Comprehensive analysis of annexin gene family and its expression in response to branching architecture and salt stress in crape myrtle.

BACKGROUND: Annexin (ANN) is calcium (Ca2+)-dependent and phospholipid binding protein family, which is involved in plant growth and development and response to various stresses. However, little known about ANN genes were identified from crape myrtle, an ornamental horticultural plant widely cultivated in the world. RESULTS: Here, 9 LiANN genes were identified from Lagerstroemia indica, and their characterizations and functions were investigated in L. indica for the first time. The LiANN genes were divided into 2 subfamilies. The gene structure, chromosomal location, and collinearity relationship were also explored. In addition, the GO annotation analysis of these LiANNs indicated that they are enriched in molecular functions, cellular components, and biological processes. Moreover, transcription factors (TFs) prediction analysis revealed that bHLH, MYB, NAC, and other TFs can interact with the LiANN promoters. Interestingly, the LiANN2/4/6-9 were demonstrated to play critical roles in the branching architecture of crape myrtle. Furthermore, the LiANN2/6/8/9 were differentially expressed under salt treatment, and a series of TFs regulating LiANN2/6/8/9 expression were predicted to play essential roles in salt resistance. CONCLUSIONS: These results shed light on profile and function of the LiANN gene family, and lay a foundation for further studies of the LiANN genes.

Transcriptome Analysis of the Salt-Treated Actinidia deliciosa (A. Chev.) C. F. Liang and A. R. Ferguson Plantlets.

The area of saline land in the world is quite large, and there is broad room for its development and usage. 'Xuxiang' is an Actinidia deliciosa variety that is tolerant to salt and can be planted in an area of light-saline land, and has good comprehensive characteristics and high economic value. However, the molecular mechanism of salt tolerance is unknown at present. To understand the molecular mechanism of salt tolerance, the leaves of A. deliciosa 'Xuxiang' were used as explants to establish a sterile tissue culture system, and plantlets were obtained using this system. One percent concentration (w/v) of sodium chloride (NaCl) was employed to treat the young plantlets cultured in Murashige and Skoog (MS) medium, then RNA-seq was used for transcriptome analysis. The results showed that the genes related to salt stress in the phenylpropanoid biosynthesis pathway and the anabolism of trehalose and maltose pathways were up-regulated; however, those genes in the plant hormone signal transduction and metabolic pathways of starch, sucrose, glucose, and fructose were down-regulated after salt treatment. The expression levels of ten genes that were up-regulated and down-regulated in these pathways were confirmed by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. The salt tolerance of A. deliciosa might be related to the expression level changes in the genes in the pathways of plant hormone signal transduction, phenylpropanoid biosynthesis, and starch, sucrose, glucose, and fructose metabolism. The increased expression levels of the genes encoding alpha-trehalose-phosphate synthase, trehalose-phosphatase, alpha-amylase, beta-amylase, feruloyl-CoA 6-hydroxylase, ferulate 5-hydroxylase, and coniferyl-alcohol glucosyl transferase might be vital to the salt stress response of the young A. deliciosa plants.

Genome-Wide Identification and Expression Profiles of C-Repeat Binding Factor Transcription Factors in Betula platyphylla under Abiotic Stress.

CBF (C-repeat binding factor) transcription factor subfamily belongs to AP2/ERF (Apetala 2/ethylene-responsive factor) transcription factor family, known for playing a vital role in plant abiotic stress response. Although some CBF transcription factors have been identified in several species, such as Arabidopsis, tobacco, tomato and poplar, research of CBF focus mainly on model plant Arabidopsis and have not been reported in Betula platyphylla yet. In this study, a total of 20 BpCBF subfamily members were identified. The conserved domains, physicochemical properties, exon-intron gene structure and the structure of conserved protein motifs of BpCBFs were analyzed via bioinformatic tools. The collinearity analysis of CBF genes was performed between Betula platyphylla and Arabidopsis thaliana, Betula platyphylla, and Populus trichocarpa. The cis-acting elements in the promoter region of BpCBFs were identified, which were mainly environmental stress-related and hormone-related element components. In this case, the expression patterns of the 20 BpCBFs upon ABA or salt treatment were investigated. Most of these transcription factors were responsive to ABA or salt stress in different plant tissues. The up-regulation trend upon cold treatment of the six cold-responsive genes validated by qRT-PCR was consistent with the result of RNA-seq. BpCBF7 showed transcription activating activity. This study sheds light on the responses of BpCBFs to abiotic stress and provides a reference for further study of CBF transcription factors in woody plants.

