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Oat (Avena sativa L.) has recently gained importance due to the discovery of a variety of health benefits and new opportunities of use. There is no efficient protocol for the production of oat doubled haploid (DH) lines. The aim of this study was to increase the efficiency of obtaining DHs of oat by the wide crossing method. The study was performed on five oat genotypes. We have compared the induction of embryos after pollination with maize, sorghum and millet pollen as well as the development of haploid embryos isolated 2, 3 and 4 weeks after pollination and cultivated on media with different sugar content. Haploid plants were treated with colchicine after or before acclimation to natural conditions. Of the three types of pollen used, the largest number of haploid embryos was obtained using maize pollen. Three weeks after pollination was the most suitable time for the isolation and cultivation of the embryos. The most efficient medium enabling the development of embryos and conversion to plants was 190-2 containing 9% of maltose. Colchicine treatment of acclimated plants provided high survival rate.

Purpose: Developing innovative precision and personalized cancer therapeutics is essential to enhance cancer survivability, particularly for prevalent cancer types such as colorectal cancer. This study aims to demonstrate various approaches for discovering new targets for precision therapies using artificial intelligence (AI) on a Polish cohort of colorectal cancer patients., Methods: We analyzed 71 patients with histopathologically confirmed advanced resectional colorectal adenocarcinoma. Whole exome sequencing was performed on tumor and peripheral blood samples, while RNA sequencing (RNAseq) was conducted on tumor samples. We employed three approaches to identify potential targets for personalized and precision therapies. First, using our in-house neoantigen calling pipeline, ARDentify, combined with an AI-based model trained on immunopeptidomics mass spectrometry data (ARDisplay), we identified neoepitopes in the cohort. Second, based on recurrent mutations found in our patient cohort, we selected corresponding cancer cell lines and utilized knock-out gene dependency scores to identify synthetic lethality genes. Third, an AI-based model trained on cancer cell line data was employed to identify cell lines with genomic profiles similar to selected patients. Copy number variants and recurrent single nucleotide variants in these cell lines, along with gene dependency data, were used to find personalized synthetic lethality pairs., Results: We identified approximately 8,700 unique neoepitopes, but none were shared by more than two patients, indicating limited potential for shared neoantigenic targets across our cohort. Additionally, we identified three synthetic lethality pairs: the well-known APC-CTNNB1 and BRAF-DUSP4 pairs, along with the recently described APC-TCF7L2 pair, which could be significant for patients with APC and BRAF variants. Furthermore, by leveraging the identification of similar cancer cell lines, we uncovered a potential gene pair, VPS4A and VPS4B, with therapeutic implications., Conclusion: Our study highlights three distinct approaches for identifying potential therapeutic targets in cancer patients. Each approach yielded valuable insights into our cohort, underscoring the relevance and utility of these methodologies in the development of precision and personalized cancer therapies. Importantly, we developed a novel AI model that aligns tumors with representative cell lines using RNAseq and methylation data. This model enables us to identify cell lines closely resembling patient tumors, facilitating accurate selection of models needed for in vitro validation., Competing Interests: Authors VMP, PS, AZ, MBa, PB, WC, OG, ŁG, MKam, BK-J, JM-G, GM, RS, JWi, MP, MJ, MWa, JK and AB were employed by Ardigen SA. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Murcia Pienkowski, Skoczylas, Zaremba, Kłęk, Balawejder, Biernat, Czarnocka, Gniewek, Grochowalski, Kamuda, Król-Józaga, Marczyńska-Grzelak, Mazzocco, Szatanek, Widawski, Welanyk, Orzeszko, Szura, Torbicz, Borys, Wohadlo, Wysocki, Karczewski, Markowska, Kucharczyk, Piatek, Jasiński, Warchoł, Kaczmarczyk, Blum and Sanecka-Duin.)

Pollution of arable land with heavy metals is a worldwide problem. Cadmium (Cd) is a toxic metal that poses a severe threat to humans' and animals' health and lives. Plants can easily absorb Cd from the soil, and plant-based food is the main means of exposure to this hazardous element for humans and animals. Phytoremediation is a promising plant-based approach to removing heavy metals from the soil, and plant growth-promoting micro-organisms such as the fungi Trichoderma can enhance the ability of plants to accumulate metals. Inoculation of Avena sativa L. (oat) with Trichoderma viride enhances germination and seedling growth in the presence of Cd and, in this study, the growth of 6-month-old oat plants in Cd-contaminated soil was not increased by inoculation with T. viride , but a 1.7-fold increase in yield was observed. The content of Cd in oat shoots depended on the Cd content in the soil. Still, it was unaffected by the inoculation with T. viride . A. sativa metallothioneins (AsMTs) participate in plant-fungi interaction, however, their role in this study depended on MT type and Cd concentration. The inoculation of A. sativa with T. viride could be a promising approach to obtaining a high yield in Cd-contaminated soil without increasing the Cd content in the plant.

Water deficit affects the growth as well as physiological and biochemical processes in plants. The aim of this study was to determine differences in physiological and biochemical responses to drought stress in two wheat cultivars-Chinese Spring (CS) and SQ1 (which are parents of a mapping population of doubled haploid lines)-and to relate these responses to final yield and agronomic traits. Drought stress was induced by withholding water for 14 days, after which plants were re-watered and maintained until harvest. Instantaneous gas exchange parameters were evaluated on the 3rd, 5th, 10th, and 14th days of seedling growth under drought. After 14 days, water content and levels of chlorophyll a + b , carotenoids, malondialdehyde, soluble carbohydrates, phenolics, salicylic acid, abscisic acid (ABA), and polyamines were measured. At final maturity, yield components (grain number and weight), biomass, straw weight, and harvest index were evaluated. Physiological and biochemical parameters of CS responded more than those of SQ1 to the 14-day drought, reflected in a greater reduction in final biomass and yield in CS. Marked biochemical differences between responses of CS and SQ1 to the drought were found for soluble carbohydrates and polyamines. These would be good candidates for testing in the mapping population for the coincidence of the genetic control of these traits and final biomass and yield.

