Metabolite accumulation and metabolic network in developing roots of Rehmannia glutinosa reveals its root developmental mechanism and quality

Protective Effects of ζ-Carotene-like Compounds against Acute UVB-Induced Skin Damage

The previous study successfully established an expression strain of ζ-carotene-like compounds (CLC) and demonstrated its remarkable antioxidant activity, which exhibited resistance to photodamage caused by UVB radiation on the skin following gavage administration. The objective of this study was to investigate the impact and mechanism of CLC on UVB-induced skin damage through topical application. Cell viability, anti-apoptotic activity, ROS scavenging ability, the inhibition of melanin synthesis, the regulation of inflammatory factors and collagen deposition were assessed in cells and mice using qRT-PCR, WB, Elisa assays, immunohistochemistry staining and biochemical kits, etc. The experimental results demonstrated that CLC-mitigated apoptosis induced by UVB irradiation up-regulated the Keap1/Nrf2/ARE antioxidant pathway to attenuate levels of ROS and inflammatory factors (NF-κB, TNF-α, IL-6 and IL-β), and suppressed MAPK/AP-1 and CAMP/PKA/CREB signaling pathways to mitigate collagen degradation, skin aging and melanin formation. In conclusion, this study underscored the potential of CLC as a safe and efficacious source of antioxidants, positioning it as a promising ingredient in the formulation of cosmetics targeting anti-aging, skin brightening and sunburn repair.

Metabolomics analysis reveals metabolite changes during freeze-drying and oven-drying of Angelica dahurica

Angelica dahurica (Angelica dahurica Fisch. ex Hoffm.) is widely used as a traditional Chinese medicine and the secondary metabolites have significant pharmacological activities. Drying has been shown to be a key factor affecting the coumarin content of Angelica dahurica. However, the underlying mechanism of metabolism is unclear. This study sought to determine the key differential metabolites and metabolic pathways related to this phenomenon. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based targeted metabolomics analysis was performed on Angelica dahurica that were freeze-drying (- 80 °C/9 h) and oven-drying (60 °C/10 h). Furthermore, the common metabolic pathways of paired comparison groups were performed based on KEEG enrichment analysis. The results showed that 193 metabolites were identified as key differential metabolites, most of which were upregulated under oven drying. It also displayed that many significant contents of PAL pathways were changed. This study revealed the large-scale recombination events of metabolites in Angelica dahurica. First, we identified additional active secondary metabolites apart from coumarins, and volatile oil were significantly accumulated in Angelica dahurica. We further explored the specific metabolite changes and mechanism of the phenomenon of coumarin upregulation caused by temperature rise. These results provide a theoretical reference for future research on the composition and processing method of Angelica dahurica.

Kampo herbal ointments for skin wound healing

The management of skin wound healing problems is a public health issue in which traditional herbal medicines could play a determining role. Kampo medicine, with three traditionally used ointments, provides interesting solutions for these dermatological issues. These ointments named Shiunkō, Chuōkō, and Shinsen taitsukō all have in common a lipophilic base of sesame oil and beeswax from which herbal crude drugs are extracted according to several possible manufacturing protocols. This review article brings together existing data on metabolites involved in the complex wound healing process. Among them are representatives of the botanical genera Angelica, Lithospermum, Curcuma, Phellodendron, Paeonia, Rheum, Rehmannia, Scrophularia, or Cinnamomum. Kampo provides numerous metabolites of interest, whose content in crude drugs is very sensitive to different biotic and abiotic factors and to the different extraction protocols used for these ointments. If Kampo medicine is known for its singular standardization, ointments are not well known, and research on these lipophilic formulas has not been developed due to the analytical difficulties encountered in biological and metabolomic analysis. Further research considering the complexities of these unique herbal ointments could contribute to a rationalization of Kampo's therapeutic uses for wound healing.

