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2. Effect of castration method on porcine skeletal muscle fiber traits and transcriptome profilesKlavdija Poklukar Žnidaršič, Anja Erbežnik, Gregor Fazarinc, Kevin Kress, Nina Batorek Lukač, Martin Škrlep, Volker Stefanski, Marjeta Čandek-Potokar, Milka Vrecl, 2024, izvirni znanstveni članek Povzetek: This study examined the effects of immunocastration and surgical castration on the histomorphometric and transcriptome traits of the porcine skeletal muscle. We hypothesized that the differences in duration of androgen deprivation resulting from different castration methods influence skeletal muscle biology in a muscle-specific manner. This was tested by analyzing samples of m. longissimus dorsi (LD) and m. semispinalis capitis (SSC) from immunocastrated (IC; n = 12), entire male (EM; n = 12), and surgically castrated (SC; n = 12) pigs using enzyme/immunohistochemical classification and histomorphometric analysis of myofibers, quantitative PCR, and RNA sequencing. The results confirmed the distinctive histomorphometric profiles of LD and SSC and the castration method related muscle-specific effects at the histomorphometric and transcriptome levels. Long-term androgen deficiency (surgical castration) significantly reduced the proportion of fast-twitch type IIa myofibers in LD (P < 0.05), whereas short-term androgen deprivation (immunocastration) reduced the cross-sectional area of oxidative type I myofibers in SSC (P < 0.05). At the transcriptional level, glycolytic LD adapted to long- and short-term androgen deprivation by upregulating genes controlling myoblast proliferation and differentiation to maintain fiber size. In contrast, increased protein degradation through the ubiquitin ligase-mediated atrophy pathway (significantly increased TRIM63 and FBXO32 expression; P < 0.05) could underly reduced crosssectional area of type I myofibers in the oxidative SSC in IC. Potential candidate genes (HK2, ARID5B, SERPINE1, and SCD) linked to specific metabolic profiles and meat quality traits were also identified in IC, providing a foundation for studying the effects of immunocastration on skeletal muscle fiber and carcass/meat quality traits.
Ključne besede: sceletal muscle, Logissimus dorsi, Semispinalis capitis, castration method, genne expression, pig
Objavljeno v DiRROS: 31.12.2024; Ogledov: 26; Prenosov: 11
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3. Non-destructive and destructive physical measurements as indicators of sugar and organic acid contents in strawberry fruit during ripeningKristyna Šimkova, Robert Veberič, Metka Hudina, Mariana Cecilia Grohar, Massimiliano Pelacci, Tina Smrke, Tea Burin, Nika Cvelbar Weber, Jerneja Jakopič, 2024, izvirni znanstveni članek Povzetek: Strawberry fruit is appreciated by consumers for its characteristic taste, which can be attributed to the balance between sugars and organic acids content, but strawberries are also a rich source of vitamin C (ascorbic acid). This study focuses on the suitability of different physical parameters, such as ripening index (IAD), firmness and total soluble solids content, as indicators of the content of sugars and organic acids during ripening. Five ripening stages were defined - green, white, ripe red, fully ripe dark red and overripe stage at five different cultivars. As the fruit ripened, the content of ascorbic acid, sugars and sugar/acid ratio increased and the organic acids content decreased, but the changes varied among cultivars. The ripening index (IAD) strongly correlated with the total sugar content (r = -0.72), total organic acids content (r = 0.70) and sugar/acid ratio (r = -0.82). Additionally, firmness correlated well with the content of sugars and organic acids. On the other hand, TSS showed a weaker correlation with the total sugar content (r = 0.38). Although, both the ripening index (I${_AD}$) and firmness showed strong correlations with sugars and organic acids content and can help distinguish unripe fruit from ripe fruit, the use of these parameters for distinguishing between different of ripe fruit (from early ripe to overripe) can be limited only to certain cultivars.
Ključne besede: strawberry, firmness, ripenning index, primary metabolites, fruit development
Objavljeno v DiRROS: 31.12.2024; Ogledov: 22; Prenosov: 9
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4. Characterization of genetic variability of common and tartary buckwheat genotypes using microsatellite markersŽelmíra Balážová, Lucia Čišecká, Zdenka Gálová, Zuzana Hromadová, Milan Chňapek, Barbara Pipan, Vladimir Meglič, 2024, izvirni znanstveni članek Ključne besede: genetic variability, varieties, common buckwheat, genetic diversity, genotypes, microsatellite markers
Objavljeno v DiRROS: 31.12.2024; Ogledov: 21; Prenosov: 5
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5. Changes in the aroma profile and phenolic compound contents of different strawberry cultivars during ripeningKristyna Šimkova, Robert Veberič, Mariana Cecilia Grohar, Massimiliano Pelacci, Tina Smrke, Tea Burin, Aljaž Medič, Nika Cvelbar Weber, Jerneja Jakopič, 2024, izvirni znanstveni članek Povzetek: Secondary metabolites, namely, phenolic and volatile organic compounds, contribute to the nutritional and organoleptic quality of the strawberry fruit. This study focuses on the changes in the content of phenolic compounds and volatile organic compounds during the ripening, from green to overripe fruit, of five strawberry cultivars (‘Asia’, ‘CIVN 766’, ‘Aprica’, ‘Clery’, and ‘Malwina’). Additionally, these changes are compared with the colour of the fruit and peroxidase and polyphenol oxidase activity. Our results show that the accumulation of secondary metabolites (phenolic and volatile organic compounds) significantly changed during the ripening process for all of the studied cultivars. As for phenolic compounds, flavanols and hydroxybenzoic acid derivatives comprised between 87 and 95% of the total phenolic compound content in unripe green fruit. In contrast, anthocyanins and hydroxycinnamic acid derivatives comprised between 64 and 77% of the total phenolic compound content in overripe fruit, except in the fruit of the cultivar ‘CIVN766’. When it comes to the aroma profile, the content of aldehydes decreased by 24–49% as the fruit ripened, and the accumulation of esters increased. Our study also shows that the ripening process differs among cultivars, and it is therefore necessary to define ripening indicators separately for each cultivar.