Genome-Wide Identification and Characterization of WRKY Transcription Factors in Betula platyphylla Suk. and Their Responses to Abiotic Stresses.

The WRKY transcription factor (TF) family is one the largest plant-specific transcription factor families. It has been proven to play significant roles in multiple plant biological processes, especially stress response. Although many WRKY TFs have been identified in various plant species, WRKYs in white birch (Betula platyphylla Suk.) remain to be studied. Here, we identified a total of 68 BpWRKYs, which could be classified into four main groups. The basic physiochemical properties of these TFs were analyzed using bioinformatics tools, including molecular weight, isoelectric point, chromosome location, and predicted subcellular localization. Most BpWRKYs were predicted to be located in the nucleus. Synteny analysis found 17 syntenic gene pairs among BpWRKYs and 52 syntenic gene pairs between BpWRKYs and AtWRKYs. The cis-acting elements in the promoters of BpWRKYs could be enriched in multiple plant biological processes, including stress response, hormone response, growth and development, and binding sites. Tissue-specific expression analysis using qRT-PCR showed that most BpWRKYs exhibited highest expression levels in the root. After ABA, salt (NaCl), or cold treatment, different BpWRKYs showed different expression patterns at different treatment times. Furthermore, the results of the Y2H assay proved the interaction between BpWRKY17 and a cold-responsive TF, BpCBF7. By transient expression assay, BpWRKY17 and BpWRKY67 were localized in the nucleus, consistent with the previous prediction. Our study hopes to shed light for research on WRKY TFs and plant stress response.

Gene Coexpression Network Analysis Indicates that Hub Genes Related to Photosynthesis and Starch Synthesis Modulate Salt Stress Tolerance in Ulmus pumila.

Ulmus pumila L. is an excellent afforestation and biofuel tree that produces high-quality wood, rich in starch. In addition, U. pumila is highly adaptable to adverse environmental conditions, which is conducive to its utilization for vegetating saline soils. However, little is known about the physiological responses and transcriptional regulatory network of U. pumila under salt stress. In this study, we exposed five main cultivars in saline-alkali land (Upu2, 5, 8, 11, and 12) to NaCl stress. Of the five cultivars assessed, Upu11 exhibited the highest salt resistance. Growth and biomass accumulation in Upu11 were promoted under low salt concentrations (<150 mM). However, after 3 months of continuous treatment with 150 mM NaCl, growth was inhibited, and photosynthesis declined. A transcriptome analysis conducted after 3 months of treatment detected 7009 differentially expressed unigenes (DEGs). The gene annotation indicated that these DEGs were mainly related to photosynthesis and carbon metabolism. Furthermore, PHOTOSYNTHETIC ELECTRON TRANSFERH (UpPETH), an important electron transporter in the photosynthetic electron transport chain, and UpWAXY, a key gene controlling amylose synthesis in the starch synthesis pathway, were identified as hub genes in the gene coexpression network. We identified 25 and 62 unigenes that may interact with PETH and WAXY, respectively. Overexpression of UpPETH and UpWAXY significantly increased the survival rates, net photosynthetic rates, biomass, and starch content of transgenic Arabidopsis plants under salt stress. Our findings clarify the physiological and transcriptional regulators that promote or inhibit growth under environmental stress. The identification of salt-responsive hub genes directly responsible for photosynthesis and starch synthesis or metabolism will provide targets for future genetic improvements.

Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed.

