Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors.

Sugarcane, a C4 plant, provides most of the world's sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane's response to various stresses will provide targets and resources for sugarcane crop improvement.

[Identification of GeERF transcription factors in Gelsmium elegans and their expression under low temperature stress].

With prominent medicinal value, Gelsemium elegans has been overexploited, resulting in the reduction of the wild resource. As a result, artificial cultivation turns out to be a solution. However, this medicinal species is intolerant to low temperature, and thus genes responding to the low temperature are important for the cultivation of this species. Based on the transcriptome database of G. elegans at 4 ℃, 29 differentially expressed GeERF genes were identified. Bioinformatics analysis of 21 GeERF gene sequences with intact open reading frames showed that 12 and 9 of the GeERF proteins respectively clustered in DREB subgroup and ERF subgroup. GeDREB1 A-1-GeERF6 B-1, with molecular weight of 23.78-50.96 kDa and length of 212-459 aa, were all predicted to be hydrophilic and in nucleus. Furthermore, the full-length cDNA sequence of GeERF2B-1 was cloned from the leaves of G. elegans. Subcellular localization suggested that GeERF2B-1 was located in the nucleus. According to the quantitative reverse-transcription PCR(qRT-PCR), GeERF2B-1 showed constitutive expression in roots, stems, and leaves of G. elegans, and the expression was the highest in roots. In terms of the response to 4 ℃ treatment, the expression of GeERF2B-1 was significantly higher than that in the control and peaked at 12 h, suggesting a positive response to low temperature. This study lays a scientific basis for the functional study of GeERF transcription factors and provides gene resources for the improvement of stress resistance of G. elegans.

Analysis of Flavonoid Metabolites in Watercress (Nasturtium officinale R. Br.) and the Non-Heading Chinese Cabbage (Brassica rapa ssp. chinensis cv. Aijiaohuang) Using UHPLC-ESI-MS/MS.

Flavonoids from plants play an important role in our diet. Watercress is a special plant that is rich in flavonoids. In this study, four important watercress varieties were compared with non-heading Chinese cabbage by ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS). A total of 132 flavonoid metabolites (including 8 anthocyanins, 2 dihydroflavone, 3 dihydroflavonol, 1 flavanols, 22 flavones, 11 flavonoid carbonosides, 82 flavonols, and 3 isoflavones) were detected. Flavonoid metabolites varied widely in different samples. Both the non-heading Chinese cabbage and the variety of watercress from Guangdong, China, had their own unique metabolites. This work is helpful to better understand flavonoid metabolites between the non-heading Chinese cabbage and the other four watercress varieties, and to provide a reliable reference value for further research.

Genome-wide identification, phylogeny, and expression analysis of Sec14-like PITP gene family in sugarcane.

KEY MESSAGE: Six Sec14-like PITP genes from sugarcane were identified, two of them were cloned, and their biological functions were characterized indicating their involvement in plant defense against biotic and abiotic stresses. Sec14, a phosphatidylinositol transfer protein (PITP) is widely present in eukaryotes. In this study, the structure and expression patterns of six Sec14-like PITP genes (ScSEC14-1, ScSEC14p, ScSFH1, ScSFH2, ScPATL1, and ScPATL2) from sugarcane were analyzed, and two of them (ScSEC14-1 and ScSEC14p) were cloned and functionally verified. Phylogenetic analysis divided these genes into four groups, including group I (ScSFH1 and ScSFH2), group II (ScPATL1 and ScPATL2), Group III (ScSEC14p), and group V (ScSEC14-1). qRT-PCR analysis showed tissue-specific expression of these genes, primarily in the root, leaf, and bud tissues. They responded differently to SA, MeJA, and ABA stresses. ScSEC14-1, ScSEC14p, and ScSFH2 were upregulated by CuCl2 and CdCl2, while ScSEC14-1, ScSFH1, ScSFH2, and ScPATL1 were upregulated by PEG and NaCl. When infected by Sporisorium scitamineum, the transcripts of ScSFH1, ScSFH2, ScPATL1, and ScPATL2 were upregulated in the resistant genotype Yacheng 05-179, while those of ScSEC14-1 and ScSEC14p were upregulated in the susceptible genotype ROC22. Subcellular localization showed that ScSEC14-1 and ScSEC14p were mainly localized in the plasma membrane and cytoplasm. Enhanced growth of Escherichia coli BL21 cells expressing ScSEC14-1 and ScSEC14p showed high tolerance to NaCl and mannitol stresses. The transient overexpression of ScSEC14-1 and ScSEC14p in Nicotiana benthamiana leaves enhanced its resistance to the infection of tobacco pathogens Ralstonia solanacearum and Fusarium solani var. coeruleum. We can conclude the involvement of ScSEC14-1 and ScSEC14p in the defense against biotic and abiotic stresses, which should facilitate further research on Sec14-like PITP gene family, especially its regulatory mechanisms in sugarcane.

