Effect of Chuanzhifang component (ZGC) on macrophage inflammatory injury based on whole gene expression profile

Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target of this formula on macrophage inflammatory injury at the overall level. Methods: A model of LPS-induced inflammation in RAW264.7 cells was constructed, and the effect of ZGC intervention on the genome-wide expression of inflammatory macrophages 3was examined by gene microarray technology, GO/KEGG enrichment analysis was performed for significantly differentially expressed genes among each group. Results: The results of genome-wide expression profiling microarray analysis showed that the ZGC intervention group upregulated the expression of 5 genes including C4bp and inhibited the expression of 22 genes including Mgat3, Psma6, and Siglecg relative to the LPS model group. KEGG signaling pathway analysis results showed that ZGC mainly acted through cytokine receptor interaction and the C-type lectin receptor signaling pathway. Conclusion: ZGC can interfere with the abnormal expression of 27 genes in inflammatory macrophages, and the related genes may exert corresponding anti-inflammatory effects by affecting cytokine receptor interactions, C-type lectin receptor signaling pathway, and TLR4/ NF-κB signaling pathway.

Effects of pyraclostrobin on growth,oxidative stress,and gene expression in relation to stress and ATP-binding cassette transporters in Tetrahymena thermophila

Pyraclostrobin(PYR),a widely used fungicide,has negative effects on fish and algae,but its toxicity in protozoa remains unclear.In this study,the effects of PYR on the growth,oxidative stress,and gene expression related to stress and ATP-binding cassette(ABC)transporters in Tetrahymena thermophila were investigated.The result showed that the 96-h IC_(50)of PYR against T.thermophila was 17.2 mg/L.Moreover,PYR inhibited the growth of T.thermophila in concentration-or time-dependent manner.A morphological study revealed that the shape and size of T.thermophila changed,and damage of cell membrane surface was observed by scanning electron microscopy after 96 h of PYR exposure.The activities of superoxide dismutase(SOD)and catalase(CAT)increased throughout the experiment.In contrast,the glutathione(GSH)content was increased at 24 h and 48 h of exposure and decreased at 96 h.Moreover,a significant increase in malondialdehyde(MDA)level was observed in T.thermophila after96 h of exposure.Furthermore,PYR upregulated the HSP703,HSP705,GPx2,and ABAC15 gene expression in the 0.1–5-mg/L groups and downregulated the HSP704,HSP90,TGR,and ABCC52 mRNA levels at 96 h of exposure.These results suggest that PYR may exert adverse effects on T.thermophila by inducing oxidative stress and changing the gene expression related to ABC transporters and stress,which may enrich the understanding of the toxicity mechanism of PYR in aquatic organisms and provide reference data for aquatic ecological risk assessments.

Decoding Retinoblastoma: Differential Gene Expression

Background: Retinoblastoma, the most common intraocular pediatric cancer, presents complexities in its genetic landscape that necessitate a deeper understanding for improved therapeutic interventions. This study leverages computational tools to dissect the differential gene expression profiles in retinoblastoma. Methods: Employing an in silico approach, we analyzed gene expression data from public repositories by applying rigorous statistical models, including limma and de seq 2, for identifying differentially expressed genes DEGs. Our findings were validated through cross-referencing with independent datasets and existing literature. We further employed functional annotation and pathway analysis to elucidate the biological significance of these DEGs. Results: Our computational analysis confirmed the dysregulation of key retinoblastoma-associated genes. In comparison to normal retinal tissue, RB1 exhibited a 2.5-fold increase in expression (adjusted p Conclusions: Our analysis reinforces the critical genetic alterations known in retinoblastoma and unveils new avenues for research into the disease’s molecular basis. The discovery of chemoresistance markers and immune-related genes opens potential pathways for personalized treatment strategies. The study’s outcomes emphasize the power of in silico analyses in unraveling complex cancer genomics.

Genome-wide identification and expression profiling of photosystem II(PsbX)gene family in upland cotton(Gossypium hirsutum L.)