Detection of the role of intestinal flora and tryptophan metabolism involved in antidepressant-like actions of crocetin based on a multi-omics approach

RATIONALE

Depression is a serious mood disorder, and crocetin has a variety of pharmacological activities, including antidepressant effect. The alterations of intestinal flora have a significant correlation with depression, and crocetin can alter the composition of intestinal flora in mice with depression-like behaviors.

OBJECTIVE

This study investigated the underlying antidepressant mechanisms of crocetin through multi-omics coupled with biochemical technique validation.

METHODS

Chronic unpredictable stress (CUMS) was used to induce mice model of depression to evaluate the antidepressant effect of crocetin through behavioral tests, and the metagenomic and metabolomic were used to explore the potential mechanisms involved. In order to verify its underlying mechanism, western blot (WB), Elisa, immune histological and HPLC techniques were used to detect the level of inflammatory cytokines and the level of metabolites/proteins related to tryptophan metabolism in crocetin-treated mice.

RESULTS

Crocetin ameliorated depression-like behaviors and increased mobility in depressive mice induced by CUMS. Metagenomic results showed that crocetin regulated the structure of intestinal flora, as well as significantly regulated the function gene related to derangements in energy metabolism and amino acid metabolism in mice with depression-like behaviors. Metabolomic results showed that the tryptophan metabolism, arginine metabolism and arachidonic acid metabolism played an essential role in exerting antidepressant-like effect of crocetin. According to multi-omics approaches and validation results, tryptophan metabolism and inflammation were identified and validated as valuable biological processes involved in the antidepressant effects of crocetin. Crocetin regulated the tryptophan metabolism in mice with depression-like behaviors, including increased aryl hydrocarbon receptor (AhR) expression, reduced indoleamine 2,3-dioxygenase 1 (IDO1) and serotonin transporter (SERT) expression in the hippocampus, elevated the content of 5-HT, kynurenic acid in serum and 5-HT, tryptophan in hippocampus. In addition, crocetin also attenuated inflammation in mice with depression-like behaviors, which presented with reducing the production of inflammatory cytokines in serum and colon. Meanwhile, crocetin up-regulated the expression of zonula occludens 1 (ZO-1) and occludin in ileum and colon to repair the intestinal barrier for preventing inflammation transfer.

CONCLUSION

Our findings clarify that crocetin exerted antidepressant effects through its anti-inflammation, repairment of intestinal barrier, modulatory on the intestinal flora and metabolic disorders, which further regulated tryptophan metabolism and impacted mitogen-activated protein kinase (MAPK) signaling pathway to enhance neural plasticity, thereby protect neural.

The Effects of NAA on the Tuberous Root Yield and Quality of Rehmannia glutinosa and Its Regulatory Mechanism by Transcriptome and Metabolome Profiling

Naphthylacetic acid (NAA) was used to increase the tuberous root yield of Rehmannia glutinosa, but the differences between its NAA-treated and control tuberous roots (NT and CG) and the regulatory mechanism of NAA effect remain unclear. In order to investigate them, NTs and CGs were used as materials, and both yield-related indices were measured; the metabolomics and transcriptomics were used to capture differentially accumulated metabolites (DAM) and to validate them via mining differentially expressed genes (DEGs), respectively. The effects of NAA treatment: increased NT mass per plant by 21.14%, through increasing the number of roots and increasing the mean root diameter; increased catalpol content by 1.2234% (p < 0.05); up-regulated 11DAMs and 596DEGs; and down-regulated 18 DAMs and 517DEGs. In particular, we discovered that NAA regulated its DAMs and biomass via 10 common metabolic pathways, and that the number of NAA-down-regulated DAMs was more than that of NAA-up-regulated DAMs in its tuberous root. Furthermore, HPLC validated the changes of several DAMs and 15 DEGs (4CL, ARF, CCoAOMT, ARGOS, etc.) associated with the yield increase and DAMs were verified by RT-qPCR. This study provided some valuable resources, such as tuberous root indices, key genes, and DAMs of Rehmannia glutinosa in response to NAA for distinguishing the CGs from NTs, and novel insights into the regulatory mechanism of NAA effects on both at the transcriptomic and metabolomic levels, so it will lay a theoretical foundation for NAA-regulated plant yield and quality, and provide references for prohibiting the uses of NAA as a swelling agent in medicinal tuber plants in China.