Identification and Functional Characterization of a Cold-Related Protein, BcHHP5, in Pak-Choi (Brassica rapa ssp. chinensis).

In plants, heptahelical proteins (HHPs) have been shown to respond to a variety of abiotic stresses, including cold stress. Up to the present, the regulation mechanism of HHP5 under low temperature stress remains unclear. In this study, BcHHP5 was isolated from Pak-choi (Brassica rapa ssp. chinensis cv. Suzhouqing). Sequence analysis and phylogenetic analysis indicated that BcHHP5 in Pak-choi is similar to AtHHP5 in Arabidopsis thaliana. Structure analysis showed that the structure of the BcHHP5 protein is relatively stable and highly conservative. Subcellular localization indicated that BcHHP5 was localized on the cell membrane and nuclear membrane. Furthermore, real-time quantitative polymerase chain reaction (RT-qPCR) analysis showed that BcHHP5 was induced to express by cold and other abiotic stresses. In Pak-choi, BcHHP5-silenced assay, inhibiting the action of endogenous BcHHP5, indicated that BcHHP5-silenced might have a negative effect on cold tolerance, which was further confirmed. All of these results indicate that BcHHP5 might play a role in abiotic response. This work can serve as a reference for the functional analysis of other cold-related proteins from Pak-choi in the future.

Isolation and functional characterization of the SpCBF1 gene from Solanum pinnatisectum.

Low temperature causes a negative impact on plant growth and development, but plants evolve a series of mechanisms to respond to chilling stress, and one of them is CBF [C-repeat (CRT)/dehydration-responsive element (DRE) binding factor] gene family which has been well studied in different crops. In this paper, a new CBF1 gene, named as SpCBF1, was isolated from frost-tolerant Solanum pinnatisectum by PCR and analyzed for its function in cold-tolerance by over-expression technique. The ORF of SpCBF1 was 666 bp long and encoded a protein of 221 amino acids with a predicted molecular mass 24.5821 kDa and theoretically isoelectric point 5.0. SpCBF1 protein contained a highly conserved specific AP2/ERF domain. SpCBF1 was expressed in all tested tissues with the highest level in tuber and the lowest in root, and induced by chilling stress (0 °C). Under natural low temperature condition (1-10 °C), plants over-expressing SpCBF1 (OE) exhibited slighter necrotic lesion and lower necrotic injury, compared with untransformed Solanum tuberosum cv. Désirée (WT) and antisense-StCBF1 control lines. Over-expression of CBF1 increased the level of COR (cold-regulated) gene transcripts in OE lines, and the physiological indexes related to cold tolerance like the contents of SOD, soluble protein, MDA, proline and soluble sugar were higher in OE lines than in WT except RWC which was lower. All these results indicated that SpCBF1 gene plays a promoting role in potato responding to cold stress.

Cloning and characterization of a potato StAN11 gene involved in anthocyanin biosynthesis regulation.