Background Photosystem II(PSII)constitutes an intricate assembly of protein pigments,featuring extrinsic and intrinsic polypeptides within the photosynthetic membrane.The low-molecular-weight transmembrane protein PsbX has been identified in PSII,which is associated with the oxygen-evolving complex.The expression of PsbX gene protein is regulated by light.PsbX’s central role involves the regulation of PSII,facilitating the binding of quinone molecules to the Qb(PsbA)site,and it additionally plays a crucial role in optimizing the efficiency of photosynthesis.Despite these insights,a comprehensive understanding of the PsbX gene’s functions has remained elusive.Results In this study,we identified ten PsbX genes in Gossypium hirsutum L.The phylogenetic analysis results showed that 40 genes from nine species were classified into one clade.The resulting sequence logos exhibited substantial conservation across the N and C terminals at multiple sites among all Gossypium species.Furthermore,the ortholo-gous/paralogous,Ka/Ks ratio revealed that cotton PsbX genes subjected to positive as well as purifying selection pressure might lead to limited divergence,which resulted in the whole genome and segmental duplication.The expression patterns of GhPsbX genes exhibited variations across specific tissues,as indicated by the analysis.Moreover,the expression of GhPsbX genes could potentially be regulated in response to salt,intense light,and drought stresses.Therefore,GhPsbX genes may play a significant role in the modulation of photosynthesis under adverse abiotic conditions.Conclusion We examined the structure and function of PsbX gene family very first by using comparative genom-ics and systems biology approaches in cotton.It seems that PsbX gene family plays a vital role during the growth and development of cotton under stress conditions.Collectively,the results of this study provide basic information to unveil the molecular and physiological function of PsbX genes of cotton plants.

A Novel Deep Learning-Based Model for Classification of Wheat Gene Expression

Deep learning(DL)plays a critical role in processing and converting data into knowledge and decisions.DL technologies have been applied in a variety of applications,including image,video,and genome sequence analysis.In deep learning the most widely utilized architecture is Convolutional Neural Networks(CNN)are taught discriminatory traits in a supervised environment.In comparison to other classic neural networks,CNN makes use of a limited number of artificial neurons,therefore it is ideal for the recognition and processing of wheat gene sequences.Wheat is an essential crop of cereals for people around the world.Wheat Genotypes identification has an impact on the possible development of many countries in the agricultural sector.In quantitative genetics prediction of genetic values is a central issue.Wheat is an allohexaploid(AABBDD)with three distinct genomes.The sizes of the wheat genome are quite large compared to many other kinds and the availability of a diversity of genetic knowledge and normal structure at breeding lines of wheat,Therefore,genome sequence approaches based on techniques of Artificial Intelligence(AI)are necessary.This paper focuses on using the Wheat genome sequence will assist wheat producers in making better use of their genetic resources and managing genetic variation in their breeding program,as well as propose a novel model based on deep learning for offering a fundamental overview of genomic prediction theory and current constraints.In this paper,the hyperparameters of the network are optimized in the CNN to decrease the requirement for manual search and enhance network performance using a new proposed model built on an optimization algorithm and Convolutional Neural Networks(CNN).

Establishment of a prognosis predictive model for liver cancer based on expression of genes involved in the ubiquitin-proteasome pathway