Effects of pH and Osmotic Changes on the Metabolic Expressions of Bacillus subtilis Strain 168 in Metabolite Pathways including Leucine Metabolism

Bacillus subtilis is often exposed to diverse culture conditions with the aim of improving hygiene or food quality. This can lead to changes in the volatile metabolite profiles related to the quality of fermented foods. To comprehensively interpret the associated metabolic expressions, changes in intracellular primary and extracellular secondary volatile metabolites were investigated by exposing B. subtilis to an alkaline pH (BP, pH 8.0) and a high salt concentration (BS, 1 M). In particular, B. subtilis was cultured in a leucine-enriched medium to investigate the formation of leucine-derived volatile metabolites. This study observed metabolic changes in several metabolic pathways, including carbohydrate metabolism, amino acid metabolism, fatty acid metabolism, and leucine degradation. The formation of proline (an osmolyte), furans, pyrrole, and monosaccharide sugars (glucose, galactose, and fructose) was enhanced in BS, whereas fatty acid derivatives (ketones and alcohols) increased in BP. In the case of leucine degradation, 3-methyl-butanal and 3-methylbutanol could be salt-specific metabolites, while the contents of 3-methylbutanoic acid and 3-methylbutylacetate increased in BP. These results show culture condition-specific metabolic changes, especially secondary volatile metabolites related to the sensory property of foods, in B. subtilis.

Regulatory Effects of Functional Soluble Dietary Fiber from Saccharina japonica Byproduct on the Liver of Obese Mice with Type 2 Diabetes Mellitus

Though the relationship between dietary fiber and physical health has been investigated widely, the use of dietary fiber from marine plants has been investigated relatively rarely. The Saccharina japonica byproducts after the production of algin contain a large amount of insoluble polysaccharide, which will cause a waste of resources if ignored. Soluble dietary fiber (SDF)prepared from waste byproducts of Saccharina japonica by alkaline hydrolysis method for the first time had a wrinkled microscopic surface and low crystallinity, which not only significantly reduced liver index, serum levels of aspartate aminotransferase (AST) and alanine amiotransferase (ALT), and liver fat accumulation damage to the livers of obese diabetic mice, but also activated the PI3K/AKT signaling pathway to increase liver glycogen synthesis and glycolysis. By LC-MS/MS employing a Nexera UPLC tandem QE high-resolution mass spectrometer, the 6 potential biomarker metabolites were screened, namely glycerophosphocholine (GPC), phosphocholine (PCho), pantothenic acid, glutathione (GSH), oxidized glutathione (GSSG), and betaine; several pathways of these metabolites were associated with lipid metabolism, glycogen metabolism, and amino acid metabolism in the liver were observed. This study further provided a detailed insight into the mechanisms of SDF from Saccharina japonica byproducts in regulating the livers of obese mice with type 2 diabetes and laid a reliable foundation for the further development and utilization of Saccharina japonica.

Study of Terpenoid Synthesis and Prenyltransferase in Roots of Rehmannia glutinosa Based on iTRAQ Quantitative Proteomics