Anthocyanins are a class of products of plant secondary metabolism and are responsible for tubers color in potato. The biosynthesis of anthocyanins is a complex biological process, in which multiple genes are involved including structural genes and regulatory genes. In this study, StAN11, a WD40-repeat gene, was cloned from potato cultivar Chieftain (Solanum tuberosum L.). StAN11 (HQ599506) contained no intron and its open reading frame (ORF) was 1,029 bp long, encoding a putative protein of 342 amino acids. In order to verify its role in anthocyanin biosynthesis, StAN11 was inserted behind the CaMV-35S promoter of pCMBIA1304 and the recombination vector was introduced into the potato cultivar Désirée plants by Agrobacterium-mediated transformation. The color of transgenic tuber skin was significantly deepened, compared to the wild-type control, which was highly consistent with the accumulation of anthocyanin and expression of StAN11 in transgenic lines tuber skin. Further analysis on the expression of Flavonone-3-hydroxylase (F3H), Dihydroflavonol reductase (DFR), Anthocyanidin synthase (ANS), and Flavonoid 3-O-glucosyl transferase (3GT) in transgenic plants revealed that only DFR was upregulated. This result suggested that StAN11 regulated anthocyanin biosynthesis in potato by controlling DFR expression and accumulation of anthocyanin could be increased through overexpression of StAN11 in the tubers with the genetic background of anthocyanin biosynthesis.

Molecular cloning and characterization of two pathogenesis-related ß-1,3-glucanase genes ScGluA1 and ScGluD1 from sugarcane infected by Sporisorium scitamineum.

KEY MESSAGE: Two ß-1,3-glucanase genes from sugarcane were cloned and characterized. They were all located in apoplast and involves in different expression patterns in biotic and abiotic stress. Smut caused by Sporisorium scitamineum is a serious disease in the sugarcane industry. ß-1,3-Glucanase, a typical pathogenesis-related protein, has been shown to express during plant-pathogen interaction and involves in sugarcane defense response. In this study, ß-1,3-glucanase enzyme activity in the resistant variety increased faster and lasted longer than that of the susceptible one when inoculated with S. scitamineum, along with a positive correlation between the activity of the ß-1,3-glucanase and smut resistance. Furthermore, two ß-1,3-glucanase genes from S. scitamineum infected sugarcane, ScGluA1 (GenBank Accession No. KC848050) and ScGluD1 (GenBank Accession No. KC848051) were cloned and characterized. Phylogenetic analysis suggested that ScGluA1 and ScGluD1 clustered within subfamily A and subfamily D, respectively. Subcellular localization analysis demonstrated that both gene products were targeted to apoplast. Escherichia coli Rosetta (DE3) cells expressing ScGluA1 and ScGluD1 showed varying degrees of tolerance to NaCl, CdCl2, PEG, CuCl2 and ZnSO4. Q-PCR analysis showed up-regulation of ScGluA1 and slight down-regulation of ScGluD1 in response to S. scitamineum infection. It suggested that ScGluA1 may be involved in the defense reaction of the sugarcane to the smut, while it is likely that ScGluD1 was inhibited. The gene expression patterns of ScGluA1 and ScGluD1, in response to abiotic stresses, were similar to sugarcane response against smut infection. Together, ß-1,3-glucanase may function in sugarcane defense mechanism for S. scitamineum. The positive responses of ScGluA1 and the negative responses of ScGluD1 to biotic and abiotic stresses indicate they play different roles in interaction between sugarcane and biotic or abiotic stresses.

Risk factors and drug discovery for cognitive impairment in type 2 diabetes mellitus using artificial intelligence interpretation and graph neural networks.

Background: Among the 382 million diabetic patients worldwide, approximately 30% experience neuropathy, and one-fifth of these patients eventually develop diabetes cognitive impairment (CI). However, the mechanism underlying diabetes CI remains unknown, and early diagnostic methods or effective treatments are currently not available. Objective: This study aimed to explore the risk factors for CI in patients with type 2 diabetes mellitus (T2DM), screen potential therapeutic drugs for T2DM-CI, and provide evidence for preventing and treating T2DM-CI. Methods: This study focused on the T2DM population admitted to the First Affiliated Hospital of Hunan College of Traditional Chinese Medicine and the First Affiliated Hospital of Hunan University of Chinese Medicine. Sociodemographic data and clinical objective indicators of T2DM patients admitted from January 2018 to December 2022 were collected. Based on the Montreal Cognitive Assessment (MoCA) Scale scores, 719 patients were categorized into two groups, the T2DM-CI group with CI and the T2DM-N group with normal cognition. The survey content included demographic characteristics, laboratory serological indicators, complications, and medication information. Six machine learning algorithms were used to analyze the risk factors of T2DM-CI, and the Shapley method was used to enhance model interpretability. Furthermore, we developed a graph neural network (GNN) model to identify potential drugs associated with T2DM-CI. Results: Our results showed that the T2DM-CI risk prediction model based on Catboost exhibited superior performance with an area under the receiver operating characteristic curve (AUC) of 0.95 (specificity of 93.17% and sensitivity of 78.58%). Diabetes duration, age, education level, aspartate aminotransferase (AST), drinking, and intestinal flora were identified as risk factors for T2DM-CI. The top 10 potential drugs related to T2DM-CI, including Metformin, Liraglutide, and Lixisenatide, were selected by the GNN model. Some herbs, such as licorice and cuscutae semen, were also included. Finally, we discovered the mechanism of herbal medicine interventions in gut microbiota. Conclusion: The method based on Interpreting AI and GNN can identify the risk factors and potential drugs associated with T2DM-CI.

