Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning

Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).

Genome-Wide Identification and Expression Analysis of the GSK3 Gene Family in Sunflower under Various Abiotic Stresses

Genes in the glycogen synthase kinase 3(GSK3)family are essential in regulating plant response to stressful conditions.This study employed bioinformatics to uncover the GSK3 gene family from the sunflower genome database.The expressions of GSK3 genes in different tissues and stress treatments,such as salt,drought,and cold,were assessed using transcriptome sequencing and quantitative real-time PCR(qRT-PCR).The study results revealed that the 12 GSK3 genes of sunflower,belonging to four classes(Classes I–IV),contained the GSK3 kinase domain and 11–13 exons.The majority of GSK3 genes were highly expressed in the leaf axil and flower,while their expression levels were relatively lower in the leaf.As a result of salt stress,six of the GSK3 genes(HaSK11,HaSK22,HaSK23,HaSK32,HaSK33,and HaSK41)displayed a notable increase in expression,while HaSK14 and HaSK21 experienced a significant decrease.With regard to drought stress,five of the GSK3 genes(HaSK11,HaSK13,HaSK21,HaSK22,and HaSK33)experienced a remarkable rise in expression.When exposed to cold stress,seven of the GSK3 genes(HaSK11,HaSK12,HaSK13,HaSK32,HaSK33,HaSK41,and HaSK42)showed a substantial increase,whereas HaSK21 and HaSK23 had a sharp decline.This research is of great importance in understanding the abiotic resistance mechanism of sunflowers and developing new varieties with improved stress resistance.

Molecular cloning,characterization and promoter analysis of LbgCWIN1 and its expression profiles in response to exogenous sucrose during in vitro bulblet initiation in lily

Lily(Lilium spp.) is an important ornamental flower, which is mainly propagated by bulbs. Cell wall invertases(CWINs), which catalyze the irreversibly conversion of sucrose into glucose and fructose in the extracellular space, are key enzymes participating in sucrose allocation in higher plants. Previous studies have shown that CWINs play an essential role in bulblet initiation process in bulbous crops, but the underlying molecular mechanism remains unclear. Here, a CWIN gene of Lilium brownii var. giganteum(Lbg) was identified and amplified from genomic DNA. Quantitative RT-PCR assays revealed that the expression level of LbgCWIN1 was highly upregulated exactly when the endogenous starch degraded in non-sucrose medium during in vitro bulblet initiation in Lbg. Phylogenetic relationship, motif, and domain analysis of LbgCWIN1 protein and CWINs in other plant species showed that all sequences of these CWIN proteins were highly conserved. The promoter sequence of LbgCWIN1 possessed a number of alpha-amylase-, phytohormone-, light-and stress-responsive cis-elements. Meanwhile, β-glucuronidase(GUS) assay showed that the 459 bp upstream fragment from the translational start site displayed maximal promoter activity. These results revealed that LbgCWIN1 might function in the process of in vitro bulblet initiation and be in the response to degradation of endogenous starch.

Expression Pattern, Interaction Network, and Functional Analysis of the Arabidopsis Botrytis Susceptible1 Interactor