Rehmannia glutinosa has important medicinal value; terpenoid is one of the main active components in R. glutinosa. In this study, iTRAQ technique was used to analyze the relative abundance of proteins in roots of R. glutinosa, and 6,752 reliable proteins were quantified. GO enrichment results indicated that most proteins were involved in metabolic process or cellular process, 57.63% proteins had catalytic activity, and 65.80% proteins were enriched in membrane-bounded organelle. In roots of R. glutinosa, there were 38 KEGG enrichments with significance, more DEPs were found in some pathways, especially the proteasome pathway and TCA cycle with 15.0% DEPs between elongation stage and expansion stage of roots. Furthermore, five KEGG pathways of terpenoid synthesis were found. Most prenyltransferases belong to FPP/GGPP synthase family, involved in terpenoid backbone biosynthesis, and all interacted with biotin carboxylase CAC2. Compared with that at the elongation stage, many prenyltransferases exhibited higher expression at the expansion stage or maturation stage of roots. In addition, eight FPP/GGPP synthase encoding genes were cloned from R. glutinosa, namely FPPS, FPPS1, GGPS, GGPS3, GGPS4, GGPS5, GPPS and GPPS2, introns were also found in FPPS, FPPS1, GGPS5 and GGPS2, and FPP/GPP synthases were more conservative in organisms, especially in viridiplantae, in which the co-occurrence of GPPS or GPPS2 was significantly higher in plants. Further analysis found that FPP/GGPP synthases of R. glutinosa were divided into three kinds, GGPS, GPPS and FPPS, and their gene expression was significantly diverse in different varieties, growth periods, or tissues of R. glutinosa. Compared with that of GGPS, the expression of GPPS and FPPS was much higher in R. glutinosa, especially at the expansion stage and maturation stage. Thus, the synthesis of terpenoids in roots of R. glutinosa is intricately regulated and needs to be further studied.

De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology

Rehmannia glutinosa is a potent medicinal plant with a significant importance in traditional Chinese medicine. Its root is enriched with various bioactive molecules mainly iridoids, possessing important pharmaceutical properties. However, the molecular biology and evolution of R. glutinosa have been largely unexplored. Here, we report a reference genome of R. glutinosa using Nanopore technology, Illumina and Hi-C sequencing. The assembly genome is 2.49 Gb long with a scaffold N50 length of 70 Mb and high heterozygosity (2%). Since R. glutinosa is an autotetraploid (4n = 56), the difference between each set of chromosomes is very small, and it is difficult to distinguish the two sets of chromosomes using Hi-C. Hence, only one set of the genome size was mounted to the chromosome level. Scaffolds covering 52.61% of the assembled genome were anchored on 14 pseudochromosomes. Over 67% of the genome consists of repetitive sequences dominated by Copia long terminal repeats and 48,475 protein-coding genes were predicted. Phylogenetic analysis corroborates the placement of R. glutinosa in the Orobanchaceae family. Our results indicated an independent and very recent whole genome duplication event that occurred 3.64 million year ago in the R. glutinosa lineage. Comparative genomics analysis demonstrated expansion of the UDP-dependent glycosyltransferases and terpene synthase gene families, known to be involved in terpenoid biosynthesis and diversification. Furthermore, the molecular biosynthetic pathway of iridoids has been clarified in this work. Collectively, the generated reference genome of R. glutinosa will facilitate discovery and development of important pharmacological compounds.

Metabolic Profiles of Brassica juncea Roots in Response to Cadmium Stress

Brassica juncea has great application potential in phytoremediation of cadmium (Cd)-contaminated soil because of its excellent Cd accumulating and high biomass. In this study, we compared the effects of Cd under 48 h and 7 d stress in roots of Brassica juncea using metabolite profiling. The results showed that many metabolic pathways and metabolites in Brassica juncea roots were altered significantly in response to Cd stress. We found that significant differences in levels of amino acids, organic acids, carbohydrates, lipids, flavonoids, alkaloids, and indoles were induced by Cd stress at different times, which played a pivotal role in the adaptation of Brassica juncea roots to Cd stress. Meanwhile, Brassica juncea roots could resist 48 h Cd stress by regulating the biosynthesis of amino acids, linoleic acid metabolism, aminoacyl-tRNA biosynthesis, glycerophospholipid metabolism, ABC transporters, arginine biosynthesis, valine, leucine and isoleucine biosynthesis, and alpha-linolenic acid metabolism; however, they regulated alpha-linolenic acid metabolism, glycerophospholipid metabolism, ABC transporters, and linoleic acid metabolism to resist 7 d Cd stress. A metabolomic expedition to the response of Brassica juncea to Cd stress will help to comprehend its tolerance and accumulation mechanisms of Cd.