Background and Aims: Histological disease activity in inflammatory bowel disease [IBD] is associated with clinical outcomes and is an important endpoint in drug development. We developed deep learning models for automating histological assessments in IBD., Methods: Histology images of intestinal mucosa from phase 2 and phase 3 clinical trials in Crohn's disease [CD] and ulcerative colitis [UC] were used to train artificial intelligence [AI] models to predict the Global Histology Activity Score [GHAS] for CD and Geboes histopathology score for UC. Three AI methods were compared. AI models were evaluated on held-back testing sets, and model predictions were compared against an expert central reader and five independent pathologists., Results: The model based on multiple instance learning and the attention mechanism [SA-AbMILP] demonstrated the best performance among competing models. AI-modelled GHAS and Geboes subgrades matched central readings with moderate to substantial agreement, with accuracies ranging from 65% to 89%. Furthermore, the model was able to distinguish the presence and absence of pathology across four selected histological features, with accuracies for colon in both CD and UC ranging from 87% to 94% and for CD ileum ranging from 76% to 83%. For both CD and UC and across anatomical compartments [ileum and colon] in CD, comparable accuracies against central readings were found between the model-assigned scores and scores by an independent set of pathologists., Conclusions: Deep learning models based upon GHAS and Geboes scoring systems were effective at distinguishing between the presence and absence of IBD microscopic disease activity., (© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation.)

As a result of oat (Avena sativa L.) × maize (Zea mays L.) crossing, maize chromosomes may not be completely eliminated at the early stages of embryogenesis, leading to the oat × maize addition (OMA) lines development. Introgression of maize chromosomes into oat genome can cause morphological and physiological modifications. The aim of the research was to evaluate the leaves' anatomy, chlorophyll a fluorescence, and yield parameter of oat doubled haploid (DH) and OMA lines obtained by oat × maize crossing. The present study examined two DH and two disomic OMA lines and revealed that they differ significantly in the majority of studied traits, apart from: the number of cells of the outer bundle sheath; light energy absorption; excitation energy trapped in PSII reaction centers; and energy dissipated from PSII. The OMA II line was characterized by larger size of single cells in the outer bundle sheath and greater number of seeds per plant among tested lines., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Warchoł et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Rapeseed oil, constituting 12% of global vegetable oil production, is susceptible to quality degradation due to stress-induced incomplete seed degreening, fatty acid oxidation, or poor nutrient accumulation. We hypothesise that the hyperphosphorylated nucleotide alarmone ppGpp (guanosine tetraphosphate), acts as a pivotal regulator of these processes, given its established roles in nutrient management, degreening, and ROS regulation in leaves. Using qPCR, UHPLC-MS/MS, and biochemical methods, our study delves into the impact of ppGpp on seed nutritional value. We observed a positive correlation between ppGpp levels and desiccation, and a negative correlation with photosynthetic pigment levels. Trends in antioxidant activity suggest that ppGpp may negatively influence peroxidases, which are safeguarding against chlorophyll decomposition. Notably, despite increasing ppGpp levels, sugars, proteins and oils appear unaffected. This newfound role of ppGpp in seed development suggests it regulates the endogenous antioxidant system during degreening and desiccation, preserving nutritional quality. Further validation through mutant-based research is needed., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Aims: Due to the lack of experimental databases, together with the chemical complexity and the dynamic nature of plants' metabolome, most of the metabolites in complex biological materials (like plant in vitro tissue cultures) are not-annotated, unidentified metabolites. In this study, a method for further metabolite characterization and classification based on the UPLC-HESI-HRMS/MS approach for small-leaved basil (Ocimum basilicum L. var. minimum Alef.) callus and cell suspension culture is presented., Key Results: A total of 2168 metabolic features were detected, out of which the database for exact mass metabolic profiling for 1949 metabolites is presented here since there is no available database dedicated to O. basilicum. We further focused on secondary metabolites (particularly phenolic compounds). The presence of 60 different phenolic compounds belonging mainly to the groups of flavonoids, glycosides, terpenoids, and phenolic acids is confirmed. By comparing relative abundances of phenolic compounds from callus culture and cell suspension culture, both grown on two types of media, via svd-PCА, univariate analysis, post-hoc tests, and heatmapping of metabolites, we provided a practical example of how resources presented here can be further applied in tissue culture-based basil metabolomics studies., Utility: This study represents the first approach toward routine targeted investigation of secondary metabolites in basil in vitro cultures and provides various opportunities for new-generation analyses., (© 2024 Scandinavian Plant Physiology Society.)

Stevia rebaudiana Bertoni possesses various medicinal and food industrial applications. This study is the first to explore the effect of the cytokinins meta-Topolin (mT; 6-(3-hydroxybenzylamino) purine), zeatin, kinetin, and BAP (6-benzylaminopurine) at concentrations of 0 (control), 5, 10, and 15 µM on shoot multiplication, as well as stevioside, rebaudioside A, phenolic acid, and flavonoid content in bioreactor cultures. The highest number of shoots (23.4 per explant) was obtained in the medium containing 5 μM of mT. However, 15 μM of mT was superior for fresh biomass production and dry biomass accumulation. Reversed-phase (RP)-HPLC analysis showed a beneficial effect of 5 μM mT on stevioside (11.43 mg/g dry weight [DW]) and rebaudioside A (10.74 mg/g DW) biosynthesis. In all conditions, the ratio of rebaudioside A/stevioside ranged from 0.75 to 1.12. The phenolic acids chlorogenic, neochlorogenic, isochlorogenic A, and rosmarinic were confirmed in the stevia extracts, as were the flavonoids isoquercetin, and quercitrin. The highest accumulations of chlorogenic and neochlorogenic acids and flavonoids were observed in shoot tissues derived from 5 µM mT, whereas 5 µM of BAP stimulated biosynthesis of chlorogenic, isochlorogenic A, and rosmarinic acids. This is the first report on the use of mT-cytokinin showing high potential in stevia cultures., (© 2023. Springer Nature Limited.)

