Master Regulatory Transcription Factors in ß-Aminobutyric Acid-Induced Resistance (BABA-IR): A Perspective on Phytohormone Biosynthesis and Signaling in Arabidopsis thaliana and Hordeum vulgare.

The endogenous stress metabolite ß-aminobutyric acid (BABA) primes plants for enhanced resistance against abiotic and biotic stress by activating a complex phytohormone signaling network that includes abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), and ethylene (ET). In this study, through stringent filtering, we identify 14 master regulatory transcription factors (TFs) from the DOF, AHL, and ERF families that potentially regulate the biosynthesis and signaling of these phytohormones. Transcriptional analysis of BABA-treated Arabidopsis thaliana and Hordeum vulgare suggests that DOF family TFs play a crucial role in stress response regulation in both species. BABA treatment in A. thaliana upregulates the TFs MNB1A and PBF and enhances the expression of the genes ICS1, EDS5, and WIN3 in the SA biosynthesis pathway, potentially boosting NPR1 and PR1 in the SA signaling pathway. Conversely, in H. vulgare, the BABA-induced upregulation of TF DOF5.8 may negatively regulate SA biosynthesis by downregulating ICS1, EDS5, and PR1. Additionally, in A. thaliana, BABA triggers the expression of TF PBF, which may result in the decreased expression of MYC2, a key gene in JA signaling. In contrast, H. vulgare exhibits increased expression of ERF2 TF, which could positively regulate the JA biosynthesis genes LOX and Tify9, along with the COI1 and JAZ genes involved in the JA signaling pathway. These findings offer new perspectives on the transcriptional regulation of phytohormones during plant priming.

First Peek into the Transcriptomic Response in Heat-Stressed Tomato Inoculated with Septoglomus constrictum.

In this study, we report the interaction between an arbuscular mycorrhizal fungus, Septoglomus constrictum, and tomato plants under heat stress. For the first time, this interaction was studied by Illumina RNA-seq, followed by a comprehensive bioinformatic analysis that investigated root and leaf tissue samples. The genome-wide transcriptional profiling displayed fewer transcriptomic changes in the root under heat-stress conditions caused by S. constrictum. The top 50 DEGs suggested significant changes in the expression of genes encoding heat-shock proteins, transporter proteins, and genes of phytohormone metabolism involving jasmonic acid signalling. S. constrictum induced the upregulation of genes associated with pathways such as 'drought-responsive' and the 'development of root hair' in the root, as well as 'glycolipid desaturation', 'intracellular auxin transport', and 'ethylene biosynthesis' in the leaf. The pathways 'biotin biosynthesis' and 'threonine degradation' were found in both investigated tissue types. Expression analysis of transcription factors showed 2 and 11 upregulated transcription factors in heat-stressed root and leaf tissues, respectively. However, we did not find shared transcription factors. Heat-stressed arbuscular mycorrhizal plants suffered less oxidative stress when exposed to high temperatures. Colorimetric tests demonstrated less accumulation of H2O2 and MDA in heat-stressed mycorrhizal plants. This phenomenon was accompanied by the higher expression of six stress genes that encode peroxidases, glutathione S-transferase and ubiquitin carboxyl-terminal hydrolase in roots and leaves. Our findings provide a new perspective on elucidating the functional metabolic processes of tomato plants under mycorrhizal-heat stressed conditions.

Dataset of conditioning effect of herbal extract-based plant biostimulants in pea (Pisum sativum).

Nowadays, many researchers, farmers and companies focus on the development of an environmentally friendly approach for enhancing field vegetable production and protection. Using next-generation plant biostimulants (PBs) could be effective to enhance tolerance to abiotic and biotic stresses, vegetable crop quality or nutrient efficiency which is particularly important for vegetables with a short growing season, such as Pisum sativum. Two herbal drug-containing plant conditioners Elice16Indures® (supercritical carbon dioxide extract SC-CO2) and Fitokondi® (aqueous extract) developed in the RIMPH Ltd (Hungary) were used in pea field experiments to monitor the potential of enhancing crop quality and defense response against different stress factors. Fresh leaves were collected after treatments for QuantSeq 3' mRNA sequencing at Illumina NextSeq 550 platform and libraries were investigated by genome-wide transcriptional profiling focusing on genes associated with defense response pathways. RNA quantification datasets are presented and 86 bp long sequence reads were pre-processed and assembled that were deposited in the National Center for Biotechnology Information (NCBI), Sequence Read Archive (SRA) and Transcriptome Shotgun Assembly (TSA) databases under the BioProject PRJNA870114. Functional annotation of transcripts and pairwise differential expression with enrichment analyses are presented here to support gene expression analysis experiments.

