Publications

Genome variation in tissue culture is of importance for commercial use in plant propagation as well as for basic research on plant growth and development. RAPD fingerprinting can be used to trace genetic or epigenetic changes at the genome level. In the present paper, results of RAPD analyses on primary tissue cultures are given with particular attention to the repeatability of the method. The significance of primer binding site competition for the discovery of qualitative and quantitative DNA polymorphism is discussed.

Research perspectives towards sustainable plant production through plant breeding on abiotic stress tolerance require interdisciplinary competence. The present paper wants to strengthen awareness of important activities or current insights in plant breeding, plant nutrition and molecular biology to facilitate approximation of the disciplines and to direct efforts in molecular biology early in development towards application. As a consequence of recent discussion on appropriate approaches in systems biology towards crop improvement, a global ‘systemic strategy’ is presented to identify functional marker candidates for abiotic stress tolerance more efficiently.

Reprogramming of primary virus-infected cells is the critical step that turns viral attacks harmful to humans by initiating super-spreading at cell, organism and population levels. To develop early anti-viral therapies and proactive administration, it is important to understand the very first steps of this process. Plant somatic embryogenesis (SE) is the earliest and most studied model for de novo programming upon severe stress that, in contrast to virus attacks, promotes individual cell and organism survival. We argued that transcript level profiles of target genes established from in vitro SE induction as reference compared to virus-induced profiles can identify differential virus traits that link to harmful reprogramming. To validate this hypothesis, we selected a standard set of genes named 'ReprogVirus'. This approach was recently applied and published. It resulted in identifying 'CoV-MAC-TED', a complex trait that is promising to support combating SARS-CoV-2-induced cell reprogramming in primary infected nose and mouth cells. In this perspective, we aim to explain the rationale of our scientific approach. We are highlighting relevant background knowledge on SE, emphasize the role of alternative oxidase in plant reprogramming and resilience as a learning tool for designing human virus-defense strategies and, present the list of selected genes. As an outlook, we announce wider data collection in a 'ReprogVirus Platform' to support anti-viral strategy design through common efforts.

SUMMARY RAPD fingerprints of individual plants of Hypericum perforatum from different accessions are discussed in this paper. From a wild population, 10 offspring were investigated by genome analyses. The results obtained revealed that the collection included significantly polymorphic genotypes. Whereas 7 of the individuals displayed identical fingerprints, obviously representing the dominant genotype of this accession, a deviating but also identical genotype was shown by 2 plants and a third genotype was represented by another plant. Additionally, genome characterization of progenies from individual plants of 4 further accessions were performed. The results show that most of the fingerprints from each accession indicated an identical mode of reproduction for H perforatum. Nevertheless, non-identical progenies could be discovered as a minor event by RAPD analyses.

