Carbohydrate Metabolic Process Research Articles

Transcriptomic analysis of Stropharia rugosoannulata reveals carbohydrate metabolism and cold resistance mechanisms under low-temperature stress

Low temperature is an important environmental factor that restricts the growth of Stropharia rugosoannulata; however, the molecular mechanisms underlying S. rugosoannulata responses to low-temperature stress are largely unknown. In this study, we performed a transcriptome analysis of a high-sensitivity strain (DQ-1) and low-sensitivity strain (DQ-3) under low-temperature stress. The liquid hyphae of S. rugosoannulata treated at 25 °C and 10 °C were analyzed by RNA-Seq, and a total of 9499 differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analyses showed that these genes were enriched in “xenobiotic biodegradation and metabolism”, “carbohydrate metabolism”, “lipid metabolism” and “oxidoreductase activity”. Further research found that carbohydrate enzyme (AA, GH, CE, and GT) genes were downregulated more significantly in DQ-1 than DQ-3 and several cellulase activities were also reduced to a greater extent. Moreover, the CAT1, CAT2, GR, and POD genes and more heat shock protein genes (HSP20, HSP78 and sHSP) were upregulated in the two strains after low-temperature stress, and the GPX gene and more heat shock protein genes were upregulated in DQ-3. In addition, the enzyme activity and qRT–PCR results showed trends similar to those of the RNA-Seq results. This result indicates that low-temperature stress reduces the expression of different AA, GH, CE, and GT enzyme genes and reduces the secretion of cellulase, thereby reducing the carbohydrate metabolism process and mycelial growth of S. rugosoannulata. Moreover, the expression levels of different types of antioxidant enzymes and heat shock proteins are also crucial for S. rugosoannulata to resist low-temperature stress. In short, this study will provide a basis for further research on important signaling pathways, gene functions and variety breeding of S. rugosoannulata related to low-temperature stress.

Strawberry FaSnRK1α Regulates Anaerobic Respiratory Metabolism under Waterlogging

Sucrose nonfermenting-1-related protein kinase 1 (SnRK1) is a central integrator of plant stress and energy starvation signalling pathways. We found that the FaSnRK1α-overexpression (OE) roots had a higher respiratory rate and tolerance to waterlogging than the FaSnRK1α-RNAi roots, suggesting that FaSnRK1α plays a positive role in the regulation of anaerobic respiration under waterlogging. FaSnRK1α upregulated the activity of anaerobic respiration-related enzymes including hexokinase (HK), phosphofructokinase (PFK), pyruvate kinase (PK), pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH) and lactate dehydrogenase (LDH). FaSnRK1α also enhanced the ability to quench reactive oxygen species (ROS) by increasing antioxidant enzyme activities. We sequenced the transcriptomes of the roots of both wild-type (WT) and FaSnRK1α-RNAi plants, and the differentially expressed genes (DEGs) were clearly enriched in the defence response, response to biotic stimuli, and cellular carbohydrate metabolic process. In addition, 42 genes involved in glycolysis and 30 genes involved in pyruvate metabolism were significantly regulated in FaSnRK1α-RNAi roots. We analysed the transcript levels of two anoxia-related genes and three ERFVIIs, and the results showed that FaADH1, FaPDC1, FaHRE2 and FaRAP2.12 were upregulated in response to FaSnRK1α, indicating that FaSnRK1α may be involved in the ethylene signalling pathway to improve waterlogging tolerance. In conclusion, FaSnRK1α increases the expression of ERFVIIs and further activates anoxia response genes, thereby enhancing anaerobic respiration metabolism in response to low-oxygen conditions during waterlogging.

Transcriptome analysis of the growth-promoting effect of volatile organic compounds produced by Microbacterium aurantiacum GX14001 on tobacco (Nicotiana benthamiana)

BackgroundPlant growth-promoting rhizobacteria (PGPR) release volatile organic compounds (VOCs), which promote plant growth.ResultsA potential PGPR strain GX14001 was isolated from marine samples, and the VOCs produced by GX14001 significantly promoted tobacco (Nicotiana benthamiana) growth in a plate experiment. Based on 16S rRNA sequence alignment and physiological and biochemical characterization, GX14001 was identified as Microbacterium aurantiacum. Comparative transcriptome analysis was conducted between GX14001 VOCs-treated tobacco and the control; it was found that 1286 genes were upregulated and 1088 genes were downregulated. Gene ontology (GO) analysis showed that upregulated genes were involved in three biological processes: polysaccharide metabolic, polysaccharide catabolic and carbohydrate metabolic. The downregulated genes were involved in six biological processes, namely cell redox homeostasis, cellular homeostasis, carbohydrate metabolic process, homeostatic process, obsolete electron transport, and regulation of biological quality. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that 190 upregulated differentially expressed genes were mainly involved in plant hormone signal transduction, phenylpropyl biosynthesis, plant–pathogen interaction, and flavonoid biosynthesis. The 148 downregulated differentially expressed genes were mainly involved in plant hormone signal transduction and the metabolism of ascorbic, aldehyde, and pyruvate acids. Further analysis revealed that many genes were differentially expressed in the metabolic pathways of plant hormone signals, which were speculated to be the main reason why GX14001 VOCs promoted tobacco growth. To further study its regulatory mechanism, we found that GX14001 promoted plant growth through auxin, salicylic acid, and gibberellin in Arabidopsis mutant experiments.ConclusionThe VOCs produced by Microbacterium aurantiacum GX14001 may promote the growth of tobacco through the auxin, salicylic acid and gibberellin pathways.