Plant growth and the process of yield formation in crops are moderated by surrounding conditions, as well as the interaction of the genetic background of plants and the environment. In the last two decades, significant climatic changes have been observed, generating unfavorable and harmful impacts on plant development. Drought stress can be considered one of the most dangerous environmental factors affecting the life cycle of plants, reducing biomass production and, finally, the yield. Plants can respond to water deficit in a wide range, which depends on the species, genetic variability within the species, the plant's ontogenesis stage, the intensity of the stress, and other potential stress factors. In plants, it is possible to observe hybrids between different taxa that certain traits adopted to tolerate stress conditions better than the parent plants. Oat × maize addition (OMA) plants are good examples of hybrids generated via wide crossing. They can exhibit morphological, physiological, and biochemical variations implemented by the occurrence of extra chromosomes of maize, as well as the interaction of maize and oat chromatin. The initial goal of the study was to identify OMA lines among plants produced by wide crossing with maize. The main goal was to investigate differences in OMA lines according to the Excised Leaf Water Loss (ELWL) test and to identify specific biochemical changes and agronomic traits under optimal water conditions and soil drought. Additionally, detection of any potential alterations that are stable in F2 and F3 generations. The aforementioned outcomes were the basis for the selection of OMA lines that tolerate growth in an environment with limited water availability. The molecular analysis indicated 12.5% OMA lines among all tested descendants of wide oat-maize crossing. The OMA lines significantly differ according to ELWL test results, which implies some anatomical and physiological adaptation to water loss from tissues. On the first day of drought, plants possessed 34% more soluble sugars compared to control plants. On the fourteen day of drought, the amount of soluble sugars was reduced by 41.2%. A significant increase of phenolic compounds was observed in the fourteen day of drought, an average of 6%, even up to 57% in line 9. Soil drought substantially reduced stem biomass, grains number, and mass per plant. Lower water loss revealed by results of the ELWL test correlated with the high yield of OMA lines. Phenolic compound content might be used as a biochemical indicator of plant drought tolerance since there was a significant correlation with the high yield of plants subjected to soil drought.

Background: Numerous studies have shown that in Crohn's disease (CD), the gut microbiota is of great importance in the induction and maintenance of inflammation in the gastrointestinal tract. Until recently, studies have focused almost exclusively on bacteria in the gut. Lately, more attention has been paid to the role of intestinal fungi., Aim: To study the gut mycobiome analysis of pediatric patients with CD (in different stages of disease activity) compared to healthy children., Methods: Fecal samples were collected from patients: With active, newly diagnosed CD ( n = 50); active but previously diagnosed and treated CD ( n = 16); non-active CD and who were in clinical remission ( n = 39) and from healthy volunteers ( n = 40). Fungal DNA was isolated from the samples . Next, next generation sequencing (MiSeq, Illumina) was performed. The composition of mycobiota was correlated with clinical and blood parameters., Results: Candida spp. were overrepresented in CD patients, while in the control group, the most abundant genus was Saccharomyces . In CD patients, the percentage of Malassezia was almost twice that of the control ( P < 0.05). In active CD patients, we documented a higher abundance of Debaryomyces hansenii ( D. hansenii ) compared to the non-active CD and control ( P < 0.05) groups. Moreover, statistically significant changes in the abundance of Mycosphaerella , Rhodotorula , and Microidium were observed. The analyses at the species level and linear discriminant analysis showed that in each group it was possible to distinguish a specific species characteristic of a given patient population. Moreover, we have documented statistically significant correlations between: D. hansenii and patient age (negative); C. zeylanoides and patient age (positive); C. dubliniensis and calprotectin (positive); C. sake and calprotectin (positive); and C. tropicalis and pediatric CD activity index (PCDAI) (positive)., Conclusion: Mycobiome changes in CD patients, and the positive correlation of some species with calprotectin or PCDAI, give strong evidence that fungi may be of key importance in the development of CD., Competing Interests: Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article., (©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved.)

Drought is one of the major threats to food security. Among several mechanisms involved in plant stress tolerance, one protein family-the plant metallothioneins (MTs)-shows great promise for enhancing drought resistance. Plant metallothioneins in oat (Avena sativa L.) have not yet been deeply analysed, and the literature lacks a comprehensive study of the whole family of plant MTs in response to drought. In this study, we showed that the number and nature of cis-elements linked with stress response in promoters of AsMTs1-3 differed depending on the MT type. Drought stress in oat plants caused an increase in the expression of AsMT2 and AsMT3 and a decrease in the expression of AsMT1 compared to well-watered plants. Moreover, the low values of relative water content, water use efficiency, net photosynthesis (P N ), transpiration (E), stomatal conductance (g s ), chlorophyll a, and carotenoid were accompanied by high levels of electrolyte leakage, internal CO 2 concentration (C i ) and abscisic acid content, and high activity of antioxidants enzymes in plants under drought stress. The present study puts forward the idea that AsMTs are crucial for oat response to drought stress not only by regulating antioxidant activity but also by changing the plant water regime and photosynthesis. Our results support the hypothesis that structural differences among types of plant MTs reflect their diversified physiological roles., (© 2023. The Author(s).)