Recently we identified a major complex trait for early de novo programming (CoV-MAC-TED) in virus-infected human cells by using an interdisciplinary approach that integrates research in plant and human cell systems.[1,2] CoV-MAC-TED included unbalanced reactive oxygen species (ROS)/reactive nitrogen species (RNS) levels connected to increased aerobic fermentation, which was linked to alpha-tubulin–based cell restructuring and control of cell cycle progression. We suggested that adaptive ROS equilibration during the first hours of stress perception might be critical for disease performance; thus, genes involved in ROS equilibration might help target therapeutic tools.[3,4] It is easier to validate traits for resilience in plants than in humans. For validation, we considered well-established unambiguous measures, such as the differential performance of plant varieties in terms of yield height and stability, based on a priori experimentation under multiple field conditions as part of the breeding and variety registration procedures. The genetic capacity for efficient cell reprogramming on isolated and combined stresses can then be studied separately in simple laboratory experiments to explore associations and a posteriori predictability. In this way, plant research can increase the efficiency of knowledge gain for the principal determinants for resilience of holobiont organisms that live under similar environmental conditions, such as water, oxygen, nutrient availability, and temperature.In plants, the small enzyme family of mitochondrial alternative oxidase (AOX) is involved in regulating ROS/RNS homeostasis and equilibration (for example, see Scheibe[5]). Its relevance for adaptive metabolism and stress behavior was widely explored across diverse plant species and environmental threats (see detailed recent reviews in Arnholdt-Schmitt et al,[1] Costa et al,[2] Scheibe,[5] Mohanapriya et al,[6] and Bharadwaj et al[7]). Its beneficial effect in respiration-related deficiencies was also studied in transgene mammals missing this enzyme.[1,2] AOX acts at the level of early cell reprogramming and maintenance. It senses stress levels and coordinates rapid metabolic reorganization for plant plasticity and adaptive plant robustness by permanently optimizing respiration.[1,2,6–9] We hypothesize that plant genotypes, which acclimate more efficiently to changing environmental conditions, have a better chance of maintaining a healthy state that translates into the desired stable higher yield and better food-quality characteristics.[7]Here, we disclose essentials of the novel insights we obtained using two rice plant genotypes, which are known through field experience to differ in multistress (such as that caused by dehydration, cold, abscisic acid application) performance and, especially, in salt tolerance.[10,11] Our results confirm the growing understanding that rapid transcript level changes during early cell reprogramming provide appropriate markers for predicting stress-tolerant phenotypes.[1]Figure 1 presents a simplified scheme that highlights our complex concept (developed and discussed in detail by Bharadwaj et al[7]) by integrating the summarized results for rice achieved during the first 24 h after seedlings were stressed by high-salt (300 mM) treatment compared with a watered control. The watered control demonstrated high transcript levels of both expressed AOX genes, AOX1a and AOX1c, from the first hour of watering in the stress-tolerant rice variety Pokkali. These levels always remained higher than that in the salt-susceptible genotype IR29 at all observed time points (1, 2, 5, 10, and 24 h; not shown, 2–10 h). Under salt treatment, we observed the following.First, there was early downregulation of AOX1a transcript levels in the tolerant variety and recovery of total AOX to control level at 24 h. AOX downregulation indicates an important issue for AOX utility,[12] and the efficiency of downregulation from initially increased levels was shown to be important for the predictability of stress-tolerance performance.[6,7] To the contrary, in the stress-susceptible genotype, the same two AOX genes were transcribed, but no pronounced early response was observed at 1 h. Instead, total AOX transcript accumulation was significantly increased at 24 h after treatment initiation, and upregulated transcription levels were indicated for both transcribed AOX genes.Second, transcript levels of phosphofructokinase (PFK), which represent glycolysis, were found at a higher level in the tolerant genotype during the first hours. This level was linked to higher transcript levels of alcohol dehydrogenase (ADH1 and ADH2), which marks aerobic fermentation. In this context, respiration via the cyclooxygenase (COX) path remained more stable. Nevertheless, during the first 2 h, in both genotypes, a slight increase (nonsignificant) was indicated compared with the control. This seems to show that the cytochrome path began to be overloaded. However, this did not reach significance and was rapidly brought down to control levels, and then to slightly below control at 24 h, which became significant only for the tolerant variety Pokkali. In addition, we suspect that genotype-dependent microbiota interaction could influence the stress-inducible sugar availability for glycolysis or aerobic fermentation.Third, during the first hours of salt treatment, the tolerant variety signaled higher energy depletion, marked by SNRK1 transcript levels, than did the susceptible genotype. This indicates the more efficient energy-dependent cell reorganization in Pokkali.Finally, in both genotypes, differential cell reorganization or restructuration was marked by distinct tubulin transcript level changes. Under salt stress, Pokkali demonstrated increased tubulin transcript accumulation against the water control between 2 and 5 h after salt treatment began, whereas IR29 tubulin transcription remained at the basal level observed at 1 h. Additional analyses indicated that cell proliferation was arrested during the first 24 h after treatment in both genotypes (not shown). This confirmed our recent conclusions from a different experimental system (induction of somatic embryogenesis by severe stress) in which we found that the cell cycle was suppressed during early cell reprogramming.[1,2] Of note, our results show parallel transcript level changes for the two most frequently expressed tubulin genes, alpha- and beta-tubulin (α-Tub and β-Tub) for both genotypes, which we also observed in the water control (not shown). Thus, these observations confirm the approach we applied in Costa et al,[2–4] in which we selected only alpha-tubulin transcript levels as a marker for differential cell reorganization during early cell reprogramming.Overall, this report supports our hypothesis that adaptive ROS equilibration can provide a powerful means of predicting the capacity for resilient performance in plant and human virus cells when viewed during early cell reprogramming at the transcript level in crucial genes and in the context of functional marker-assisted description of energy-dependent cell reorganization and cell cycle regulation. Furthermore, our group studied exhaustively the diversity of polymorphisms in AOX genes related to diverse environments. We suggest that AOX gene diversity in target cells within an individual plant might be a trait that, by itself, allows rapid switching between diverse allelic sequences for acclimation. In parallel, we identified allelic transcript level profiles in the gene ASMTL (N-acetylserotonin methyltransferase-like) in human epithelial nasal cells, which link under viral stress to ROS/RNS balancing. Considering our overall results, we propose that these findings should be explored as promising sources of functional markers that could support prediction of differential disease development.[13,14]Supplemental data are available online with the article.

