14 results on '"Sabolić, Iva"'
Search Results
2. Incorporating evolutionary based tools in cephalopod fisheries management
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Sabolić, Iva, Baltazar-Soares, Miguel, and Štambuk, Anamaria
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- 2021
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3. Plastic and genomic change of a newly established lizard population following a founder event.
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Sabolić, Iva, Mira, Óscar, Brandt, Débora Y. C., Lisičić, Duje, Stapley, Jessica, Novosolov, Maria, Bakarić, Robert, Cizelj, Ivan, Glogoški, Marko, Hudina, Tomislav, Taverne, Maxime, Allentoft, Morten E., Nielsen, Rasmus, Herrel, Anthony, and Štambuk, Anamaria
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LIZARD populations , *GENOTYPE-environment interaction , *HERITABILITY , *PHENOTYPIC plasticity , *POPULATION differentiation , *LACERTIDAE , *PHENOTYPES - Abstract
Understanding how phenotypic divergence arises among natural populations remains one of the major goals in evolutionary biology. As part of competitive exclusion experiment conducted in 1971, 10 individuals of Italian wall lizard (Podarcis siculus (Rafinesque‐Schmaltz, 1810)) were transplanted from Pod Kopište Island to the nearby island of Pod Mrčaru (Adriatic Sea). Merely 35 years after the introduction, the newly established population on Pod Mrčaru Island had shifted their diet from predominantly insectivorous towards omnivorous and changed significantly in a range of morphological, behavioural, physiological and ecological characteristics. Here, we combine genomic and quantitative genetic approaches to determine the relative roles of genetic adaptation and phenotypic plasticity in driving this rapid phenotypic shift. Our results show genome‐wide genetic differentiation between ancestral and transplanted population, with weak genetic erosion on Pod Mrčaru Island. Adaptive processes following the founder event are indicated by highly differentiated genomic loci associating with ecologically relevant phenotypic traits, and/or having a putatively adaptive role across multiple lizard populations. Diverged traits related to head size and shape or bite force showed moderate heritability in a crossing experiment, but between‐population differences in these traits did not persist in a common garden environment. Our results confirm the existence of sufficient additive genetic variance for traits to evolve under selection while also demonstrating that phenotypic plasticity and/or genotype by environment interactions are the main drivers of population differentiation at this early evolutionary stage. [ABSTRACT FROM AUTHOR]
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- 2024
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4. Plastic and genomic change of a newly established lizard population following a founder event
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Sabolić, Iva, primary, Mira, Óscar, additional, Brandt, Débora Y. C., additional, Lisičić, Duje, additional, Stapley, Jessica, additional, Novosolov, Maria, additional, Bakarić, Robert, additional, Cizelj, Ivan, additional, Glogoški, Marko, additional, Hudina, Tomislav, additional, Taverne, Maxime, additional, Allentoft, Morten E., additional, Nielsen, Rasmus, additional, Herrel, Anthony, additional, and Štambuk, Anamaria, additional
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- 2023
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5. Different approaches in microRNA analysis
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Jenko Bizjan, Barbara, Stančič, Bine, Sabolić, Iva, Štalekar, Maja, Prosenc Zmrzljak, Uršula, Jenko Bizjan, Barbara, Stančič, Bine, Sabolić, Iva, Štalekar, Maja, and Prosenc Zmrzljak, Uršula
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MicroRNA might serve as a predictive biomarker for treatment response in stem cell treatment in knee osteoarthritis. Different sample types are going to be collected to enlighten the true biological role. MicroRNA analysis necessitates diverse approaches based on the sample type. In this study, we examined microRNA profiles in plasma samples, synovial fluid, and adipose-derived fat tissue. We conducted a comparative analysis of different microRNA analysis methods to assess the data. The first approach involved a series of steps, including adapter trimming, quality filtering, size filtering, and mapping of all reads to the human reference genome (GRCh38.p12). Subsequently, genome-mapped reads were aligned to known miRNA sequences from miRBase. Reads that did not match miRNAs were subjected to further classification using additional databases, such as RNAcentral. The second pipeline also encompassed adapter trimming, quality filtering, and size filtering. Additionally, it involved collapsing individual reads into repeat sequences, followed by alignment to the mature index of miRBase. Unaligned reads were classified as isomiRs based on their alignment to the hairpin index of miRBase. We processed sequences from three plasma samples, three adipose fat tissue samples, and three synovial fluid samples. Although there were slight variations in microRNA read counts, the average ratio between counts was 0.92 (SD=0.29). Notably, the second pipeline yielded higher read counts compared to the first pipeline. The results obtained from both microRNA bioinformatic pipelines demonstrated similar outcomes, suggesting that the choice of pipeline is unlikely to have a significant impact on the derived biological insights.