E3 ubiquitin ligases are participated in numerous processes, regulating the response to biotic and abiotic stresses. Botrytis susceptible1 interactor (BOI) is a RING (Really Interesting New Gene)-type E3 ligase that mediates the ubiquitination of BOS1 (Botrytis susceptible1), a transcription factor involved in stress and pathogen responses. Although BOI is an E3 ligase, there are reports to show that BOI interacts with target proteins such as DELLAs or CONSTANS to repress gibberellin responses and flowering without the degradation of the target proteins. In this article, we utilize diversified methods to comprehensively analyze the expression pattern, interaction network and function of BOI gene. Firstly, 1800 bp upstream region of BOI gene from Arabidopsis thaliana (Arabidopsis) genome was isolated, and fused GUS reporter gene. The resulting expression cassette was introduced into wild-type Arabidopsis through Agrobacterium-mediated transformation. The result demonstrated that BOI gene was expressed predominantly in leaves, siliques, young roots, and flowering tissues, indicating that BOI gene may be involved in multiple processes in plant growth and development in Arabidopsis. Besides, eight candidate interacting proteins were obtained from the Arabidopsis cDNA library via yeast two-hybrid technology, including EXO70E2 (AT5G61010), WRKY7 (AT4G24240), WRKY11 (AT4G31550), WRKY17 (AT2G24570), UBP20 (AT4G17895), L5 (AT1G12290), SAUR9 (AT4G36110) and TCP21 (AT5G08330). Functional analysis of these candidate interacting proteins manifested that they related to multiple pathways, including biological and abiotic stress, programmed cell death, protein degradation, material metabolism and transcriptional regulation. In addition, the results of the transient assay proclaimed that BOI protein affects the protein stability of EXO70E2 and L5 through its E3 ubiquitin ligase activity. Our results provide novel clues for a better understanding of molecular mechanisms underlying BOI-mediated regulations.

Genome-Wide Identification of Tomato (Solanum lycopersicum L.) CKX Gene Family and Expression Analysis in the Callus Tissue under Zeatin Treatment

The cytokinin oxidase/dehydrogenase(CKX)enzyme is essential for controlling thefluctuating levels of endogen-ous cytokinin(CK)and has a significant impact on different aspects of plant growth and development.Nonethe-less,there is limited knowledge about CKX genes in tomato(Solanum lycopersicum L.).Here we performed genome-wide identification and analysis of nine SlCKX family members in tomatoes using bioinformatics tools.The results revealed that nine SlCKX genes were unevenly distributed onfive chromosomes(Chr.1,Chr.4,Chr.8,Chr.10,and Chr.12).The amino acid length,isoelectric points,and molecular weight of the nine SlCKX proteins ranged from 453 to 553,5.77 to 8.59,and 51.661 to 62.494 kD,respectively.Subcellular localization analysis indi-cated that SlCKX2 proteins were located in both the vacuole and cytoplasmic matrix;SlCKX3 and SlCKX5 pro-teins were located in the vacuole;and SlCKX1,4,6,7,8,and 9 proteins were located in the cytoplasmic matrix.Furthermore,we observed differences in the gene structures and phylogenetic relationships of SlCKX proteins among different members.SlCKX1-9 were positioned on two out of the three branches of the CKX phylogenetic tree in the multispecies phylogenetic tree construction,revealing their strong conservation within phylogenetic subgroups.Unique patterns of expression of CKX genes were noticed in callus cultures exposed to varying con-centrations of exogenous ZT,suggesting their roles in specific developmental and physiological functions in the regeneration system.These results may facilitate subsequent functional analysis of SlCKX genes and provide valu-able insights for establishing an efficient regeneration system for tomatoes.

Genome-Wide Discovery and Expression Profiling of the SWEET Sugar Transporter Gene Family in Woodland Strawberry (Fragaria vesca) under Developmental and Stress Conditions: Structural and Evolutionary Analysis

The SWEET(sugar will eventually be exported transporter)family proteins are a recently identified class of sugar transporters that are essential for various physiological processes.Although the functions of the SWEET proteins have been identified in a number of species,to date,there have been no reports of the functions of the SWEET genes in woodland strawberries(Fragaria vesca).In this study,we identified 15 genes that were highly homolo-gous to the A.thaliana AtSWEET genes and designated them as FvSWEET1–FvSWEET15.We then conducted a structural and evolutionary analysis of these 15 FvSWEET genes.The phylogenetic analysis enabled us to categor-ize the predicted 15 SWEET proteins into four distinct groups.We observed slight variations in the exon‒intron structures of these genes,while the motifs and domain structures remained highly conserved.Additionally,the developmental and biological stress expression profiles of the 15 FvSWEET genes were extracted and analyzed.Finally,WGCNA coexpression network analysis was run to search for possible interacting genes of FvSWEET genes.The results showed that the FvSWEET10 genes interacted with 20 other genes,playing roles in response to bacterial and fungal infections.The outcomes of this study provide insights into the further study of FvSWEET genes and may also aid in the functional characterization of the FvSWEET genes in woodland strawberries.

