Spela Baebler

National Institute of Biology - Nacionalni inštitut za biologijo | NIB · Dept. Biotechnology & Systems Biology

Potato virus Y (PVY) is the most economically important virus affecting potato production. PVY manipulates the plant cell machinery in order to successfully complete the infecting cycle. On the other side, the plant activates a sophisticated multilayer immune defense response to combat viral infection. The balance between these mechanisms, dependin...

While activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to restriction of pathogen remain mostly unknown. We studied the immunity network response conditioned by the potato Ny‐1 gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the bi...

Hypersensitive response (HR)‐conferred resistance is associated with induction of programmed cell death and pathogen spread restriction in its proximity. The exact role of chloroplastic reactive oxygen species and its link with salicylic acid (SA) signaling in HR remain unexplained. To unravel this, we performed a detailed spatiotemporal analysis o...

Plant biofactories are a promising platform for sustainable production of high-value compounds, among which are insect sex pheromones, a green alternative to conventional insecticides in agriculture. Recently, we have constructed transgenic Nicotiana benthamiana plants (“Sexy Plants”, SxP) that successfully produce a blend of moth (Lepidoptera) sex...

Ethylene response factors (ERFs) have been associated with biotic stress in Arabidopsis, while their function in non‐model plants is still poorly understood. Here we investigated the role of potato ERF StPti5 in plant immunity. We show that StPti5 acts as a susceptibility factor. It negatively regulates potato immunity against potato virus Y and Ra...

Potato, the most important non-cereal crop, is highly water and space efficient but susceptible to abiotic stress such as heat, drought, or flooding. Climate change is severely increasing the likelihood of such stresses to occur individually, sequentially, or simultaneously. However, the understanding of acclimation to abiotic stress in crops in ge...

Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge networ...

Most biosynthetic gene clusters (BGC) encoding the synthesis of important microbial secondary metabolites, such as antibiotics, are either silent or poorly expressed; therefore, to ensure a strong pipeline of novel antibiotics, there is a need to develop rapid and efficient strain development approaches. This study uses comparative genome analysis...

Insect physiology and reproduction depend on several terpenoid compounds, whose biosynthesis is mainly unknown. One enigmatic group of insect monoterpenoids are mealybug sex pheromones, presumably resulting from the irregular coupling activity of unidentified isoprenyl diphosphate synthases (IDSs). Here, we performed a comprehensive search for IDS...

Stress Knowledge Map (SKM, https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs describing current knowledge of biochemical, signalling, and regulatory molecular interactions in plants: a highly curated model of plant stress signalling (PSS, 543 reactions) and a large comprehensive knowledge network (CK...

Most of the biosynthetic gene clusters (BGC) encoding the biosynthesis of important microbial secondary metabolites, such as antibiotics, are either silent or poorly expressed; therefore, robust technologies are required to secure the production of natural products for both drug discovery and any subsequent commercial fermentation processes. Indust...

Many insect species rely on diverse terpenoids for their development and interorganismal interactions. However, little is known about terpenoid biosynthesis in insects. The monoterpenoid sex pheromones of mealybugs and scale insects (Coccoidea) are particularly enigmatic, with several species producing unique structures presumed to result from the...

We developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. pISA-tree was initiated by end-user requirements thus its strong points are practicality and low maintenance cost. It enables on-the-fly creation of enriched directory tree structure (projec...

The role of programmed cell death (PCD) in hypersensitive response (HR)-conferred resistance depends on the type of host–pathogen interaction and therefore has to be studied for each individual pathosystem. Here we present and explain the protocol for studying the role of PCD in HR-conferred resistance in potato plants in the interaction with the v...

We have developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. It enables on-the-fly creation of enriched directory tree structure (project/Investigation/Study/Assay) via a series of sequential batch files in a standardised manner based on the ISA...

Arthropods crop pests are responsible for 20% of global annual crop losses, a figure predicted to increase in a changing climate where the ranges of numerous species are projected to expand. At the same time, many insect species are beneficial, acting as pollinators and predators of pest species. For thousands of years, humans have used increasingl...