Comparative analysis of tuberous root metabolites between cultivated and wild varieties of Rehmannia glutinosa by widely targeted metabolomics

Differential metabolites between tuberous roots from cultivated variety (ZP) and wild variety (YS) of Rehmannia glutinosa were analyzed by widely targeted metabolomics, and annotated to KEGG pathways. 228 secondary metabolites (SM) in ZP and YS were detected, of which 58 were differential metabolites (DM), including 41 flavonoids, 10 phenolic acids, 3 terpenoids, 2 alkaloids and 2 others, and 170 were unchanged; Among 58 DMs, 44 (75.9%) were up-regulated in YS, of which 30 were unique to YS, while 14 (24.1%) were down-regulated in YS, of which 10 were unique to ZP; Among flavonoids, 33 (80.5%) were more highly expressed in YS than in ZP; Among phenolic acids, 7 (70%) were more highly expressed in YS than in ZP; 12 of 58 DMs were annotated into 17 types of KEGG pathways. Among them, benzoic acid and p-Coumaryl alcohol were up-regulated in YS, and annotated into 10 pathways (58.8%) and 4 pathways (23.5%), respectively. In addition, much of DMs possess various pharmacological effects. These results indicated better quality of YS than ZP and the necessity of YS domestication. Taken together, this study will provide a reference for the scientific introduction, comprehensive development and utilization of wild Rehmannia glutinosa.

FUNCTIONAL METABOLOMICS DECIPHER BIOCHEMICAL FUNCTIONS AND ASSOCIATED MECHANISMS UNDERLIE SMALL-MOLECULE METABOLISM

Metabolism is the collection of biochemical reactions enabled by chemically diverse metabolites, which facilitate different physiological processes to exchange substances and synthesize energy in diverse living organisms. Metabolomics has emerged as a cutting-edge method to qualify and quantify the metabolites in different biological matrixes, and it has the extraordinary capacity to interrogate the biological significance that underlies metabolic modification and modulation. Liquid chromatography combined with mass spectrometry (LC/MS), as a robust platform for metabolomics analysis, has increased in popularity over the past 10 years due to its excellent sensitivity, throughput, and versatility. However, metabolomics investigation currently provides us with only phenotype data without revealing the biochemical functions and associated mechanisms. This limitation indeed weakens the core value of metabolomics data in a broad spectrum of the life sciences. In recent years, the scientific community has actively explored the functional features of metabolomics and translated this cutting-edge approach to be used to solve key multifaceted questions, such as disease pathogenesis, the therapeutic discovery of drugs, nutritional issues, agricultural problems, environmental toxicology, and microbial evolution. Here, we are the first to briefly review the history and applicable progression of LC/MS-based metabolomics, with an emphasis on the applications of metabolic phenotyping. Furthermore, we specifically highlight the next era of LC/MS-based metabolomics to target functional metabolomes, through which we can answer phenotype-related questions to elucidate biochemical functions and associated mechanisms implicated in dysregulated metabolism. Finally, we propose many strategies to enhance the research capacity of functional metabolomics by enabling the combination of contemporary omics technologies and cutting-edge biochemical techniques. The main purpose of this review is to improve the understanding of LC/MS-based metabolomics, extending beyond the conventional metabolic phenotype toward biochemical functions and associated mechanisms, to enhance research capability and to enlarge the applicable scope of functional metabolomics in small-molecule metabolism in different living organisms.