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- 2023
6. Developing bioinformatics pipeline for processing environmental DNA metabarcoding sequencing data
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Sabolić, Iva, Markulin, Lucija, Muha, Teja Petra, Jenko, Barbara, Prosenc Zmrzljak, Uršula, Sabolić, Iva, Markulin, Lucija, Muha, Teja Petra, Jenko, Barbara, and Prosenc Zmrzljak, Uršula
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Environmental DNA (eDNA) is DNA present in an environmental sample, originating from any biological material released from organisms living in that environment. This DNA can be isolated, amplified, sequenced, and analyzed in order to examine the taxonomic richness and abundance of different organism groups in the targeted environment. Methods of eDNA metabarcoding thus offer a unique opportunity to systematically streamline and scale-up regular biological assessments across many different environments of interest. Recently, as a part of the project funded by European structural and investment funds, Labena d.o.o. company established a modern laboratory in Zagreb focused on the research and provision of services in the field of eDNA. In collaboration with the Institute Ruđer Bošković we have been working on developing tests for analysis of water quality based on the eDNA and, as part of the standardization and optimization of sample-to-results eDNA analysis process, we developed a custom bioinformatics pipeline to facilitate efficient and effective eDNA sequencing data analysis. The pipeline was was written in Bash and utilizes several different algorithms to filter, trim, merge, denoise and classify targeted eDNA sequences. Python-based scripts which allow automatically download, filter, and format the data available on various online platforms were included in the pipeline to facilitate the curation of custom reference databases needed for taxonomic classification of targeted organism groups. User-friendly and interactive pipeline report generation, comprised of both wet- and dry-lab step-bystep sample statistics and graphical representations or the main results, is supported using Rmarkdown and Plotly and DataTables libraries. The pipeline is containerized in Docker, allowing for easier environment building and pipeline deployment.
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- 2023
7. Marine Pollutant Tributyltin Affects DNA Methylation and Fitness of Banded Murex (Hexaplex trunculus) Populations
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Šrut, Maja, primary, Sabolić, Iva, additional, Erdelez, Anita, additional, Grbin, Dorotea, additional, Furdek Turk, Martina, additional, Bakarić, Robert, additional, Peharda, Melita, additional, and Štambuk, Anamaria, additional
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- 2023
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8. Grounds for an Appeal in Enforcement Proceedings
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Sabolić, Iva, Bratković, Marko, Uzelac, Alan, and Maganić, Aleksandra
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Protiv rješenja o ovrsi na temelju ovršne isprave kao pravni lijekovi strankama su na raspolaganju žalba uz koju se kao komplementarna pravna sredstva nalaze opozicijska i opugnacijska tužba te revizija. Žalba zauzima centralno mjesto u sustavu pravnih lijekova protiv rješenja o ovrsi na temelju ovršne isprave. Mogu je izjaviti i ovrhovoditelj i ovršenik. Žalba ovrhovoditelja u odnosu na žalbu ovršenika razlikuje se svojim karakteristikama i žalbenim razlozima zbog kojih se može podnijeti. Također, ovrhovoditelj može izjaviti samo redovnu žalbu dok ovršenik može izjaviti redovnu i, uz ispunjenje posebnih uvjeta, izvanrednu žalbu. Samo ovršenik može izjaviti žalbu zbog opozicijskih i opugnacijskih žalbenih razloga. U slučaju izjavljivanja izvanredne žalbe ili redovne žalbe