BACKGROUND The ubiquitin-proteasome pathway(UPP)has been proven to play important roles in cancer.AIM To investigate the prognostic significance of genes involved in the UPP and develop a predictive model for liver cancer based on the expression of these genes.METHODS In this study,UPP-related E1,E2,E3,deubiquitylating enzyme,and proteasome gene sets were obtained from the Kyoto Encyclopedia of Genes and Genomes(KEGG)database,aiming to screen the prognostic genes using univariate and multivariate regression analysis and develop a prognosis predictive model based RESULTS Five genes(including autophagy related 10,proteasome 20S subunit alpha 8,proteasome 20S subunit beta 2,ubiquitin specific peptidase 17 like family member 2,and ubiquitin specific peptidase 8)were proven significantly correlated with prognosis and used to develop a prognosis predictive model for liver cancer.Among training,validation,and Gene Expression Omnibus sets,the overall survival differed significantly between the high-risk and low-risk groups.The expression of the five genes was significantly associated with immunocyte infiltration,tumor stage,and postoperative recurrence.A total of 111 differentially expressed genes(DEGs)were identified between the high-risk and low-risk groups and they were enriched in 20 and 5 gene ontology and KEGG pathways.Cell division cycle 20,Kelch repeat and BTB domain containing 11,and DDB1 and CUL4 associated factor 4 like 2 were the DEGs in the E3 gene set that correlated with survival.CONCLUSION We have constructed a prognosis predictive model in patients with liver cancer,which contains five genes that associate with immunocyte infiltration,tumor stage,and postoperative recurrence.

The Influence of Aerial Exposure on Sea Anemones Aulactinia veratra Mucin Genes Expression Using the RNA Sequencing

Mucin genes are the main component of mucus. The sea anemone species, Aulactinia veratra (Phylum Cnidaria) contains different types of mucin genes. In the intertidal zone, A. veratra is found to be exposed to air during the low tide and produces large quantities of mucus as an external covering. The relation between low tide and mucus secretion is still unclear, and what is the role of mucin during arial exposure is not yet investigated. This study hypothesised that the mucin genes in A. veratra would have significantly high expression in response to aerial exposure. Therefore, the aim of current study was to examine and analyses the response of A. veratra mucins in response to an experiment involving three hours of aerial exposure. To achieve this, aim the RNA-sequencing and bioinformatics analyses were used to examine the expression profile of A. veratra mucin genes in response to aerial exposure. The generated results have shown that, Mucin4-like and mucin5B-like were up-regulated in response to the three hours of aerial exposure in A. veratra. This finding shows a significant role of mucin5B-like and mucin4-like genes in response to air stress at low tide. The data generated from this study could be used in conjunction with future mucin gene studies of sea anemones and other cnidarians to compare A. veratra mucin gene expression results across time, and to extend our understanding of mucin stress response in this phylum.

Characterization of Caspase Gene Family Members in Spotted Sea Bass(Lateolabrax maculatus)and Their Expression Profiles in Response to Vibrio harveyi Infection

The caspase gene family is a crucial gene cluster that regulates apoptosis which contribute to programmed cell death,cell proliferation and differentiation,and several immune responses.In our study,a complete set of 12 caspase genes were identified in spotted sea bass Lateolabrax maculatus.These genes were divided into three subfamilies:2 inflammatory caspases(casp-1 and casp-14-like),5 apoptosis initiators(casp-2,casp-8a,casp-8b,casp-9,and casp-10),and 5 apoptosis executioners(casp-3a,casp-3b,casp-3-like,casp-6,and casp-7).Their phylogenetic relationships,synteny and gene structures were systematically analyzed.Furthermore,the relative expression profiles of the caspase family members in the liver,intestine,head kidney,and spleen were measured by q PCR after infection with Vibrio harveyi.The results showed that the overall mRNA levels of the caspase genes were dramatically increased after V.harveyi infection,and the expression patterns varied among genes and tissues.More caspase genes underwent pronounced expression changes in the head kidney and spleen than in the liver or intestine,mainly after 48 h of the challenge.Specifically,casp-3a,casp-3b,casp-3-like,casp-6,casp-7,casp-8a,casp-8b,casp-10,and casp-14-like in the head kidney,and casp-3-like,casp-6,casp-7,and casp-14-like in the spleen,were the most responsive caspase genes which may contribute significantly to immune regulation in spotted sea bass.Additionally,the apoptosis level in head kidney and spleen after infection were examined using the Caspase assay.Our study provides a systemic overview of the caspase gene family in spotted sea bass after V.harveyi infection and lays a foundation for further deciphering the biological roles of these caspase genes.