Light-emitting diodes (LEDs) have emerged as efficient light sources for promoting in vitro plant growth and primary and secondary metabolite biosynthesis. This study investigated the effects of blue, red, and white-red LED lights on plant biomass growth, photosynthetic pigments, soluble sugars, phenolic compounds, the production of Amaryllidaceae alkaloids, and the activities of antioxidant enzymes in Leucojum aestivum L. cultures. A white fluorescent light was used as a control. The plants that were grown under white-red and red light showed the highest fresh biomass increments. The blue light stimulated chlorophyll a , carotenoid, and flavonoid production. The white-red and blue lights were favourable for phenolic acid biosynthesis. Chlorogenic, p -hydroxybenzoic, caffeic, syringic, p -coumaric, ferulic, sinapic, and benzoic acids were identified in plant materials, with ferulic acid dominating. The blue light had a significant beneficial effect both on galanthamine (4.67 µg/g of dry weight (DW)) and lycorine (115 µg/g DW) biosynthesis. Red light treatment increased catalase and superoxide dismutase activities, and high catalase activity was also observed in plants treated with white-red and blue light. This is the first report to provide evidence of the effects of LED light on the biosynthesis of phenolic acid and Amaryllidaceae alkaloids in L. aestivum cultures, which is of pharmacological importance and can propose new strategies for their production.

Glaucous (811, L35, and RXL10) and non-glaucous (811bw, L35bw, and RXL10bw) near-isogenic lines (NILs) of rye (Secale cereale L.) forming three pairs of inbred lines were the subject of the research. The research aimed to study the relationship between wax cover attributes and the physio-biochemical drought reactions and yield of rye NILs and to uncover the differences in drought resistance levels of these lines. The greatest differences between glaucous and non-glaucous NILs were observed in the RXL10/RXL10bw pair. Of particular note were the stable grain number and the thousand grain weight of the non-glaucous line RXL10bw under drought and the accompanying reactions, such as an approximately 60% increase in MDA and a two-fold increase in wax amount, both of which were significantly higher than in the glaucous line RXL10 and in other NILs. The surprisingly high level of MDA in the RXL10bw line requires further analysis. Moreover, additional wax crystal aggregates were found under drought conditions on the abaxial leaf surface of the glaucous lines 811 and RXL10. The use of rye NILs indicated that line-specific drought resistance could be associated with wax biosynthetic pathways involved in physiological and biochemical responses important for increased drought resistance., (© 2022. The Author(s).)

Leucojum aestivum is known for its ability to biosynthesize alkaloids with therapeutic properties, among which galanthamine used for the treatment of Alzheimer's disease. New sources of this alkaloid are still being explored. In this study, a novel strain PLV of endophytic bacterium Paenibacillus lautus was isolated from in vitro L. aestivum plants. We report the whole genome sequence of that strain and its capacity to produce alkaloids and growth regulators. The effect of elicitation with autoclaved bacteria on the production of alkaloids was examined. Ten alkaloids were identified in bacteria extracts: galanthamine, lycorine, ismine, lycoramine, haemanthamine, tazettine, galanthine, homolycorine, 1,2-dihydrochlidanthine, and hippeastrine. The mean contents of galanthamine and lycorine were 37.51 µg/g of dry weight (DW) and 129.93 µg/g of DW, respectively. Moreover, isolated P. lautus strain synthesized: indole-3-acetic acid, t-zeatin, c-zeatin, kinetin, gibberellin A 1 , abscisic acid, salicylic acid, benzoic acid. In vitro elicitation of cultures with P. lautus increased dry biomass, stimulated galanthamine and lycorine production, contributed to 8,9-desmethylenebis (oxy)-7,9 dimethoxy-crinan biosynthesis, change pigments content, and antioxidant enzymes activities. Our findings for the first time point out that galanthamine can be synthesized by an microorganism. Moreover isolated strain can be used as a new elictor of Amaryllidaceae alkaloids biosynthesis., (© 2022. The Author(s).)

Background: Development of new cultivars is one of the vital options for adapting agriculture to climate change, and the production of doubled haploid (DH) plants can make a significant contribution to accelerating the breeding process. Oat is one of the cereals with particular health benefits, but it unfortunately still remains recalcitrant to haploidization. Our previous studies have clearly demonstrated that post-pollination with hormone treatment is a key step in haploid production through wide hybridization and indicated it as the most effective method for this species. Therefore, we subsequently addressed the problem of the influence of 2,4-dichlorophenoxyacetic acid (2,4-D) concentration on consecutive stages of DH production., Methods: Twenty-nine genotypes were tested, 9,465 florets were pollinated with maize pollen 2 days after emasculation and then treated with 2,4-D at 50 mg/L and 100 mg/L., Results: The applied treatments did not reveal any differences in the number of obtained haploid embryos. However, almost twice as many haploid plants formed on MS medium after applying a higher auxin concentration and 20% more successfully acclimatized. Moreover, 100 mg/L 2,4-D treatment resulted in twice as many DH lines that produced almost three times more seeds compared to 50 mg/L treatment. Nevertheless, the results have confirmed the existence of strong genotypic variation, which may significantly limit the development of an effective and economically feasible method that could be incorporated into breeding programs., Competing Interests: The authors declare there are no competing interests., (©2022 Juzoń et al.)

A critical step in the production of doubled haploids is a conversion of the haploid embryos into plants. Our study aimed to recognize the reasons for the low germination rate of Avena sativa haploid embryos obtained by distant crossing with maize. Oat cultivars of 'Krezus' and 'Akt' were investigated regarding embryo anatomy, the endogenous phytohormone profiles, and antioxidant capacity. The zygotic embryos of oat were used as a reference. It was found that twenty-one days old haploid embryos were smaller and had a less advanced structure than zygotic ones. Morphology and anatomy modifications of haploid embryos were accompanied by extremely low levels of endogenous auxins. Higher levels of cytokinins, as well as tenfold higher cytokinin to auxin ratio in haploid than in zygotic embryos, may suggest an earlier stage of development of these former. Individual gibberellins reached higher values in 'Akt' haploid embryos than in the respective zygotic ones, while the differences in both types of 'Krezus' embryos were not noticed. Additionally to the hormonal regulation of haploid embryogenesis, the poor germination of oat haploid embryos can be a result of the overproduction of reactive oxygen species, and therefore higher levels of low molecular weight antioxidants and stress hormones., (© 2022. The Author(s).)

