General Analysis of Heat Shock Factors in the Cymbidium ensifolium Genome Provided Insights into Their Evolution and Special Roles with Response to Temperature.

Heat shock factors (HSFs) are the key regulators of heat stress responses and play pivotal roles in tissue development and the temperature-induced regulation of secondary metabolites. In order to elucidate the roles of HSFs in Cymbidium ensifolium, we conducted a genome-wide identification of CeHSF genes and predicted their functions based on their structural features and splicing patterns. Our results revealed 22 HSF family members, with each gene containing more than one intron. According to phylogenetic analysis, 59.1% of HSFs were grouped into the A subfamily, while subfamily HSFC contained only two HSFs. And the HSF gene families were differentiated evolutionarily between plant species. Two tandem repeats were found on Chr02, and two segmental duplication pairs were observed on Chr12, Chr17, and Chr19; this provided evidence for whole-genome duplication (WGD) events in C. ensifolium. The core region of the promoter in most CeHSF genes contained cis-acting elements such as AP2/ERF and bHLH, which were associated with plant growth, development, and stress responses. Except for CeHSF11, 14, and 19, each of the remaining CeHSFs contained at least one miRNA binding site. This included binding sites for miR156, miR393, and miR319, which were responsive to temperature and other stresses. The HSF gene family exhibited significant tissue specificity in both vegetative and floral organs of C. ensifolium. CeHSF13 and CeHSF15 showed relatively significant expression in flowers compared to other genes. During flower development, CeHSF15 exhibited markedly elevated expression in the early stages of flower opening, implicating critical regulatory functions in organ development and floral scent-related regulations. During the poikilothermic treatment, CeHSF14 was upregulated over 200-fold after 6 h of heat treatment. CeHSF13 and CeHSF14 showed the highest expression at 6 h of low temperature, while the expression of CeHSF15 and CeHSF21 continuously decreased at a low temperature. The expression patterns of CeHSFs further confirmed their role in responding to temperature stress. Our study may help reveal the important roles of HSFs in plant development and metabolic regulation and show insight for the further molecular design breeding of C. ensifolium.

A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome.

Auxin Response Factors (ARFs) mediate auxin signaling and govern diverse biological processes. However, a comprehensive analysis of the ARF gene family and identification of their key regulatory functions have not been conducted in Melastoma dodecandrum, leading to a weak understanding of further use and development for this functional shrub. In this study, we successfully identified a total of 27 members of the ARF gene family in M. dodecandrum and classified them into Class I-III. Class II-III showed more significant gene duplication than Class I, especially for MedARF16s. According to the prediction of cis-regulatory elements, the AP2/ERF, BHLH, and bZIP transcription factor families may serve as regulatory factors controlling the transcriptional pre-initiation expression of MedARF. Analysis of miRNA editing sites reveals that miR160 may play a regulatory role in the post-transcriptional expression of MeARF. Expression profiles revealed that more than half of the MedARFs exhibited high expression levels in the stem compared to other organs. While there are some specific genes expressed only in flowers, it is noteworthy that MedARF16s, MedARF7A, and MedARF9B, which are highly expressed in stems, also demonstrate high expressions in other organs of M. dodecandrum. Further hormone treatment experiments revealed that these MedARFs were sensitive to auxin changes, with MedARF6C and MedARF7A showing significant and rapid changes in expression upon increasing exogenous auxin. In brief, our findings suggest a crucial role in regulating plant growth and development in M. dodecandrum by responding to changes in auxin. These results can provide a theoretical basis for future molecular breeding in Myrtaceae.

Recombinant Streptomyces netropsis transglutaminase expressed in Komagataella phaffii (Pichia pastoris) and applied in plant-based chicken nugget.

Transglutaminase (TG, EC 2.3.2.13) is widely used to modify functional properties in food systems, which can catalyze cross-linking reaction of proteins. In this work, microbial transglutaminase (MTG) from Streptomyces netropsis was heterologously expressed in the methylotrophic yeast Komagataella phaffii (Pichia pastoris). The specific activity of recombinant microbial transglutaminase (RMTG) was 26.17 ± 1.26 U/mg, and the optimum pH and temperature were measured as 7.0 and 50 °C, respectively. Bovine serum albumin (BSA) was used as a substrate to evaluate the effect of cross-linking reaction, and we found that RMTG had significant (p < 0.05) cross-linking effect for more than 30 min reactions. RMTG was further utilized in the investigation of plant-based chicken nuggets. Results showed that the hardness, springiness and chewiness of nuggets increased, and the adhesiveness decreased after RMTG treatment, which can prove that RMTG has the potential to improve the texture properties of plant-based chicken nuggets.