Computational identification and characterization of vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici) CAZymes in tomato xylem sap

Fusarium oxysporum f. sp. lycopersici is a devastating plant pathogenic fungi known for wilt disease in the tomato plant and secrete cell wall degrading enzymes. These enzymes are collectively known as carbohydrate-active enzymes (CAZymes), crucial for growth, colonization and pathogenesis. Therefore, the present study was aimed to identify and annotate pathogen CAZymes in the xylem sap of a susceptible tomato variety using downstream proteomics and meta servers. Further, structural elucidation and conformational stability analysis of the selected CAZyme families were done through homology modeling and molecular dynamics simulation. Among all the fungal proteins identified, the carbohydrate metabolic process was found to be enriched. Most of the annotated CAZymes belonged to the hydrolase and oxidoreductase families, and 90% were soluble and extracellular. Moreover, using a publically available interactome database, interactions were observed between the families acting on chitin, hemicellulose and pectin. Subsequently, important catalytic residues were identified in the candidate CAZymes belonging to carbohydrate esterase (CE8) and glycosyl hydrolase (GH18 and GH28). Further, essential dynamics after molecular simulation of 100 ns revealed the overall behavior of these CAZymes with distinct global minima and transition states in CE8. Thus, our study identified some of the CAZyme families that assist in pathogenesis and growth through host cell wall deconstruction with further structural insight into the selected CAZyme families. Communicated by Ramaswamy H. Sarma

RNA-Seq-Based Transcriptomics Study to Investigate the Genes Governing Nitrogen Use Efficiency in Indian Wheat Cultivars.

High NUE (nitrogen use efficiency) has great practical significance for sustainable crop production. Wheat is one of the main cultivated crops worldwide for human food and nutrition. However, wheat grain productivity is dependent upon cultivars with high NUE in addition to the application of nitrogen fertilizers. In order to understand the molecular mechanisms exhibiting a high NUE response, a comparative transcriptomics study was carried out through RNA-seq analysis to investigate the gene expression that regulates NUE, in root and shoot tissue of N-efficient (PBW677) and N-inefficient (703) cultivars under optimum and nitrogen (N) stress. Differentially expressed gene analysis revealed a total of 2,406 differentially expressed genes (DEGs) present in both the contrasting cultivars under N stress. The efficient genotype PBW677 had considerably more abundant DEGs with 1,653 (903 roots +750 shoots) compared to inefficient cultivar PBW703 with 753 (96 roots +657 shoots). Gene ontology enrichment and pathway analysis of these DEGs suggested that the two cultivars differed in terms of adaptive mechanism. Gene enrichment analysis revealed that among the upregulated and downregulated genes the overrepresented and underrepresented gene categories belonged to biological processes like DNA binding, response to abiotic stimulus, photosynthesis, carbon fixation, carbohydrate metabolic process, nitrogen compound metabolic process, nitrate transport, and translation in cultivar PBW677, while the enriched biological processes were nucleosome assembly, chromatin remodeling, DNA packaging, lipid transport, sulfur compound metabolic process, protein modifications, and protein folding and refolding in N inefficient cultivar PBW703. We found several transcription factors (MYB, WRKY, RING finger protein, zinc finger protein, transporters, NRT1, amino acid transporters, sugar), protein kinases, and genes involved in N absorption, transportation, and assimilation to be highly expressed in high NUE cultivar PBW677. In our study, we report 13 potential candidate genes which showed alternate gene expression in the two contrasting cultivars under study. These genes could serve as potential targets for future breeding programs.

An Integrated Analysis of Transcriptome and miRNA Sequencing Provides Insights into the Dynamic Regulations during Flower Morphogenesis in Petunia

Published genome sequences can facilitate multiple genome sequencing studies of flower development, which can serve as the basis for later analysis of variation in flower phenotypes. To identify potential regulators related to flower morphology, we captured dynamic expression patterns under five different developmental stages of petunia flowers, a popular bedding plant, using transcriptome and miRNA sequencing. The significant transcription factor (TF) families, including MYB, MADS, and bHLH, were elucidated. MADS-box genes exhibited co-expression patterns with BBR-BPC, GATA, and Dof genes in different modules according to a weighted gene co-expression network analysis. Through miRNA sequencing, a total of 45 conserved and 26 novel miRNAs were identified. According to GO and KEGG enrichment analysis, the carbohydrate metabolic process, photosynthesis, and phenylalanine metabolism were significant at the transcriptomic level, while the response to hormone pathways was significantly enriched by DEmiR-targeted genes. Finally, an miRNA–RNA network was constructed, which suggested the possibility of novel miRNA-mediated regulation pathways being activated during flower development. Overall, the expression data in the present study provide novel insights into the developmental gene regulatory network facilitated by TFs, miRNA, and their target genes.