Oat ( Avena sativa L.) cultivars 'Bingo' and 'Chwat' were used to compare the embryogenesis competence of another culture. Despite the embryo-like structures obtained from both tested cultivars, only 'Chwat' produced green plantlets, which confirmed the cultivar dependency. 'Chwat' produced the highest number of embryo-like structures and green plantlets (0.7/100 anthers and 0.1/100 anthers, respectively). The embryo-like structure formation also depended on cold pretreatment combined with Cu 2+ , Zn 2+ , or Ag + ion supplementation, which was applied during the tiller pretreatment or added to the induction media. The highest number of embryo-like structures (2.1/100 anthers) were observed on anthers derived from the tillers kept in a 50% Hoagland medium with the addition of 10 µM of CuSO 4 . In turn, the induction media supplemented with the ions Cu 2+ , Zn 2+ , or Ag + increased neither the number of embryo-like structures nor the green plantlet production compared to the control conditions. However, such ion applications turned out to be most effective when the induction medium was enriched with 25 µM of AgNO 3 and left to obtain the highest number of embryo-like structures and green plantlets (0.8/100 anthers and 0.2/100 anthers, respectively). Therefore, more attention should be paid to the possibilities of adjusting the media nutrient composition, as this may be the only way to significantly increase the efficiency of this method.

Wide hybridization is one of the haploid-inducing techniques that can accelerate the breeding process. Obtaining new cultivars is crucial to solve the problem of the constantly growing world population and global increase in demand for food, feed and renewable energy under changing environmental conditions. Here, we present a detailed protocol for obtaining oat (Avena sativa L.) doubled haploids (DHs) by pollination with maize (Zea mays L.). After fertilization, not only oat homozygotes, but also oat × maize hybrid zygotes can be formed, and during early embryo development, maize chromosomes are preferentially eliminated, which ultimately results in haploid plant formation. This chapter describes a method to produce oat DHs by crossing oat with maize, covering all steps from crossings to haploid plant regeneration and chromosome doubling., (© 2021. Springer Science+Business Media, LLC, part of Springer Nature.)

Production of doubled haploids (DHs) by androgenesis is a promising and convenient alternative to traditionally used breeding techniques. Low response of anther culture and strong genotype dependency in the development of embryo-like structures (ELS) was reported for oat (Avena sativa L.). Total homozygosity has been reached in one generation. This chapter describes a step-by-step protocol that can be useful for androgenesis studies and oat DH line production through anther culture., (© 2021. Springer Science+Business Media, LLC, part of Springer Nature.)

The oat × maize chromosome addition (OMA) lines, as hybrids between C3 and C4 plants, can potentially help us understand the process of C4 photosynthesis. However, photosynthesis is often affected by adverse environmental conditions, including drought stress. Therefore, to assess the functioning of the photosynthetic apparatus in OMA lines under drought stress, the chlorophyll content and chlorophyll a fluorescence (CF) parameters were investigated. With optimal hydration, most of the tested OMA lines, compared to oat cv. Bingo, showed higher pigment content, and some of them were characterized by increased values of selected CF parameters. Although 14 days of drought caused a decrease of chlorophylls and carotenoids, only slight changes in CF parameters were observed, which can indicate proper photosynthetic efficiency in most of examined OMA lines compared to oat cv. Bingo. The obtained data revealed that expected changes in hybrid functioning depend more on the specific maize chromosome and its interaction with the oat genome rather than the number of retained chromosomes. OMA lines not only constitute a powerful tool for maize genomics but also are a source of valuable variation in plant breeding, and can help us to understand plant susceptibility to drought. Our research confirms more efficient functioning of hybrid photosynthetic apparatus than oat cv. Bingo, therefore contributes to raising new questions in the fields of plant physiology and biochemistry. Due to the fact that the oat genome is not fully sequenced yet, the mechanism of enhanced photosynthetic efficiency in OMA lines requires further research.

Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods to infer protein levels from other omics measurements, we leveraged crowdsourcing via the NCI-CPTAC DREAM proteogenomic challenge. We asked for methods to predict protein and phosphorylation levels from genomic and transcriptomic data in cancer patients. The best performance was achieved by an ensemble of models, including as predictors transcript level of the corresponding genes, interaction between genes, conservation across tumor types, and phosphosite proximity for phosphorylation prediction. Proteins from metabolic pathways and complexes were the best and worst predicted, respectively. The performance of even the best-performing model was modest, suggesting that many proteins are strongly regulated through translational control and degradation. Our results set a reference for the limitations of computational inference in proteogenomics. A record of this paper's transparent peer review process is included in the Supplemental Information., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

The aim of the present study was to evaluate the effect of osmotic stress caused by polyethylene glycol (PEG) 6000 in hydroponic culture on wheat seedlings of drought-resistant Chinese Spring (CS) and drought-susceptible SQ1 cultivar, and to examine the alleviative role of exogenous polyamines (PAs) applied to the medium. The assessment was based on physiological (chlorophyll a fluorescence kinetics, chlorophyll and water content) as well as biochemical (content of carbohydrates, phenols, proline, salicylic and abscisic acid, activity of low molecular weight antioxidants) parameters, measured after supplementation with PAs (putrescine, spermidine and spermine) on the 3rd, 5th and 7th day of the treatment. The results indicate that PAs ameliorate the effects of stress, indirectly and conditionally inducing stress tolerance of wheat seedlings. In contrast to the susceptible SQ1, the resistant CS cultivar activated its protective mechanisms, adjusting the degree of their activation to the level of the stress, depending on the genetic resources of the plant. Increased accumulation of antioxidants in the resistant CS in response to stress after the application of PAs confirms the hypothesis that PAs are involved in the signaling pathway determining the antioxidative response and the tolerance of wheat plants to drought stress.

