Decoding exercise-induced atomic components and prognostic shifts in endometrial carcinoma through differentially expressed genes

Background:This study aimed to portray the atomic intelligence and prognostic implications of differentially expressed genes and their involvement in biological pathways in endometrial carcinoma,with a specific focus on the impacts of exercise on cancer.Methods:We utilized a multi-faceted approach,including volcano plots,Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses,Venn diagrams,protein-protein interaction networks,Kaplan-Meier survival analysis,Gene Set Variety Analysis,and single-cell transcriptomic analysis.Furthermore,we profiled tumor mutational scenes,assessed the prognostic value of immune-related features,and conducted a comprehensive examination of genetic variations and their impact on tumor mutational burden across different cancer types.Multidimensional genomic interactions and methylation elements were also investigated.Using real-time quantitative PCR and immunofluorescence staining,the effects of B-cell lymphoma 2(BCL2)silencing on TNF-αand caspase-3 gene expression were evaluated.Results:Our study identified a noteworthy number of differentially expressed genes in endometrial carcinoma with potential links to athletic performance traits.BCL2 expression levels were found to be associated with survival outcomes,and its changeability across cancers was related to immune cell infiltration and immune checkpoint gene expression.Single-cell investigations uncovered cellular complexity within tumor microenvironments and critical biological pathways in BCL2-overexpressing cells.The expression flow and mutational effect of BCL2 in endometrial carcinoma were characterized,and the prognostic implications of immune-related features were assessed.Hereditary variations,including copy number variations and their relationship with gene expression and tumor mutational burden,were investigated.Multidimensional genomic transaction highlighted the essential role of regulatory genes in cancer pathogenesis.Silencing of the BCL2 gene significantly inhibited the proliferation of HEC-108 cells and promoted apoptosis,as evidenced by decreased TNF-αgene expression and increased caspase-3 gene expression.Immunofluorescence staining further confirmed these results.Conclusion:This study gives a point-by-point understanding of the atomic intelligence and prognostic implications in endometrial carcinoma and across various other cancers.BCL2’s role as a modulatory factor within the tumor-resistant environment and its potential impact on disease prognosis and response to immunotherapy were underscored.The multidimensional genomic analysis provides insights into the complex interaction between genetic and epigenetic variables in cancer,which may shed light on future therapeutic strategies.This study indicates that silencing the BCL2 gene can significantly inhibit tumor cell proliferation and promote apoptosis through the regulation of the TNF-αand caspase-3 pathways.

Effects of Mycobacterium vaccae vaccine in a mouse model of tuberculosis: protective action and differentially expressed genes

Background:Tuberculosis is a leading cause of death worldwide.BCG is an effective vaccine,but not widely used in many parts of the world due to a variety of issues.Mycobacterium vaccae(M.vaccae)is another vaccine used in human subjects to prevent tuberculosis.In the current study,we investigated the potential mechanisms of M.vaccae vaccination by determining differentially expressed genes in mice infected with M.tuberculosis before and after M.vaccae vaccination.Methods:Three days after exposure to M.tuberculosis H37 Rv strain(5×10~5 CFU),adult BALB/c mice randomly received either M.vaccae vaccine(22.5μg)or vehicle via intramuscular injection(n=8).Booster immunization was conducted 14 and 28 days after the primary immunization.Differentially expressed genes were identified by microarray followed by standard bioinformatics analysis.Results:M.vaccae vaccination provided protection against M.tuberculosis infection(most prominent in the lungs).We identified 2,326 upregulated and 2,221 downregulated genes in vaccinated mice.These changes could be mapped to a total of 123 signaling pathways(68 upregulated and 55 downregulated).Further analysis pinpointed to the MyD88-dependent TLR signaling pathway and PI3 K-Akt signaling pathway as most likely to be functional.Conclusions:M.vaccae vaccine provided good protection in mice against M.tuberculosis infection,via a highly complex set of molecular changes.Our findings may provide clue to guide development of more effective vaccine against tuberculosis.