Low light intensity elongates period and defers peak time of photosynthesis: a computational approach to circadian-clock-controlled photosynthesis in tomato.

Photosynthesis is involved in the essential process of transforming light energy into chemical energy. Although the interaction between photosynthesis and the circadian clock has been confirmed, the mechanism of how light intensity affects photosynthesis through the circadian clock remains unclear. Here, we propose a first computational model for circadian-clock-controlled photosynthesis, which consists of the light-sensitive protein P, the core oscillator, photosynthetic genes, and parameters involved in the process of photosynthesis. The model parameters were determined by minimizing the cost function ( [Formula: see text]), which is defined by the errors of expression levels, periods, and phases of the clock genes (CCA1, PRR9, TOC1, ELF4, GI, and RVE8). The model recapitulates the expression pattern of the core oscillator under moderate light intensity (100 µmol m -2 s-1). Further simulation validated the dynamic behaviors of the circadian clock and photosynthetic outputs under low (62.5 µmol m-2 s-1) and normal (187.5 µmol m-2 s-1) intensities. When exposed to low light intensity, the peak times of clock and photosynthetic genes were shifted backward by 1-2 hours, the period was elongated by approximately the same length, and the photosynthetic parameters attained low values and showed delayed peak times, which confirmed our model predictions. Our study reveals a potential mechanism underlying the circadian regulation of photosynthesis by the clock under different light intensities in tomato.

A novel dirigent protein gene with highly stem-specific expression from sugarcane, response to drought, salt and oxidative stresses.

Dirigent and dirigent-like family proteins contain a number of proteins involved in lignification or in the response to pathogen infection and abiotic stress in plants. In the present study, a full-length cDNA sequence of a dirigent-like gene designated ScDir (GenBank Accession Number JQ622282) was obtained from sugarcane based on the stem full-length cDNA library. The ScDir gene was 819-bp long, including a 564-bp ORF encoding 187 amino acid residues. The protein N-terminus contained signal peptides at amino acid residues of 1-25 and transmembrane regions at 7-26 aa. A his-tagged ScDir protein with an estimated molecular mass of 27.4 kDa was expressed in Escherichia coli system. The expressed ScDir protein had increased the host cell's tolerance to PEG and NaCl. When an endogenous GAPDH gene was used as internal control, results from real-time qPCR demonstrated that the ScDir mRNA amount in sugarcane stems was significantly higher than that in the roots, leaves and buds by 18.64 ± 0.48, 25,635.16 ± 2,966.03 and 721.50 ± 8.17-fold, respectively. The ScDir transcript levels in sugarcane seedling increased under H(2)O(2), PEG or NaCl stress. The expression level of ScDir was significantly upregulated under PEG stress, and the highest level was observed at 12 h after stress. Thus, both the ScDir-hosted cell performance and the enhanced expressions in sugarcane imply that the ScDir gene is involved in the response to abiotic stresses of drought, salts and oxidation. The transcription of the ScDir gene is highly stem-specific, as revealed by real-time qPCR. Key message A novel sugarcane Sc-Dir gene, DIRd subfamily, which is highly stalk-specific expression and involved in the response to artificial stresses of drought, salts, and oxidatives.

LSAP: A Machine Learning Method for Leaf-Senescence-Associated Genes Prediction.