Ključne besede: Fragaria × ananassa, volatile organic compounds, phenolics, fruit development, cultivar
Objavljeno v DiRROS: 31.12.2024; Ogledov: 22; Prenosov: 9
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6. Improved adhesion of bacterial cellulose on plasma-treated cotton fabric for development of all-cellulose biocompositesLinda Ogrizek, Janja Lamovšek, Gregor Primc, Mirjam Leskovšek, Alenka Vesel, Miran Mozetič, Marija Gorjanc, 2024, izvirni znanstveni članek Ključne besede: all-cellulose biocomposite, bacterial cellulose, cotton, oxygen plasma, surface changes, adhesion
Objavljeno v DiRROS: 31.12.2024; Ogledov: 20; Prenosov: 8
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7. Short-term storage in a modified atmosphere affects the chemical profile of blueberry (Vaccinium corymbosum L.) fruitTina Smrke, Nika Cvelbar Weber, Jaka Razinger, Aljaž Medič, Robert Veberič, Metka Hudina, Jerneja Jakopič, 2024, izvirni znanstveni članek Povzetek: Short-term modified-atmosphere storage with an adjusted CO$_2$ and/or O$_2$ concentration could recover blueberry fruit infested with the larvae of quarantine pests. However, this could significantly affect the fruit quality. In our experiment we investigated the performance of highbush blueberry Bluecrop fruit (firmness, peel color, individual phenolics, sugars, and organic acids) under four short-term storage regimes: (1) a regular atmosphere with 0.03% CO$_2$, 21% O$_2$, and 78% N$_2$ at 22 °C, i.e., the control; (2) a regular atmosphere with 0.03% CO$_2$, 21% O$_2$, and 78% N$_2$ at 2 ; (3) a modified atmosphere with 10% CO$_2$, 5% O$_2$, and 85% N$_2$ at 2 °C; and (4) a modified atmosphere with 100% CO$_2$ at 2 °C. Fruit sampling took place after 24 h, 48 h, and 72 h. Fruit firmness was not significantly altered by storage regime or duration, while some significant, but minor, changes were detected in the color parameters. Regarding the primary metabolites, the sugar/organic acid ratio stagnated in the first 48 h in all storage regimes. The content of the majority of the individual phenolics was significantly higher in the fruit stored under control conditions. From our results, we can conclude that the short-term storage of highbush blueberry Bluecrop fruit for 24 h in a cold atmosphere does not affect the phenolic content, and storage for 48 h does not affect the total sugar/organic acid ratio, regardless of the atmosphere composition.
Ključne besede: bluecrop, peel color, primary metabolites, phenolics
Objavljeno v DiRROS: 31.12.2024; Ogledov: 24; Prenosov: 8
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8. Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheatYuqi He, Kaixuan Zhang, Yaliang Shi, Mateja Germ, Zlata Luthar, Ivan Kreft, Dagmar Janovská, Vladimir Meglič, Meiliang Zhou, 2024, izvirni znanstveni članek Povzetek: Background: Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. Results: Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency. Conclusions: This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.
Ključne besede: domestication, migration, artificial selection, buckwheat, genomics
Objavljeno v DiRROS: 31.12.2024; Ogledov: 20; Prenosov: 8
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9. Potential of different common (Fagopyrum esculentum Moench) and Tartary (Fagopyrum tataricum (L.) Gaertn.) buckwheat accessions to sustainably manage surrounding weedsY Vieites-Álvarez, MI Hussain, Manuel J. Reigosa, Aleš Kolmanič, Vladimir Meglič, Petra Hlásná Čepková, Meiliang Zhou, Dagmar Janovská, Adela M. Sánchez-Moreiras, 2024, izvirni znanstveni članek Ključne besede: agroecology, allelopathy, buckwheat, polyphenols, root exudates, sustainable weed management
Objavljeno v DiRROS: 31.12.2024; Ogledov: 23; Prenosov: 9
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10. AmiCa : atlas of miRNA-gene correlations in cancerNina Hauptman, Jože Pižem, 2024, izvirni znanstveni članek Povzetek: The increasing availability of RNA sequencing data has opened up numerous opportunities to analyze various RNA interactions, including microRNA-target interactions (MTIs). In response to the necessity for a specialized tool to study MTIs in cancer and normal tissues, we developed AmiCa (https://amica.omics.si/), a web server designed for comprehensive analysis of mature microRNA (miRNA) and gene expression in 32 cancer types. Data from 9498 tumor samples and 626 normal samples from The Cancer Genome Atlas were obtained through the Genomic Data Commons and used to calculate differential expression and miRNA-target gene (MTI) correlations. AmiCa provides data on differential expression of miRNAs/genes for cancers for which normal tissue samples were available. In addition, the server calculates and presents correlations separately for tumor and normal samples for cancers for which normal samples are available. Furthermore, it enables the exploration of miRNA/gene expression in all cancer types with different miRNA/gene expression. In addition, AmiCa includes a ranking system for genes and miRNAs that can be used to identify those that are particularly highly expressed in certain cancers compared to other cancers, facilitating targeted and cancer-specific research. Finally, the functionality of AmiCa is illustrated by two case studies.
Ključne besede: miRNA, gene, expression, cancer, correlation, gene prioritization
Objavljeno v DiRROS: 31.12.2024; Ogledov: 26; Prenosov: 9
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