Natural immunity stimulation using ELICE16INDURES® plant conditioner in field culture of soybean.

Recently, climate change has had an increasing impact on the world. Innate defense mechanisms operating in plants - such as PAMP-triggered Immunity (PTI) - help to reduce the adverse effects caused by various abiotic and biotic stressors. In this study, the effects of ELICE16INDURES® plant conditioner for organic farming, developed by the Research Institute for Medicinal Plants and Herbs Ltd. Budakalász Hungary, were studied in a soybean population in Northern Hungary. The active compounds and ingredients of this product were selected in such a way as to facilitate the triggering of general plant immunity without the presence and harmful effects of pathogens, thereby strengthening the healthy plant population and preparing it for possible stress effects. In practice, treatments of this agent were applied at two different time points and two concentrations. The conditioning effect was well demonstrated by using agro-drone and ENDVI determination in the soybean field. The genetic background of healthier plants was investigated by NGS sequencing, and by the expression levels of genes encoding enzymes involved in the catalysis of metabolic pathways regulating PTI. The genome-wide transcriptional profiling resulted in 13 contigs related to PAMP-triggered immunity and activated as a result of the treatments. Further analyses showed 16 additional PTI-related contigs whose gene expression changed positively as a result of the treatments. The gene expression values of genes encoded in these contigs were determined by in silico mRNA quantification and validated by RT-qPCR. Both - relatively low and high treatments - showed an increase in gene expression of key genes involving AOC, IFS, MAPK4, MEKK, and GST. Transcriptomic results indicated that the biosyntheses of jasmonic acid (JA), salicylic acid (SA), phenylpropanoid, flavonoid, phytoalexin, and cellular detoxification processes were triggered in the appropriate molecular steps and suggested that plant immune reactions may be activated also artificially, and innate immunity can be enhanced with proper plant biostimulants.

Corrigendum to "Natural immunity stimulation using ELICE16INDURES® plant conditioner in field culture of soybean" [Heliyon 9 (1), (January 2023) Article e12907].

[This corrects the article DOI: 10.1016/j.heliyon.2023.e12907.].

'Garlic-lipo'4Plants: Liposome-Encapsulated Garlic Extract Stimulates ABA Pathway and PR Genes in Wheat (Triticum aestivum).

Recently, environmentally friendly crop improvements using next-generation plant biostimulants (PBs) come to the forefront in agriculture, regardless of whether they are used by scientists, farmers, or industries. Various organic and inorganic solutions have been investigated by researchers and producers, focusing on tolerance to abiotic and biotic stresses, crop quality, or nutritional deficiency. Garlic has been considered a universal remedy ever since antiquity. A supercritical carbon dioxide garlic extract encapsulated in nanoscale liposomes composed of plant-derived lipids was examined as a possible PB agent. The present study focused on the characterization of the genes associated with the pathways involved in defense response triggered by the liposome nanoparticles that were loaded with supercritical garlic extracts. This material was applied to Triticum aestivum in greenhouse experiments using foliar spraying. The effects were examined in a large-scale genome-wide transcriptional profiling experiment by collecting the samples four times (0 min, used as a control, and 15 min, 24 h, and 48 h after spraying). Based on a time-course expression analysis, the dynamics of the cellular response were determined by examining differentially expressed genes and applying a cluster analysis. The results suggested an enhanced expression of abscisic acid (ABA) pathway and pathogenesis-related (PR) genes, of which positive regulation was found for the AP2-, C2H2-, HD-ZIP-, and MYB-related transcription factor families.