zbog opozicijskih ili opugnacijskog razloga nedostatka legitimacije može doći do pokretanja parnice radi proglašenja ovrhe nedopuštenom. Parnica se pokreće podnošenjem tužbe koja se naziva opozicijska ili opugnacijska tužba. U Ovršnom zakonu opozicijski i opugnacijski žalbeni razlozi nabrojani su kao jedni od razloga zbog kojih je žalba protiv rješenja o ovrsi osobito dopuštena. Opozicijski žalbeni razlozi su 1) prestanak tražbine, 2) odgođeno, zabranjeno, izmijenjeno ili onemogućeno ispunjenje tražbine te 3) zastara. To su razlozi pogrešne primjene materijalnog prava te pogrešno utvrđenog činjeničnog stanja. Opugnacijski žalbeni razlozi su: 1) nedostatak legitimacije, 2) nedostatak ovršnosti, 3) pactum de non petendo, 4) protek roka te 5) neispunjenje uvjeta. To su razlozi koji se odnose na bitne povrede odredaba ovršnog postupka.
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- 2021
9. Genomic patterns of phenotypic adaptation in Italian wall lizard Podarcis siculus (Rafinesque-Schmaltz, 1810)
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Sabolić, Iva and Štambuk, Anamaria
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PRIRODNE ZNANOSTI. Biologija ,udc:57(043.3) ,population genomics ,populacijska genomika ,genomic adaptation ,zajedniĉki okoliš ,Podarcis siculus, rapid evolution, common garden, heritability, population genomics, genomic adaptation ,Podarcis siculus ,heritability ,Biološke znanosti. Fizička antropologija. Bioraznolikost ,nasljednost ,NATURAL SCIENCES. Biology ,genomska adaptacija ,Biological sciences. Physical anthropology. Biodiversity ,common garden ,rapid evolution ,brza evolucija - Abstract
Within a competitive exclusion experiment conducted in 1971, five pairs of Podarcis siculus lizards were transferred from islet Pod Kopište to a nearby islet of Pod Mrĉaru in the Adriatic Sea. In only 35 years the newly established population exhibited significant morphological and ecological changes. This study combines experimental common garden approach with population genomics tools to discriminate between plastic and genomic response in Pod Mrĉaru population. Crossing experiment in common garden pointed towards medium to high heritability of diverged phenotypic traits related to head shape, indicating they hold enough additive genetic variance to evolve under selection. Genotyping by sequencing elucidated genome-wide divergence between Pod Mrĉaru and Pod Kopište populations. 18 loci putatively under selection were found to be associated with divergent phenotypic traits in source and newly established population, and/or differences in ecological variables among multiple P. siculus populations, suggesting rapid genomic adaptation on the islet of Pod Mrĉaru. 1971. godine pet pari gušterice Podarcis siculus je u sklopu istraţivanja kompetitivne ekskluzije prebaĉeno s otoĉića Pod Kopište na susjedni otoĉić Pod Mrĉaru u Jadranskom moru. U samo 35 godina nakon introdukcije novoustanovljena populacija je razvila znaĉajne ekološke i morfološke razlike. Ovo istraţivanje kombinira pokus zajedniĉkog okoliša s metodama populacijske genomike u svrhu razluĉivanja izmeĊu plastiĉnih i genomskih prilagodba u populaciji s otoka Pod Mrĉaru. Eksperiment kriţanja u zajedniĉkom okolišu je ukazao na srednje visoku nasljednost fenotipskih obiljeţja vezanih uz oblik glave, što sugerira da sadrţe dovoljno aditivne genetske varijabilnosti da evoluiraju pod utjecajem selekcije. Genotipiziranje putem sekvenciranja je pokazalo diferencijaciju na razini cijelog genoma izmeĊu populacija s Pod Mrĉaru i Pod Kopište. 18 lokusa identificiranih kao potencijalno pod utjecajem selekcije povezani su s divergirajućim fenotipskim obiljeţjima u ishodišnoj i novoustanovljenoj populaciji i/ili varijacijom u okolišnim ĉimbenicima meĊu mnogobrojnim nativnim populacijama P. siculus, što ukazuje na brzu genomsku adaptaciju populacije na otoku Pod Mrĉaru.