De novo assembly of a fruit transcriptome set identifies AmMYB10 as a key regulator of anthocyanin biosynthesis in Aronia melanocarpa

Aronia is a group of deciduous fruiting shrubs, of the Rosaceae family, native to eastern North America. Interest in Aronia has increased because of the high levels of dietary antioxidants in Aronia fruits. Using Illumina RNA-seq transcriptome analysis, this study investigates the molecular mechanisms of polyphenol biosynthesis during Aronia fruit development. Six A. melanocarpa (diploid) accessions were collected at four fruit developmental stages. De novo assembly was performed with 341 million clean reads from 24 samples and assembled into 90,008 transcripts with an average length of 801 bp. The transcriptome had 96.1% complete according to Benchmarking Universal Single-Copy Orthologs (BUSCOs). The differentially expressed genes (DEGs) were identified in flavonoid biosynthetic and metabolic processes, pigment biosynthesis, carbohydrate metabolic processes, and polysaccharide metabolic processes based on significant Gene Ontology (GO) biological terms. The expression of ten anthocyanin biosynthetic genes showed significant up-regulation during fruit development according to the transcriptomic data, which was further confirmed using qRT-PCR expression analyses. Additionally, transcription factor genes were identified among the DEGs. Using a transient expression assay, we confirmed that AmMYB10 induces anthocyanin biosynthesis. The de novo transcriptome data provides a valuable resource for the understanding the molecular mechanisms of fruit anthocyanin biosynthesis in Aronia and species of the Rosaceae family.

Systematic analysis of changes across different developmental stages of the mushroom Sarcomyxa edulis

Sarcomyxa edulis is a widely harvested mushroom of Northeastern Asia. Its development can be divided into six stages: growth of mycelium until occupying half the bag (B1), mycelium under low-temperature stimulation after occupying the entire bag (B2), appearance of mycelium in primordia (B3), primordia (B4), mycelium at the harvest stage (B5), and mature fruiting body (B6). Differentially expressed gene (DEG) analysis and weighted gene coexpression network analysis (WGCNA) are important bioinformatic methods for screening key genes. To explore the growth and development mechanisms of the mushroom S. edulis and clarify its genetic background, DEG and WGCNA analyses were combined to screen key genes at different developmental stages. From A1 to A6, respectively, 459, 97, 885, 169, 277, and 712 key genes were identified. Then the Gene Ontology (GO) terms and KEGG pathways of key genes were analyzed, and GO and KEGG analyses were performed on all genes across different periods using GSEA. In summary, the genes in A1 were mainly involved in amino sugar and nucleotide sugar metabolism, structural molecule activity, and oxidative phosphorylation. At the A2 stage, genes were mainly involved in peptidase activity, peroxidase activity, oxidoreductase activity, antioxidant activity, biosynthesis of secondary metabolites, and glycolysis and gluconeogenesis. A3 genes were involved in gene expression, RNA metabolism, spliceosome, RNA transport, and ribosome biogenesis. A4 genes were mainly involved in the biosynthesis of secondary metabolites, proteasome complex, cellular protein complex assembly, actin filament-based processes, oxidative phosphorylation, and carbon metabolism. The A5 stage genes were involved in the carbohydrate metabolic process, polysaccharide metabolic process, and the biosynthesis of secondary metabolites, leucine, isoleucine, and ABC transporters. Finally, A6 genes were mainly involved in the cell cycle, meiosis of yeast, MAPK signaling pathway, cellular response to DNA damage stimulus, DNA metabolic process, DNA replication, and DNA repair. The combination of multiple analyses provides us with an in-depth understanding of the network that regulates mushroom development.

Identification and validation of ram sperm proteins associated with cryoinjuries caused by the cryopreservation process

The change of sperm protein profile after the cryopreservation process may influence fertilization and early embryonic development. The purpose of the present study was to identify ram sperm proteomic modifications induced by the cryopreservation process using the isobaric tags for relative and absolute quantification labeling technology (iTRAQ) coupled with the parallel reaction monitoring (PRM) technology. Semen samples were collected from five Yunnan semi-fine wool rams using an electroejaculator. Sperm motility (CASA), plasma membrane (HOST test), and acrosome integrity (FITC-PSA) were evaluated after freeze-thawing. The total proteins of fresh and frozen-thawed sperm were extracted and purified, followed by identifying ram sperm proteomic modifications using the isobaric tags for relative and absolute quantification labeling technique (iTRAQ) coupled with the parallel reaction monitoring (PRM) technology. The results showed a significant reduction (P < 0.05) in all sperm parameters after thawing. 126 differentially abundant proteins (DAPs) were identified through comparison of the proteomes between fresh and frozen-thawed sperm. Among them, 90 proteins were down-regulated after the cryopreservation process. The remaining 36 proteins were up-regulated in frozen-thawed sperm. The results of functional annotation demonstrated the potential relationship of 10 DAPs with oxidoreductase activity. 18 and 15 DAPs may be involved in the stress and carbohydrate metabolic process, respectively. Furthermore, 8 DAPs may be functionally associated with reproduction. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results demonstrated the primary enrichment of these identified DAPs in metabolic activities, disease, and oxidative phosphorylation. In order to confirm the reliability of the iTRAQ results, the changing trends of 10 proteins analyzed by PRM were similar to those of the corresponding proteins identified by iTRAQ. In conclusion, the cryopreservation process modifies the proteome of ram sperm, possibly leading to compromised fertility of post-thaw sperm. Additionally, the identified DAPs in this study may function as potential biomarkers for assessing the post-thaw quality of ram semen.

