well sorted with symmetrical curve. Petrographic analysis, carried out through microscopic and macroscopic observations of the pebbles and their prepared thin sections, showed that the selected non-carbonate pebbles can be classified as metagranitic and effusive rock pebbles. These originate from the Drava terraces and, as such, do not belong to the original material of Ploče Beach
The biochemical mechanisms of polysaccharide degradation in freshwater ecosystems
No full textSlatkovodni ekosustavi imaju ključnu ulogu u globalnom ciklusu ugljika, pri čemu bakterije razgrađuju polisaharide kroz mehanizme kolaboracije, oportunizma i sebičnosti. Utjecaj okolišnih čimbenika na strukturu mikrobnih zajednica istražen je prostorno-vremenskom analizom pomoću visoko protočnog sekvenciranja DNA. Mehanizmi razgradnje polisaharida praćeni su inkubacijama s fluorescentno označenim polisaharidima, dok su ključne bakterijske skupine identificirane kombinacijom sekvenciranja i fluorescencijske in situ hibridizacije. Sekvenciranjem metagenoma dodatno su otkriveni prostorno i sezonski specifični geni za razgrdanju ispitanih polisaharida. Rezultati su pokazali da mikrobne zajednice slatkovodnog povezanog ekosustava, unatoč sezonskim promjenama, zadržavaju stabilnost kroz temeljni središnji mikrobiom. Dokazana je i prisutnost sebičnog mehanizma razgradnje polisaharida, s varijacijama između jezera različitih trofičkih stanja i sezona. Bakterije iz koljena Bacteroidota, Planctomycetota, Proteobacteria i Verrucomicrobiota odgovorne su za razgradnju polisaharida. Ova disertacija produbljuje razumijevanje uloge mikrobnih zajednica u razgradnji polisaharida, ključnih za kruženje ugljika unutar slatkovodnih ekosustava.Freshwater ecosystems play a key role in the global carbon cycle, where bacteria degrade polysaccharides through sharing, scavenging and selfish mechanisms. Environmental influence on microbial community structures was investigated through spatiotemporal analysis using high-throughput DNA sequencing. Polysaccharide degradation mechanisms were tracked using fluorescently labelled polysaccharides incubations, while bacteria involved were identified through a combination of sequencing and fluorescence in situ hybridization. Metagenomic sequencing revealed spatially and seasonally specific genes responsible for the polysaccharide degradation. The results revealed stabile microbial communities in the freshwater network ecosystem through core microbiome, despite seasonal variations. Polysaccharide degradation thorough selfish mechanism among bacteria was proven, varying across lakes with different trophic states and seasons. Bacteria from the phyla Bacteroidota, Planctomycetota, Proteobacteria, and Verrucomicrobiota were identified as key polysaccharide degraders. This dissertation advances understanding of microbial role in polysaccharide degradation, an essential process for carbon cycling within freshwater ecosystem
IgG glycosylation in women: Puberty, pregnancy, and menopause
No full textImunoglobulin G (IgG) najzastupljenija je izoforma imunoglobulina u krvotoku čovjeka. Nglikani vezani na IgG utječu na efektorske funkcije ovog antitijela i na taj način reguliraju
imunološki odgovor. Kompozicija IgG glikoma značajno se mijenja u pubertetu, trudnoći i
menopauzi kao direktna posljedica promjena u koncentraciji estrogena. Međutim, točni
mehanizmi kojima estrogen dovodi do promjene glikozilacije IgG-a nisu poznati. Cjelogenomske
studije povezanosti su otkrile kako je gen ABCF2 reguliran estrogenom uključen u glikozilaciju
IgG-a. Kako bismo potvrdili ulogu gena ABCF2 u tom procesu, povećali smo njegovu ekspresiju
u staničnoj liniji FreeStyle-293-F koja stabilno eksprimira fuzijski protein dCas9-VPR i luči
molekule IgG u stanični medij. Povećana ekspresija gena ABCF2 nakon manipulacije stanica
alatom CRISPR/dCas9-VPR rezultirala je povećanom razinom galaktoziliranih glikoformi IgG-a
(G1 i G2) i istovremenim smanjenjem agalaktoziliranih glikoformi IgG-a (G0) što sugerira da
ABCF2, gen reguliran estrogenom, najvjerojanije sudjeluje u regulaciji glikozilacije IgG-a.Immunoglobulin G (IgG) is the most abundant immunoglobulin isoform in the human