Whole-volume histogram analysis of spectral-computed tomography iodine maps characterizes HER2 expression in gastric cancer

BACKGROUND Although surgery remains the primary treatment for gastric cancer(GC),the identification of effective alternative treatments for individuals for whom surgery is unsuitable holds significance.HER2 overexpression occurs in approximately 15%-20%of advanced GC cases,directly affecting treatment-related decisions.Spectral-computed tomography(sCT)enables the quantification of material compositions,and sCT iodine concentration parameters have been demonstrated to be useful for the diagnosis of GC and prediction of its invasion depth,angioge-nesis,and response to systemic chemotherapy.No existing report describes the prediction of GC HER2 status through histogram analysis based on sCT iodine maps(IMs).AIM To investigate whether whole-volume histogram analysis of sCT IMs enables the prediction of the GC HER2 status.METHODS This study was performed with data from 101 patients with pathologically confirmed GC who underwent preoperative sCT examinations.Nineteen parameters were extracted via sCT IM histogram analysis:The minimum,maximum,mean,standard deviation,variance,coefficient of variation,skewness,kurtosis,entropy,percentiles(1st,5th,10th,25th,50th,75th,90th,95th,and 99th),and lesion volume.Spearman correlations of the parameters with the HER2 status and clinicopathological parameters were assessed.Receiver operating characteristic curves were used to evaluate the parameters’diagnostic performance.RESULTS Values for the histogram parameters of the maximum,mean,standard deviation,variance,entropy,and percentiles were significantly lower in the HER2+group than in the HER2–group(all P<0.05).The GC differentiation and Lauren classification correlated significantly with the HER2 status of tumor tissue(P=0.001 and 0.023,respectively).The 99th percentile had the largest area under the curve for GC HER2 status identification(0.740),with 76.2%,sensitivity,65.0%specificity,and 67.3%accuracy.All sCT IM histogram parameters correlated positively with the GC HER2 status(r=0.237-0.337,P=0.001-0.017).CONCLUSION Whole-lesion histogram parameters derived from sCT IM analysis,and especially the 99th percentile,can serve as imaging biomarkers of HER2 overexpression in GC.

Gene expression analysis of cytokines and MMPs in melatonin and rhBMP-2 enhanced bone remodeling

BACKGROUND In the medical and dental fields,there is a need for studies of new therapeutic approaches for the treatment of bone defects that cause extensive bone loss.Melatonin may be an important endogenous biological factor for bone remodeling,and growth factors may enhance the repair process.AIM To evaluate the gene expression of cytokines(IL-1β,IL-6,IL-10 and TNF-α),markers of osteoclastogenesis(RANK,RANKL and OPG)and MMPs(MMP-1,MMP-2,MMP-8 and MMP-13)from the treatment of melatonin associated with an osteogenic membrane and rhBMP-2 on the recovery of a bone injury.METHODS Sixty-four rats were used and divided into 9 experimental groups and were formed according to the treatment carried out in the region of the bone lesion,which varied between the combination of 1,10 and 100μmol/L of melatonin.Gene Expression analysis was performed using real time-PCR by reading the concentration of total RNA and reverse transcription.RESULTS There were differences between groups when compared with clot or scaffold control,and improvement with a higher concentration of melatonin or rhBMP-2.The combination melatonin(1μg)with 5μg of rhBMP-2,using the guided bone regeneration technique,demonstrated some effects,albeit mild,on bone repair of critical bone defects.CONCLUSION This indicates that the approach for administering these substances needs to be reassessed,with the goal of ensuring their direct application to the affected area.Therefore,future research must be carried out,seeking to produce materials with these ideal characteristics.