Physiological and Molecular Characterization of an Oxidative Stress-Resistant Saccharomyces cerevisiae Strain Obtained by Evolutionary Engineering.

Oxidative stress is a major stress type observed in yeast bioprocesses, resulting in a decrease in yeast growth, viability, and productivity. Thus, robust yeast strains with increased resistance to oxidative stress are in highly demand by the industry. In addition, oxidative stress is also associated with aging and age-related complex conditions such as cancer and neurodegenerative diseases. Saccharomyces cerevisiae, as a model eukaryote, has been used to study these complex eukaryotic processes. However, the molecular mechanisms underlying oxidative stress responses and resistance are unclear. In this study, we have employed evolutionary engineering (also known as adaptive laboratory evolution – ALE) strategies to obtain an oxidative stress-resistant and genetically stable S. cerevisiae strain. Comparative physiological, transcriptomic, and genomic analyses of the evolved strain were then performed with respect to the reference strain. The results show that the oxidative stress-resistant evolved strain was also cross-resistant against other types of stressors, including heat, freeze-thaw, ethanol, cobalt, iron, and salt. It was also found to have higher levels of trehalose and glycogen production. Further, comparative transcriptomic analysis showed an upregulation of many genes associated with the stress response, transport, carbohydrate, lipid and cofactor metabolic processes, protein phosphorylation, cell wall organization, and biogenesis. Genes that were downregulated included those related to ribosome and RNA processing, nuclear transport, tRNA, and cell cycle. Whole genome re-sequencing analysis of the evolved strain identified mutations in genes related to the stress response, cell wall organization, carbohydrate metabolism/transport, which are in line with the physiological and transcriptomic results, and may give insight toward the complex molecular mechanisms of oxidative stress resistance.

Metabolic Variation Dictates Cardiac Pathogenesis in Patients With Tetralogy of Fallot.

BackgroundHerein, we aimed to analyze cardiac metabolic reprogramming in patients with tetralogy of Fallot (ToF).MethodsCardiac metabolic reprogramming was analyzed through comprehensive bioinformatics analysis, which included gene set enrichment, gene set variation, and consensus clustering analyses, so as to assess changes in metabolic pathways. In addition, full-spectrum metabolomics analysis was performed using right atrial biopsy samples obtained from patients with ToF and atrial septal defect (ASD) before cardiopulmonary bypass; ultrahigh performance liquid chromatography–tandem mass spectrometry (UPLC–MS/MS) was used to construct a metabolic map of cardiac metabolic reprogramming in cyanotic congenital heart disease.ResultsThe metabolic maps of carbohydrate metabolic process and heme metabolism were significantly activated, while bile acid metabolism, lipid droplet, and lipid binding were primarily restrained in ToF samples as compared with that in ASD samples. The reprogramming of butanoate metabolism was identified basing on the UPLC–MS/MS detection and analysis in myocardial hypoxia damage in cyanotic heart disease. Finally, the butanoate metabolism–related hub regulators ALDH5A1 and EHHADH were identified and they were significantly downregulated in ToF samples.ConclusionsThe metabolic network of butanoate metabolism involved ALDH5A1 and EHHADH, which could contribute to myocardial tissue damage in cyanotic congenital heart of ToF. Our results provide further insights into the mechanisms underlying metabolic reprogramming in cyanotic congenital heart disease and could lead to the identification of potential therapeutic targets.

Дикарбонільний стрес: гіпотеза клітинного пошкодження в умовах гіпоксії. Пусковий механізм розвитку мультиорганної дисфункції

