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Povzetek: The Slovenian autochthonous breed, Krškopolje pig, is known for high fatness and better adaptability to different environmental conditions and feed resources. However, the metabolic processes underlying these adaptations, especially in response to different diets, have not yet been studied. A deeper understanding of these mechanisms could provide valuable insights into the breed’s adaptability to different environmental conditions. Therefore, the main objective of this study was to evaluate the effect of a low-protein (LP) diet on adipose tissue in Krškopolje pigs reared in either organic outdoor (n = 2 × 12) or conventional indoor (n = 2 × 14) systems. In the outdoor system, the LP diet had no effect on adipocyte size compared to the control (high-protein) diet, while it increased lipogenic enzyme activities and monounsaturated fatty acid content, and decreased polyunsaturated fatty acid content (p < 0.05). RNA sequencing revealed the upregulation of 28 genes and the downregulation of 37 genes. The upregulated genes were mainly involved in lipid metabolism (ACLY, FASN, ACACA, MOGAT2), oxidative stress, and mitochondrial function. In the indoor system, pigs on the LP diet had smaller adipocytes (p < 0.05), whereas no differences were detected in the lipogenic enzyme activities or fatty acid composition (p > 0.10). RNA sequencing revealed 30 upregulated and 28 downregulated genes. In the indoor system, heat shock proteins (HSP70.2, HSPA6) were upregulated in pigs on the LP diet, while genes involved in the innate immune system (MSR1, TREM2, CSF3R) were downregulated. To conclude, the present study showed that LP diet affected adipose tissue metabolism and gene expression in Krškopolje pigs, with different transcriptomic responses observed in outdoor and indoor rearing conditions.
Ključne besede: pig, local breed, low-protein diet, indoor system, outdoor system, subcutaneous adipose tissue, RNA-sequencing, nCounter gene expression assay
Objavljeno v DiRROS: 12.05.2025; Ogledov: 122; Prenosov: 21
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Povzetek: Abscission is a tightly regulated process in which plants shed unnecessary, infected, damaged, or aging organs, as well as ripe fruits, through predetermined abscission zones in response to developmental, hormonal, and environmental signals. Despite its importance, the underlying mechanisms remain incompletely understood. This study highlights the deleterious effects of abscission on chloroplast ultrastructure in the cells of the tomato flower pedicel abscission zone, revealing spatiotemporal differential gene expression and key transcriptional networks involved in chloroplast vesiculation during abscission. Significant changes in chloroplast structure and vesicle formation were observed 8 and 14 h after abscission induction, coinciding with the differential expression of vesiculation-related genes, particularly with upregulation of Senescence-Associated Gene 12 (SAG12) and Chloroplast Vesiculation (CV). This suggests a possible vesicle transport of chloroplast degrading material for recycling by autophagy-independent senescence-associated vacuoles (SAVs) and CV-containing vesicles (CCVs). Ethylene signaling appears to be involved in the regulation of these processes, as treatment with a competitive inhibitor of ethylene action, 1-methylcyclopropene, delayed vesiculation, reduced the expression of SAG12, and increased expression of Curvature Thylakoid 1A (CURT1A). In addition, chloroplast vesiculation during abscission was associated with differential expression of photosynthesis-related genes, particularly those involved in light reactions, underscoring the possible functional impact of the observed structural changes. This work provides new insights into the molecular and ultrastructural mechanisms underlying abscission and offers potential new targets for agricultural or biotechnological applications.
Ključne besede: abscission, chloroplast vesiculation, CURT1A, CV-containing vesicle, senescence-associated vacuole, ethylene, gene expression, tomato flower pedicel
Objavljeno v DiRROS: 10.01.2025; Ogledov: 375; Prenosov: 199
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Povzetek: Understanding what drives protein abundance is essential to biology, medicine, and biotechnology. Driven by evolutionary selection, an amino acid sequence is tailored to meet the required abundance of a proteome, underscoring the intricate relationship between sequence and functional demand. Yet, the specific role of amino acid sequences in determining proteome abundance remains elusive. Here we show that the amino acid sequence alone encodes over half of protein abundance variation across all domains of life, ranging from bacteria to mouse and human. With an attempt to go beyond predictions, we trained a manageable-size Transformer model to interpret latent factors predictive of protein abundances. Intuitively, the model's attention focused on the protein's structural features linked to stability and metabolic costs related to protein synthesis. To probe these relationships, we introduce MGEM (Mutation Guided by an Embedded Manifold), a methodology for guiding protein abundance through sequence modifications. We find that mutations which increase predicted abundance have significantly altered protein polarity and hydrophobicity, underscoring a connection between protein structural features and abundance. Through molecular dynamics simulations we revealed that abundance-enhancing mutations possibly contribute to protein thermostability by increasing rigidity, which occurs at a lower synthesis cost.
Ključne besede: molecular biology, biotechnology, bioinformatics, deep learning, gene expression, synthetic biology, protein abundance, amino acid sequence, evolutionary selection, transformer model, MGEM (Mutation guided by an embedded manifold)
Objavljeno v DiRROS: 17.12.2024; Ogledov: 325; Prenosov: 171
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Povzetek: In the field, plants are challenged by more than one biotic stressor at the same time. In this study, the molecular interactions between potato (Solanum tuberosum L.), Colorado potato beetle (Leptinotarsa decemlineata Say; CPB) and Potato virus YNTN (PVYNTN) were investigated through analyses of gene expression in the potato leaves and the gut of the CPB larvae, and of the release of potato volatile compounds. CPB larval growth was enhanced when reared on secondary PVYNTN-infected plants, which was linked to decreased accumulation of transcripts associated with the antinutritional properties of potato. In PVYNTN-infected plants, ethylene signalling pathway induction and induction of auxin response transcription factors were attenuated, while no differences were observed in jasmonic acid (JA) signalling pathway. Similarly to rearing on virus-infected plants, CPB larvae gained more weight when reared on plants silenced in JA receptor gene (coi1). Although herbivore-induced defence mechanism is regulated predominantly by JA, response in coi1-silenced plants only partially corresponded to the one observed in PVYNTN-infected plants, confirming the role of other plant hormones in modulating this response. The release of β-barbatene and benzyl alcohol was different in healthy and PVYNTN-infected plants before CPB larvae infestation, implicating the importance of PVYNTN infection in plant communication with its environment. This was reflected in gene expression profiles of neighbouring plants showing different degree of defence response. This study thus contributes to our understanding of plant responses in agro-ecosystems.
Ključne besede: insect midgut transcriptional response, gene expression, plant defence, volatile organic compounds, potato
Objavljeno v DiRROS: 02.08.2024; Ogledov: 676; Prenosov: 309
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Povzetek: Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software for synthetic biology. It includes a library of plant biological parts organized in structural categories and a set of rules describing how to assemble these parts into large constructs. Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments. The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs. Therefore the plant grammar implemented in GenoCAD will help plant biologists take advantage of methods from synthetic biology to design expression vectors supporting their research projects.
Ključne besede: plasmid construction, plant genetics, gene expression
Objavljeno v DiRROS: 26.07.2024; Ogledov: 592; Prenosov: 344
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