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Iskalni niz: "ključne besede" (sequencing) .

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Evolution of a hybrid zone of willows (Salix L.) in the Alps analysed by RAD-seq and morphometrics
Pia Marinček, 2022, magistrsko delo

Povzetek: Natural hybridization of plants can result in many outcomes with several evolutionary consequences, such as hybrid speciation and introgression. Natural hybrid zones can arise as a result of fluctuating climate during the exchange of glacial and interglacial periods, where species retract and expand their territories, resulting in secondary contacts. On mountain ranges, such as the European Alps, hybrid zones of alpine species are frequently formed where different lineages meet. Willows are a large genus of woody plants with an immense capability of interspecific crossing. About 33 species of this genus inhabit the Alps, where intermediate phenotypes were frequently observed and proclaimed as hybrids, but rarely examined in detail. One of the reasons was a lack of informative molecular markers and suitable analytical tools to analyse this highly diverse and convergent genus. With the development of the RAD-seq technology, several questions regarding willow phylogeny and hybridization could be answered. In this study, a putative hybrid zone of two sister species, S. foetida and S. waldsteiniana, was investigated to study the genomic structure of populations within and outside their contact zone, to find evidence for hybrid speciation or introgression, and to analyse if morphological phenotypes are reflected by their genotypes. Individuals of the two species were sampled across their distribution range in the Alps and examined with the use of RADseq data and morphometric analyses. The results showed that a hybrid zone between the two species was established within the range of their contact zone. Patterns of genetic admixture in homoploid hybrids indicated introgression with asymmetric backcrossing to one of the parental species. Morphometric characteristics of hybrids supported the molecular data and showed intermediacy with a bias towards S. waldsteiniana. Only one potentially divergent hybrid lineage was observed, hinting to a possibility of localised hybrid speciation events.
Ključne besede: alpine plants, hybridization, morphometry, RAD sequencing, master thesis
Objavljeno v DiRROS: 17.01.2025; Ogledov: 104; Prenosov: 36
.pdf Celotno besedilo (4,66 MB)

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Massively parallel measurement of protein–protein interactions by sequencing using MP3-seq
Alexandr Baryshev, Benjamin Groves, Cirstyn Michel, David Baker, Ajasja Ljubetič, Georg Seelig, 2024, izvirni znanstveni članek

Ključne besede: proteins, proteins interactions, sequencing, MP3-seq
Objavljeno v DiRROS: 30.10.2024; Ogledov: 298; Prenosov: 941
.pdf Celotno besedilo (4,42 MB)
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5.
Selection on the vascular-remodeling BMPER gene is associated with altitudinal adaptation in an insular lizard
Nina Guerra Serén, Catarina Pinho, Rodrigo Megía-Palma, Prem Aguilar, Anamarija Žagar, Pedro Andrade, Miguel A. Carretero, 2024, izvirni znanstveni članek

Povzetek: High altitude imposes several extreme constraints on life, such as low oxygen pressure and high levels of ultraviolet radiation, which require specialized adaptations. Many studies have focused on how endothermic vertebrates respond to these challenging environments, but there is still uncertainty on how ectotherms adapt to these conditions. Here, we used whole-genome sequencing of low-altitude (100–600 m) and high-altitude (3,550 m) populations of the wide-ranging Tenerife lizard Gallotia galloti to uncover signatures of selection for altitudinal adaptation. The studied populations show reduced differentiation, sharing similar patterns of genetic variation. Selective sweep mapping suggests that signatures of adaptation to high altitude are not widespread across the genome, clustering in a relatively small number of genomic regions. One of these regions contains BMPER, a gene involved with vascular remodeling, and that has been associated with hypoxia-induced angiogenic response. By genotyping samples across 2 altitudinal transects, we show that allele frequency changes at this locus are not gradual, but rather show a well-defined shift above ca. 1,900 m. Transcript and protein structure analyses on this gene suggest that putative selection likely acts on noncoding variation. These results underline how low oxygen pressure generates the most consistent selective constraint in high-altitude environments, to which vertebrates with vastly contrasting physiological profiles need to adapt in the context of ongoing climate change.
Ključne besede: high altitude, adaptations, ectotherms, whole-genome sequencing, selective sweep, BMPER gene, hypoxia, genomics
Objavljeno v DiRROS: 08.10.2024; Ogledov: 332; Prenosov: 120
.pdf Celotno besedilo (1,54 MB)
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6.
Conservation of molecular responses upon viral infection in the non-vascular plant Marchantia polymorpha
Eric Ros-Moner, Tamara Jiménez-Góngora, Luis Villar-Martin, Lana Vogrinec, Víctor M. González-Miguel, Denis Kutnjak, Ignacio Rubio-Somoza, 2024, izvirni znanstveni članek

Povzetek: After plants transitioned from water to land around 450 million years ago, they faced novel pathogenic microbes. Their colonization of diverse habitats was driven by anatomical innovations like roots, stomata, and vascular tissue, which became central to plant-microbe interactions. However, the impact of these innovations on plant immunity and pathogen infection strategies remains poorly understood. Here, we explore plant-virus interactions in the bryophyte Marchantia polymorpha to gain insights into the evolution of these relationships. Virome analysis reveals that Marchantia is predominantly associated with RNA viruses. Comparative studies with tobacco mosaic virus (TMV) show that Marchantia shares core defense responses with vascular plants but also exhibits unique features, such as a sustained wound response preventing viral spread. Additionally, general defense responses in Marchantia are equivalent to those restricted to vascular tissues in Nicotiana, suggesting that evolutionary acquisition of developmental innovations results in re-routing of defense responses in vascular plants.
Ključne besede: plant-virus interactions, bryophytes, virome analysis, high-throughput sequencing, virology, pathogenic, innovations, interactions, RNA viruses, plant defense response, botany
Objavljeno v DiRROS: 02.10.2024; Ogledov: 309; Prenosov: 295
.pdf Celotno besedilo (3,00 MB)
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7.
Soil microbiome along the carpathian mountains
Nejc Suban, Olivera Maksimović, Nataša Šibanc, Tijana Martinović, Eva Dařenová, Matjaž Čater, Tine Grebenc, 2024, objavljeni povzetek znanstvenega prispevka na konferenci