The nucleus architecture of hybrid crop plants is not a well-researched topic, yet it can have important implications for their genetic stability and usefulness in the successful expression of agronomically desired traits. In this work we studied the spatial distribution of introgressed maize chromatin in oat × maize addition lines with the number of added maize chromosomes varying from one to four. The number of chromosome additions was confirmed by genomic in situ hybridization (GISH). Maize chromosome-specific simple sequence repeat (SSR) markers were used to identify the added chromosomes. GISH on 3-D root and leaf nuclei was performed to assess the number, volume, and position of the maize-chromatin occupied regions. We revealed that the maize chromosome territory (CT) associations of varying degree prevailed in the double disomic lines, while CT separation was the most common distribution pattern in the double monosomic line. In all analyzed lines, the regions occupied by maize CTs were located preferentially at the nuclear periphery. A comparison between the tissues showed that the maize CTs in the leaf nuclei are positioned closer to the center of the nucleus than in the root nuclei. These findings shed more light on the processes that shape the nucleus architecture in hybrids.

Background: Leucojum aestivum L. is an important medicinal plant which produces Amaryllidaceae alkaloids, especially galanthamine and lycorine. Research is currently exploring the possibility of producing these alkaloids using biotechnological methods, including in vitro cultures. The biosynthesis of alkaloids may be affected by the types and concentrations of carbohydrate sources used in the medium. In the present investigation we performed such studies on in vitro cultures of L. aestivum with a view to obtaining plant material of good quality, characterized, in particular, by a high content of valuable Amaryllidaceae alkaloids., Methods: We examined the effects of various types of carbohydrate sources-sucrose, glucose, fructose and maltose-at different concentrations (30, 60 and 90 g/L)-on the quality of L. aestivum plants grown in the RITA ® bioreactor. The plants' quality was assessed by their biomass increments, as well by as analysing photosynthetic pigments, endogenous sugar, phenolics and Amaryllidaceae alkaloid content. We also investigated the effect of sugars on the activity of the antioxidant enzymes catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD)., Results: The highest biomass increments were observed in plants cultivated in the medium containing 90 g/L sucrose. The highest CAT activity was noted in cultures growing in the medium supplemented with 90 g/L maltose, while the highest POD activity was observed in the presence of 90 g/L fructose and 60 g/L maltose. No differences in SOD activity were observed. Moreover, the sugars did not affect the contents of chlorophyll a and carotenoids, whereas the highest amount of chlorophyll b was recorded in plants growing in the medium with 60 g/L maltose. No statistically significant differences were observed in the contents of endogenous sugars and phenolics in any in vitro conditions. However, the addition of sugar had a decisive effect on the biosynthesis of the Amaryllidaceae alkaloids. The highest distribution of alkaloids occurred in plants cultured in the medium containing 60 g/L sucrose. Six Amaryllidaceae alkaloids were detected in the plant tissue. The addition of 30 g/L fructose in the medium resulted in the accumulation of five alkaloids, including ismine, which was not identified in other analysed tissues. The highest concentration of galanthamine was observed in plants cultured in the presence of 30 g/L fructose and 60 g/L sucrose (39.2 and 37.5 µg/g of dry weight (DW), respectively). The plants grown in the medium containing 60 g/L sucrose exhibited the highest lycorine content (1048 µg/g of DW)., Conclusions: The type and concentration of sugar used in the medium have an essential influence on the biosynthesis of Amaryllidaceae alkaloids in L. aestivum plants cultured in a RITA ® bioreactor. The results point to an interesting approach for commercial production of galanthamine and lycorine., Competing Interests: The authors declare that they have no competing interests., (© 2020 Ptak et al.)

Designing a molecule with desired properties is one of the biggest challenges in drug development, as it requires optimization of chemical compound structures with respect to many complex properties. To improve the compound design process, we introduce Mol-CycleGAN-a CycleGAN-based model that generates optimized compounds with high structural similarity to the original ones. Namely, given a molecule our model generates a structurally similar one with an optimized value of the considered property. We evaluate the performance of the model on selected optimization objectives related to structural properties (presence of halogen groups, number of aromatic rings) and to a physicochemical property (penalized logP). In the task of optimization of penalized logP of drug-like molecules our model significantly outperforms previous results.

A doubled haploid population of 94 lines from the Chinese Spring × SQ1 wheat cross (CSDH) was used to evaluate additive and epistatic gene action effects on total phenolic content, grain yield of the main stem, grain number per plant, thousand grain weight, and dry weight per plant at harvest based on phenotypic and genotypic observations of CSDH lines. These traits were evaluated under moderate and severe drought stress and compared with well-watered plants. Plants were grown in pots in an open-sided greenhouse. Genetic parameters, such as additive and epistatic effects, affecting total phenolic content, were estimated for eight year-by-drought combinations. Twenty-one markers showed a significant additive effect on total phenolic content in all eight year-by-drought combinations. These markers were located on chromosomes: 1A, 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4A, and 4D. A region on 4AL with a stable QTL controlling the phenolic content, confirmed by various statistical methods is particularly noteworthy. In all years and treatments, three markers significantly linked to QTLs have been identified for both phenols and yield. Thirteen markers were coincident with candidate genes. Our results indicated the importance of both additive and epistatic gene effects on total phenolic content in eight year-by-drought combinations.