Актуальність. Різноманітні критичні стани організму часто асоційовані з розвитком гіпоксії, у результаті чого активуються механізми гліколізу, під впливом звільнення стресових гормонів розвивається гіперглікемія. Показано, що в умовах анаеробного гліколізу на тлі гіперглікемії в клітинах продукуються токсичні речовини, що викликають гліколізування протеїнів та нуклеїнових кислот. Разом із порушенням функції клітинних білків виникає мітохондріальна дисфункція, що призводить до енергетичного дефіциту та порушення функціонування органів. Мета дослідження: виявити провідні механізми дикарбонільного стресу, їх значення для формування критичних станів організму та визначити найбільш перспективні способи корекції для фахівців у галузі інтенсивної терапії. Матеріали та методи. Детальне вивчення результатів сучасних наукових досліджень процесів вуглеводного обміну при патологічних станах на підставі інформації, поданої в Інтернеті. Результати. Провідна роль у пошкодженні клітинних структур організму при дикарбонільному стресі належить гліоксалю та метилгліоксалю. Ці хімічні сполуки утворюються як побічні продукти анаеробного гліколізу. Збільшенню їх синтезу сприяють активація анаеробного гліколізу та гіперглікемія. Дикарбонільні сполуки вступають у хімічні реакції з амінними групами протеїнів, нуклеїнових кислот та інших біологічно активних сполук, порушуючи їх функціонування. Природна детоксикація здійснюється гліоксалазною системою за участю відновленого глутатіону, що є основним компонентом антиоксидантної системи. Прогресування окислювального стресу та поява антиоксидантного дефіциту зумовлюють збільшення тяжкості пошкоджень, що викликає підвищене утворення гліоксалю та метилгліоксалю. Профілактика дикарбонільного стресу здійснюється за допомогою збільшення потужності антиоксидантної системи, насамперед за рахунок зростання утворення відновленого глутатіону. Для нейтралізації токсичних дикарбонільних метаболітів можуть бути використані препарати, що виконують функцію «пасток». Перспективне застосування терапії, що спрямована на усунення мітохондріальної дисфункції. Висновки. Нова проблема пошкодження організму в умовах дикарбонільного стресу диктує необхідність аналізу та переоцінки численної кількості заходів інтенсивної терапії. Докладне вивчення особливостей вуглеводного обміну при різних критичних станах, включаючи визначення концентрації гліоксалю та метилгліоксалю, моніторинг рівня глікемії та кліренсу лактату в поєднанні з поверненням до оцінювання стану компенсації функції прооксидантної/антиоксидантної системи організму, є одним із перспективних напрямів наукових досліджень у клініці, що має розпочатися. Фахівці з інтенсивної терапії щоденно стикаються із ситуаціями, коли дикарбонільний стрес може виступати як один із дійсних механізмів формування органної та мультиорганної дисфункції й визначає розвиток декомпенсації життєво важливих функцій. Навчитися протистояти йому є актуальною найближчою задачею.

Combined Transcriptomics and Metabolomics Analysis Reveals the Molecular Mechanism of Salt Tolerance of Huayouza 62, an Elite Cultivar in Rapeseed (Brassica napus L.).

Soil salinity is one of the most significant abiotic stresses affecting crop yield around the world. To explore the molecular mechanism of salt tolerance in rapeseed (Brassica napus L.), the transcriptome analysis and metabolomics analysis were used to dissect the differentially expressed genes and metabolites in two rapeseed varieties with significant differences in salt tolerance; one is an elite rapeseed cultivar, Huayouza 62. A total of 103 key differentially expressed metabolites (DEMs) and 53 key differentials expressed genes (DEGs) that might be related to salt stress were identified through metabolomics and transcriptomics analysis. GO and KEGG analysis revealed that the DEGs were mainly involved in ion transport, reactive oxygen scavenging, osmotic regulation substance synthesis, and macromolecular protein synthesis. The DEMs were involved in TCA cycle, proline metabolism, inositol metabolism, carbohydrate metabolic processes, and oxidation-reduction processes. In addition, overexpression of BnLTP3, which was one of the key DEGs, could increase tolerance to salt stress in Arabidopsis plants. This study reveals that the regulation mechanism of salt tolerance in rapeseed at the transcriptome and metabolism level and provides abundant data for further in-depth identification of essential salt tolerance genes.

Population Evolution, Genetic Diversity and Structure of the Medicinal Legume, Glycyrrhiza uralensis and the Effects of Geographical Distribution on Leaves Nutrient Elements and Photosynthesis.

Glycyrrhiza uralensis is a valuable medicinal legume, which occurs widely in arid and semi-arid regions. G. uralensis demand has risen steeply due to its high medical and commercial value. Interpret genome-wide information can stimulate the G. uralensis development as far as its increased bioactive compound levels, and plant yield are concerned. In this study, leaf nutrient concentration and photosynthetic chlorophyll index of G. uralensis were evaluated to determine the G. uralensis growth physiology in three habitats. We observed that G. uralensis nutrient levels and photosynthesis differed significantly in three regions (p < 0.05). Whole-genome re-sequencing of the sixty G. uralensis populations samples from different habitats was performed using an Illumina HiSeq sequencing platform to elucidate the distribution patterns, population evolution, and genetic diversity of G. uralensis. 150.06 Gb high-quality clean data was obtained after strict filtering. The 895237686 reads were mapped against the reference genome, with an average 89.7% mapping rate and 87.02% average sample coverage rate. A total of 6985987 SNPs were identified, and 117970 high-quality SNPs were obtained after filtering, which were subjected to subsequent analysis. Principal component analysis (PCA) based on interindividual SNPs and phylogenetic analysis based on interindividual SNPs showed that the G. uralensis samples could be categorized into central, southern, and eastern populations, which reflected strong genetic differentiation due to long periods of geographic isolation. In this study, a total of 131 candidate regions were screened, and 145 candidate genes (such as Glyur001802s00036258, Glyur003702s00044485, Glyur001802s00036257, Glyur007364s00047495, Glyur000028s00003476, and Glyur000398s00034457) were identified by selective clearance analysis based on Fst and θπ values. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed significant enrichment of 110 GO terms including carbohydrate metabolic process, carbohydrate biosynthetic process, carbohydrate derivative biosynthetic process, and glucose catabolic process (p < 0.05). Alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, and fatty acid degradation pathways were significantly enriched (p < 0.05). This study provides information on the genetic diversity, genetic structure, and population adaptability of the medicinal legumes, G. uralensis. The data obtained in this study provide valuable information for plant development and future optimization of breeding programs for functional genes.