Supplementation of the Plant Conditioner ELICE Vakcina® Product with ß-Aminobutyric Acid and Salicylic Acid May Lead to Trans-Priming Signaling in Barley (Hordeum vulgare).

Plant immunological memory, priming, is a defense mechanism that can be triggered by external stimuli, leading to the activation of biochemical pathways and preparing plants for disease resistance. Plant conditioners improve yield and crop quality through nutrient efficiency and abiotic stress tolerance, which is enhanced by the addition of resistance- and priming-induced compounds. Based on this hypothesis, this study aimed to investigate plant responses to priming actives of different natures, including salicylic acid and beta-aminobutyric acid, in combination with the plant conditioning agent ELICE Vakcina®. Phytotron experiments and RNA-Seq analyses of differentially expressed genes using the combinations of these three investigated compounds were performed in a barley culture to investigate possible synergistic relationships in the genetic regulatory network. The results indicated a strong regulation of defense responses, which was enhanced by supplemental treatments; however, both synergistic and antagonistic effects were enhanced with one or two components, depending on the supplementation. The overexpressed transcripts were functionally annotated to assess their involvement in jasmonic acid and salicylic acid signaling; however, their determinant genes were highly dependent on the supplemental treatments. Although the effects overlapped, the potential effects of trans-priming the two supplements tested could be largely separated.

Transcriptome profiling dataset of different developmental stage flowers of soybean (Glycine max).

The dynamic of flower development is a key agronomic characteristic affecting soybean yield. RNA-seq dataset of field-cultivated soybean flowers in four developmental stages including flower buds, and early, mature, and overblown stage flowers are reported in this paper. Gene Expression (Gex) library construction and Illumina NextSeq550 sequencing were carried out to produce 86 bp long forward reads. Reads were preprocessed and deposited in the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) database. These SRA depositions are under the BioProject accession: PRJNA807844. A reference transcriptome dataset was de novo assembled using these SRA reads. Annotation, differential expression, and gene set enrichment analyses were performed and deposited in the Mendeley Data.

RNA-seq datasets of field rapeseed (Brassica napus) cultures conditioned by Elice16Indures® biostimulator.

Elice16Indures® Plant Conditioner combines the effects of a number of herbs to increase the yield of dicotyledonous plants in the field. This crop enhancer can also be used in organic farming applying low doses with ULV spraying by drone. Reducing the ecological footprint is the basis for sustainable crop production. By using the crop enhancer, a better crop can be achieved with less impact on the environment. EU Member States attach great importance to rapeseed (Brassica napus). Due to its versatility, it is one of the supported plants. Plant conditioner applied in different phenological phases (BBCH 51 and BBCH 67) of winter oilseed rape at a dose of 240 g/ha of. By using Elice16Indures, the value of the vegetation index and the yield can be increased. RNA-seq data set of field Elice16Indures-treated and non-treated (control) rapeseed plants are presented. For RNA-seq experiments, two samples were taken from leaf tissues in the phenological phase of BBCH 69 from control and treated plots, 2 days after treatment. Illumina NextSeq 550 sequence reads were uploaded to the NCBI SRA database after preprocessing. Combined read sets were de novo assembled and functional annotation with the output transcripts were performed. The entire dataset of identified coding sequences (transcripts) was deposited in the NCBI TSA database. The SRA and TSA datasets are under the BioProject access PRJNA838472. The data series reported in this study may open up new opportunities to increase the efficiency of organic rapeseed production.

RNA-seq datasets of field soybean cultures conditioned by Elice16Indures® biostimulator.

The herbal drug-containing plant conditioner Elice16Indures® may help elicit plant immune responses in field dicotyledonous cultures. Application of this conditioner is also allowed in organic farming and recommended its drone spraying application in small doses. In this way, even distribution and better yields may be reached leading to economical and safe plant growing. The high protein content soy is an important food both in animal and human aspects which ecological cultivation is gaining prominence over GMO technology in the European Union. We present RNA-seq datasets of control and Elice16Indures treated soybean plants cultivated in field conditions from 01/05/2020 to 20/07/2020. For RNA seq experiments six samples were collected from vegetative tissues two times during the vegetation cycle: before and in flowering after 48 h of drone exposure. The 86 bp long Illumina NextSeq 550 reads were preprocessed and deposited in the NCBI SRA database. De novo assembly of combined read sets was performed and transcripts were deposited in the NCBI TSA database. Data of functional analysis of annotated transcripts are presented. The SRA and TSA datasets are under the Bioproject accession PRJNA778970. The presented datasets may help new strategies of ecological production of soy.