Background: The oat × maize addition (OMA) lines are used for mapping of the maize genome, the studies of centromere-specific histone (CENH3), gene expression, meiotic chromosome behavior and also for introducing maize C4 photosynthetic system to oat. The aim of our study was the identification and molecular-cytogenetic characterization of oat × maize hybrids., Methods: Oat DH lines and oat × maize hybrids were obtained using the wide crossing of Avena sativa L. with Zea mays L. The plants identified as having a Grande-1 retrotransposon fragment, which produced seeds, were used for genomic in situ hybridization (GISH)., Results: A total of 138 oat lines obtained by crossing of 2,314 oat plants from 80 genotypes with maize cv. Waza were tested for the presence of maize chromosomes. The presence of maize chromatin was indicated in 66 lines by amplification of the PCR product (500 bp) generated using primers specific for the maize retrotransposon Grande-1 . Genomic in situ hybridization (GISH) detected whole maize chromosomes in eight lines (40%). All of the analyzed plants possessed full complement of oat chromosomes. The number of maize chromosomes differed between the OMA lines. Four OMA lines possessed two maize chromosomes similar in size, three OMA-one maize chromosome, and one OMA-four maize chromosomes. In most of the lines, the detected chromosomes were labeled uniformly. The presence of six 45S rDNA loci was detected in oat chromosomes, but none of the added maize chromosomes in any of the lines carried 45S rDNA locus. Twenty of the analyzed lines did not possess whole maize chromosomes, but the introgression of maize chromatin in the oat chromosomes. Five of 66 hybrids were shorter in height, grassy type without panicles. Twenty-seven OMA lines were fertile and produced seeds ranging in number from 1-102 (in total 613). Sixty-three fertile DH lines, out of 72 which did not have an addition of maize chromosomes or chromatin, produced seeds in the range of 1-343 (in total 3,758). Obtained DH and OMA lines were fertile and produced seeds., Discussion: In wide hybridization of oat with maize, the complete or incomplete chromosomes elimination of maize occur. Hybrids of oat and maize had a complete set of oat chromosomes without maize chromosomes, and a complete set of oat chromosomes with one to four retained maize chromosomes., Competing Interests: Zygmunt Nita and Krystyna Werwińska are employed by Plant Breeding Strzelce Ltd., PBAI Group.

Background: Melatonin (MEL) is a signaling molecule in plants that affects developmental processes during vegetative and reproductive growth. Investigations have proved that exogenously applied MEL also has the potential to improve seed germination and plant development., Methods: In the present study, seeds of stevia, a species with a very low germination rate, were germinated on an agar gel (AG) containing MEL at various concentrations (5, 20, 100, and 500 µM) in light. Seeds germinated on AG without MEL were used as controls. For the first 24 or 48 h of germination, the seeds were maintained in darkness as a pre-incubation step. Some seeds were not exposed to this pre-incubation step., Results: At concentrations of 20 and 5 µM, MEL significantly improved germination, but only in seeds pre-incubated in darkness for 24 h ( p  < 0.001). At concentrations of 100 and 500 µM, MEL had an inhibitory effect on germination, regardless of the pre-incubation time. Melatonin also affected plantlet properties. At a concentration of 20 µM, MEL increased plantlet fresh weight and leaf numbers. At a concentration of 5 µM, it promoted plantlet height. Regarding root development, the most favorable MEL concentration was 500 µM. Biochemical analysis revealed that MEL promoted higher pigment concentrations but hampered superoxide dismutase activity. On the other hand, the concentrations of sugars and phenolics, as well as the activities of catalase and peroxidase, increased at a MEL concentration of 500 µM., Discussion: The results suggest that MEL can improve germination of positively photoblastic stevia seeds and that it can play a role in plantlet development. However, the effects observed in the present study depended on the quantity of MEL that was applied., Competing Interests: The authors declare there are no competing interests.

Background: Allergic asthma is the most prevalent phenotype of severe asthma where treatment with omalizumab (OMB) has been proven to be particularly beneficial. In Poland, OMB therapy is available and reimbursed within a drug programme where strict inclusion and exclusion criteria are defined. The objective of this study was to present a descriptive analysis regarding the trends in outcomes (clinical, quality of life, costs) among a cohort of patients who satisfy inclusion criteria for the initiation of OMB treatment and who successfully responded to OMB according to a set of objective criteria., Methods: A retrospective analysis of data collected during the 52 weeks of OMB treatment was carried out. The study population was adolescents and adults with severe allergic asthma that was uncontrolled despite a combination of high-dose inhaled corticosteroids (ICS)/long-acting beta-agonists (LABA) and/or other controllers (leukotriene receptor antagonists (LTRA), sustained-release theophylline, and short- or long-acting muscarinic antagonists (SAMA/LAMA), who were the first to finish the one-year treatment. A clinical and cost analysis for patients included in the programme was conducted comparing the one-year pre-treatment period to the one-year treatment period outcomes., Results: Data of 85 patients who completed the first year of therapy were reviewed and analysed. Add-on OMB treatment resulted in a median decrease in exacerbation rate of 66% relative to the baseline and a reduction in oral steroid (OCS) dose by an average of 7.7 mg. At the end of the 52 weeks of therapy the changes in the quality of life questionnaire (AQLQ) and the asthma control questionnaire (ACQ) scores were 1.86 and 1.45 points, respectively. The mean cost of asthma treatment increased by an average of 15,979 EUR per patient per year (baseline period - 802 EUR/patient/year; OMB treatment - 16,781 EUR/patient/year). The cost to avoid one exacerbation was 17721 EUR., Conclusion: The clinical outcomes for the observed subset of patients were highly improved. At the same time, costs of the treatment increased, mainly due to the high OMB costs. Other costs associated with a lower number of hospitalizations and ED and office visits and a reduction in OCS dose decreased. These descriptive data can be used for further investigation in defining patients who benefit the most from OMB treatment in clinical practice.

Background: Ghrelin, leptin and insulin, generally considered as regulators of energy homeostasis of the organism may be related to fetal and early postnatal growth. Numerous studies have confirmed the presence of these hormones in the cells of the fetus indicating their importance in development at early stages of life., Methods: This study analyzed active and total ghrelin by radioimmunoassay (RIA), leptin and insulin concentrations by enzyme-linked immunosorbent assay (ELISA) in 65 cord blood samples, from term newborns, and measured the birth anthropometric parameters [birth weight (BW), head circumference, chest, stomach, thigh and arm circumference]., Results: Active ghrelin (AG) concentrations correlated negatively with BW, head circumference, stomach and thigh circumference. When divided by gender, AG correlated negatively with males' BW, stomach and thigh circumference. Females' head circumference correlated negatively with AG. Cord leptin correlated positively with arm circumference. When divided by gender, cord leptin was positively associated with BW and stomach circumference in male newborns and with thigh and arm circumference in female newborns. Insulin concentrations tended to correlate positively with BW in male newborns., Conclusions: In summary, it was confirmed that cord blood ghrelin, leptin and insulin correlate with anthropometric parameters at birth. This study showed a negative correlation of AG with anthropometric parameters, which may emphasize that this hormone is an indicator of growth restriction. This is in contrast to cord leptin and insulin, which are more connected with overgrowth. Taking all the results into consideration, the metabolic status of the fetus and newborn is an essential component in understanding the regulation of perinatal development.