bloodstream. Different N-glycans attached to IgG directly influence this antibody's effector
functions and regulate the immune response. IgG glycome composition is changed significantly
during puberty, pregnancy, and menopause, as a direct consequence of the change in estrogen
concentration. However, the exact mechanisms by which estrogen modulates IgG glycosylation
are unknown. Genome-wide association studies have shown that the estrogen-regulated gene
ABCF2 is associated with IgG glycosylation. To functionally validate the role of the ABCF2 gene
in this process, I overexpressed it in the FreeStyle-293-F cell line that stably expresses the dCas9-
VPR fusion protein and secretes IgG. Overexpression of the ABCF2 gene resulted in an increased
level of galactosylated IgG glycoforms (G1 and G2) and a simultaneous decrease in
agalactosylated glycoforms of IgG (G0), suggesting that estrogen-regulated gene ABCF2 has a
role in the regulation of IgG glycosylation
Characterization of human osteoblasts isolated from fresh and frozen bone tissue
No full textPoznavanje građe koštanog tkiva i razumijevanje funkcije stanica i signalnih molekula važno
je za napredak regenerativne medicine. Kosti su najčešće transplantirana muskuloskeletna
tkiva. Autologne kosti smatraju se zlatnim standardnom osiguravajući osteogenezu,
osteokondukciju i osteoindukciju. Krioprezervacijom 10%-tnim dimetil sulfoksidom (DMSO),
tkiva se dugotrajno pohranjuju na ultraniskim temperaturama < -80 °C s ciljem održavanja
vitalnosti stanica (npr. autologni osteohondralni graft). Korištenje autolognih kostiju je
limitirano, zato se koristi alogeno koštano tkivo (npr. glava bedrene kosti) osiguravajući
osteokondukciju i osteoindukciju. Pohranjuju se bez korištenja krioprotektanta na ultraniskim
temperaturama. Zamrzavanje ima mali utjecaj na mehanička svojstva koštanog tkiva te
umanjuje imunogenost. Kost je izgrađena od stanica osteoblasta, osteoklasta, osteocita i stanica
koje oblažu površinu kosti. Osteoblasti imaju ulogu u izgradnji, remodeliranju i regeneraciji
koštanog tkiva. Obzirom na potencijalno štetne i citotoksične učinke DMSO-a na pacijente,
važno je ispitati njegovo djelovanje na koštano tkivo i stanice jer uloga krioprotektanta kod
pohrane muskuloskeletnih tkiva nije u potpunosti jasna. U ovome istraživanju se ispituju i
uspoređuju citološka i molekularna svojstva osteoblasta izoliranih iz svježeg koštanog tkiva te
tkiva pohranjenog s i bez DMSO-a u periodu od 15 i 30 dana. Morfologija, vijabilnost,
mogućnost proliferacije i genska ekspresija osnovne su karakteristike stanica na koje
krioprotektant može imati utjecaja.Knowing the structure of bone tissue and understanding the function of cells and signaling
molecules is important for the progress of regenerative medicine. Bones are the most frequently
transplanted musculoskeletal tissues. Autologous bone is considered the gold standard,
providing osteogenesis, osteoconduction and osteoinduction. By cryopreservation with 10%
dimethyl sulfoxide (DMSO), tissues are stored for a long time at ultra-low temperatures < -80
°C with the aim of maintaining cell vitality (eg autologous osteochondral graft). The use of
autologous bones is limited, that's why allogeneic bone tissue (eg femoral head) is used,
ensuring osteoconduction and osteoinduction. They are stored without the use of
cryoprotectants at ultra-low temperatures. Freezing has little effect on the mechanical properties
of bone tissue and reduces immunogenicity. Bone is made up of osteoblasts, osteoclasts,
osteocytes and bone lining cells. Osteoblasts play a role in the construction, remodeling and
regeneration of bone tissue. Considering the potentially harmful and cytotoxic effects of DMSO
on patients, it is important to examine its effect on bone tissue and cells, because the role of
cryoprotectants in the storage of musculoskeletal tissues is not entirely clear. In this research,
the cytological and molecular properties of osteoblasts isolated from fresh bone tissue and tissue
stored with and without DMSO for a period of 15 and 30 days are examined and compared.