Treatment with catalpol protects against cisplatin-induced renal injury through Nrf2 and NF-κB signaling pathways

Cisplatin (CP) is one of the most widely used chemotherapy drugs for cancer treatment, but it often leads to nephrotoxicity. It is well known that catalpol exhibits antioxidant and anti-inflammatory functions, thus the present study aimed to investigate the potential protective effects of catalpol on CP-induced kidney injury in rats, in addition to determining the underlying mechanisms. Sprague-Dawley rats were treated with 25, 50 or 100 mg/kg catalpol for two days, injected with 20 mg/kg cisplatin and catalpol on day 3 and sacrificed on day 4. The histological analysis of isolated kidney tissues was performed using hematoxylin and eosin staining, cleaved caspase-3 expression levels were analyzed using western blotting and the expression levels of inflammatory cytokines in the tissues, including tumor necrosis factor α (TNF-α), interleukin (IL)-1β, IL-6, IL-8, IL-10 and inducible nitric oxide synthase (iNOS) were evaluated using ELISAs. Furthermore, the mRNA and protein expression levels of nuclear factor erythroid 2-related factor 2 (Nrf2), heme oxygenase 1 (HO-1), kelch-like ECH-associated protein 1 (Keap1), NF-κB and inhibitory κB (IκB) were determined using reverse transcription-quantitative PCR and western blotting, respectively. The results revealed that the treatment with catalpol prevented the histopathological injury and renal dysfunction caused by CP. In addition, catalpol significantly suppressed the CP-induced apoptosis of tubular cells, inhibited the CP-induced upregulation of TNF-α, IL-1β, IL-6, IL-8 and iNOS and promoted the production of the anti-inflammatory cytokine IL-10. Additionally, the mRNA and protein expression levels of Nrf2, HO-1 and IκB in the kidney tissues were increased, whereas the expression levels of Keap1 and NF-κB were significantly decreased following the treatment with catalpol. In conclusion, these results suggested that catalpol may inhibit CP-induced renal injury and suppress the associated inflammatory response through activating the Nrf2 and inhibiting the NF-κB signaling pathways, respectively.

Current advances in acteoside biosynthesis pathway elucidation and biosynthesis

Acteoside is an important bioactive natural product distributed in many plant species, composed of four moieties such as caffeic acid, glucose, rhamnose and phenylethyl alcohol, and possesses some bioactivities such as anti-inflammatory, anti-oxidant, neuro-protective, anti-tumor and so on. However, acteoside content in medicinal plants is low, and acteoside stability is bad, so acteoside biosynthesis is a problem. Recent years, acteoside biosynthesis pathway elucidation and bio-production have been widely investigated, so many achievements have been made up to now. In this study, we reviewed current advances in both the elucidation and bio-production such as the putative methods and enzymatic determination of acteoside biosynthesis pathway, functional analyses of the roles of some candidate genes for verbascoside biosynthesis by transgenic technology, acteoside production via metabolic engineering and synthetic biology approaches and plant tissue culture. Moreover, we first established a combined putative acteoside biosynthesis pathway based on its recent studies in animals, plants and microbes. Meanwhile, we pointed out both problems to shortcomings, and highlighted its future development trend. These results will provide references for the complete elucidation of acteoside biosynthesis pathway and the improvement of acteoside content in medicinal plants and acteoside production via microbial and plant metabolic engineering and synthetic biology approaches, and inform the readers critically of the latest developments of them.

Analysis of Young Shoots of 'Anji Baicha' (Camellia sinensis) at Three Developmental Stages Using Nontargeted LC-MS-Based Metabolomics