Plant leaves, which convert light energy into chemical energy, serve as a major food source on Earth. The decrease in crop yield and quality is caused by plant leaf premature senescence. It is important to detect senescence-associated genes. In this study, we collected 5853 genes from a leaf senescence database and developed a leaf-senescence-associated genes (SAGs) prediction model using the support vector machine (SVM) and XGBoost algorithms. This is the first computational approach for predicting SAGs with the sequence dataset. The SVM-PCA-Kmer-PC-PseAAC model achieved the best performance (F1score = 0.866, accuracy = 0.862 and receiver operating characteristic = 0.922), and based on this model, we developed a SAGs prediction tool called "SAGs_Anno". We identified a total of 1,398,277 SAGs from 3,165,746 gene sequences from 83 species, including 12 lower plants and 71 higher plants. Interestingly, leafy species showed a higher percentage of SAGs, while leafless species showed a lower percentage of SAGs. Finally, we constructed the Leaf SAGs Annotation Platform using these available datasets and the SAGs_Anno tool, which helps users to easily predict, download, and search for plant leaf SAGs of all species. Our study will provide rich resources for plant leaf-senescence-associated genes research.

Cloning and Functional Analysis of NoMYB60 Gene Involved in Flavonoid Biosynthesis in Watercress (Nasturtium officinale R. Br.).

The MYB60 gene belongs to the R2R3-MYB subfamily, which includes the MYB31/30/96/94 genes. Although these genes have been shown to respond to heat and drought stresses, their role in flavonoid synthesis remains unclear. In this study, NoMYB60 was cloned from watercress and its structure and function were analyzed. Sequence structure analysis showed that NoMYB60 had a highly conserved R2R3 DNA-binding region at the N-terminus. Under the treatment of ABA, SA or MeJA, the expression level of NoMYB60 first significantly increased and then decreased, indicating that ABA, SA and MeJA positively regulated NoMYB60. The subcellular localization of NoMYB60-GFP indicated that NoMYB60 was localized in the nuclear region, which is consistent with the molecular characterization of the transcription factor. Gene silencing experiments were also performed to further test the function of NoMYB60. The result showed that virus-induced silencing of NoMYB60 affected the expression of enzyme genes in flavonoid synthesis pathways and promoted the synthesis of flavonoids. Moreover, we discovered that NoMYB60 interacts with NoBEH1/2. In this study, provides a reference for research on the regulation mechanism of flavonoid synthesis in Cruciferae and other crops.

Red Light Resets the Expression Pattern, Phase, and Period of the Circadian Clock in Plants: A Computational Approach.

Recent research in the fields of biochemistry and molecular biology has shown that different light qualities have extremely different effects on plant development, and optimizing light quality conditions can speed up plant growth. Clock-regulated red-light signaling, can enhance hypocotyl elongation, and increase seedling height and flower and fruit productivity. In order to investigate the effect of red light on circadian clocks in plants, a novel computational model was established. The expression profiles of the circadian element CCA1 from previous related studies were used to fit the model. The simulation results were validated by the expression patterns of CCA1 in Arabidopsis, including wild types and mutants, and by the phase shifts of CCA1 after red-light pulse. The model was used to further explore the complex responses to various photoperiods, such as the natural white-light/dark cycles, red/white/dark cycles, and extreme 24 h photoperiods. These results demonstrated that red light can reset the expression pattern, period, and phase of the circadian clock. Finally, we identified the dependence of phase shifts on the length of red-light pulse and the minimum red-light pulse length required for producing an observable phase shift. This work provides a promising computational approach to investigating the response of the circadian clock to other light qualities.

Interactive Analysis of Epidemic Situations Based on a Spatiotemporal Information Knowledge Graph of COVID-19.

In view of the lack of data association in spatiotemporal information analysis and the lack of spatiotemporal situation analysis in knowledge graphs, this article combines the semantic web of the geographic knowledge graph with the visual analysis model of spatial information and puts forward the comprehensive utilization of the related technologies of the geographic knowledge graph and big data visual analysis. Then, it realizes the situational analysis of COVID-19 (Coronavirus Disease 2019) and the exploration of patient relationships through interactive collaborative analysis. The main contributions of the paper are as follows. (1) Based on the characteristics of the geographic knowledge graph, a patient entity model and an entity relationship type and knowledge representation method are proposed, and a knowledge graph of the spatiotemporal information of COVID-19 is constructed. (2) To analyse the COVID-19 patients' situations and explore their relationships, an analytical framework is designed. The framework, combining the semantic web of the geographic knowledge graph and the visual analysis model of geographic information, allows one to analyse the semantic web by using the node attribute similarity calculation, key stage mining, community prediction and other methods. (3)An efficient epidemic prevention and anti-epidemic method is proposed which is of referential significance. It is based on experiments and the collaborative analysis of the semantic web and spatial information, allowing for real-time situational understanding, the discovery of patients' relationships, the analysis of the spatiotemporal distribution of patients, super spreader mining, key node analysis, and the prevention and control of high-risk groups.