RNA-sequencing expression profile and functional analysis of retinal pigment epithelium in atrophic age-related macular degeneration

The retinal pigment epithelium(RPE)is fundamental to sustaining retinal homeostasis.RPE abnormality leads to visual defects and blindness,including age-related macular degeneration(AMD).Although breakthroughs have been made in the treatment of neovascular AMD,effective intervention for atrophic AMD is largely absent.The adequate knowledge of RPE pathology is hindered by a lack of the patients'RPE datasets,especially at the single-cell resolution.In the current study,we delved into a large-scale single-cell resource of AMD donors,in which RPE cells were occupied in a substantial proportion.Bulk RNA-seq datasets of atrophic AMD were integrated to extract molecular characteristics of RPE in the pathogenesis of atrophic AMD.Both in vivo and in vitro models revealed that carboxypeptidase X,M14 family member 2(CPXM2),was specifically expressed in the RPE cells of atrophic AMD,which might be induced by oxidative stress and involved in the epithelial-mesenchymal transition of RPE cells.Additionally,silencing of CPXM2 inhibited the mesenchymal phenotype of RPE cells in an oxidative stress cell model.Thus,our results demonstrated that CPXM2 played a crucial role in regulating atrophic AMD and might serve as a potential therapeutic target for atrophic AMD.

How Rustic Videos Influence Youth’s Linguistic Expression: An Analysis Based on Semiotics, Meme Theory and Media Spectacle Theory

The surge in popularity of rustic videos has spawned a great number of Internet memes, such as Internet trendy words growing from dialects and strange pronunciations, picture memes made from video screenshots, and mesmerizing music with a vernacular flavor. Due to their reproducibility, social interaction, and involvement, these rustic videos adhere to the fundamental logic of the propagation of online memes. Rustic videos are widely disseminated as online memes on TikTok (the Chinese version), are often reproduced and used by young people in social contact, and have become a unique linguistic symbol in modern internet culture. As a symbolic carrier that transports the consciousness of the video creator and viewer, it is widely employed in the communication and engagement of young people on a regular basis, progressively altering their linguistic expression. This specific semiotic interaction has deconstructed and recreated the conventional media culture spectacle. This research examines the influence of rustic videos on TikTok on the linguistic expressions of modern youth from the perspectives of meme theory and semiotics, as well as the impact of rustic videos on the media spectacle from the standpoint of media spectacle theory. It also examines in depth the effects of the popularity of rustic videos on China’s economy and culture.

Comparative Analysis of Ki-67 Protein as a Proliferative Expression Index in Cutaneous Basal and Squamous Cell Carcinoma in Federal Medical Centre Umuahia, Nigeria

Background: Evaluating the tumor proliferative index helps predict clinical behavior and provides prognostic insights for cutaneous basal cell carcinoma (cBCC) and squamous cell carcinoma (cSCC). Objective: This study aimed to identify differences in the proliferative indices among variants of cBCC and cSCC diagnosed at a tertiary healthcare center. Method: Skin biopsies histologically diagnosed as cBCC and cSCC between 2012 and 2018 at the Federal Medical Centre (FMC) Umuahia, Abia State, Nigeria, were analyzed. Archival formalin-fixed, paraffin-embedded (FFPE) tissue blocks were retrieved along with clinical data, and were prepared on charged microscope slides and the immunohistochemical staining was carried out. The primary antibody used in this study was clone BioCare CRM325C (RM) and adenotonsillar tissue blocks/slides served as positive controls. Ki-67 immunohistochemistry was performed on fresh 4µm sections of the tumor specimens. Results: The application of Ki-67 immunoperoxidase on both BCC and SCC cohort, yielded an intense observable brownish nuclear stain in areas of dense proliferating tumour cells on both cutaneous tumours. The average Ki-67 index for all cSCC cases was 24.7%, with a range of 2.3% - 80%, while the mean for cBCC was 15.8%, ranging from 1.2% - 45.6%. Variants with high proliferative indices were observed in 11.9% of cBCC cases and 29.1% of cSCC cases. Among the low proliferative index category, cSCC accounted for 5.4%, while cBCC represented 14.3%. For mild proliferative indices, cSCC cases made up 7.3% and cBCC, 11.9%. The majority of cases showed moderate proliferative indices, with 61.9% for cBCC and 58.2% for cSCC. Overall, there was a significant difference in proliferative indices between cSCC, cBCC, and their variants. Conclusion: The study found a significantly higher rate of cell proliferation, measured by Ki-67 immunostaining, in cSCC and its variants compared to cBCC. However, certain variants of cBCC also exhibited high Ki-67 expression, indicating they can be as aggressive as some cSCC variants.