Understanding the molecular mechanisms of potato development and responses to environmental stressors is of utmost importance for achieving stable crop yields. RNA sequencing (RNA-Seq) provides an insight into responses of all of the organism genes to the environmental and developmental cues and thus provides insights into underlying modes of actio...

Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly...

Background Natural products are a valuable source of biologically active compounds that have applications in medicine and agriculture. One disadvantage with natural products is the slow, time-consuming strain improvement regimes that are necessary to ensure sufficient quantities of target compounds for commercial production. Although great efforts...

Due to increased frequency of cyanobacterial blooms and emerging evidence of cyanotoxicity in biofilm, reliable methods for early cyanotoxin threat detection are of major importance for protection of human, animal and environmental health. To complement the current methods of risk assessment, this study aimed to evaluate selected qPCR assays for de...

Hypersensitive response (HR)-conferred resistance is associated with an induction of programmed cell death (PCD) and pathogen spread restriction in its proximity. While the pivotal role of salicylic acid (SA) in the restriction of pathogen spread during HR has been confirmed, the exact role of chloroplastic reactive oxygen species and the link betw...

In this work, the kinetic model based on the previously developed metabolic and glycan reaction networks of the ovarian cells of the Chinese hamster ovary (CHO) cell line was improved by the inclusion of transcriptomic data that took into account the values of the RPKM gene (Reads per Kilobase of Exon per Million Reads Mapped). The transcriptomic (...

Imatinib mesylate (IM) is an anticancer drug that belongs to tyrosine kinase inhibitors. We report the results of the first investigation of the chronic exposure of zebrafish (Danio rerio) to IM. The exposure to IM (0.01, 1 and 100 μg/L) was initiated in adult fish and continued through hatching and the offspring generation for seven months. In add...

Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly...

Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors...

In a tolerant plant–virus interaction, viral multiplication is sustained without substantial effects on plant growth or reproduction. Such interactions are, in natural environments, frequent and sometimes even beneficial for both interactors. Here we compiled evidence showing that small RNAs modulate plant immune responses and growth, hence adjusti...

While activation of resistance (R) proteins has been intensively studied, the mechanisms acting downstream of R protein activation remain elusive. We studied effector-triggered immunity (ETI) conditioned by the potato Ny-1 gene against potato virus Y. Transcriptomic, ultrastructural and biochemical analyses of four consecutive tissue sections in an...

Molecular response of plants to viruses is a mixture of the plant responses to intracellular virus multiplication and defense responses. The balance between these mechanisms and environment determines the outcome of the interaction, resulting in either compatible or incompatible interaction. Plants have developed three different strategies to count...

Slovensko društvo za biologijo rastlin je 17. in 18. septembra 2018 v Biološkem središču v Lju- bljani organiziralo že 7. simpozij o rastlinski biologiji z mednarodno udeležbo. Zanimiv program z dvanajstimi vabljenimi predavatelji je privabil preko 100 udeležencev iz kar 12 držav, ki so svoje delo predstavili še v okviru 19 kratkih predavanj in 40...

Modern, high-throughput methods for the analysis of genetic information, gene and metabolic products and their interactions offer new opportunities to gain comprehensive information on life processes. The data and knowledge generated open diverse application possibilities with enormous innovation potential. To unlock that potential skills in genera...

To develop novel crop-breeding strategies, it is crucial to understand the mechanisms underlying the interaction between plants and their pathogens. Network modelling represents a powerful tool that can unravel properties of complex biological systems. In this study, we aimed to use network modelling to better understand immune signalling in potato...

Hypersensitive response (HR)-conferred resistance to viral infection restricts the virus spread and is accompanied by the induction of cell death, manifested as the formation of necrotic lesions. While it is known that salicylic acid is the key component in the orchestration of the events restricting viral spread in HR, the exact function of the ce...

Dynamics of lesion expansion in cv. Rywal after PVY N605-GF Pinoculation. Lesions expansion was followed by DinoLite digital microscope in 13 independent experiments. Black arrows indicate some of the lesions which continuously expanded even in later dpi, while red arrows indicate some of the lesions which became fully developed already in early ti...