RAPD fingerprints of individual plants of Hypericum perforatum from different accessions are discussed in this paper. From a wild population, 10 offspring were investigated by genome analyses. The results obtained revealed that the collection included significantly polymorphic genotypes. Whereas 7 of the individuals displayed identical fingerprints, obviously representing the dominant genotype of this accession, a deviating but also identical genotype was shown by 2 plants and a third genotype was represented by another plant. Additionally, genome characterization of progenies from individual plants of 4 further 164accessions were performed. The results show that most of the fingerprints from each accession indicated an identical mode of reproduction for H. perforatum. Nevertheless, non-identical progenies could be discovered as a minor event by RAPD analyses. [Article copies available for afee from The Haworth Document Delivery Service: 1-800-HAWORTH. E-mail address: <getinfo@haworthpressinc.com> Website: <https://www.HaworthPress.com> © 2002 by The Haworth Press, Inc. All rights reserved.]

Rapid genomic DNA variation due to methylation and copy number alteration was observed in carrot root explants 6 h after inoculation and during a 36-h peri

Backgroung Selection of reference genes (RGs) for normalization of PCR-gene expression data includes two crucial steps: determination of the among-sample transcriptionally more stable genes and subsequent choosing of the most suitable genes as internal controls. Both steps can be carried-out through generally accepted strategies each having different strengths and weaknesses. The present study proposes to reinforce normalization of gene expression data by integrating and adding analytical revision at critical steps of those accepted procedures. Especially crucial is to counterbalance a higher representative number of RGs with a correspondent increase in their average transcriptional instability or a generalised co-expression trend among the samples. This methodological study used in vitro olive adventitious rooting as an experimental system, since the underlying morphogenetic process -wich is common to diverse species- is still not completely understood. Results Firstly, RG candidates were ranked according to transcriptional stability following a simple statistical method that reduces biasing effects of concomitant, systematic biological variations associated to experimental conditions, such as the variations caused by gene co-regulation. Those types of systematic co-variation are unconsidered by several popular ad hoc informatics programmes. To select the adequate genes among those already ranked, an algorithm of one of the ad hoc informatics programmes (GeNorm) was adapted to allow partial automatization of RG selection for any strategy of transcriptional-gene stability ordering. In order to delve into the resulting possible RG sets suitability for inter-assay comparisons and technical-error compensation, separate statistics were formulated. The achieved results were compared with those obtained by standard stability ranking methods. Finally, a double evaluation was performed to accurately contrast two choice RG sets. The whole strategy was applied to a panel considering several independent factors, but the suitability of the obtained putative RG sets was tested for cases restricted to fewer variables. H2B , OUB and ACT are valid for normalization in transcriptional studies on olive microshoot rooting when comparing treatments, time points and assays. Conclusions The set of genes identified as internal reference is now available for wider expression studies on any target gene in similar biological systems. The overall methodology aims to constitute a guide for general application.