Bibliometric analysis of phosphoglycerate kinase 1 expression in breast cancer and its distinct upregulation in triple-negative breast cancer

BACKGROUND Phosphoglycerate kinase 1(PGK1)has been identified as a possible biomarker for breast cancer(BC)and may play a role in the development and advancement of triple-negative BC(TNBC).AIM To explore the PGK1 and BC research status and PGK1 expression and mecha-nism differences among TNBC,non-TNBC,and normal breast tissue.METHODS PGK1 and BC related literature was downloaded from Web of Science Core Co-llection Core Collection.Publication counts,key-word frequency,cooperation networks,and theme trends were analyzed.Normal breast,TNBC,and non-TNBC mRNA data were gathered,and differentially expressed genes obtained.Area under the summary receiver operating characteristic curves,sensitivity and specificity of PGK1 expression were determined.Kaplan Meier revealed PGK1’s prognostic implication.PGK1 co-expressed genes were explored,and Gene Onto-logy,Kyoto Encyclopedia of Genes and Genomes,and Disease Ontology applied.Protein-protein interaction networks were constructed.Hub genes identified.RESULTS PGK1 and BC related publications have surged since 2020,with China leading the way.The most frequent keyword was“Expression”.Collaborative networks were found among co-citations,countries,institutions,and authors.PGK1 expression and BC progression were research hotspots,and PGK1 expression and BC survival were research frontiers.In 16 TNBC vs non-cancerous breast and 15 TNBC vs non-TNBC datasets,PGK1 mRNA levels were higher in 1159 TNBC than 1205 non-cancerous breast cases[standardized mean differences(SMD):0.85,95%confidence interval(95%CI):0.54-1.16,I²=86%,P<0.001].PGK1 expression was higher in 1520 TNBC than 7072 non-TNBC cases(SMD:0.25,95%CI:0.03-0.47,I²=91%,P=0.02).Recurrence free survival was lower in PGK1-high-expression than PGK1-low-expression group(hazard ratio:1.282,P=0.023).PGK1 co-expressed genes were concentrated in ATP metabolic process,HIF-1 signaling,and glycolysis/gluconeogenesis pathways.CONCLUSION PGK1 expression is a research hotspot and frontier direction in the BC field.PGK1 may play a strong role in promoting cancer in TNBC by mediating metabolism and HIF-1 signaling pathways.