Time-course gene expression profiling data of Triticum aestivum treated by supercritical CO2 garlic extract encapsulated in nanoscale liposomes.

The biostimulant phytochemicals as alternatives to synthetic chemicals are gaining ground in sustainable agricultural production nowadays. The medicinal herb, garlic (Allium sativum) has a spectacular therapeutic reputation due to its antimicrobial properties. The effectiveness of supercritical carbon dioxide (SC-CO2) extraction of A. sativum could help preserve bioactive compounds and be used as a biostimulant agent. The SC-CO2 garlic was formulated in liposomes and used as a nanoscale drug delivery system to reach better efficiency of penetration and translocation. The SC-CO2 garlic extracts were used in Triticum aestivum time-course experiments to monitor conditioning effects such as improving crop quality and priming its defense responses against different pathogens. Fresh leaves were collected after SC-CO2 garlic exposure at 15 min, 24, and 48 hours for QuantSeq 3' mRNA sequencing at Illumina NextSeq 550 platform. RNA quantification datasets are presented. Raw data such as Illumina 85bp single-end read sequences and reconstructed transcripts were deposited in the NCBI SRA and TSA databases under the BioProject PRJNA808851. Functional annotation of transcripts and time-course expression data are presented here to support gene expression analysis experiments.

Transcriptome datasets of ß-Aminobutyric acid (BABA)-primed mono- and dicotyledonous plants, Hordeum vulgare and Arabidopsis thaliana.

The non-protein amino acid ß-Aminobutyric acid (BABA) may trigger the immune responses of plants to various biotic and abiotic stresses leading to a long-term resistance (primed state). We present RNA-seq datasets of BABA - primed mono- and dicotyledonous plants, such as Arabidopsis thaliana and Hordeum vulgare. Illumina NextSeq550 sequencing were carried out after 72 h of BABA exposure. 87 bp long sequence reads were preprocessed of treated and control samples and deposited in the NCBI SRA database. Transcriptome datasets were de novo assembled of each species and deposited in the NCBI TSA database. These SRA and TSA depositions are under the Bioproject accession: PRJNA791573. Pairwise differential expression with enrichment analyses were performed and the most specific DEGs were determined and annotated in both plants.

Liposomal Formulation of Botanical Extracts may Enhance Yield Triggering PR Genes and Phenylpropanoid Pathway in Barley (Hordeum vulgare).

This work aimed to study the plant conditioning effect and mode of action of a plant-based biostimulant used in organic farming. This new generation plant biostimulant, named ELICE16INDURES®, is rich in plant bio-active ingredients containing eleven supercritical botanical extracts encapsulated in nano-scale liposomes. The dose-response (10 to 240 g ha-1) relationship was tested in a field population of autumn barley (Hordeum vulgare) test crop, and underlying molecular mechanisms were studied. Applying nanotechnology, cell-identical nanoparticles may help the better uptake and delivery of active ingredients increasing resilience, vitality, and crop yield. The amount of harvested crops showed a significant increase of 27.5% and 39.9% interconnected to higher normalized difference vegetation index (NDVI) of 20% and 25% after the treatment of low and high dosages (20 and 240 g ha-1), respectively. Illumina NextSeq 550 sequencing, gene expression profiling, and KEGG-pathway analysis of outstanding dosages indicated the upregulation of pathogenesis-related (PR) and other genes-associated with induced resistance-which showed dose dependency as well.

New complete mitogenome datasets and their characterization of the European catfish (Silurus glanis).