BACKGROUND: Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been characterized, however, the roles of long noncoding RNAs (lncRNAs) remain unknown. RESULTS: In this work, totally 2815 novel lncRNAs were discovered in S. polyrhiza by strand-specific RNA sequencing, of which 185 (6.6%) were expressed differentially under salinity condition. Co-expression analysis indicated that the trans-acting lncRNAs regulated their co-expressed genes functioning in amino acid metabolism, cell- and cell wall-related metabolism, hormone metabolism, photosynthesis, RNA transcription, secondary metabolism, and transport. In total, 42 lncRNA-mRNA pairs that might participate in cis-acting regulation were found, and these adjacent genes were involved in cell wall, cell cycle, carbon metabolism, ROS regulation, hormone metabolism, and transcription factor. In addition, the lncRNAs probably functioning as miRNA targets were also investigated. Specifically, TCONS_00033722, TCONS_00044328, and TCONS_00059333 were targeted by a few well-studied salt-responsive miRNAs, supporting the involvement of miRNA and lncRNA interactions in the regulation of salt stress responses. Finally, a representative network of lncRNA-miRNA-mRNA was proposed and discussed to participate in duckweed salt stress via auxin signaling. CONCLUSIONS: This study is the first report on salt-responsive lncRNAs in duckweed, and the findings will provide a solid foundation for in-depth functional characterization of duckweed lncRNAs in response to salt stress.

The long non-coding RNA lncRNA973 is involved in cotton response to salt stress.

BACKGROUND: Long non-coding (lnc) RNAs are a class of functional RNA molecules greater than 200 nucleotides in length, and lncRNAs play important roles in various biological regulatory processes and response to the biotic and abiotic stresses. LncRNAs associated with salt stress in cotton have been identified through RNA sequencing, but the function of lncRNAs has not been reported. We previously identified salt stress-related lncRNAs in cotton (Gossypium spp.), and discovered the salt-related lncRNA-lncRNA973. RESULTS: In this study, we identified the expression level, localization, function, and preliminary mechanism of action of lncRNA973. LncRNA973, which was localized in the nucleus, was expressed at a low level under nonstress conditions but can be significantly increased by salt treatments. Here lncRNA973 was transformed into Arabidopsis and overexpressed. Along with the increased expression compared with wild type under salt stress conditions in transgenic plants, the seed germination rate, fresh weights and root lengths of the transgenic plants increased. We also knocked down the expression of lncRNA973 using virus-induced gene silencing technology. The lncRNA973 knockdown plants wilted, and the leaves became yellowed and dropped under salt-stress conditions, indicating that the tolerance to salt stress had decreased compared with wild type. LncRNA973 may be involved in the regulation of reactive oxygen species-scavenging genes, transcription factors and genes involved in salt stress-related processes in response to cotton salt stress. CONCLUSIONS: LncRNA973 was localized in the nucleus and its expression was increased by salt treatment. The lncRNA973-overexpression lines had increased salt tolerance compared with the wild type, while the lncRNA973 knockdown plants had reduced salt tolerance. LncRNA973 regulated cotton responses to salt stress by modulating the expression of a series of salt stress-related genes. The data provides a basis for further studies on the mechanisms of lncRNA973-associated responses to salt stress in cotton.

Physiological and Transcriptomic Responses of Chinese Cabbage (Brassica rapa L. ssp. Pekinensis) to Salt Stress.

Salt stress is one of the major abiotic stresses that severely impact plant growth and development. In this study, we investigated the physiological and transcriptomic responses of Chinese cabbage "Qingmaye" to salt stress, a main variety in North China. Our results showed that the growth and photosynthesis of Chinese cabbage were significantly inhibited by salt treatment. However, as a glycophyte, Chinese cabbage could cope with high salinity; it could complete an entire life cycle at 100 mM NaCl. The high salt tolerance of Chinese cabbage was achieved by accumulating osmoprotectants and by maintaining higher activity of antioxidant enzymes. Transcriptomic responses were analyzed using the digital gene expression profiling (DGE) technique after 12 h of treatment by 200 mM NaCl. A total of 1235 differentially expressed genes (DEGs) including 740 up- and 495 down-regulated genes were identified. Functional annotation analyses showed that the DEGs were related to signal transduction, osmolyte synthesis, transcription factors, and antioxidant proteins. Taken together, this study contributes to our understanding of the mechanism of salt tolerance in Chinese cabbage and provides valuable information for further improvement of salt tolerance in Chinese cabbage breeding programs.

Short communication: Effect of storage temperature on the solubility of milk protein concentrate 80 (MPC80) treated with NaCl or KCl.