'Anji Baicha' (Camellia sinensis) is a low-temperature-sensitive tea variety. During the development of young shoots, the leaves of 'Anji Baicha' exhibit periodic albinism. The quality of 'Anji Baicha' is closely related to the color of the fresh leaves, with whiter leaves affording a higher amino acid content and superior sensory quality after processing. However, the metabolic mechanism of its quality formation is still unclear. In this study, we analyzed the metabolomic changes of young shoots of 'Anji Baicha' and screened for metabolic markers that may be involved in the periodic albinism. Positive- and negative-mode UPLC-QTOF-MS was applied to the metabolomic analysis of young leaves of 'Anji Baicha' during three developmental stages (i.e., the pre-albescent, albescent, and regreening stages). The results revealed significant differences in the metabolic profiles of the young leaves at the three stages. The differential metabolites were mainly related to the pathways of flavonoid, phenylpropanoid, and amino acid biosynthesis. The concentrations of several amino acids (primarily l-theanine, l-glutamate, N₂ -acetyl-l-ornithine, l-aspartic acid, d-proline, l-glutamine, l-leucine, and pyroglutamic acid) and 12-OPDA were significantly higher in the albescent stage. In contrast, during the albescent stages, the concentrations of several carbohydrates (d-fructose, β-d-galactopyranose, 3-O-fucopyranosyl-2-acetamido-2-deoxyglucopyranose, galactose-β-1, 4-xylose acetyl-maltose, and 2-fucosyllactose) were significantly lower. Moreover, catechins (mainly epigallocatechin and catechin derivatives), dimeric catechins (primarily proanthocyanidins), and flavonol and flavonol/flavone glycosides (mainly kaempferol, myricetin, quercetin, cyanidin, and delphinidin glycosides) were detected at the highest levels in the regreening or pre-albescent stages. The obtained results enhance the current understanding of the metabolic mechanisms of periodic albinism and quality development formation in 'Anji Baicha'. PRACTICAL APPLICATION: The obtained results not only provide information regarding differential metabolites but also advance the understanding of the mechanism of periodic albinism in 'Anji Baicha' at the metabolite level and open up new possibilities for the genetic improvement of tea cultivars.

Physiological and Metabolomic Analysis of Cold Plasma Treated Fresh-Cut Strawberries

Cold plasma technology offers new opportunities to the decontamination and preservation of fruits and vegetables. In the present research, strawberries were cut into four wedges and then treated with dielectric barrier discharge plasma at 45 kV for 1 min and stored for 1 week (4 °C). Metabolomic analysis suggested that plasma treatment improved the biosynthesis of the metabolites in the "flavones and flavonol biosynthesis" pathway and "biosynthesis of phenylpropanoids" pathway in fresh-cut strawberries. Physiological assay demonstrated that plasma treatment maintained the texture properties and inhibited microbial growth of fresh-cut strawberries. In addition, plasma treatment also promoted the accumulation of total phenolics, total flavonoid, and anthocyanin by enhancing the critical enzyme activities and activating related gene expression in phenylpropanoid as well as reactive oxygen species metabolism, which contributed greatly to the enhancement of antioxidant capacity of strawberry wedges. Our investigation provided a new perspective of the effect of plasma treatment on the safety and quality of strawberry wedges and suggested that cold plasma treatment holds promise as an emerging processing technology for improving the quality and antioxidant activity of postharvest fruits and vegetables.

Algorithmic and Stochastic Representations of Gene Regulatory Networks and Protein-Protein Interactions

BACKGROUND

Latest studies reveal the importance of Protein-Protein interactions on physiologic functions and biological structures. Several stochastic and algorithmic methods have been published until now, for the modeling of the complex nature of the biological systems.

OBJECTIVE

Biological Networks computational modeling is still a challenging task. The formulation of the complex cellular interactions is a research field of great interest. In this review paper, several computational methods for the modeling of GRN and PPI are presented analytically.

METHODS

Several well-known GRN and PPI models are presented and discussed in this review study such as: Graphs representation, Boolean Networks, Generalized Logical Networks, Bayesian Networks, Relevance Networks, Graphical Gaussian models, Weight Matrices, Reverse Engineering Approach, Evolutionary Algorithms, Forward Modeling Approach, Deterministic models, Static models, Hybrid models, Stochastic models, Petri Nets, BioAmbients calculus and Differential Equations.

RESULTS

GRN and PPI methods have been already applied in various clinical processes with potential positive results, establishing promising diagnostic tools.

CONCLUSION

In literature many stochastic algorithms are focused in the simulation, analysis and visualization of the various biological networks and their dynamics interactions, which are referred and described in depth in this review paper.