Potato tuber degradation is regulated by carbohydrate metabolism: Results of transcriptomic analysis.

Tuber number is an essential factor determining yield and commodity in potato production. The initiation number has long been considered the sole determinant of the final total tuber number. In this study, we observed that tuber numbers at harvest were lower than at the tuber bulking stage; some formed tubers that were smaller than 3 cm degraded during development. Carbohydrate metabolism plays a crucial role in tuber degradation by coordinating the source–sink relationship. The contents of starch and sucrose, and the C:N ratio, are dramatically reduced in degradating tubers. Transcriptomic study showed that “carbohydrate metabolic processes” are Gene Ontology (GO) terms associated with tuber degradation. A polysaccharide degradation‐related gene, LOC102601831, and a sugar transport gene, LOC102587850 (SWEET6a), are dramatically up‐regulated in degradating tubers according to transcriptomic analysis, as validated by qRT‐PCT. The terms “peptidase inhibitor activity” and “hydrolase activity” refer to the changes in molecular functions that degradating tubers exhibit. Nitrogen supplementation during potato development alleviates tuber degradation to a certain degree. This study provides novel insight into potato tuber development and possible management strategies for improving potato cultivation.

Proteomic analysis of hexahydro-β-acids/hydroxypropyl-β-cyclodextrin inhibit Listeria monocytogenes.

Food safety affected by food-borne pathogen has received increasing attention by researchers. Listeria monocytogenes (L. monocytogenes), widespread in the environment, could easily cause some diseases. The aim of this study was to investigate how L. monocytogenes ATCC 19,115 regulated and shaped its proteome in response to hexahydro-β-acids (HBA) formed inclusion complex with hydroxypropyl-β-cyclodextrin (HP-β-CD), compared to untreated cells growing under optimal conditions. HP-β-CD enhanced the solubility of HBA to 0.589g/100mL. The minimum inhibitory concentration (MIC) and the minimal bactericidal concentration (MBC) of HBA/HP-β-CD to L. monocytogenes were 25μg/mL and 100μg/mL, respectively. Scanning electron microscope (SEM) images demonstrated that HBA could destroy the cell membrane of L. monocytogenes. The proteomic analysis revealed that 2882 proteins were initially identified, among which 153 and 201 proteins were differentially upregulated and downregulated respectively. Changes of L. monocytogenes proteome in response to treatments were mainly related to carbohydrate metabolism, protein synthesis, ribosome composition proteins, cell wall composition proteins, and cell division anomalies process. This research is conducive to understanding the molecular mechanisms underlying the inhibiting effects of HBA/HP-β-CD against L. monocytogenes, providing novel insights for further development of HBA/HP-β-CD antimicrobial agents. KEY POINTS: • MIC and MBC of HBA/HP-β-CD to L. monocytogenes were 25μg/mL and 100μg/mL. • HBA/HP-β-CD cause significant changes in bacterial proteome. • The process of ribosome composition and carbohydrate metabolism was inhibited.

Features of correction of markers of hepatocyte cytolysis and the degree of hepatocyte steatosis in patients with nonalcoholic steatohepatitis and type 2 diabetes with diabetic kidney disease