Expression Profiles and Response to Exogenous Hormones of β-Fructofuranosidase Gene BmSuc1 in Silkworms(Bombyx mori)

[Objectives]In order to clarify the regulatory effects of insect hormones on the expression of BmSuc1 and provide a reference for further analysis of the function and expression regulation mechanism of BmSuc1,this study explored the expression profiles of BmSuc1 in different tissues and periods of silkworm larvae and the expression changes of BmSuc1 after treatment with exogenous hormones.[Methods]By using the real-time fluorescence quantitative PCR technique,the expression characteristics of BmSuc1 were detected in different periods,different tissues and after treatment with exogenous hormones during the development of silkworm larvae.The expression of BmSuc1 and 20E receptor gene USP was detected after RNA interference with double-stranded RNA(dsRNA)of USP.[Results]The relative expression of BmSuc1 gene in the midgut was the highest,followed by the silk glands,epidermis and hemolymph.However,there was much lower or almost no expression in other tissues.In addition,the BmSuc1 expression profile exhibited a pulse-like pattern in silkworm larvae.The expression level of BmSuc1 was higher at each instar stage before molting,late fifth instar before cocooning and prepupal stage.Silkworm larvae at day 2 of the fifth instar were treated with 20-hydroxyecdysone(20E)and juvenile hormone(JH).It was found that the expression of BmSuc1 was extremely significantly higher at 12 and 18 h after 20E treatment than the control group injected with 0.1%dimethyl sulfoxide(DMSO)(P<0.01,the same below).But there were no significant difference in BmSuc1 expression between the JH treatment and the control group during the measurement time range(P>0.05).The dsRNA of USP was synthesized in vitro and injected into silkworm larvae at day 3 of the fifth instar.It was showed that the USP relative expression was extremely significantly down-regulated at 24 and 36 h after injection,which indicated that dsRNA interference was successful.RNAi of USP would block 20E signal transduction,and the expression of BmSuc1 was inhibited and significantly down-regulated at 24 and 36 h after injection of dsRNA of USP(P<0.05).[Conclusions]The BmSuc1 expression peaks appeared in the molting of silkworm larvae and the metamorphosis of larvae to pupae,which suggests that BmSuc1 may be involved in the metamorphic development process of silkworms.Treatment with exogenous ecdysone 20E can activate the expression of BmSuc1,but blocking the 20E signal transduction pathway may suppress expression of BmSuc1.It indicates that BmSuc1 as a downstream target gene in the 20E signal transduction pathway is directly or indirectly regulated by 20E signals.

Integrated analysis of gene expression profiles reveals prognostic biomarkers for immunotherapy in cancer

Tumor immunotherapy has emerged as a promising method in cancer treatment,but patient responses vary,necessitating personalized strategies and prognostic biomarkers.This study aimed to identify prognostic factors and construct a predictive model for patient survival outcomes and immunotherapy response.We curated six immunotherapy datasets representing diverse cancer types and treatment regimens.After data preprocessing,patients were stratified based on immunotherapy response.Differential gene expression analysis identified 22 genes consistently dysregulated across multiple datasets.Functional analysis provided critical insights,highlighting the enrichment of these dysregulated genes in immune response pathways and tumor microenvironment-related processes.To create a robust prognostic model,we meticulously employed a multistep approach.Initially,the identified 22 genes underwent rigorous univariate Cox regression analysis to evaluate their individual associations with patient survival outcomes.Genes showing statistical significance(p-values<0.05)at this stage advanced to the subsequent multivariate Cox regression analysis,which aimed to address potential confounding factors and collinearity among genes.From this analysis,we ultimately identified four key genes—ST6GALNAC2,SNORA65,MFAP2,and CDKN2B—that were significantly associated with patient survival outcomes.Incorporating these four key genes along with their corresponding coefficients,we constructed a predictive model.This model’s efficacy was validated through extensive Cox regression analyses,demonstrating its robustness in predicting patient survival outcomes.Furthermore,our model exhibited promising predictive capability for immunotherapy response,providing a potential tool for anticipating treatment efficacy.These findings provide insights into immunotherapy response mechanisms and suggest potential prognostic biomarkers for personalized treatment.Our study contributes to advancing cancer immunotherapy and personalized medicine.