The bZIP Transcription Factors in Current Jasmine Genomes: Identification, Characterization, Evolution and Expressions.

Jasmine, a recently domesticated shrub, is renowned for its use as a key ingredient in floral tea and its captivating fragrance, showcasing significant ornamental and economic value. When cultivated to subtropical zone, a significant abiotic stress adaptability occurs among different jasmine varieties, leading to huge flower production changes and plantlet survival. The bZIP transcription factors (TFs) are reported to play indispensable roles in abiotic stress tolerance. Here, we performed a genome-level comparison of bZIPs using three-type jasmine genomes. Based on their physicochemical properties, conserved motif analysis and phylogenetic analysis, about 63 bZIP genes were identified and clustered in jasmine genomes, noting a difference of one member compared to the other two types of jasmines. The HTbZIP genes were categorized into 12 subfamilies compared with A. thaliana. In cis-acting element analysis, all genes contained light-responsive elements. The abscisic acid response element (ABRE) was the most abundant in HTbZIP62 promoter, followed by HTbZIP33. Tissue-specific genes of the bZIPs may play a crucial role in regulating the development of jasmine organs and tissues, with HTbZIP36 showing the most significant expressions in roots. Combined with complicated protein interactions, HTbZIP62 and HTbZIP33 might play a crucial role in the ABA signaling pathway and stress tolerance. Combined with RT-qPCR analysis, SJbZIP37/57/62 were more sensitive to ABA response genes compared with other bZIPs in DJ amd HT genomes. Our findings provide a useful resource for further research on the regulation of key genes to improve abiotic stress tolerance in jasmine.

The collaborative mode by PmSVPs and PmDAMs reveals neofunctionalization in the switch of the flower bud development and dormancy for Prunus mume.

Prunus mume (Rosaceae, Prunoideae) serves as an excellent ornamental woody plant with a large-temperature-range cultivation scope. Its flower buds require a certain low temperature to achieve flowering circulation. Thus, it is important to delve into the processes of flower bud differentiation and dormancy, which affected its continuous flowering. These processes are generally considered as regulation by the MADS-box homologs, SHORT VEGETATIVE PHASE (SVP), and DORMANCY-ASSOCIATED MADS-BOX (DAM). However, a precise model on their interdependence and specific function, when acting as a complex in the flower development of P. mume, is needed. Therefore, this study highlighted the integral roles of PmDAMs and PmSVPs in flower organ development and dormancy cycle. The segregation of PmDAMs and PmSVPs in a different cluster suggested distinct functions and neofunctionalization. The expression pattern and yeast two-hybrid assays jointly revealed that eight genes were involved in the floral organ development stages, with PmDAM1 and PmDAM5 specifically related to prolificated flower formation. PmSVP1-2 mingled in the protein complex in bud dormancy stages with PmDAMs. Finally, we proposed the hypothesis that PmSVP1 and PmSVP2 could combine with PmDAM1 to have an effect on flower organogenesis and interact with PmDAM5 and PmDAM6 to regulate flower bud dormancy. These findings could help expand the current molecular mechanism based on MADS-box genes during flower bud development and dormancy.

Associations between CYP3A4, CYP3A5 and SCN1A polymorphisms and carbamazepine metabolism in epilepsy: A meta-analysis.

BACKGROUND AND OBJECTIVE: CYP3A4 (rs2242480), CYP3A5 (rs776746) and SCN1A (rs3812718 and rs2298771) gene polymorphisms were previously indicated to be associated with carbamazepine (CBZ) metabolism and resistance in epilepsy. However, previous studies regarding the effects of these polymorphisms still remain controversial. Therefore, we performed a meta-analysis to evaluate whether the four polymorphisms are associated with CBZ metabolism and resistance. METHODS: The PubMed, EMBASE, Cochrane library, Chinese National Knowledge Infrastructure, Chinese Science and Technique Journals Database, China Biology Medicine disc and Wan Fang Database were searched up to January 2021 for appropriate studies regarding the association of rs2242480, rs776746, rs3812718 and rs2234922 polymorphisms with CBZ metabolism and resistance. The meta-analysis was conducted by Review Manager 5.3 software. RESULTS: Eighteen studies involving 2546 related epilepsy patients were included. We found that the G allele of CYP3A4 rs2242480 markedly decreased the plasma CBZ concentration in epilepsy. For CYP3A5 rs776746 polymorphism, the GG genotype (homozygote codominant model: GG vs. AA) and GG + GA genotype (dominant model: GG + GA vs. AA and recessive model: GG vs. GA + AA) were respectively found to be significantly associated with increased CBZ plasma concentration. Additionally, it was also found that the SCN1A rs3812718 A allele was significantly associated with decreased CBZ plasma concentration and increased CBZ resistance. However, no association was observed between SCN1A rs2298771 polymorphism and CBZ metabolism and resistance. CONCLUSION: The CYP3A4 rs2242480, CYP3A5 rs776746 and SCN1A rs3812718 polymorphisms may play important roles in CBZ metabolism and resistance, while SCN1A rs2298771 polymorphism is not associated with CBZ in epilepsy. These findings would improve the individualized therapy of epileptic patients in clinics.