The relevance of the problem of the comorbid course of nonalcoholic steatohepatitis, type 2 diabetes and diabetic kidney disease lies in the rapid progression of all comorbid diseases, decompensation of carbohydrate metabolism processes, and the development of hepatocellular and renal failure. The specified comorbid diseases have a number of mutually burdening mechanisms, the elimination of which will contribute to achieving clinical remission of diseases, compensation of the functional potential of the liver and kidneys. The aim of the study was to find out the probable effect of the complex of metformin, rosuvastatin and bicyclol on the markers of hepatocyte cytolysis in patients with non-alcoholic steatohepatitis and type 2 diabetes with diabetic kidney disease, the degree of hepatocyte steatosis and the stage of liver fibrosis, which are markers of the progression of non-alcoholic steatohepatitis. Materials and methods. Depending on the prescribed treatment, the examined patients were randomly divided into 2 groups: (1 group – control: 28 people) received a hypocaloric diet taking into account the restrictions of diet No. 9, essential phospholipids (Essentiale forte H 300 mg 2 capsules 3 times a day ) for 90 days in order to treat active non-alcoholic steatohepatitis, for type 2 diabetes and hyperlipidemia metformin hydrochloride (Metformin-Teva 1000 mg per day, rosuvastatin (Rosuvastatin-Teva 5 mg once a day) was prescribed for 90 days. Group 2 consisted of patients (32 people), who, in addition to similar dietary recommendations, hypoglycemic and hypolipidemic therapy, instead of essential phospholipids, additionally received the drug Bicyclol 25 mg 3 times a day for 90 days. The average age of the patients was (53,8±3,52) years. Group comparison for the presentation of reference values of homeostasis indicators was made by 30 healthy persons of the appropriate age. Research results and their discussion. The analysis of indicators of cytolytic syndrome activity indicates that the activity of ALT increased before treatment (by 3,6 times, p&lt;0,05) – after treatment it decreased in patients of groups 1 and 2: by 2.2 and 3,7 times, respectively (p&lt;0,05) with the presence of a probable intergroup difference (p&lt;0,05). At the same time, the increased indicator of steatosis of hepatocytes before treatment, which exceeded the reference values by 4,0 times (p&lt;0,05) – under the influence of treatment also probably decreased in patients of 1 and 2 observation groups – by 1.2 and 1.8 times, respectively (p&lt;0,05) with the presence of a probable intergroup difference (p&lt;0,05). Thus, both traditional treatment with essential phospholipids and the drug Bicyclol actively affect and during 90 treatments contribute to the reduction of the main components of the pathological process in the liver in non-alcoholic steatohepatitis – cytolysis and fatty dystrophy of hepatocytes, but Bicyclol as part of complex hypoglycemic and hypolipidemic therapy has a more intense effect. It should also be pointed out that the effect of traditional therapy and the activity of liver fibrosis, according to previous studies, was probably lower than the proposed Bicyclol therapy. Thus, the significantly increased FibroTest indicator before treatment (3,2 times, p&lt;0,05) in patients with non-alcoholic steatohepatitis with comorbid diabetes mellitus and diabetic kidney disease in the dynamics of treatment in patients of group 1 decreased by 10,7% (p&lt; 0,05), and in patients of group 2 – by 40,0% (р&lt;0,05) with the presence of a probable intergroup difference (р&lt;0,05). The obtained data indicate a favorable anti-inflammatory effect of Bicyclol, which is aimed at inhibiting and preventing liver fibrosis. Conclusions from the study. Complex therapy with metformin, rosuvastatin in combination with bicyclol in people with comorbid non-alcoholic steatohepatitis, type 2 diabetes and diabetic kidney disease for 3 months contributed to the elimination of hepatocyte cytolysis syndrome, a significant decrease in steato-test and fibrotest indicators (p&lt;0.05), probable reducing the intensity of liver tissue fibrosis.

FEATURES OF CORRECTION OF MARKERS OF HEPATOCYTE CYTOLYSIS AND THE DEGREE OF HEPATOCYTE STEATOSIS IN PATIENTS WITH NONALCOHOLIC STEATOHEPATITIS AND TYPE 2 DIABETES WITH DIABETIC KIDNEY DISEASE