Prognostic significance of CDKN2A expression in colon adenocarcinoma: insights from TCGA analysis

Background:The cyclin-dependent kinase inhibitor 2a(CDKN2A)gene,identified as the multiple tumor suppressor gene,functions as a regulatory gene implicated in cancer pathogenesis.Its significance lies in its pivotal involvement in the genesis of various tumors;notwithstanding,the precise connection between CDKN2A and c olon adenocarcinoma(COAD)remains undisclosed.Methods:The objective of this research was to assess the predictive importance of CDKN2A in COAD by analyzing data from The Cancer Genome Atlas database.Logistic regression,signed rank test,Wilcoxon test,and Kruskal-Wallis test were used to examine CDKN2A expression levels and clinicopathological features.Univariate and multivariate Cox r egression analyses and Kaplan-Meier analysis found prognostic variables.Additionally,gene set enrichment analysis identified key CDKN2A expression pathways.The study additionally examined CDKN2A expression with tumor immune infiltration using The Cancer Genome Atlas data and single sample gene set enrichment analysis.Results:The results of this investigation indicated a substantial connection between higher CDKN2A expression and negative outcomes in terms of overall survival and disease-related survival among COAD patients.Gene set enrichment analysis indicated a tight link between CDKN2A and both the cell cycle and hedgehog signaling pathways.Subsequent evaluation employing single sample gene set enrichment analysis demonstrated a positive link between CDKN2A expression with infiltration by iDCs,whereas a negative correlation was detected with infiltration by helper T cells.Conclusion:In conclusion,the present study gives strong data supporting the predictive value of CDKN2A and its possible usefulness as a biomarker for COAD.Additionally,our results show a reasonable link between CDKN2A expression and immune influx in COAD,putting light on the role of CDKN2A in the control of the tumor microenvironment.Nevertheless,additional studies are needed to confirm the underlying mechanisms of these relationships and to discover the therapeutic possibilities of targeting CDKN2A in the treatment of COAD.

The prognostic and immunological impacts of DCX expression:a pan-cancer analysis

Background:Doublecortin(DCX),a microtubule-associated protein,is best known for its critical role in neuronal migration during neural development,where it stabilizes microtubules and guides neurons to their proper positions.Recently,DCX has been implicated in various cancer processes,suggesting it may influence tumor progression and the tumor microenvironment.Emerging evidence indicates that DCX can modulate cell migration,invasion,and interaction with immune cells,making it a potential player in oncogenesis.However,the role of DCX across different cancer types and its potential as a prognostic biomarker remain underexplored,necessitating a comprehensive analysis.Methods:We utilized The Cancer Genome Atlas to extract data on DCX expression in tumor and adjacent normal tissues across diverse cancer types.Differential expression analysis was conducted using differential expression sequencing 2.Survival analysis was performed with Kaplan-Meier estimates and Cox proportional hazards models.Correlations between DCX expression and tumor mutational burden,microsatellite instability,and immune infiltration were examined using Spearman’s correlation.Results:DCX showed variable expression across cancer types,with significant overexpression in certain tumors such as liver and lung cancer and downexpression in others like breast cancer.High DCX expression was correlated with poor prognosis in adrenocortical carcinoma but with better outcomes in low-grade glioma.Additionally,DCX expression was significantly associated with various immune markers and chemokines,suggesting a role in modulating the immune microenvironment.Conclusion:Our findings highlight the complex role of DCX in cancer,underlining its potential as a prognostic marker and its involvement in immune-related pathways.Targeting DCX could represent a novel approach to modulating tumor behavior and enhancing immune response in cancer therapy.

Identification,evolution,expression and protein interaction analysis of genes encoding B-box zinc-finger proteins in maize

The B-box(BBX)family of proteins consists of zinc-finger transcription factors with one or two highly conserved B-box motifs at their N-termini.BBX proteins play crucial roles in various aspects of plant growth and development,including seedling photomorphogenesis,shade avoidance,flowering time,and biotic and abiotic stress responses.Previous studies have identified many different BBXs from several plant species,although the BBX family members in maize are largely unknown.Genome-wide identification and comprehensive analysis of maize BBX(ZmBBX)expression and interaction networks would therefore provide valuable information for understanding their functions.In this study,36 maize BBXs in three major clades were identified.The ZmBBXs within a given clade were found to share similar domains,motifs,and genomic structures.Gene duplication analyses revealed that the expansion of BBX proteins in maize has mainly occurred by segmental duplication.The expression levels of ZmBBXs were analyzed in various organs and tissues,and under different abiotic stress conditions.Protein–protein interaction networks of ZmBBXs were established using bioinformatic tools and verified by bimolecular fluorescence complementation(BiFC)assays.Our findings can facilitate a greater understanding of the complexity of the ZmBBX family and provide novel clues for unravelling ZmBBX protein functions.