Graph neural network and multi-data heterogeneous networks for microbe-disease prediction.

The research on microbe association networks is greatly significant for understanding the pathogenic mechanism of microbes and promoting the application of microbes in precision medicine. In this paper, we studied the prediction of microbe-disease associations based on multi-data biological network and graph neural network algorithm. The HMDAD database provided a dataset that included 39 diseases, 292 microbes, and 450 known microbe-disease associations. We proposed a Microbe-Disease Heterogeneous Network according to the microbe similarity network, disease similarity network, and known microbe-disease associations. Furthermore, we integrated the network into the graph convolutional neural network algorithm and developed the GCNN4Micro-Dis model to predict microbe-disease associations. Finally, the performance of the GCNN4Micro-Dis model was evaluated via 5-fold cross-validation. We randomly divided all known microbe-disease association data into five groups. The results showed that the average AUC value and standard deviation were 0.8954 ± 0.0030. Our model had good predictive power and can help identify new microbe-disease associations. In addition, we compared GCNN4Micro-Dis with three advanced methods to predict microbe-disease associations, KATZHMDA, BiRWHMDA, and LRLSHMDA. The results showed that our method had better prediction performance than the other three methods. Furthermore, we selected breast cancer as a case study and found the top 12 microbes related to breast cancer from the intestinal flora of patients, which further verified the model's accuracy.

Identification of AHSA1 as a Potential Therapeutic Target for Breast Cancer: Bioinformatics Analysis and in vitro Studies.

BACKGROUND: Shenling Baizhu Powder (SBP), a famous Traditional Chinese Medicine (TCM) formulation, has been widely used in the adjuvant treatment of cancers, including breast cancer. This study aims to identify potential new targets for breast cancer treatment based on the network pharmacology of SBP. METHODS: By analyzing the relationship between herbs and target proteins, potential targets of multiple herbs in SBP were identified by network pharmacology analysis. Besides, by comparing the data of breast cancer tissue with normal tissue, upregulated genes in two breast cancer expression profiles were found. Thereafter, the expression level and prognosis of activator of heat shock protein 90 (HSP90) ATPase activity 1 (AHSA1) were further analyzed in breast cancer by bioinformatics analysis, and the network module of AHSA1 binding protein was constructed. Furthermore, the effect of knocking down AHSA1 on the proliferation, migration, and invasion of breast cancer cells was verified by MTT, clone formation assay, and transwell assay. RESULTS: Vascular endothelial growth factor A (VEGFA), intercellular adhesion molecule 1 (ICAM1), chemokine (C-X-C motif) ligand 8 (CXCL8), AHSA1, and serpin family E member 1 (SERPINE1) were associated with multiple herbs in SBP. AHSA1 was remarkably upregulated in breast cancer tissues and positively correlated with poor overall survival and disease metastasis- free survival. Furthermore, knockdown of AHSA1 significantly inhibited the migration and invasion in MCF-7 and MDA-MB-231 breast cancer cells but had no obvious effect on proliferation. In addition, among the proteins that bind to AHSAl, the network composed of proteasome, chaperonin, and heat shock proteins is closely connected, and these proteins are associated with poor prognosis in a variety of cancers. CONCLUSION: AHSA1 is positively correlated with breast cancer progression and might act as a novel therapeutic target for breast cancer.

Differential gene expression in sugarcane in response to challenge by fungal pathogen Ustilago scitaminea revealed by cDNA-AFLP.