Morphology, viability, the possibility of proliferation and gene expression are the basic
characteristics of cells on which the cryoprotectant can have an effect
Transfer of chemical contaminants across food chains from freshwater to terrestrial ecosystems
No full textOnečišćenje okoliša je kontinuirani proces koji se smatra jednim od najvećih problema s kojima
se suvremeno društvo suočava, a posljedično dovodi do štetnog utjecaja na zdravlje ljudi, životinja
i biljaka. Tvari koje uzrokuju proces onečišćenja zovemo onečišćivala. Onečišćivala se dijele na
anorganske i organske. Prijenos kemijskih onečišćivala putem hranidbenih lanaca najčešće se
odvija bioakumulacijom, biokoncentracijom, biomagnifikacijom i bioamplifikacijom. Vodeni
kukci su upravo ti koji povezuju vodene i kopnene hranidbene mreže obzirom da njihov životni
ciklus uključuje vodene i kopnene faze života, stoga predstavljaju važnu međustanišnu vezu preko
koje se odvija protok energije i hranjivih tvari, ali i prijenos zagađivača u druge ekosustave. Zbog
svega navedenoga, potreban je interdisciplinaran pristup za istraživanje ekoloških i evolucijskih
učinaka onečišćivala u okolišu, što pruža osnovu za njihovo praćenje, posebice u slatkovodnim
ekosustavima gdje su učinci onečišćenja posebno kritični.Environmental pollution represents an ongoing and challenging issue, making it one of the
foremost problems faced by society today. It has far-reaching negative impacts on the well-being
of humans, animals, and plants alike. Substances that accelerate the pollution process are
commonly referred to as pollutants, which can be categorized into two primary groups: inorganic
and organic pollutants. The transfer of chemical pollutants within ecosystems predominantly
occurs through processes such as bioaccumulation, bioconcentration, biomagnification and
bioamplification. Aquatic insects connect aquatic and terrestrial food webs, since their life cycle
includes aquatic and terrestrial life stages, therefore they represent an important interhabitat link
through which the flow of energy and nutrients takes place, as well as the transfer of pollutants to
other ecosystems. Consequently, an interdisciplinary approach is needed to investigate ecological
and evolutionary impacts of contaminants, which provides the foundation for biomonitoring
effects, particularly in freshwater ecosystems where the impacts of pollution are especially critical
The role of estrogen and estrogen receptors in the metastatic potential of head and neck tumors
No full textMuškarci imaju dva do četiri puta veći rizik od razvijanja tumora glave i vrata (TGV) od žena,
neovisno o etiološkom agensu. Stoga se smatra da izloženost estrogenu ženama pruža zaštitu
od nastanka i metastaziranja TGV. Estrogeni svoju funkciju ostvaruju vezanjem za receptore
estrogena, koji se mogu podijeliti na jezgrene (ERα i ERβ) i membranske receptore estrogena
(GPER1 i NaV1.2). Vezanjem estrogena dolazi do aktivacije transkripcije određenih gena i/ili
signalnih kaskada, koje naposlijetku utječu na gensku ekspresiju. Metodom RT-qPCR određen
je ekspresijski profil gena za receptore estrogena u uzorcima zdrave sluznice usne šupljine,
primarnih tumora i metastatskih limfnih čvorova te u staničnoj liniji Detroit 562 nakon tretmana
17β-estradiolom. Pomoću testa zacjeljivanja rana provjerena je migracijska sposobnost stanica
nakon tretmana 17β-estradiolom i tamoksifenom. Rezultati su pokazali da bi ERα i ERβ mogli