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- 2021
10. Proximate and ultimate drivers of variation in bite force in the insular lizards Podarcis melisellensis and Podarcis sicula
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Taverne, Maxime, primary, King-Gillies, Nina, additional, Krajnović, Maria, additional, Lisičić, Duje, additional, Mira, Óscar, additional, Petricioli, Donat, additional, Sabolić, Iva, additional, Štambuk, Anamaria, additional, Tadić, Zoran, additional, Vigliotti, Chloé, additional, Wehrle, Beck, additional, and Herrel, Anthony, additional
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- 2020
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11. Rapid evolution in Italian wall lizard (Podarcis siculus)
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Lisičić, Duje, Sabolić, Iva, Mira, Óscar, Šrut, Maja, Soares, Miguel, Dennis, Stuart, Dorotea Polović1, Ivan Cizelj4 , Bakarić, Robert, Glogoški, Marko, Stapley, Jessica, Herrel, Anthony, and Štambuk, Anamaria
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Biological introduction, island effect, phenotypic plasticity, Podarcis siculus, rapid evolution - Abstract
The modern synthesis defines evolution as a change in genotypic (or allelic) frequencies from one generation to the next. Evolution is usually regarded as slow process of gradual change of a species, and as such, is difficult to be tested and witnessed in shorter time span. Yet, there is growing evidence from modern scientific studies that relative quick changes in some populations emerged. Biological invasions are especially good models to study the rate and extent of evolutionary events upon encountering novel environments, especially on islands ecosystem. Here, we present one lizard species as a model for rapid evolution. Podarcis siculus is typical small lacertid lizard widely distributed through Eastern Adriatic islands. One of these populations has been subjected to experimental introductions of known date and location that have given rise to a spectacular phenotypic divergence in morphology and ecology in a relatively short time span of 35 years. The evolutionary rates observed between divergent P. siculus populations are among the highest ever recorded in natural populations, making this system as excellent model for studying rapid evolution. The main issue in such systems is to discriminate between evolution and phenotypic plasticity. There is a ongoing research project led by assist. prof. Anamaria Štambuk from Faculty of Science of University of Zagreb with aim to do so. The project combines common garden crossing experiments and population genomic to test weather observed the rapid phenotypic divergence has a genetic background indicating rapid evolution or it is result on inherited phenotypic plasticity.
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- 2018
12. Defining connectivity of exploited octopus and shrimp populations across the Mediterranean
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Štambuk, Anamaria, Sabolić, Iva, Baltazar-Soares, Miguel, Mira, Óscar, Bakarić, Robert, Raicevich, Sasa, Albo Puigserver, Marta, Battaglia, Pietro, Božanić, Jakša, Company, Joan B., Cegonho, Rute, Partidario, Maria Rosario, Rotllant, Guiomar, Barros, Margarida, Špika, Matea, and Hudina, Sandra
- Abstract
Fourth International Marine Connectivity (iMarCo) Conference, 8-9 October 2018, Crete, Greece.-- 1 page, In this era of fast global change, defining connectivity and adaptive potential of exploited marine stocks is a key requirement towards sustainability of fisheries. Though the use of genetics tools is not very pervasive in fisheries management, evolutionary concepts that derive from its use provide the much needed information regarding stock structure and its adaptation capacity. In our study, we examine the integration of evolutionary-based knowledge in fisheries sustainable management and conservation of two target species: common octopus, Octopus vulgaris and red shrimp Aristeus antennatus. To that end, we sampled 19 octopus and 12 red shrimp populations across the Mediterranean. Populations were genotyped using genotyping by sequencing (GBS) approach and a number of polymorphic genetic markers (SNPs) was validated for each species and population. In order to assess stock structure, genetic differentiation among populations was estimated with F-statistics and patterns of genomic variation across spatial scales were obtained, providing evidence of connectivity. To investigate occurrences of local adaptation, the data set was tested for evolution under selection. Here we provide high resolution perspective on stock structure, connectivity and local adaptation of octopus and red shrimp in the Mediterranean and indicate fishery areas that are critical to preserve, contributing directly to the sustainable management of Mediterranean fishery populations