Identification of Differentially Expressed Genes Associated with Cotton Fiber Development in a Chromosomal Substitution Line(CS-B22sh)

One of the impediments in the genetic improvement of cotton fiber is the paucity of information about genes associated with fiber development.Availability of chromosome arm substitution line CS-

A comparative analysis of differentially expressed genes in rostral and caudal regions after spinal cord injury in rats

The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular and biological process alterations that occur after SCI for therapy development.The differences between the rostral and caudal regions around an SCI lesion have received little attention.Here,we analyzed the differentially expressed genes between rostral and caudal sites after injury to determine the biological processes in these two segments after SCI.We identified a set of differentially expressed genes,including Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1,between rostral and caudal regions at different time points following SCI.Functional enrichment analysis indicated that these genes were involved in response to mechanical stimulus,blood vessel development,and brain development.We then chose Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1 for quantitative real-time PCR and Fn1 for immunostaining validation.Our results indicate alterations in different biological events enriched in the rostral and caudal lesion areas,providing new insights into the pathology of SCI.

Muscle Biological Characteristics of Differentially Expressed Genes in Wujin and Landrace Pigs

The biological chemistry would be responsible for the meat quality. This study tried to investigate the transcript expression profile and explain the characteristics of differentially expressed genes between the Wujin and Landrace pigs. The results showed that 526 differentially expressed genes were found by comparing the transcript expression profile of muscle tissue between Wujin and Landrace pigs. Among them, 335 genes showed up-regulations and 191 genes showed down-regulations in Wujin pigs compared with the Landrace pigs. Gene ontology （GO） analysis indicated that the differentially expressed genes were clustered into three groups involving in protein synthesis, energy metabolism and immune response. Kyoto encyclopedia of genes and genomes （KEGG） pathway analysis found that these differentially expressed genes participated in protein synthesis metabolism, energy metabolism and immune response pathway. The Database for Annotation, Visualization and Integrated Discovery （DAVID） analysis of protein function and protein domains function also confirmed that differentially expressed genes belonged to protein synthesis, energy metabolism and immune response. Genes related protein synthesis metabolism pathway in Landrace was higher than in Wujin pigs. However, differentially expressed genes related energy metabolism and immune response was up-regulated in Wujin pigs compared with Landrace pigs. Quantitative real-time RT-PCR on selected genes was used to confirm the results from the microarray. These suggested that the genes related to protein synthesis, energy metabolism and immune response would contribute to the growth performance, meat quality as well as anti-disease capacity.

Analysis on differentially expressed genes in watermelon rind color based on RNA–Seq

In order to screen the genes controlling watermelon rind color and luster, the experiment was carried out with yellow watermelon skin mutants as tester and green wild type watermelon as control, and transcriptome sequencing and bioinformatics analysis were done. The results show that 34.27 Gb clean data were got by transcriptome sequencing. There are 261 differentially expressed genes among Y_1_vs_G_1, Y_2_vs_G_2 and Y_3_vs_G_3. The pathways contenting most differentially expressed genes are plant hormone signal transduction pathway, phenylpropanoid biosynthesis pathway, photosynthesis pathway, starch and sucrose metabolism pathway. 9-cis-epoxycarotenoid dioxygenase(Cla002942), alcohol dehydrogenase(Cla004992), photosystem Ⅰ reaction center subunit Ⅲ, chloroplastic(precursor)(Cla009181), long-chain acyl coenzyme A synthetase(Cla017341), threonine dehydratase biosynthetic(Cla018352) candidates genes were screened out.

Analysis of differentially expressed genes in Verruca vulgaris vs.adjacent normal skin by RNA-sequencing

Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca vulgaris in the Chinese population.This study aimed to obtain comprehensive transcript information of verruca vulgaris by RNA sequencing.Methods:High-throughput sequencing was performed on three fresh verruca vulgaris samples and adjacent normal skin on the Illumina sequencing platform.The transcriptomes were analyzed using bioinformatics and the differentially expressed genes(DEGs)were verified by immunohistochemistry.Verruca vulgaris exhibited a unique molecular signature.Results:In total,1,643 DEGs were identified in verruca vulgaris compared to normal skin.The functions of the DEGs were studies by Gene Ontology(GO)enrichment,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis,DEGs Reactome analysis,disease annotation function,and STRING protein-protein interaction(PPI)network analysis.The results revealed 595 GO terms associated with the cell cycle,signal transduction,immune system,signaling molecules,and interaction.The Reactome analysis revealed enrichment in reversible hydration of carbon dioxide and BMP signaling,while the disease annotation function revealed that the enriched DEGs are involved in keratosis disorders.The STRING PPI network showed that the edges with the highest density mainly included the 2′-5′oligoadenylate synthase(OAS)family-related proteins.Furthermore,the M-code analysis found ISG15,IRF7,and OASL were scored as significant modules and their high expression compared to the control was verified by immunohistochemistry.Conclusion:These findings contribute to the genetic information of verruca vulgaris in the Chinese population,revealing that interferon-stimulated genes may play essential roles in verruca vulgaris.