Ključne besede: soil microbiome, next-generation sequencing, climate change, forest soil, fungi, bacteria
Objavljeno v DiRROS: 02.09.2024; Ogledov: 410; Prenosov: 114
.pdf Celotno besedilo (632,77 KB)

8.
Detection of plant viruses using nanopore highthroughput sequencing : validation report
Anja Pecman, Veronika Bukvič, Ana Vučurović, Irena Bajde, Jakob Brodarič, Nataša Mehle, Denis Kutnjak, 2023, končno poročilo o rezultatih raziskav

Ključne besede: diagnostics, method validation, nanopores, high-throughput sequencing
Objavljeno v DiRROS: 02.09.2024; Ogledov: 496; Prenosov: 1563
.pdf Celotno besedilo (6,04 MB)
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9.
Metrological evaluation of DNA extraction method effects on the bacterial microbiome and resistome in sputum
Aleksander Benčič, Nataša Toplak, Simon Koren, Alexandra Bogožalec Košir, Mojca Milavec, Viktorija Tomič, Dane Lužnik, Tanja Dreo, 2024, izvirni znanstveni članek

Povzetek: Targeted high-throughput sequencing (HTS) has revolutionized the way we look at bacterial communities. It can be used for the species-specific detection of bacteria as well as for the determination of the microbiome and resistome and can be applied to samples from almost any environment. However, the results of targeted HTS can be influenced by many factors, which poses a major challenge for its use in clinical diagnostics. In this study, we investigated the impact of the DNA extraction method on the determination of the bacterial microbiome and resistome by targeted HTS using principles from metrology and diagnostics such as repeatability and analytical sensitivity. Sputum samples spiked with Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa at three different concentrations (103–106 cells/mL) were used. DNA was extracted from each sample on 2 separate days in three replicates each using three different extraction methods based on cetrimonium bromide, magnetic beads, and silica membranes. All three spiked bacteria were detected in sputum, and the DNA extraction method had no significant effect on detection. However, the DNA extraction method had significant effects on the composition of the microbiome and the resistome. The sequencing results were repeatable in the majority of cases. The silica membrane-based DNA extraction kit provided the most repeatable results and the highest diversity of the microbiome and resistome. Targeted HTS has been shown to be a reliable tool for determining the microbiome and resistome; however, the method of DNA extraction should be carefully selected to minimize its impact on the results.
Ključne besede: targeted high-throughput sequencing, bacterial microbiome, resistome, bacteria detection, DNA extraction, metrology, diagnostics, repeatability
Objavljeno v DiRROS: 30.08.2024; Ogledov: 387; Prenosov: 273
.pdf Celotno besedilo (996,30 KB)
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10.
In-depth comparison of adeno-associated virus containing fractions after CsCl ultracentrifugation gradient separation
Mojca Janc, Kaja Zevnik, Ana Dolinar, Tjaša Jakomin, Maja Štalekar, Katarina Bačnik, Denis Kutnjak, Magda Tušek-Žnidarič, Lorena Zentilin, Dmitri G. Fedorov, David Dobnik, 2024, izvirni znanstveni članek

Povzetek: Recombinant adeno-associated viruses (rAAVs) play a pivotal role in the treatment of genetic diseases. However, current production and purification processes yield AAV-based preparations that often contain unwanted empty, partially filled or damaged viral particles and impurities, including residual host cell DNA and proteins, plasmid DNA, and viral aggregates. To precisely understand the composition of AAV preparations, we systematically compared four different single-stranded AAV (ssAAV) and self-complementary (scAAV) fractions extracted from the CsCl ultracentrifugation gradient using established methods (transduction efficiency, analytical ultracentrifugation (AUC), quantitative and digital droplet PCR (qPCR and ddPCR), transmission electron microscopy (TEM) and enzyme-linked immunosorbent assay (ELISA)) alongside newer techniques (multiplex ddPCR, multi-angle light-scattering coupled to size-exclusion chromatography (SEC-MALS), multi-angle dynamic light scattering (MADLS), and high-throughput sequencing (HTS)). Suboptimal particle separation within the fractions resulted in unexpectedly similar infectivity levels. No single technique could simultaneously provide comprehensive insights in the presence of both bioactive particles and contaminants. Notably, multiplex ddPCR revealed distinct vector genome fragmentation patterns, differing between ssAAV and scAAV. This highlights the urgent need for innovative analytical and production approaches to optimize AAV vector production and enhance therapeutic outcomes.
Ključne besede: recombinant adeno-associated viruses (rAAVs), CsCl ultracentrifugation gradient, analytical methods, digital droplet PCR (ddPCR), transmission electron microscopy (TEM), analytical ultracentrifugation (AUC), size-exclusion chromatography coupled with multi-angle light scattering (SEC-MALS), Illumina sequencing, virology
Objavljeno v DiRROS: 07.08.2024; Ogledov: 500; Prenosov: 383
.pdf Celotno besedilo (8,47 MB)
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