A previous study in our laboratory showed that addition of 150 mM NaCl or KCl into diafiltration water improved the solubility of freshly made milk protein concentrate 80 (MPC80). In the present study, the objectives were (1) to evaluate the solubility of NaCl- or KCl-treated MPC80 samples kept at varying temperatures and then stored for extensive periods at room temperature (21 °C ± 1 °C); and (2) to determine if MPC80 samples stored at different temperatures and protein conformation can be grouped or categorized together. Freshly manufactured MPC80 samples were untreated (control), processed with NaCl, or processed with KCl. One set of sample bags was stored at 4 °C; second and third sets of bags were kept at 25 °C and 55 °C for 1 mo (31 d) and then transferred to room temperature (21 °C ± 1 °C) storage conditions for 1 yr (365 d). Samples were tested for nitrogen solubility index (NSI) and for protein changes by Fourier-transform infrared (FTIR) spectroscopy. Analysis of variance results for NSI showed 2 significantly different groupings of MPC80 samples. The more soluble group contained samples treated with NaCl or KCl and stored at either 4 °C or 25 °C. These samples had mean NSI >97.5%. The less soluble groups contained all control samples, regardless of storage temperature, and NaCl- or KCl-treated samples stored at 55 °C. These samples had mean NSI from 39.5 to 58%. Within each of these groups (more soluble and less soluble), no significant differences in solubility were detected. Pattern recognition analysis by soft independent modeling of class analogy (SIMCA) was used to assess protein changes during storage by monitoring the amide I and amide II (1,700(-1) to 1,300 cm(-1)) regions. Dominant bands were observed at 1,385 cm(-1) for control, 1,551 cm(-1) for KCl-treated samples, and 1,694 cm(-1) for NaCl-treated samples. Moreover, SIMCA clustered the MPC80 samples stored at 4 °C separately from samples stored at 25 °C and 55 °C. This study demonstrates that (1) the addition of NaCl or KCl during MPC80 manufacture reduces the deleterious changes in solubility upon prolonged storage at 4 °C or 25 °C, and (2) the solubility of samples stored at 55 °C is poor irrespective of salt treatment.

Salinity tolerance and desalination properties of a Haematococcus lacustris strain from eastern Hungary.

Nowadays the increasing amount of saline wastewaters has given rise to various biological desalination processes, among which the application possibilities of microalgae represents a priority research area. Next to "real" aquatic species (members of phytoplankton or phytobenthon), species from ephemeral aquatic habitats or aeroterrestrial algae also could be good candidates of research studying salt tolerance or desalination ability, since salinity stress is often referred as "physiological drought" and species from ephemeral habitats can be characterized by high drought tolerance. In this study, the salinity tolerance, salt and nutrient removal ability of a Haematococcus lacustris strain from eastern Hungary were investigated. Vegetative cells showed low salt tolerance, survival was ensured by the formation of cysts up to a sodium-chloride concentration of 2,000 mg l-1. Although relatively moderate (a max. 30%) conductivity reduction and chloride removal were observed, notable (nearly 100%) nitrate and phosphate removal occurred even in the presence of 2,000 mg l-1 NaCl. Carotenoid accumulation was observed earlier and in higher extent in salt treated cultures than in drying out ones, although the amount of astaxanthin-esters was significantly higher in the cultures of drying out experiment than in the corresponding cultures of salt treatment characterized with similar chloride content. Our results suggest that algae isolates from ephemeral aquatic habitats endangered by regular drying out (exposed to special salt stress), could have notable salt tolerance and consequently successful applicability in nutrient removal processes from slightly saline wastewaters. The accumulation of valuable metabolites (such as astaxanthin) as a response to salinity stress, could enhance the economic value of the biomass.

Surface Reconstruction Enhanced Li-Rich Cathode Materials for Durable Lithium-Ion Batteries.

Regulating the distribution of surface elements in lithium-rich cathode materials can effectively change the electrochemical performance of cathode materials. Considering that the enrichment of Mn element on the surface is the main reason for the irreversible phase transition and dissolution of its surface structure, which in turn is the main reason for performance degradation. Based on the molten salt-assisted sintering method, a lithium rich cathode material with surface rich Ni and Co is designed and prepared. The surface enrichment of Ni and Co effectively reduces the dissolution of Mn, promotes the occurrence of irreversible collapse of surface structure from layered phase to rock salt phase on the material surface, improves the stability of surface crystal phase structure, and improves the cycling stability of positive electrode materials. Notably, after 500 cycles at 1 C current density, the discharge-specific capacity attained 189.8 mAh g -1, with a capacity retention rate of 88.9%, indicating a 42.1% improvement in capacity retention. Molten salt treatment is widely used in the modification of positive electrode materials. The research work will provide new ideas for improving the stability of lithium rich materials and promoting their commercial applications.