Genome-wide identification of TPS genes in sesame and analysis of their expression in response to abiotic stresses

Trehalose and its precursor,trehalose-6-phosphate,play critical roles in plant metabolism and response to abiotic stresses.Trehalose-6-phosphate synthase(TPS)is a key enzyme in the trehalose synthesis pathway.Hence this study identified TPS genes in sesame(SiTPSs)and examined their expression patterns under various abiotic stresses.Totally,ten SiTPSs were identified and comprehensively characterized.SiTPSs were found to be unevenly distributed on five out of 13 sesame chromosomes and were predicted to be localized in chloroplasts and vacuoles of cells.Phylogenetic analysis classified SiTPS proteins into two groups(I and II),which was supported by gene structure and conserved motif analyses.Analysis of cis-acting elements in promoter regions of SiTPSs revealed that they might primarily involve developmental and environmental responses.SiTPSs exhibited different expression patterns in different tissues and under different abiotic stresses.Most group II SiTPS genes(SiTPS4-SiTPS10)were strongly induced by drought,salt,waterlogging,and osmotic stress.Particularly,SiTPS10 was the most significantly up-regulated under various abiotic stresses,indicating it is a candidate gene for improving sesame tolerance to multiple abiotic stresses.Our results provide insight into the TPS gene family in sesame and fundamental resources for genomics studies towards dissecting SiTPS genes’functions.

Identification of key genes underlying clinical features of hepatocellular carcinoma based on weighted gene co‑expression network analysis and bioinformatics analysis

Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagnosis and treatment. Methods: GSE84598 chip data were downloaded from the GEO database, and module genes closely related to the clinical features of HCC were extracted by comprehensive weighted gene co‑expression network analysis. Hub genes were identified through protein interaction network analysis by the maximum clique centrality (MCC) algorithm;Finally, the expression of hub genes was validated by TCGA database and the Kaplan Meier plotter online database was used to evaluate the prognostic relationship between hub genes and HCC patients. Results: By comparing the gene expression data between HCC tissue samples and normal liver tissue samples, a total of 6 262 differentially expressed genes were obtained, of which 2 207 were upregulated and 4 055 were downregulated. Weighted gene co‑expression network analysis was applied to identify 120 genes of key modules. By intersecting with the differentially expressed genes, 115 candidate hub genes were obtained. The results of enrichment analysis showed that the candidate hub genes were closely related to cell mitosis, p53 signaling pathway and so on. Further application of the MCC algorithm to the protein interaction network of 115 candidate hub genes identified five hub genes, namely NUF2, RRM2, UBE2C, CDC20 and MAD2L1. Validation of hub genes by TCGA database revealed that all five hub genes were significantly upregulated in HCC tissues compared to normal liver tissues;Moreover, survival analysis revealed that high expression of hub genes was closely associated with poor prognosis in HCC patients. Conclusions: This study identifies five hub genes by combining multiple databases, which may provide directions for the clinical diagnosis and treatment of HCC.

