Conservation and Expression Patterns Divergence of Ascorbic Acid d-mannose/l-galactose Pathway Genes in Brassica rapa

Application of Chitosan@Fe3O4 Nanoparticle-Modified Screen-Printed Graphene-Based Electrode for Simultaneous Analysis of Nitrite and Ascorbic Acid in Hydroponics and Fruit Juice

In this work, the development of screen-printed electrodes modified with chitosan-coated magnetite nanoparticles (CTS@Fe3O4/SPGNE) for the simultaneous determination of nitrite (NO2-) and ascorbic acid (AA-) is presented. The study investigated various ratios of graphene to chitosan-coated magnetite nanoparticles (CTS@Fe3O4), as well as the optimal pH. These factors were examined due to their impact on the selectivity and sensitivity of the analysis. The results indicated that a graphene paste to CTS@Fe3O4 ratio of 16:1.0 g and a pH of 4 were optimal for the analysis of both NO2- and AA-. Additionally, the behavior of the proposed electrode, its analytical performance, and interference studies were thoroughly examined. Furthermore, the CTS@Fe3O4/SPGNE electrode shows potential for the simultaneous determination of NO2- and AA- in hydroponics and fruit juice samples.

Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages

BACKGROUND

In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages.

RESULTS

Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations.

CONCLUSIONS

This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.

The Biochemistry and Effectiveness of Antioxidants in Food, Fruits, and Marine Algae

It is more effective to maintain good health than to regain it after losing it. This work focuses on the biochemical defense mechanisms against free radicals and their role in building and maintaining antioxidant shields, aiming to show how to balance, as much as possible, the situations in which we are exposed to free radicals. To achieve this aim, foods, fruits, and marine algae with a high antioxidant content should constitute the basis of nutritional elements, since natural products are known to have significantly greater assimilation efficiency. This review also gives the perspective in which the use of antioxidants can extend the life of food products, by protecting them from damage caused by oxidation as well as their use as food additives.

Genetic and biochemical strategies for regulation of L-ascorbic acid biosynthesis in plants through the L-galactose pathway

Vitamin C (L-ascorbic acid, AsA) is an essential compound with pleiotropic functions in many organisms. Since its isolation in the last century, AsA has attracted the attention of the scientific community, allowing the discovery of the L-galactose pathway, which is the main pathway for AsA biosynthesis in plants. Thus, the aim of this review is to analyze the genetic and biochemical strategies employed by plant cells for regulating AsA biosynthesis through the L-galactose pathway. In this pathway, participates eight enzymes encoded by the genes PMI, PMM, GMP, GME, GGP, GPP, GDH, and GLDH. All these genes and their encoded enzymes have been well characterized, demonstrating their participation in AsA biosynthesis. Also, have described some genetic and biochemical strategies that allow its regulation. The genetic strategy includes regulation at transcriptional and post-transcriptional levels. In the first one, it was demonstrated that the expression levels of the genes correlate directly with AsA content in the tissues/organs of the plants. Also, it was proved that these genes are light-induced because they have light-responsive promoter motifs (e.g., ATC, I-box, GT1 motif, etc.). In addition, were identified some transcription factors that function as activators (e.g., SlICE1, AtERF98, SlHZ24, etc.) or inactivators (e.g., SlL1L4, ABI4, SlNYYA10) regulate the transcription of these genes. In the second one, it was proved that some genes have alternative splicing events and could be a mechanism to control AsA biosynthesis. Also, it was demonstrated that a conserved cis-acting upstream open reading frame (5'-uORF) located in the 5'-untranslated region of the GGP gene induces its post-transcriptional repression. Among the biochemical strategies discovered is the control of the enzyme levels (usually by decreasing their quantities), control of the enzyme catalytic activity (by increasing or decreasing its activity), feedback inhibition of some enzymes (GME and GGP), subcellular compartmentation of AsA, the metabolon assembly of the enzymes, and control of AsA biosynthesis by electron flow. Together, the construction of this basic knowledge has been establishing the foundations for generating genetically improved varieties of fruits and vegetables enriched with AsA, commonly used in animal and human feed.

Incorporation of Nanocatalysts for the Production of Bio-Oil from Staphylea holocarpa Wood

Biomass has been recognized as the most common source of renewable energy. In recent years, researchers have paved the way for a search for suitable biomass resources to replace traditional fossil fuel energy and provide high energy output. Although there are plenty of studies of biomass as good biomaterials, there is little detailed information about Staphylea holocarpa wood (S. holocarpa) as a potential bio-oil material. The purpose of this study is to explore the potential of S. holocarpa wood as a bio-oil. Nanocatalyst cobalt (II) oxide (Co₃O₄) and Nickel (II) oxide (NiO) were used to improve the production of bio-oil from S. holocarpa wood. The preparation of biofuels and the extraction of bioactive drugs were performed by the rapid gasification of nanocatalysts. The result indicated that the abundant chemical components detected in the S. holocarpa wood extract could be used in biomedicine, cosmetics, and biofuels, and have a broad industrial application prospect. In addition, nanocatalyst cobalt tetraoxide (Co₃O₄) could improve the catalytic cracking of S. holocarpa wood and generate more bioactive molecules at high temperature, which is conducive to the utilization and development of S. holocarpa wood as biomass. This is the first time that S. holocarpa wood was used in combination with nanocatalysts. In the future, nanocatalysts can be used to solve the problem of sustainable development of biological resources.