imati ulogu u razvoju TGV, ali da tamoksifen vjerojatno nije pogodan oblik liječenja TGV.Men are at a two- to fourfold higher risk of developing head and neck cancers (HNC) than women, regardless of aetiological agent. Therefore, estrogen is considered to provide protection from HNC development and metastasis in women. Estrogens exert their function by binding to estrogen receptors, which can be divided into nuclear (ERα and ERβ) and membrane estrogen receptors (GPER1 and NaV1.2). Estrogen binding activates the transcription of certain genes and/or signaling cascades, which ultimately regulate gene expression. RT-qPCR was used to determine the expression profile of estrogen receptor genes in healthy mucosa, primary tumor and metastatic lymph node samples as well as the cell line Detroit 562 after 17β-estradiol treatment. The wound healing assay was used to study cell migration after 17β-estradiol and tamoxifen treatment. Results showed that ERα and ERβ might be involved in HNC development, but tamoxifen probably isn't a suitable treatment option for HNC
Study of the evolution of the number of chromosomes in healthy and tumor cells using the macrokaryotype concept
No full textStanična dioba je proces od temeljne važnosti za život čiji je ispravan tijek nužan za propagaciju roditeljskog kariotipa, skupa kromosoma u stanici, u novonastalim stanicama kćerima. Ipak, moguć je nastanak pogrešaka tijekom diobe. Jedna od pogrešaka do koje može doći jest nepravilna raspodjela kromosoma. Ona dovodi do odstupanja kariotipa stanica kćeri od kariotipa roditeljskih stanica. Promjena kariotipa stanica nekih mikroorganizama može služiti boljoj prilagodbi tih organizama na okolinu, a u stanicama sisavaca može promovirati tumorigenezu. Dugodose žne posljedice pogrešne podjele kromosoma i drugih procesa na evoluciju kariotipa nisu potpuno istražene. Da bi se identificirali temeljni mehanizmi koji su zaslužni za odredeni tijek evolucije kariotipa populacije stanica, praktično je koristiti matematičke modele. U ovom radu korišten je koncept makrokariotipa za vizualizaciju evolucije populacije stanica kvasca primjenom na rezultate iz literature. Pronadeno je da se u početku evolucije pojavljuju kariotipi koji imaju kombinacije isključivo 3 i 4 kopije kromosoma, što sugerira da stanice zadržavaju uravnotežen broj kromosoma. Korištenjem pristupa srednjeg polja odredena je dinamika evolucije kariotipa te je pronadeno da upravo stanice koje imaju 3 i 4 kopije kromosoma moraju biti one koje su najbolje prilagodene okolini - moraju imati najveći stanični fitness. Zaključno, eksperimenti i teorija sugeriraju da uravnotežen sastav kariotipa odreduje smjer evolucije populacije stanica kvasca.Cell division is a process of fundamental importance for life, the correct course of which is necessary for the propagation of the parental karyotype, the set of chromosomes in the parent cell, in newly formed daughter cells. However, errors may occur during division. One of the errors that can occur is the irregular distribution of chromosomes. It leads to the deviation of the karyotype of the daughter cells from the karyotype of the parent cells. Changes in the karyotype of the cells of some microorganisms can serve the purpose of better adaptation of the organisms to their environment, on the other hand, in mammalian cells such changes can promote tumorigenesis. The long-term consequences of missegregation and other processes on karyotype evolution are not fully understood. To identify the fundamental mechanisms that are responsible for a certain course of evolution of the karyotype of a population of cells, it is practical to use mathematical models. In this work, the macro-karyotype concept