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.

Metabolomics and gene expression levels reveal the positive effects of teaseed oil on lifespan and aging process in Caenorhabditis elegans

As an irreplaceable dietary constituent,lipids play a vital important role in health,but their effects on aging process and longevity are still not well known yet.In this paper,the metabolic profiling and gene expression levels of Caenorhabditis elegans were investigated to explore the effects of different edible oils on senescence and lifespan.The results showed that teaseed oil(TO)could prolong the life expectancy and slow down the aging process of C.elegans.Compared to the control group,the intake of lard oil(LO)and TO increased the expression levels of genes related to inhibition of protein aggregation(akt-1,daf-16,hsf-1,hsp-16.2)and lipid metabolism(daf-7,daf-1,mdt-15,lipl-4,fat-5,fat-6,fat-7),with a more significant alteration in TO group.Metabolomics revealed that palm oil can upregulated plenty of fatty acids(palmitic acid,stearic acid,tetracosanoic acid),together with some amino acids(tryptophan,L-aspartate,L-valine)and carbohydrate(D-glucose),while the trend was opposite in TO group.Besides,moderate-to-strong correlations were found between differential metabolites and changed genes.In general,this paper claimed that TO could prolong lifespan and slow down aging process via regulating the lipids,amino acids and carbohydrates metabolism.

Analysis of gene expression profiles in pancreatic carcinoma by using cDNA microarray

OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarray and detect target genes for further study. METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and 4 cases of moderate-differentiated pancreatic carcinoma were studied by means of cDNA microarray consisting of 18 000 genes. RESULTS: 1484 and 1353 different expressed genes were observed in two cancer samples respectively. We identified 455 genes altered with the same tendency in both samples, including 102 up-regulated and 353 down-regulated genes. There were 274 known genes and 181 unknown genes; 27.8% and 52.0% genes respectively had an expression level in cancer that was 2-fold higher or lower than that in normal samples. Tumor suppressor genes, growth factors and receptor genes, signal conduction genes, transcription factor genes were identified. CONCLUSIONS: cDNA microarray is an efficient and high-throughout method to investigate gene expression profiles in pancreatic carcinoma. MBD1, EDG1 and gene hypermethylation mechanism would play an important role in the pathogenesis of pancreatic carcinoma.

The mRNA Expression Profiles of Five Heat Shock Protein Genes from Frankliniella occidentalis at Different Stages and Their Responses to Temperatures and Insecticides

The westem flower thrips, Frankliniella occidental＆ （Pergande） is a highly invasive pest that is able to exploit many crops across a wide range of environmental conditions. Five full-length cDNAs of heat shock protein （HSP） genes （Fo-HSP90, Fo-HSP70, Fo-HSP60, Fo-HSP40 and Fo-HSP28.9） were cloned from F. occidentalis, and their expression profiles were investigated under conditions of thermal stress and insecticide exposure, and at different stages during development, using real-time quantitative PCR. All five gene sequences showed high similarity to homologs in other species, indicating the conserved fimction of this gene family. HSP60 represents an informative phylogenetic marker at the ordinal taxonomic level within Insecta, but HSP90, which has two homologous copies in Hymenoptera, was not informative. The expression of Fo-HSPs under thermal stress suggests that Fo-HSP90, Fo-HSP70, and Fo-HSP28.9 are inducible by both cold and heat stress, Fo-HSP40 is only heat-inducible, and Fo-HSP60 is thermally insensitive. There were two patterns of cold induction of Fo-HSPs： one is from 0 to 4℃ and the other is around -8℃. All five Fo-HSPs genes were induced by exposure to sublethal concentrations of the insecticide avermectin. The expression of the five Fo-HSPs during different developmental stages suggests that they all play a role in development of F. occidentalis.