Genome-Wide Identification and Expression Profiling of CONSTANS-Like Genes in Pepper (Capsicum annuum): Gaining an Insight to Their Phylogenetic Evolution and Stress-Specific Roles

CONSTANS-like (COL) genes play important regulatory roles in multiple growth and development processes of plants but have rarely been studied in Capsicum annuum. This study explored the evolutionary relationship and expression patterns of COL genes from C. annuum. A total of 10 COL genes were identified in the genome of the cultivated pepper Zunla-1 and were named CaCOL01-10. These genes were unequally distributed among five chromosomes and could be divided into three groups based on differences in gene structure characteristics. During evolutionary history, duplications and retentions were divergent among different groups of COL genes. Tandem duplication caused amplification of group I genes. Genetic distance among COL genes was the largest in group III, suggesting that group III genes undergo more relaxed selection pressure compared with the other groups. Expression patterns of CaCOLs in tissues were significantly different, with CaCOL08 exhibiting the highest expression in stem and leaf. Some COL orthologous genes showed markedly different expression patterns in pepper compared with tomato, such as COL_1 orthologs, which may be involved in fruit development in pepper. In addition, CaCOLs participated in the regulation of abiotic stresses to varying degrees. Five CaCOL genes were induced by cold, and CaCOL02 and CaCOL03 were specifically upregulated by cold and downregulated by heat. This study provides a theoretical basis for the in-depth understanding of the functions of COL genes in pepper and their molecular mechanisms involved in growth and development and responses to abiotic stresses.

TWAS results are complementary to and less affected by linkage disequilibrium than GWAS

A genome-wide association study (GWAS) is used to identify genetic markers associated with phenotypic variation. In contrast, a transcriptome-wide association study (TWAS) detects associations between gene expression levels and phenotypic variation. It has previously been shown that in the cross-pollinated species, maize (Zea mays), GWAS, and TWAS identify complementary sets of trait-associated genes, many of which exhibit characteristics of true positives. Here, we extend this conclusion to the self-pollinated species, Arabidopsis thaliana and soybean (Glycine max). Linkage disequilibrium (LD) can result in the identification, via GWAS, of false-positive associations. In all three analyzed plant species, most trait-associated genes identified via TWAS are well separated physically from other candidate genes. Hence, TWAS is less affected by LD than is GWAS, demonstrating that TWAS is particularly well suited for association studies in genomes with slow rates of LD decay, such as soybean. TWAS is reasonably robust to the plant organs/tissues used to determine expression levels. In summary, this study confirms that TWAS is a promising approach for accurate gene-level association mapping in plants that is complementary to GWAS, and established that TWAS can exhibit substantial advantages relative to GWAS in species with slow rates of LD decay.

The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype

Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales, ornate leaves, extended vegetative phase, and nutritional quality are some of the characters potentially selected by humans during domestication. We used a combination of developmental studies and transcriptomics to understand the vegetative domestication syndrome of kale. To identify candidate genes that are responsible for the evolution of domestic kale, we searched for transcriptome-wide differences among three vegetative B. oleracea morphotypes. RNA-seq experiments were used to understand the global pattern of expressed genes during a mixture of stages at one time in kale, cabbage, and the rapid cycling kale line TO1000. We identified gene expression patterns that differ among morphotypes and estimate the contribution of morphotype-specific gene expression that sets kale apart (3958 differentially expressed genes). Differentially expressed genes that regulate the vegetative to reproductive transition were abundant in all morphotypes. Genes involved in leaf morphology, plant architecture, defense, and nutrition were differentially expressed in kale. This allowed us to identify a set of candidate genes we suggest may be important in the kale domestication syndrome. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve Cole crop production.

Responses of Phragmites australis to copper stress: A combined analysis of plant morphology, physiology and proteomics

Few relevant research attempts have been made to determine heavy metal resistance mechanisms of rhizomatous perennial plants. Thus, it is pertinent to investigate the physiological and biochemical changes in Phragmites australis under metal-stressed conditions to facilitate the development of strategies to enhance copper (Cu) tolerance. We measured parameters related to plant growth and development, metal translocation and physiological responses of P. australis subjected to Cu stress. In addition, the differentially expressed proteins (DEP) were evaluated using the isobaric tag for relative and absolute quantification (iTRAQ) system. A large amount of copper accumulates in the roots of P.australis, but the growth parameters were not sensitive to Cu. However, the high concentration of Cu reduced the content of chlorophyll a and chlorophyll b, and the expression of important photosynthesis proteins PsbD, PsbO and PsaA were all down-regulated, so photosynthesis was inhibited. In contrast, the content of ascorbic acid and proline both increased with the increase of copper stress. P.australis fixed a large amount of Cu in its roots, limiting the migration of Cu to other parts of the plant. Moreover, Cu stress can affect photosynthesis by inhibiting the activity of PSI, PSII and LHCII. In addition, P.australis synthesizes ascorbic acid through the D-mannose/L-galactose pathway, and synthesizes proline through the ornithine pathway. Ascorbic acid and proline can increase Cu tolerance and protect photosynthesis. These results provide a theoretical basis for understanding the tolerance and repair mechanisms of plants in response to heavy metal pollution.