Differential gene expression in sugarcane during sugarcane-Ustilago scitaminea interaction was conducted in a smut-resistant genotype. Using cDNA-AFLP along with silver staining, a total of 136 transcript-derived fragments (TDFs) were found to be differentially expressed in response to challenge by U. scitaminea. Forty TDFs, 34 newly induced plus six with obvious upregulated expression after infection, were sequenced and validated by RT-PCR analysis. These results demonstrated that the expression of 37 out of these TDFs in RT-PCR analysis was consistent with that in cDNA-AFLP analysis. Based on BlastX in NCBI, 28 TDFs were assumed to function in sugarcane under U. scitaminea stress. Analysis of expression profile of three TDFs revealed that they responded differently after infection with U. scitaminea, and the transcription was significantly enhanced. The response of two TDFs, SUC06 and SUC09, occurred before that of SUC10. This study enriches our knowledge of the molecular basis for sugarcane response to U. scitaminea infection.

Transcriptome and Small RNA Combined Sequencing Analysis of Cold Tolerance in Non-heading Chinese Cabbage.

BACKGROUND: Non-heading Chinese cabbage (Brassica rapa ssp. chinensis) is an important leaf vegetable grown worldwide. However, there has currently been not enough transcriptome and small RNA combined sequencing analysis of cold tolerance, which hinders further functional genomics research. RESULTS: In this study, 63.43 Gb of clean data was obtained from the transcriptome analysis. The clean data of each sample reached 6.99 Gb, and the basic percentage of Q30 was 93.68% and above. The clean reads of each sample were sequence aligned with the designated reference genome (Brassica rapa, IVFCAASv1), and the efficiency of the alignment varied from 81.54 to 87.24%. According to the comparison results, 1,860 new genes were discovered in Pak-choi, of which 1,613 were functionally annotated. Among them, 13 common differentially expressed genes were detected in all materials, including seven upregulated and six downregulated. At the same time, we used quantitative real-time PCR to confirm the changes of these gene expression levels. In addition, we sequenced miRNA of the same material. Our findings revealed a total of 34,182,333 small RNA reads, 88,604,604 kinds of small RNAs, among which the most common size was 24 nt. In all materials, the number of common differential miRNAs is eight. According to the corresponding relationship between miRNA and its target genes, we carried out Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the set of target genes on each group of differentially expressed miRNAs. Through the analysis, it is found that the distributions of candidate target genes in different materials are different. We not only used transcriptome sequencing and small RNA sequencing but also used experiments to prove the expression levels of differentially expressed genes that were obtained by sequencing. Sequencing combined with experiments proved the mechanism of some differential gene expression levels after low-temperature treatment. CONCLUSION: In all, this study provides a resource for genetic and genomic research under abiotic stress in Pak-choi.

Repair function of essential oil from Crocodylus Siamensis (Schneider, 1801) on the burn wound healing via up-regulated growth factor expression and anti-inflammatory effect.

ETHNOPHARMACOLOGICAL RELEVANCE: Crocodile oil has been used by traditional physicians around the world to treat wound healing and inflammation. However, the scientific rationale and mechanism behind its use in vivo has not been fully researched. AIMS OF THE STUDY: We mainly investigated the mechanism during crocodile oil treatment of up-regulated growth factor expression and anti-inflammatory on burn wound healing in rats. MATERIALS AND METHODS: The moisture and nitric oxide (NO) levels in the skin of rats were analyzed in the first 14 days after burn and the changes of the structure of the skin tissues in the wound healing were studied by hematoxylin-eosin (H.E.) staining within 21 days after scald. The inflammatory factor on burn wound healing in rats was dected by ELISA kits and Q-PCR. the expression of a variety of growth factors (TGF-ß1, VEGE-α, EGF) and PCNA in the skin tissue after burns was evaluated using immunohistochemistry. The down-regulated phosphorylation of p38 MAPK in the wound healing was confirmed by Western-blot analysis. In addition, TEM was used to observe the ultrastructure of scalded skin. RESULTS: This study showed that crocodile oil could significantly reduce the protein and mRNA levels of TNF-α, IL-1ß and IL-6. And it was found that the phosphorylation of p38 MAPK was down-regulated in the wound healing (p < 0.05). Meanwhile, crocodile oil can promote the expression of a variety of growth factors (TGF-ß1, VEGE-α, EGF) and PCNA in the skin tissue after burns, and promote the repair of collagen fibers in the dermis, preventing the production of melanin and maintain the appearance of repaired skin.