We present new complete mitogenome sequences of Silurus glanis (S. glanis) from 4 samples such as male and female individuals from two countries (Hungary, Czech Republic). The complete mitochondria were determined from genome sequencing by using Illumina MiSeq platform resulting in long, 300 bp. paired-end reads. De novo assembly was performed resulting in one nod (scaffold) covering the total mitochondria in each sample. The mitochondrial genomes were circular, double-stranded molecules of 16,524 bp in length and consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. These sequences were deposited in the NCBI GeneBank under the accession numbers (MW796040, MW796041, MW796042, MW796043) and compared with the only available S. glanis mitochondrial genome (NC_014261.1) sequenced by unidentified technology and showed 99% similarity. We found in seq1 82, in seq2 82, seq3 83, seq4 82 nucleotide alterations involving 10 protein-coding genes and meaning 29 amino acid substitutions as well.

Epithelioid hemangioma of liver-The first reported case.

Epithelioid hemangioma, otherwise known as angiolymphoid hyperplasia with eosinophilia, is a rare benign vasoproliferative disease with an unknown etiology. We report the case of a 42-year-old man with routine bloods test showing mildly elevated serum bilirubin level. CT scan revealed a lesion in the left liver lobe not typical of FNH. PET/CT scan and a dynamic liver MRI were consistent with a malignant mass. Surgical resection was performed. Histopathology of the 45 mm mass reported well-defined, slightly lobular proliferations of capillary-sized vessels around several central muscular vessels. Although the endothelial cells revealed a "hobnail" appearance, none of them showed pleomorphism or mitotic activity. Endothelial cells showed reactivity for the endothelial markers (CD34, CD31) and smooth muscle was detected in the blood vessel walls via immunohistochemistry. Despite its benign nature, epithelioid hemangioma of the liver can lead to a diagnostic and therapeutic dilemma due to the malignant looking features on imaging modalities.

[Effects of supplementation with the antioxidant flavonoid, silymarin, in chronic hepatitis C patients treated with peg-interferon + ribavirin. A placebo-controlled double blind study]. / Az antioxidáns flavonoid silymarin szupplementációja hatásának placebokontrollos vizsgálata PEG-IFN + ribavirin antivirális kezelésben részesülô krónikus C-hepatitises betegekben.

UNLABELLED: Since oxidative stress may play a pathogenetic role in chronic hepatitis C, and sustained virological response to antiviral therapy is limited in HCV1 genotype infection, a double blind study was performed in HCV1 patients treated with pegylated interferon + ribavirin, to assess the efficacy of supplementation with the antioxidant flavonoid silymarin. PATIENTS AND METHODS: Thirty-two naive HCV1 positive patients with biopsy proven chronic hepatitis C, to be treated with pegylated interferon + ribavirin, have been randomized: group A): 16 patients have been given the antiviral therapy for 6-12 months plus placebo for the first 3 months; group B): 16 patients have been treated with pegylated interferon + ribavirin for 6-12 months plus silymarin, 2 x 166 mg/day, was given for 3 months. Serum alanine aminotransferase and HCV-RNA levels as well as parameters of oxidative stress such as plasma or red blood cell hemolysate, malondialdehyde, superoxide dismutase, glutathione peroxidase, catalase and myeloperoxidase were determined after 0, 1, 3, 6 and 12 months during the treatment. Sustained virological response as undetectable serum HCV RNA was evaluated 24 weeks after the end of therapy. RESULTS: In the silymarin group, a more rapid decrease in the malondialdehyde level as well as a marked decrease in superoxide dismutase and an increase in myeloperoxidase activity after month 12 were found, alanine aminotransferase normalized in 6/16 (vs control 9/16) cases, and sustained virological response occurred in 3/16 (vs 7/16) patients. DISCUSSION/CONCLUSION: Although silymarin supportation to antiviral therapy improved oxidative stress, it was able to affect favourably neither the alanine aminotransferase nor the sustained virological response. These contradictory findings may be related to randomization bias as patients in study group B had more negative predictors of response: they were older with higher fibrosis score and even with more severe pretreatment baseline oxidative stress. Regarding the recently published in vitro experiments with silybinin on HCV replication as well as the newest convincing clinical observations, we do suggest further studies with more than three times higher doses of silymarin in controlled trials to assess the value of this supplementation in antivirally treated HCV patients.