The relevance of the problem of the comorbid course of nonalcoholic steatohepatitis, type 2 diabetes and diabetic kidney disease lies in the rapid progression of all comorbid diseases, decompensation of carbohydrate metabolism processes, and the development of hepatocellular and renal failure. The specified comorbid diseases have a number of mutually burdening mechanisms, the elimination of which will contribute to achieving clinical remission of diseases, compensation of the functional potential of the liver and kidneys. The aim of the study was to find out the probable effect of the complex of metformin, rosuvastatin and bicyclol on the markers of hepatocyte cytolysis in patients with non-alcoholic steatohepatitis and type 2 diabetes with diabetic kidney disease, the degree of hepatocyte steatosis and the stage of liver fibrosis, which are markers of the progression of non-alcoholic steatohepatitis. Materials and methods. Depending on the prescribed treatment, the examined patients were randomly divided into 2 groups: (1 group – control: 28 people) received a hypocaloric diet taking into account the restrictions of diet No. 9, essential phospholipids (Essentiale forte H 300 mg 2 capsules 3 times a day ) for 90 days in order to treat active non-alcoholic steatohepatitis, for type 2 diabetes and hyperlipidemia metformin hydrochloride (Metformin-Teva 1000 mg per day, rosuvastatin (Rosuvastatin- Teva 5 mg once a day) was prescribed for 90 days. Group 2 consisted of patients (32 people), who, in addition to similar dietary recommendations, hypoglycemic and hypolipidemic therapy, instead of essential phospholipids, additionally received the drug Bicyclol 25 mg 3 times a day for 90 days. The average age of the patients was (53,8±3,52) years. Group comparison for the presentation of reference values of homeostasis indicators was made by 30 healthy persons of the appropriate age. Research results and their discussion. The analysis of indicators of cytolytic syndrome activity indicates that the activity of ALT increased before treatment (by 3,6 times, p&lt;0,05) – after treatment it decreased in patients of groups 1 and 2: by 2.2 and 3,7 times, respectively (p&lt;0,05) with the presence of a probable intergroup difference (p&lt;0,05). At the same time, the increased indicator of steatosis of hepatocytes before treatment, which exceeded the reference values by 4,0 times (p&lt;0,05) – under the influence of treatment also probably decreased in patients of 1 and 2 observation groups – by 1.2 and 1.8 times, respectively (p&lt;0,05) with the presence of a probable intergroup difference (p&lt;0,05). Thus, both traditional treatment with essential phospholipids and the drug Bicyclol actively affect and during 90 treatments contribute to the reduction of the main components of the pathological process in the liver in non-alcoholic steatohepatitis – cytolysis and fatty dystrophy of hepatocytes, but Bicyclol as part of complex hypoglycemic and hypolipidemic therapy has a more intense effect. It should also be pointed out that the effect of traditional therapy and the activity of liver fibrosis, according to previous studies, was probably lower than the proposed Bicyclol therapy. Thus, the significantly increased FibroTest indicator before treatment (3,2 times, p&lt;0,05) in patients with non-alcoholic steatohepatitis with comorbid diabetes mellitus and diabetic kidney disease in the dynamics of treatment in patients of group 1 decreased by 10,7% (p&lt; 0,05), and in patients of group 2 – by 40,0% (р&lt;0,05) with the presence of a probable intergroup difference (р&lt;0,05). The obtained data indicate a favorable anti-inflammatory effect of Bicyclol, which is aimed at inhibiting and preventing liver fibrosis. Conclusions from the study. Complex therapy with metformin, rosuvastatin in combination with bicyclol in people with comorbid non-alcoholic steatohepatitis, type 2 diabetes and diabetic kidney disease for 3 months contributed to the elimination of hepatocyte cytolysis syndrome, a significant decrease in steato-test and fibrotest indicators (p&lt;0.05), probable reducing the intensity of liver tissue fibrosis.

Induced Hepatic Glutathione and Metabolomic Alterations Following Mixed Pesticide and Fertilizer Exposures in Juvenile Leopard Frogs (Lithobates sphenocephala).

The increasing use of agrochemicals, alone and in combination, has been implicated as a potential causative factor in the decline of amphibians worldwide. Fertilizers and pesticides are frequently combined into single-use tank mixtures for agricultural applications to decrease costs while meeting the food demands of a growing human population. Limited data are available on the effects of increased nitrogen levels in nontarget species, such as amphibians, and therefore investigating alterations in the nitrogen cycle and its impacts on amphibians needs to be considered in best management practices going forward. The objective of the present study was to elucidate the impact of fertilizer (urea) and herbicide (atrazine and/or alachlor) tank mixtures on the hepatic metabolome of juvenile leopard frogs as well as to investigate alterations in oxidative stress by relating these changes to glutathione (GSH) levels. Herbicide exposure only moderately increased this parameter in amphibians, however, urea alone and in combination with either atrazine or alachlor statistically elevated GSH levels. Interestingly, urea also inhibited pesticide uptake: calculated bioconcentration factors were greatly decreased for atrazine and alachlor when urea was present in the exposure mixture. Metabolomic profiling identified fluxes in hepatic metabolites that are involved in GSH and carbohydrate metabolic processes as well as altered intermediates in the urea cycle. Ultimately, understanding the biological impacts of nitrogenous fertilizers alone and in combination with pesticide exposure will inform best management practices to conserve declining amphibian populations worldwide. Environ Toxicol Chem 2022;41:122-133. © 2021 SETAC.

Transcriptomic and Physiological Response of Durum Wheat Grain to Short-Term Heat Stress during Early Grain Filling

In a changing climate, extreme weather events such as heatwaves will be more frequent and could affect grain weight and the quality of crops such as wheat, one of the most significant crops in terms of global food security. In this work, we characterized the response of Triticum turgidum L. spp. durum wheat to short-term heat stress (HS) treatment at transcriptomic and physiological levels during early grain filling in glasshouse experiments. We found a significant reduction in grain weight (23.9%) and grain dimensions from HS treatment. Grain quality was also affected, showing a decrease in starch content (20.8%), in addition to increments in grain protein levels (14.6%), with respect to the control condition. Moreover, RNA-seq analysis of durum wheat grains allowed us to identify 1590 differentially expressed genes related to photosynthesis, response to heat, and carbohydrate metabolic process. A gene regulatory network analysis of HS-responsive genes uncovered novel transcription factors (TFs) controlling the expression of genes involved in abiotic stress response and grain quality, such as a member of the DOF family predicted to regulate glycogen and starch biosynthetic processes in response to HS in grains. In summary, our results provide new insights into the extensive transcriptome reprogramming that occurs during short-term HS in durum wheat grains.