Differential Gene Expression Profiles in Acute Hepatic Failure Model in Mice Infected with MHV-3 Virus Intervened by Anti-hepatic Failure Compound

Differential gene expression profiles in Balb/cJ mouse model of acute hepatic failure infected with MHV-3 virus intervened by anti-hepatic failure compound （AHFC） and the changes of cytokines regulated by genes were investigated. The Balb/cj mice were divided into AHFC-intervened group and control group randomly. Acute hepatic failure model of Balb/cJ mice infected with MHV-3 virus was established. The survival rate in the two groups was observed. It was found that the survival rate in the AHFC-intervened group and control group was 90% and 50% respectively 48 h after intraperitoneal injection of MHV-3 （P〈0.05）. Before and after the experiment, the cytokines in peripheral blood of the survival mice were determined, and RNA was extracted from survival mouse liver tissue for the analysis of the differential gene expression by a 36 kb mouse oligonuleotide DNA array. In all the genes of microarray there were 332 genes expressed differently in the two groups, in which 234 genes were up-regulated and 78 genes down-regulated. Through clustering analysis, the differential expression of immune related genes, including TNF receptor superfamily, Kctd9, Bcl-2, Fgl2, IL-8, IL-6, IFN-7, TNF-α etc. might be related with the curative effectiveness of AHFC. It was suggested that AHFC can balance the immune state of mouse model of acute hepatic failure infected with MHV-3 virus mainly through regulating the expression of immune related genes, decrease the immune damage and inhibit liver cell apoptosis of mouse acute hepatic failure model obviously so as to increase the survival rate of mouse models of acute hepatic failure.

Gene expression profiles in gastric mucosa of sleep deprivation rats

INTRODUCTIONStress has been shown to induce gastric mucosallesions and lower the effectiveness of the mucosa asa barrier.In rats,gastric ulcers can beproduced by cold-restraint stress and it isfrequently employed as a model for the study of themechanisms of stress on ulcer formation.Cold-restraint stress however is not normally

Expression profiles of sex-related genes in gonads of genetic male Takifugu rubripes after 17β-estradiol immersion

Estradiol treatment during early life stages of tiger puffer Takifugu rubripes induces feminization in genetic males.However,the ovaries in genetic males may revert to testes once estradiol treatment is halted.Therefore studies should investigate molecular mechanisms underlying ovary-to-testis recovery in genetic males after treatment.In the present study,tiger puffer were exposed to 10,and 100μg/L 17β-estradiol(E 2)from 15 to 100 days post-hatching(dph),then gonad phenotypes and expression profi les of six sex-related genes(cyp19a,foxl2,dmrt1,amh,sox9a,and sox9b)were characterized after the exposure.Results showed that both 10 and 100μg/L E2 induced ovarian development in genetic males at 100 dph.However,all ovaries induced by 10μg/L E2 first developed into intersexual gonads and subsequently reverted to testes after the exposure.As for treatment of 100μg/L E2,while the rest of the ovaries maintained morphological stability,percentages of intersexual gonads reached 38%-57%,and none were reverted to testes.Increased mRNA levels of cyp19a,foxl2 and sox9b and decreased mRNA levels of dmrt1,amh,and sox9a were observed during the ovarian development in genetic males.While contrary gene expression profiles were detected during ovary-to-testis transformation.The mRNA levels of all the six genes were increased during the development of intersexual gonads.These results indicated that up-regulation of dmrt1,amh and sox9a is associated with initial ovary-to-intersexual transformation,and suppression of foxl2,cyp19a and sox9b is essential for complete ovary-to-testis recovery in genetic males.This research will help to trace the molecular processes underlying gonadal transformation in teleosts.