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- 2018
13. Biomarker response of Mediterranean mussels Mytilus galloprovincialis regarding environmental conditions, pollution impact and seasonal effects
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Grbin, Dorotea, primary, Sabolić, Iva, additional, Klobučar, Goran, additional, Dennis, Stuart R., additional, Šrut, Maja, additional, Bakarić, Robert, additional, Baković, Vid, additional, Brkanac, Sandra Radić, additional, Nosil, Patrik, additional, and Štambuk, Anamaria, additional
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- 2019
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14. Accumulation of biotoxins in bivalves (Mollusca, Bivalvia)
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Sabolić, Iva and Lajtner, Jasna
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biotoksini ,PRIRODNE ZNANOSTI. Biologija ,NATURAL SCIENCES. Biology ,biotoxins ,bivalves ,školjkaši - Abstract
Mikroskopske planktonske alge predstavljaju glavni izvor hrane za školjkaše koji ih filtriraju iz okolne vode. No, među sekundarnim metabolitima alga, identificirani su neki koji su snažni toksini i koji mogu imati negativan učinak na ljudsko zdravlje i okoliš (okadaična kiselina, domoična kiselina, saxitoksini, brevetoksini). Biotoksini povezani sa slučajevima otrovanja ljudi produkt su nekih vrsta dinoflagelata, dijatomeja i modrozelenih algi. Mnogo vrsta školjkaša koje ljudi koriste za prehranu akumuliraju fitoplanktonske biotoksine u svojim tkivima. Konzumacijom školjkaša sa visokom koncentracijom akumuliranih biotoksina u ljudi dolazi do različitih simptoma na temelju kojih se razlikuju četiri vrste oboljenja. To su dijareično trovanje školjkašima (DSP), paralizirajuće trovanje školjkašima (PSP), trovanje školjkašima s posljedičnim gubitkom pamćenja (ASP) i neurotoksično trovanje školjkašima (NSP). Zbog mogućega ozbiljnog utjecaja na ljudsko zdravlje i okoliš, u većini zemalja se provodi kontinuirani monitoring i testovi za detekciju biotoksina akumuliranih u školjkašima. Tijekom zadnjih nekoliko desetaka godina sve su učestalija izvješća o cvjetanju potencijalno toksičnih algi i pojavi oboljenja u ljudi za što je glavni krivac povećana antropološka eutrofikacija vodenih sustava. Microscopic planktonic algae are the main food source for filter-feeding bivalves. However, among the secondary algal metabolites, several have been identified as potent toxins that can have negative effects on human health and environment (okadaic acid, domoic acid, saxitoxins, brevetoxins). Biotoxins associated with human intoxication are product of several species of dinoflagellates, diatoms and blue-green algae. The variety of shellfish species used in human nutrition can accumulate phytotoxins in their edible tissue. By consumption of shellfish with high concentration of accumulated biotoxins, people can develop different symptoms of intoxication, based on which we distinguish four serious poisoning syndromes. These are diarrhetic shellfish poisoning (DSP), paralytic shellfish poisoning (PSP), amnesic shellfish poisoning (ASP) and neurotoxic shellfish poisoning (NSP). Because of possible serious effect on human health and environment, number of countries conducts continuous algal monitoring and assays for accumulated biotoxins detection in shellfish. Over the past few decades reports of blooms of potentially toxic algae and appearance of human intoxication have become more frequent, and it seems that the increase in anthropological eutrophication of water bodies is the main cause.
- Published
- 2012
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