was used for visualizing the evolution of the yeast cell population by applying the concept to results from the literature. Karyotypes with combinations of only 3 and 4 copies of chromosomes were found early in evolution, suggesting that cells maintain a balanced number of chromosomes. Using the mean-field approach, the dynamics of karyotype evolution were determined and it was found that cells with 3 and 4 copies of chromosomes must be the ones that thrive in the given environment - they must have higher cell fitness. In conclusion, both experiments and theory suggest that a balanced karyotype composition determines the direction of yeast cell evolution
Plan upravljanja istraživačkim podacima - Livadni procjepak (Chouardia litardierei, Hyacinthaceae) kao istraživački sustav ekološke divergencije (IP-2020-02-8099)_2025
No full textPlan upravljanja istraživačkim podacima za istraživački projekt Hrvatske zaklade za znanost: Livadni procjepak (Chouardia litardierei, Hyacinthaceae) kao istraživački sustav ekološke divergencije (IP-2020-02-8099) za cjelokupno projektno razdoblje (01.01.2021. - 31.05.2025.)
GENETIC VARIABILITY AND PHYLOGENY OF EPSTEIN-BARR VIRUS IN INFECTIOUS MONONUCLEOSIS
No full textVirus Epstein-Barr (EBV) pripada porodici Orthoherpesviridae čiji se genom sastoji od
dvolančane linearne DNA. Temeljem varijabilnosti sekvencija pojedinih gena, EBV se
klasificira u različite tipove, podtipove i varijante. Ciljevi ovog istraživanja bili su odrediti
varijabilnost gena LMP-1, EBNA-1, EBNA-2, BLLF1 i promotora Zp u infektivnoj
mononukleozi (IM), filogenetskom analizom proučiti arhitekturu virusne populacije te
provjeriti mogućnost koinfekcije metodom sekvenciranja nove generacije u uzorcima s više
varijanti gena LMP-1. Najčešća varijanta gena LMP-1 bila je divlji tip, dok su druge varijante
(China1, Med-, North Carolina) i rekombinanti bili rjeđe zastupljeni. Analizom gena EBNA-1
dokazani su prototipovi P-ala i P-thr te novootkriveni polimorfizam Arg594Lys. Analizom
gena EBNA-2 dokazana su oba tipa virusa uz novotkrivenu adiciju Leu212. Najzastupljeniji
podtip gena BLLF1 bio je BLLF1-a s polimorfizmom Q201, dok je najčešća varijanta
promotora Zp bio Zp-P. Rezultati ovog rada pokazali su, po prvi puta, molekularnu raznolikost
EBV-a u IM u ovom geografskom području.Epstein-Barr virus (EBV) belongs to the Orthoherpesviridae family whose genome consists of
double-stranded linear DNA. Based on the variability of individual gene sequences, EBV is
classified into different types, subtypes and variants. The aims of this study were to determine
the variability of LMP-1, EBNA-1, EBNA-2, BLLF1 genes and Zp promoter in infectious
mononucleosis (IM), to study the architecture of the viral population by phylogenetic analysis,
and to check the possibility of co-infection using the new generation sequencing method in
samples with multiple variants of the LMP-1 gene. The most frequent variant of the LMP-1
gene was the wild type, while other variants (China1, Med-, North Carolina) and recombinants
were less frequently represented. The analysis of the EBNA-1 gene showed the presence of
prototypes P-ala and P-thr and the newly discovered polymorphism Arg594Lys. Analysis of
the EBNA-2 gene showed the presence of both viral types as well as newly discovered addition
of Leu212. The most frequent BLLF1 gene subtype was BLLF1-a with the Q201
polymorphism, while the most common variant of the Zp promoter was Zp-P. The results of
this study showed, for the first time, the extent of the molecular diversity of EBV in IM in this
geographical area