Dynamic Expression Profiles of Marker Genes in Osteogenic Differentiation of Human Bone Marrow-derived Mesenchymal Stem Cells

Objective To observe the expression profiles of osteoblast-related genes in human mesenchymal stem cells(MSCs) derived from bone marrow during osteogenic differentiation. Methods MSCs were induced to differentiate with MSC osteogenic differentiation medium for 7, 14, 21 and 28 days respectively. Alizarin Red staining was used to detect matrix mineralization. Expression of osteoblast-related genes, including osteocalcin, osteopontin, Runt-related transcription factor 2(Runx2), alkaline phosphatase and collagen type Ⅰ, was assessed with quantitative reverse transcription-polymerase chain reaction. Results On day 14 after induction of differentiation, cells were stained positively with Alizarin Red. The expression levels of these genes exhibited an upward trend as induction time was prolonged. Exposure to osteogenic differentiation medium less than 21 days did not significantly induce osteocalcin expression; osteocalcin expression levels in the differentiated cells induced for 21 and 28 days were 1.63 and 2.46 times as high as the undifferentiated cells respectively(all P<0.05). Stimulation with MSC osteogenic differentiation medium over 14 days significantly enhanced bone marrow-derived MSCs to express osteopontin and Runx2 genes(all P<0.05). Osteogenic differentiation medium could significantly induce the expressions of alkaline phosphatase and collagen type Ⅰgenes(all P<0.05). Their expressions reached the peak levels on day 21, which were increased more than 4- and 3-fold respectively. Conclusion Human bone marrow-derived MSCs could exhibit the sequential expression pattern of osteoblast marker genes during osteogenic differentiation in vitro.

Gene expression profiles associated with osteoblasts differentiated from bone marrow stromal cells

Objective:To study the changes of gene expression profiles associated with osteoblasts differentiated from rat bone marrow stromal cells in vitro by gene chip technique.Methods:rat Rone marrow stromal cells were isolated and cultured,and differentiation was induced by dexamethasone,β-glycerol phosphate and vitamin C.Cellular mRNA was extracted and reverse transcribed into cDNA,thus related genes expression differences were detected by gene expression profile chip.Results:Calcifying nodules were visible in the induced cells.There were27.7%genes expressed differentially,three times more than the normal and induced cells,and some genes were related to transcription,translation,glycosylation modification.Extracellular matrix,signal molecules and metabolism were up—regulated.Conclusions:The gene chip technique can be used to detect the multi-gene different expression in the differentiationinduceed rat BMSCs,and these differentially expressed genes are necessary genes related to rat BMSCs proliferation and induction of osteoblastic differentiation.

Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes

The biological function of the novel zinc-finger SWIM domain-containing protein family(ZSWIM)during embryonic development remains elusive.Here,we conducted a genome-wide analysis to explore the evolutionary processes of the ZSWIM gene family members in mice,Xenopus tropicalis,zebrafish,and humans.We identified nine putative ZSWIM genes in the human and mouse genome,eight in the Xenopus genome,and five in the zebrafish genome.Based on multiple sequence alignment,three members,ZSWIM5,ZSWIM6,and ZSWIM8,demonstrated the highest homology across all four species.Using available RNA sequencing(RNAseq)data,ZSWIM genes were found to be widely expressed across different tissues,with distinct tissuespecific properties.To identify the functions of the ZSWIM protein family during embryogenesis,we examined temporal and spatial expression patterns of zswim family genes in Xenopus embryos.Quantitative real-time polymerase chain reaction(qRT-PCR)revealed that each member had a distinct expression profile.Whole-mount in situ hybridization showed that both zswim1 and zswim3 were maternally expressed genes;zswim5 and zswim6were expressed throughout embryogenesis and displayed dynamic expression in the brain,eyes,somite,and bronchial arch at the late tailbud stages;zswim7 was detected in the eye area;zswim8 showed a dynamic expression pattern during the tailbud stages,with expression detected in the brain,eyes,and somite;zswim9 was faintly expressed throughout embryonic development.This study provides a foundation for future research to delineate the functions of ZSWIM gene members.