The associations of CYP19A1 rs700518 polymorphism with bone mineral density and risk of osteoporosis: a meta-analysis.

Osteoporosis is now a worldwide public health problem that seriously endangers human health, but its causes have not yet been fully clarified. Recently, increasing evidence suggested that polymorphisms in CYP19A1 gene were associated with osteoporosis risk and bone mineral density (BMD), but results remained conflicting. We herein performed a meta-analysis based on evidence currently available from the literature to make a more precise estimation of these relationships. The PubMed, Embase, Cochrane library, CNKI (China National Knowledge Infrastructure), and Wan Fang databases were searched for eligible studies. Odds ratio (OR), mean difference (MD), and 95% confidence interval (CI) were applied to assess the strength of these relationships. A total of 8 studies involving 2632 subjects were included in our meta-analysis. We observed that the AG genotype of CYP19A1 rs700518 was significantly associated with lower BMD values of lumbar spine and femoral neck (AG vs. GG: p = .001 and.01, respectively). However, this polymorphism had no obvious impacts on osteoporosis risk according to current available data. In conclusion, the present meta-analysis showed that CYP19A1 rs700518 polymorphism may be a potential candidate biomarker for osteoporosis screening, early diagnosis, and treatment, which will help improve individualized therapy of osteoporosis patients in clinics.

The associations of HLA-DRB1 gene polymorphisms with late-onset myasthenia gravis: a meta-analysis.

BACKGROUND: Late-onset myasthenia gravis (LOMG) is one of the major subgroups of the MG. Intensive evidence suggested that polymorphisms in HLA-DRB1 gene were associated with LOMG risk, but the results remained inconsistent. Therefore, a meta-analysis is conducted to make a more precise evaluation between HLA-DRB1 alleles and LOMG. METHODS: The PubMed, EMBASE, Cochrane library, Chinese National Knowledge Infrastructure (CNKI), and Wan Fang and Technology of Chongqing (VIP) Database were searched for eligible studies. The pooled odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were applied to assess the association between HLA-DRB1 alleles and LOMG. RESULTS: A total of 11 studies involving 5513 people were included in our meta-analysis. The results showed that DRB1 07 and 0403 alleles were risk factors for LOMG (1.83 [1.12, 2.98], P = 0.02; 7.05 [2.62, 18.92], P = 0.0001, respectively), while DRB1 0301 and 1301 alleles were identified as protective factors for LOMG (0.44 [0.31, 0.62], P < 0.00001; 0.38 [0.23, 0.62], P = 0.0001, respectively). As for the HLA-DRB1 04 and 14 alleles, our subgroup analysis showed that there were significant associations between these alleles and LOMG in Caucasians (2.21 [1.14, 4.27], P = 0.02; 2.82 [1.29, 6.14], P = 0.009, respectively). CONCLUSIONS: These results confirmed the association of DRB1 alleles (0301, 04, 0403, 07, 1301, and 14) and LOMG, which might provide potential promising biomarkers for prediction of LOMG risk.

Association between EPHX1 polymorphisms and carbamazepine metabolism in epilepsy: a meta-analysis.