Decoupling of nutrient stoichiometry in Suaeda glauca (Bunge) senesced leaves under salt treatment.

The stoichiometry of senesced leaves is pivotal in nutrient cycling and can be significantly influenced by soil salinization, a rising global issue threatening the functionality of ecosystems. However, the impacts of soil salinization on senesced leaf stoichiometry are not fully understood. In this study, we conducted a pot experiment with varying soil salt concentrations to examine their influence on the concentrations and stoichiometric ratios of nitrogen (N), phosphorus (P), sodium (Na), potassium (K), calcium (Ca), magnesium (Mg), and zinc (Zn) in the senesced leaves of Suaeda glauca (Bunge). Compared to the control group, salt treatments significantly enhanced Na concentration while diminishing the concentrations of K, Ca, Mg, Zn, N, and P. Interestingly, as salinity levels escalated, N concentration maintained stability, whereas P concentration exhibited an increasing trend. Moreover, K, Ca, and Mg significantly declined as salt levels rose. Salt treatments brought about significant changes in stoichiometric ratios, with the N:P, K:Na, N:Na, N:Mg, and Ca : Mg ratios dropping and the N:Ca and N:K ratios rising, illustrating the varying nutrient coupling cycles under different salt conditions. These findings shed light on the plasticity of stoichiometric traits in S. glauca senesced leaves in response to soil salinization shifts, which could potentially offer insights into nutrient cycling reactions to soil salinization.

Physiological and transcriptomic analyses revealed the change of main flavor substance of Zygosaccharomyces rouxii under salt treatment.

Zygosaccharomyces rouxii was a highly salt-tolerant yeast, playing an important role in soy sauce fermentation. Previous studies reported that Z. rouxii under salt treatment produces better fermented food. However, the detailed change of main flavor substance was not clear. In this study, the physiological and transcriptomic analyses of Z. rouxii under salt treatment was investigated. The results revealed the high salt tolerance of Z. rouxii. Analysis of physiological data showed that the proportion of unsaturated fatty acids was significantly increased with the increment of salt concentrations. The analysis of organic acids showed that the content of succinic acid was significantly higher in the salt-treated Z. rouxii while oxalic acid was only identified at the 18% salt concentration-treated group. Results of volatile substances analysis showed that concentrations of 3-methyl-1-butanol and phenylethyl alcohol were significantly increased with the increment of salt concentrations. A comparison of transcriptome data showed that the genes involved in the TCA cycle and the linoleic acid synthesis process exhibited different expressions, which is consistent with the results of physiological data. This study helps to understand the change of main flavor substance of Z. rouxii under salt treatment and guide their applications in the high salt liquid state fermentation of the soy sauce.

Mechanism of cadmium tolerance in Salicornia europaea at optimum levels of NaCl.

Many saline-alkali soils around the world are polluted by the heavy metal Cd, restricting the development of agriculture and ecology in those regions. The halophyte Salicornia europaea L. is capable of growing healthily in Cd-contaminated saline-alkali soil, suggesting that the species is tolerant to stress caused by both salt and heavy metals. In this study, the mechanism of Cd tolerance in this species was explored under 200 mM NaCl. Flame spectrophotometric assays for ions content and spectrophotometric for organic soluble substances, antioxidant enzyme activity, phytochelatins (PCs) content and phytochelatin synthase (PCS) activity, the photosynthetic parameters by portable photosynthesis measurement system, genes expression by qRT-PCR analysis were carried out. Cd treatment significantly decreased the dry weight, photosynthetic rate, K+ , Zn2+ , and Fe2+/3+ content, while significantly increasing Na+ and Cd+ , soluble organic matter, and reactive oxygen species (ROS) levels. Compared with Cd treatment at 0 mM NaCl, Cd treatment at 200 mM NaCl significantly increased dry weight and photosynthetic rate while significantly decreasing ROS content through increased antioxidant enzyme activity. When exposed to Cd stress, treatment with 200 mM NaCl significantly increased PCs content and PCS activity and up-regulated the expression of the phytochelatin synthase genes CDA1 and PCS1 were, thereby increasing resistance to Cd. NaCl treatment increases the tolerance of S. europaea to the heavy metal Cd by growing rapidly, reducing the quantity of Cd2+ from entering the plant shoots, increasing the levels of PCs that chelate Cd2+ , thereby reducing its toxicity.