Obtaining oat DH lines is only effective via wide crossing with maize. Seven hundred haploid embryos from 21 single F 1 progeny obtained from wide crosses with maize were isolated, divided into four groups according to their size (<0.5 mm, 0.5-0.9 mm, 1.0-1.4 mm, and ≥1.5 mm), and transferred into 190-2 regeneration medium with different growth regulators: 0.5 mg L -1 kinetin (KIN) and 0.5 mg L -1 1-naphthaleneacetic acid (NAA); 1 mg L -1 zeatin (ZEA) and 0.5 mg L -1 NAA; or 1 mg L -1 dicamba (DIC), 1 mg L -1 picloram (PIC), and 0.5 mg L -1 kinetin (KIN). Among all isolated embryos, approximately 46.1% were between 1.0-1.4 mm, while the smallest group of embryos (7.1%) were those <0.5 mm. The ability of haploid embryos to germinate varied depending on oat genotypes and the size of embryos. Haploid embryos <0.5 mm were globular and did not germinate, whereas embryos ≥1.5 mm had clearly visible coleoptiles, radicles, and scutella, and were able to germinate. Germination of oat haploid embryos varied depending on growth regulators in the regeneration medium. Most haploid embryos germinated on medium with 0.5 mg L -1 NAA and 0.5 mg L -1 KIN, while the fewest germinated on medium with 1 mg L -1 DIC, 1 mg L -1 PIC, and 0.5 mg L -1 KIN. One hundred thirty germinated haploid embryos converted into haploid plants. Fifty oat DH lines were obtained after colchicine treatment.

Unlabelled: The costs incurred for treatment of patients with asthma are an important part of health care in the budget of each country. The aim of the study was to evaluate the direct and indirect costs of asthma in Poland. The study was based on questionnaires completed by professionals--allergists and pneumonologists of 13 centers in which is conducted the diagnosis and treatment of asthma., Materials and Methods: The costs of asthma were determined from the payer perspective (NHF) and from the perspective of social security (ZUS). The study evaluated the direct costs of one patient with asthma in 2012, and indirect costs, as measured by human capital or friction costs. The study involved 128 people, including 84 women and 44 men, mean age 51.04+/11.41 years., Results: Among the most frequent concomitant diseases: allergic rhinitis (93.75%), gastro-oesophageal reflux (38.54%), urticaria (16.67%), atopic dermatitis (21.88%) were present. The average monthly cost of drugs in 2012 amounted to PLN 251.32 (61.29 EURO, 2012 EURO 1 year=4.1 PLN), including patient,s copayment amounted to PLN 65.48 (EUR 15.97). The study showed that the direct cost per patient was 3240,88 PLN (790,46 EURO,). The Indirect cost, calculated using the human capital was for an average PLN 17,579.18 (4287.6 EURO) per patient, and using the method of friction costs was PLN 5974.06 (EUR 1,457.2)., Conclusions: Estimating the cost of the disease often depends on the adopted method of analysis, but in the study group, a significant advantage of the indirect costs of the disease was observed. The effectiveness of the treatment of asthma in Poland should also be aimed at reducing the indirect costs of illness., (© 2015 MEDPRESS.)

Introduction and Objective: The growing epidemic of childhood obesity has forced scientists to search for methods to prevent feeding disorders. Increasing interest in appetite regulating hormones has revealed their influence on energy homeostasis after birth or even in utero., State of Knowledge: The presence of ghrelin in the stomach of human foetuses and the distinctive production in the pancreas of neonates suggests the role of ghrelin in pre- and post-natal development. The neonatal period appears to be a critical time for the formation of adipose tissue-hypothalamus circuits, thus the amount of adipocytes in foetal life may be a major regulator of food intake. Insulin's orexigenic effect in the arcuate nucleus of the hypothalamus can be a major modulator of foetal development., Objective: This review, based on available literature, aims to analyses the role of appetite regulating hormones in foetal development., Summary: Different concentrations of hormones, such as ghrelin, leptin and insulin during foetal life raises the question whether or not they can be modulated, thereby avoiding obesity before birth. Children with pancreas agenesis showed smaller body size at birth, which emphasises the probable role of insulin in foetal growth. Study of sheep foetuses with IUGR confirmed these finding. Appetite-regulating hormones show different roles in foetal development and seem to be essential in the perinatal period.

Introduced research was connected with exposure of liverword Marchantia polymorpha in selected places in the area of Krakow. Places differing in regard to average concentration of air pollution [especially for (synergistic) effects NO2 and SO2]. Purpose of research was to check correlation between exposure to different concentrations of NO2 and SO2 (in regard to their synergistic effects) and possible differences in dynamics of growth of M. polymorpha. Samples of M. polymorpha located in soil, which was standardly analysed (in regard to contents of trace elements) before and after exposure. Research was simultaneously performed with similar exposure culture in vitro of Petunia hybrida. To growing tissues of petunia was used standard Murashige & Skoog medium and was protected against infections (with using filter of fibre). Described biomonitoring was completed by measurements of concentration of NO2 and SO2 by passive method with use of samplers of Amaya and Krochmal, in the same places, where was located exposure of plants. Observed was inhibition of growth in places, where was high concentration both gases.