Dynamics of lesion expansion in Rywal after PVY N605-GFP infection.

Dynamics of lesion expansion in NahG-Rywal after PVY N605-GFP inoculation. Lesions expansion was followed by DinoLite digital microscope in 5 independent experiments. We observed unlimited expansion of all analyzed lesions.

(A) Number of lesions with the PVY N605-GFP accumulation detected outside the cell death zone after inoculation. Results from seven independent experiments (Exp 1–7) are presented for cv. Rywal and NahG-Rywal. At each time point (3–12 dpi) one or two plants (A,B) were analyzed (one leaf per plant). Number of positive lesions (number of lesions with...

Dynamics of lesion expansion in NahG-Rywal after PVY N605-GFP infection.

Number of lesions developed on potato leaves after inoculation with PVY N605-GFP. Lesions were counted in 16 cv. Rywal and 11 NahG-Rywal plants on all three inoculated leaves from 3 to 7 dpi and on 11 dpi to study the dynamics of lesions formation. (A) Numbers of lesions observed on each plant leaf at each time point is shown. X: detached leaf for...

The probability that the observed lesion was formed until the particular day post inoculation. The probability was calculated after PVY N605-GFP inoculation of cv. Rywal (A) and NahG-Rywal (B) plants by nonlinear regression model with logistic function.

Relative PVY RNA abundance in the systemic leaves in Rywal and NahG-Rywal plants after PVY inoculation. Relative PVY RNA abundance was determined in upper non-inoculated leaves 4 weeks after inoculation with PVY N605-GFP. Results were obtained from two independent experiments. Relative abundance of PVY RNA was followed using quantitative PCR. RNA w...

Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors...

List of primers for sequencing and colony PCR. (PDF)

Primers for sequencing and colony PCR. (PDF)

Transformation efficiencies of homemade chemically competent and electrocompetent E. coli. (PDF)

Primers used for the construction of Plant X-tender expression vectors. (PDF)

Oligonucleotides used for the amplification of Level 0 subunits by PCR. A) Oligonucleotides used for the amplification of Level 0 subunit for the assembly of expression cassette p35S::H2BRFP_tNOS. B) Oligonucleotides used for the amplification of Level 0 subunits for the assembly of multigene construct p35S::H2BRFP_tNOS + pNOS::ECFP_t35S. Nucleotid...

Optimization of assembly and transformation methods for the insert cloning into Plant X-tender expression vectors. Expression cassette p35S::H2BRFP_tNOS (insert 1) and multigene construct p35S::H2BRFP_tNOS + pNOS::CFP_t35S (insert 2) were separately assembled into pCAMBIA_ASX to determine optimal conditions for insert cloning into the expression ve...

Potato virus Y is the most economically important potato viral pathogen. We aimed at unraveling the roles of small RNAs (sRNAs) in the complex immune signaling network controlling the establishment of tolerant response of potato cv. Désirée to the virus. We constructed a sRNA regulatory network connecting sRNAs and their targets to link sRNA level...

Virus-induced systemic necrosis accounts for great yield losses in potato (Solanum tuberosum L.) cultivars susceptible to necrotic strain of Potato virus Y (PVYNTN). To extend our understanding of systemic necrosis, the tissue of healthy and PVYNTN infected potato tubers (necrotic and non-necrotic) during storage was profiled for host gene expressi...

To provide means for novel crop breeding strategies, it is crucial to understand the mechanisms underlying the interaction between plants and their pathogens. Network modelling represents a powerful tool that can unravel properties of complex biological systems. Here, we build on a reliable Arabidopsis ( Arabidopsis thaliana L.) immune signalling m...

Potato virus Y is the most economically important potato viral pathogen. We aimed at unraveling the roles of small RNAs (sRNAs) in the complex immune signaling network controlling the establishment of tolerant response of potato cv. Désirée to the virus. We constructed a sRNA regulatory network connecting sRNAs and their targets to link sRNA level...

Background Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platfo...