Differential Response of Phenol Metabolism Associated with Antioxidative Network in Elicited Grapevine Suspension Cultured Cells under Saline Conditions.

Highly productive trans-resveratrol (t-R) grapevine suspension cultured cells (SCC) and two effective elicitors, methyl jasmonate (MJ) and randomly methylated ß-cyclodextrins (CDs), were used to analyze the extent to which salt treatments alter the production of bioactive phenolic compounds. The expression/activity profile of the enzymes involved in phenol metabolism and antioxidant networks were also studied. A marked extracellular accumulation of phenolic compounds, especially t-R, was found in SCC elicited with CDs and/or MJ under saline conditions. However, the treatments with MJ alone and all those combined with salt favored the intracellular accumulation of catechin and ferulic acid. The salt-induced accumulation of phenolics was correlated with the higher total antioxidant capacity values found in cells, suggesting that cellular redox homeostasis under saline conditions was largely maintained by increasing phenolic compound production. These higher levels of phenolics found in elicited cells under saline conditions fit well with the highest activity of phenylalanine ammonia-lyase. Moreover, antioxidant enzyme activities were boosted in treatments with MJ and/or in those combined with salt and decreased in those treated with CDs. These results suggest a differential response of the antioxidative network to the presence of elicitors under saline conditions.

Ultrasonic­assisted molten salt hydrates pretreated Eucheuma cottonii residues as a greener precursor for third-generation l-lactic acid production.

This study aims to establish an efficient pretreatment method that facilitates the conversion of sugars from macroalgae wastes, Eucheuma cottonii residues (ECRs) during hydrolysis and subsequently enhances l-lactic acid (L-LA) production. Hence, ultrasonic-assisted molten salt hydrates (UMSHs) pretreatment was proposed to enhance the accessibility of ECRs to hydrolyze into glucose through dilute acid hydrolysis (DAH). The obtained hydrolysates were employed as the substrate in producing L-LA by separate hydrolysis and fermentation (SHF). The maximum glucose yield (97.75 %) was achieved using UMSHs pretreated ECRs with 40 wt% ZnCl2 at 80 °C for 2 h and followed with DAH. The optimum glucose to L-LA yield obtained for SHF was 90.08 % using 5 % (w/w) inoculum cell densities of B. coagulans ATCC 7050 with yeast extract (YE). A comparable performance (89.65 %) was obtained using a nutrient combination (lipid-extracted Chlorella vulgaris residues (CVRs), vitamin B3, and vitamin B5) as a partial alternative for YE.

Transcriptomic Responses of Cordyceps militaris to Salt Treatment During Cordycepins Production.

Cordycepin is a major bioactive compound found in Cordyceps militaris (C. militaris) that exhibits a broad spectrum of biological activities. Hence, it is potentially a bioactive ingredient of pharmaceutical and cosmetic products. However, overexploitation and low productivity of natural C. militaris is a barrier to commercialization, which leads to insufficient supply to meet its existing market demands. In this study, a preliminary study of distinct concentrations of salt treatments toward C. militaris was conducted. Although the growth of C. militaris was inhibited by different salt treatments, the cordycepin production increased significantly accompanied by the increment of salt concentration. Among them, the content of cordycepin in the 7% salt-treated group was five-fold higher than that of the control group. Further transcriptome analysis of samples with four salt concentrations, coupled with Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, several differentially expressed genes (DEGs) were found. Finally, dynamic changes of the expression patterns of four genes involved in the cordycepin biosynthesis pathway were observed by the quantitative real-time PCR. Taken together, our study provides a global transcriptome characterization of the salt treatment adaptation process in C. militaris and facilitates the construction of industrial strains with a high cordycepin production and salt tolerance.