BackgroundEPHX1 gene polymorphisms were recently acknowledged as an important source of individual variability in carbamazepine metabolism, but the result of that association still remains controversial. Aim of the review To obtain a more precise estimation of the associations between EPHX1 polymorphisms and carbamazepine metabolism and resistance. Methods The PubMed, EMBASE, Cochrane library, Chinese National Knowledge Infrastructure, Chinese Science and Technique Journals Database, China Biology Medicine disc and Wan fang Database were searched for appropriate studies regarding the rs1051740 and rs2234922 polymorphisms of EPHX1 up to September 2019. The meta-analysis was carried out using the Review Manager 5.3 software. The mean difference and 95% confidence interval were applied to assess the strength of the relationship. Results A total of 7 studies involving 1118 related epilepsy patients were included. EPHX1 rs1051740 polymorphism was significantly associated with adjusted concentrations of both carbamazepine (CC vs. TT: P = 0.02; CC vs. CT + TT: P = 0.005) and carbamazepine-10,11-epoxide (CC vs. CT + TT: P = 0.03). Furthermore, EPHX1 rs2234922 polymorphism was also observed to be significantly associated with decreased adjusted concentrations of carbamazepine-10,11-trans dihydrodiol (GG vs. GA + AA: P = 0.04) and CBZD:CBZE ratio (GG vs. AA: P = 0.008; GG vs. GA + AA: P = 0.0008). Nevertheless, the pooled analysis showed that the EPHX1 polymorphisms had no significant effect on CBZ resistance. Conclusion EPHX1 rs1051740 and rs2234922 polymorphisms may affect the carbamazepine metabolism; but carbamazepine resistance was not related to any of the single nucleotide polymorphisms investigated. These findings provided further evidence for individualized therapy of epilepsy patients in clinics.

Associations between UGT2B7 polymorphisms and cancer susceptibility: A meta-analysis.

BACKGROUND: UGT2B7 was recently acknowledged as a new critical enzyme involved in biotransformation of a variety of carcinogens, whose function was reported to be significantly associated with its encoding gene (UGT2B7) polymorphisms. However, results regarding the associations between single nucleotide polymorphisms (SNPs) of UGT2B7 and cancer risk still remained controversial. Therefore, a meta-analysis was conducted to further elucidate the role of UGT2B7 SNPs on cancer susceptibilities. METHODS: PubMed, EMBASE, Cochrane library, Chinese National Knowledge Infrastructure (CNKI), Technology of Chongqing (VIP) and Wan Fang Database were searched for eligible studies until March 2019. All analysis was carried out using the Review Manager 5.3 software. Subgroup analyses were performed by cancer types, ethnicity or source of controls. RESULTS: 13 studies with a total of 7688 cancer cases and 11,281 controls were included in this meta-analysis. The results showed that UGT2B7 rs7439366 increased the colorectal cancer risk in dominant model (OR = 0.76, 95% CI = 0.61-0.95, P = 0.02). However, as for the rs7435335 and rs12233719, we did not find their associations with cancer risk in all genetic models. In addition, the rs7441774 was found to be associated with breast cancer risk and significantly reduced papillary thyroid cancer risk in rs3924194 was also observed. Nevertheless, these findings remained to be further proven in future studies since these 2 SNPs were only respectively involved in 1 study. CONCLUSION: This meta-analysis confirmed the association of UGT2B7 rs7439366 with colorectal cancer risk, which may be a potential promising biomarker for prediction of colorectal cancer risk.

A general strategy for the ultrafast surface modification of metals.

Surface modification is an essential step in engineering materials that can withstand the increasingly aggressive environments encountered in various modern energy-conversion systems and chemical processing industries. However, most traditional technologies exhibit disadvantages such as slow diffusion kinetics, processing difficulties or compatibility issues. Here, we present a general strategy for the ultrafast surface modification of metals inspired by electromigration, using aluminizing austenitic stainless steel as an example. Our strategy facilitates the rapid formation of a favourable ductile surface layer composed of FeCrAl or ß-FeAl within only 10 min compared with several hours in conventional processes. This result indicates that electromigration can be used to achieve the ultrafast surface modification of metals and can overcome the limitations of traditional technologies. This strategy could be used to aluminize ultra-supercritical steam tubing to withstand aggressive oxidizing environments.

Synthesis of advanced aluminide intermetallic coatings by low-energy Al-ion radiation.

Metals that work at high temperatures (for instance, superalloys in gas-turbines) depend on thermally grown oxide (TGO, commonly alumina) to withstand corrosion attack. Nickel Aluminide (NiAl) as one superior alumina TGO former plays an important role in protective coatings for turbine blades in gas-turbine engines used for aircraft propulsion and power generation. Lowering TGO growth rate is essentially favored for offering sustainable protection, especially in thermal barrier coatings (TBC). However, it can only be achieved currently by a strategy of adding the third element (Pt or reactive elements) into NiAl during traditional diffusion- or deposition-based synthesis of the coating. Here we present a highly flexible Al-ion radiation-based synthesis of advanced NiAl coatings, achieving low TGO growth rate without relying on the third element addition. Our results expand the strategy for lowering TGO growth rate and demonstrate potentials for ion radiation in advancing materials synthesis.