Transcriptome and weighted gene co-expression network analysis of jujube(Ziziphus jujuba Mill.)fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation

Proanthocyanidin(PA)is an important bioactive compound with multiple physiological benefits in jujube(Ziziphus jujube Mill.).However,the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been investigated.Here,the profiling of PA,(+)-catechin and(–)-epicatechin and transcriptome sequencing of three jujube cultivars from Xinjiang Uyghur Autonomous Region of China at five developmental stages were analyzed.The levels of total PAs and catechin exhibited a decreased trend over jujube ripening,and epicatechin content of two jujube cultivars increased first and then declined.Transcriptome analysis revealed that the differentially expressed genes(DEGs)were mainly enriched in ribosome,glycolysis/gluconeogenesis,fructose and mannose metabolism.17 DEGs encoding PAL,CHS,CHI,CHS,F3'H,LAR,ANR,C4Hs,4CLs,FLSs,DFRs and UFGTs involved in PA biosynthesis were relatively abundant.The highly transcribed LAR gene may greatly contribute to epicatechin accumulation.A weighted gene co-expression network analysis(WGCNA)was performed,and a network module including 1620 genes highly correlated with content of Pas and catechin was established.We identified 58 genes including 9 structural genes and 49 regulatory genes related to PA biosynthesis and regulation in the WGCNA module.Sixteen genes encoding 9 families of transcriptional factors(i.e.,MYB,bHLH,ERF,bZIP,NAC,SBP,MIKC,HB,WRKY)were considered as hub genes.The results of qRT-PCR analysis validating 10 genes were well consistent with the transcriptome data.These findings provide valuable knowledge to facilitate its genetic studies and molecular breeding.

CHDTEPDB:Transcriptome Expression Profile Database and Interactive Analysis Platform for Congenital Heart Disease

CHDTEPDB(URL:http://chdtepdb.com/)is a manually integrated database for congenital heart disease(CHD)that stores the expression profiling data of CHD derived from published papers,aiming to provide rich resources for investigating a deeper correlation between human CHD and aberrant transcriptome expression.The develop-ment of human diseases involves important regulatory roles of RNAs,and expression profiling data can reflect the underlying etiology of inherited diseases.Hence,collecting and compiling expression profiling data is of critical significance for a comprehensive understanding of the mechanisms and functions that underpin genetic diseases.CHDTEPDB stores the expression profiles of over 200 sets of 7 types of CHD and provides users with more convenient basic analytical functions.Due to the differences in clinical indicators such as disease type and unavoidable detection errors among various datasets,users are able to customize their selection of corresponding data for personalized analysis.Moreover,we provide a submission page for researchers to submit their own data so that increasing expression profiles as well as some other histological data could be supplemented to the database.CHDTEPDB is a user-friendly interface that allows users to quickly browse,retrieve,download,and analyze their target samples.CHDTEPDB will significantly improve the current knowledge of expression profiling data in CHD and has the potential to be exploited as an important tool for future research on the disease.

Genome wide investigation of Hsf gene family in Phoebe bournei:identification,evolution,and expression after abiotic stresses

Heat shock transcription factors(Hsfs)have important roles during plant growth and development and responses to abiotic stresses.The identification and func-tion of Hsf genes have been thoroughly studied in various herbaceous plant species,but not woody species,especially Phoebe bournei,an endangered,unique species in China.In this study,17 members of the Hsf gene family were identi-fied from P.bournei using bioinformatic methods.Phyloge-netic analysis indicated that PbHsf genes were grouped into three subfamilies:A,B,and C.Conserved motifs,three-dimensional structure,and physicochemical properties of the PbHsf proteins were also analyzed.The structure of the PbHsf genes varied in the number of exons and introns.Pre-diction of cis-acting elements in the promoter region indi-cated that PbHsf genes are likely involved in responses to plant hormones and stresses.A collinearity analysis dem-onstrated that expansions of the PbHsf gene family mainly take place via segmental duplication.The expression levels of PbHsf genes varied across different plant tissues.On the basis of the expression profiles of five representative PbHsf genes during heat,cold,salt,and drought stress,PbHsf pro-teins seem to have multiple functions depending on the type of abiotic stress.This systematic,genome-wide investigation of PbHsf genes in P.bournei and their expression patterns provides valuable insights and information for further func-tional dissection of Hsf proteins in this endangered,unique species.