Effects of Salt Treatment Time on the Metabolites, Microbial Composition, and Quality Characteristics of the Soy Sauce Moromi Extract.

Salt is one of the most important factors for fermented foods, but the effect of salt treatment time on the quality of fermented foods has rarely been studied. In this study, the effect of different salt treatment times (0, 48, and 96 h) after the start of fermentation on the quality of the soy sauce moromi extract (SSME) was investigated. As the salt treatment time was delayed, the population of Aspergillus oryzae, Lactobacillaceae, and Enterococcaecea in SSME increased, whereas the population of Staphylococcaceae and Bacillaceae decreased, leading to changes in the enzymatic activity and metabolite profiles. In particular, the contents of amino acids, peptides, volatile compounds, acidic compounds, sugars, and secondary metabolites were significantly affected by the salt treatment time, resulting in changes in the sensory quality and appearance of SSME. The correlation data showed that metabolites, bacterial population, and sensory parameters had strong positive or negative correlations with each other. Moreover, based on metabolomics analysis, the salt treatment-time-related SSME metabolomic pathway was proposed. Although further studies are needed to elucidate the salt treatment mechanism in fermented foods, our data can be useful to better understand the effect of salt treatment time on the quality of fermented foods.

In silico analysis of glycosyltransferase 2 family genes in duckweed (Spirodela polyrhiza) and its role in salt stress tolerance.

Plant glycosyltransferase 2 (GT2) family genes are involved in plant abiotic stress tolerance. However, the roles of GT2 genes in the abiotic resistance in freshwater plants are largely unknown. We identified seven GT2 genes in duckweed, remarkably more than those in the genomes of Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, Nymphaea tetragona, Persea americana, Zostera marina, and Ginkgo biloba, suggesting a significant expansion of this family in the duckweed genome. Phylogeny resolved the GT2 family into two major clades. Six duckweed genes formed an independent subclade in Clade I, and the other was clustered in Clade II. Gene structure and protein domain analysis showed that the lengths of the seven duckweed GT2 genes were varied, and the majority of GT2 genes harbored two conserved domains, PF04722.12 and PF00535.25. The expression of all Clade I duckweed GT2 genes was elevated at 0 h after salt treatment, suggesting a common role of these genes in rapid response to salt stress. The gene Sp01g00794 was highly expressed at 12 and 24 h after salt treatment, indicating its association with salt stress resilience. Overall, these results are essential for studies on the molecular mechanisms in stress response and resistance in aquatic plants.

PCR Amplifiable DNA from Breast Disease FFPE Section for Mutational Analysis.

Formalin-fixed paraffin-embedded (FFPE) tissue specimens have been a staple of research, providing precious resources for molecular and genomic studies. However, the biggest challenge is the extraction of high-quality DNA from FFPE tissues, given that the integrity of DNA is critically affected by formalin fixation. Formaldehyde induces crosslinks in DNA that renders single or double-stranded DNA breaks. Such breaks cause extensive fragmentation that directly influences the quality of DNA purified and the number of templates available for PCR amplification. Thus, protocol for DNA purification from FFPE tissues must effectively extract highly fragmented DNA and reverse cross-linking caused by formalin fixation. DNA extraction methods available in the literature were selected and modified at different stages to optimize a protocol that extracts DNA of sufficient quality and fragment size to be detectable by PCR. Archived FFPE tissues belonged to patients with triple negative breast cancer (TNBC) and benign breast disease were used for the protocol optimization. The best optimized protocol was then used to amplify Exon 4 region of Proviral integration site for Moloney murine leukemia virus1 (Pim1) kinase gene to analyze any probable somatic mutations both in TNBCs and benign breast diseases. Of the 12 different protocols developed, best quality DNA in terms of fragment size and purity was obtained when Tween20 lysis buffer was used for both deparaffinization and overnight digestion along with high salt precipitation. Optimized protocol was then validated by extracting DNAs from 10 TNBCs and 5 benign breast disease specimens with consistent purity and fragment size. PCR amplification and subsequent Sanger's sequencing revealed the presence of mutations in the Exon 4 region of Pim1 kinase. Deparaffinization and overnight digestion in Tween20 lysis buffer along with high salt precipitation yielded the best quality PCR amplifiable DNA for mutational analysis.