[The significance of elastic staining in detecting vascular invasion in colorectal carcinoma]. / Az elasztikus rostfestés jelentôôsége a colorectalis carcinomák vascularis invázióinak kimutatása szempontjából.

Venous invasion (VI) is one of the most important prognostic factors in colorectal carcinomas (CRC). The interobserver variation of this feature varies between 10% and 89.5%, mainly due to the specimen processing and staining. VI was assessed using haematoxylin and eosin (H+E) alone in 611 cases and with elastic stain (orcein-haematoxylin) in 243 CRCs. The stage, the pattern of invasion and the presence of intramural and extramural VI were determined. VI was identified in 27.45% of the H+E stained sections and in 67.1% using elastic stain counterstained with haematoxylin. The incidence of VI proved stage dependent as it has been noted in 13% of Dukes A, 36% of Dukes B, 80% of Dukes C and in 83% of CRCs with distant metastasis. The pattern of invasion is strongly connected to the VI, accordingly, VI could be identified in 82% of CRCs with invasive and only in 44% with expansive margin. The use of elastic stain did not help in differentiation of extramural tumour deposits due to the damage of elastic membranes in the vascular walls and the presence of elastic fibres in the lymph node capsule. As a conclusion, the routine use of elastic stains in our practice doubled the identification of VI. The frequency of VI depends on the stage and pattern of invasion in CRCs. As it is more likely to occur in the advanced CRCs, the use of elastic stain is even more suggested in Dukes B carcinomas with invasive margin.

Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weed Ambrosia artemisiifolia L. (Asteraceae).

The highly allergenic and invasive weed Ambrosia artemisiifolia L. is a monoecius plant with separated male and female flowers. The genetic regulation of floral morphogenesis is a less understood field in the reproduction biology of this species. Therefore the objective of this work was to investigate the genetic control of sex determination during floral organogenesis. To this end, we performed a genome-wide transcriptional profiling of vegetative and generative tissues during the plant development comparing wild-growing and in vitro cultivated plants. RNA-seq on Illumina NextSeq 500 platform with an integrative bioinformatics analysis indicated differences in 80 floral gene expressions depending on photoperiodic and endogenous initial signals. Sex specificity of genes was validated based on RT-qPCR experiments. We found 11 and 16 uniquely expressed genes in female and male transcriptomes that were responsible particularly to maintain fertility and against abiotic stress. High gene expression of homologous such as FD, FT, TFL1 and CAL, SOC1, AP1 were characteristic to male and female floral meristems during organogenesis. Homologues transcripts of LFY and FLC were not found in the investigated generative and vegetative tissues. The repression of AP1 by TFL1 homolog was demonstrated in male flowers resulting exclusive expression of AP2 and PI that controlled stamen and carpel formation in the generative phase. Alterations of male and female floral meristem differentiation were demonstrated under photoperiodic and hormonal condition changes by applying in vitro treatments.

Prognostic factors in Hungarian breast cancer patients.

BACKGROUND: Breast cancer is the most common cancer among women, with variable outcomes, justifying a continuous search for new parameters to predict accurate prognosis and indicate suitable adjuvant therapy for patients. MATERIALS AND METHODS: Fourty-four stage I-III breast cancer specimens were investigated immunohistochemically for the expression of cyclooxygenase-2 enzyme (COX-2), hormone receptors, tumor suppressor gene p53, oncogene HER2 and proliferation marker Ki-67. Additionally, twelve specimens were also investigated for the presence of the phosphorylated extracellular signal-regulated kinase (pERK). RESULTS: It was demonstrated that expressions of biological markers were related to each other (ER to p53 and Ki-67, COX-2 to ER, PgR, Ki-67 and p53, Ki-67 to p53 and PgR, p53 to PgR). CONCLUSION: Our data indicate that concomitant immunohistochemical evaluation of cyclooxygenase-2, hormone receptors, p53 and Ki-67 may be of clinical value in determining an accurate prognosis.