Molecular Evolutionary and Expression Pattern Analysis of AKR Genes Shed New Light on GalUR Functional Characteristics in Brassica rapa

The aldo-keto reductase (AKR) superfamily plays a major role in oxidation-reduction in plants. _D-galacturonic acid reductase (GalUR), an ascorbic acid (AsA) biosynthetic enzyme, belongs to this superfamily. However, the phylogenetic relationship and evolutionary history of the AKR gene family in plants has not yet been clarified. In this study, a total of 1268 AKR genes identified in 36 plant species were used to determine this phylogenetic relationship. The retention, structural characteristics, and expression patterns of AKR homologous genes in Brassica rapa and Arabidopsis thaliana were analyzed to further explore their evolutionary history. We found that the AKRs originated in algae and could be divided into A and B groups according to the bootstrap value; GalURs belonged to group A. Group A AKR genes expanded significantly before the origin of angiosperms. Two groups of AKR genes demonstrated functional divergence due to environmental adaptability, while group A genes were more conservative than those in group B. All 12 candidate GalUR genes were cloned, and their expression patterns under stress were analyzed, in Pak-choi. These genes showed an obvious expression divergence under multiple stresses, and BrcAKR22 exhibited a positive correlation between its expression trend and AsA content. Our findings provide new insights into the evolution of the AKR superfamily and help build a foundation for further investigations of GalUR’s functional characteristics.

Advances in the Regulation of In Vitro Paclitaxel Production: Methylation of a Y-Patch Promoter Region Alters BAPT Gene Expression in Taxus Cell Cultures

Plant cell biofactories represent a promising solution to the increasing demand for plant-derived compounds, but there are still limiting factors that prevent optimal production, including the loss of yield during in vitro maintenance. Our results reveal a clear correlation between genomic methylation levels and a progressive decline in taxane production in Taxus spp. cell cultures. A comparative study of two cell lines, one 10 years old and low productive and the other new and high productive, revealed important differences in appearance, growth, taxane accumulation and expression levels of several taxane biosynthetic genes. Differences in taxane content and gene expression profile indicate an altered pathway regulation and that the BAPT gene, located in the center of the expression network of taxane biosynthetic genes, is active in a potentially flux-limiting step. The methylation patterns of the BAPT gene were studied in both cell lines by bisulfite sequencing, which revealed high rates of CHH methylated cytosines on the core promoter. Using a bioinformatics approach, this hotspot was identified as a Y-patch promoter element. The Y-patch may play a key role in the epigenetic regulation of the taxane biosynthetic pathway, which would open up novel genetic engineering strategies toward stable and high productivity.

Does vitamin C have the ability to augment the therapeutic effect of bone marrow-derived mesenchymal stem cells on spinal cord injury?

Methylprednisolone (MP) is currently the only drug confirmed to exhibit a neuroprotective effect on acute spinal cord injury (SCI). Vitamin C (VC) is a natural water-soluble antioxidant that exerts neuroprotective effects through eliminating free radical damage to nerve cells. Bone marrow mesenchymal stem cells (BMMSCs), as multipotent stem cells, are promising candidates in SCI repair. To evaluate the therapeutic effects of MP, VC and BMMSCs on traumatic SCI, 80 adult male rats were randomly divided into seven groups: control, SCI (SCI induction by weight-drop method), MP (SCI induction, followed by administration of 30 mg/kg MP via the tail vein, once every other 6 hours, for five times), VC (SCI induction, followed by intraperitoneal administration of 100 mg/kg VC once a day, for 28 days), MP + VC (SCI induction, followed by administration of MP and VC as the former), BMMSCs (SCI induction, followed by injection of 3 × 10⁶ BMMSCs at the injury site), and BMMSCs + VC (SCI induction, followed by BMMSCs injection and VC administration as the former). Locomotor recovery was assessed using the Basso Mouse Scale. Injured spinal cord tissue was evaluated using hematoxylin-eosin staining and immunohistochemical staining. Expression of transforming growth factor-beta, tumor necrosis factor-alpha, and matrix metalloproteinase-2 genes was determined using real-time quantitative PCR. BMMSCs intervention better promoted recovery of nerve function of rats with SCI, mitigated nerve cell damage, and decreased expression of transforming growth factor-beta, tumor necrosis factor-alpha, and matrix metalloproteinase-2 genes than MP and/or VC. More importantly, BMMSCs in combination with VC induced more obvious improvements. These results suggest that VC can enhance the neuroprotective effects of BMMSCs against SCI.