ANALYSES ON DIFFERENTIALLY EXPRESSED GENES ASSOCIATED WITH HUMAN BREAST CANCER

Objective： To investigate the molecular etiology of breast cancer by way of studying the differential expression and initial function of the related genes in the occurrence and development of breast cancer. Methods： Two hundred and eighty-eight human tumor related genes were chosen for preparation of the oligochips probe, mRNA was extracted from 16 breast cancer tissues and the corresponding normal breast tissues, and cDNA probe was prepared through reverse-transcription and hybridized with the gene chip. A laser focused fluorescent scanner was used to scan the chip.The different gene expressions were thereafter automatically compared and analyzed between the two sample groups. Cy3/Cy5〉3.5 meant significant up-regulation. Cy3/Cy5〈0.25 meant significant down-regulation. Results： The comparison between the breast cancer tissues and their corresponding normal tissues showed that 84 genes had differential expression in the Chip. Among the differently expressed genes, there were 4 genes with significant down-regulation and 6 with significant up-regulation. Compared with normal breast tissues, differentially expressed genes did partially exist in the breast cancer tissues. Conclusion： Changes in multi-gene expression regulations take place during the occurrence and development of breast cancer; and the research on related genes can help understanding the mechanism of tumor occurrence.

Identification and analysis of differentially expressed genes involved in dark-induced photoperiod response and senescence of soybean leaves by suppression subtractive hybridization

A cDNA subtractive library enriched for dark-induced up-regulated ESTs was constructed by suppression subtractive hybridization(SSH) from leaf tissues of soybean cultivar DongNong L13 treated with short-day(8-h light/16-h dark) and long-day(16-h light/8-h dark) conditions.A total of 148 clones were sequenced,representing 76 unique ESTs which corresponded to about 20% of 738 clones from the cDNA library and showed a significant up-regulation of at least three fold verified by dot blot hybridization.The putative functions of ESTs were predicted by Blastn and Blastx.The 43 differentially expressed genes identified by subtractions were classified according to their putative functions generated by Blast analysis.Genetic functional analysis indicated that putative proteins encoded by these genes were related to diverse functions during organism development,which include biological regulation pathways such as transcription,signal transduction and programmed cell death,protein,nucleic acid and carbohydrate macromolecule degradation,the cell wall modification,primary and secondary metabolism and stress response.Two soybean transcription factors enhanced in SD conditions,GAMYB-binding protein and DNA binding protein RAV cDNAs that may be involved in SD soybean photoperiod response,had been isolated using 5'-and 3'-rapid amplification of cDNA ends(RACE)(Genbank Accession numbers DQ112540 and DQ147914).

Identification of overlapping differentially expressed genes in hepatocellular carcinoma,breast cancer,and depression by bioinformatics analysis

Objective:This study aimed to determine the presence of statistically significant relationships between these factors using bioinformatics analysis to identify overlapping differentially expressed genes(DEGs).Methods:The expression microarray data of GSE19665,GSE65194 and GSE12654 were obtained by GEO2R.Then,the overlapping DEGs of hepatocellular carcinoma(HCC),breast cancer(BC)and depression were analyzed by Gene Ontology,Kyoto Encyclopedia of Genes and Genomes and protein-protein interaction networks.Finally,the protein-protein interaction network was constructed by STRING and DEGs were sorted by Cytoscape.Results:The results indicated that multiple genes,including RNA-binding protein with multiple splicing,GATA binding protein 6,angiotensin II receptor type 1,ETS variant 6,TNF receptor superfamily member 17,aurora kinase A,integrin subunit alpha 6 and fibrinogen-like protein 2 might be common factors related to HCC,BC and depression.Conclusion:These results indicate that the genetic profile of HCC,BC and depression,may yield valuable insights for our understanding of the underlying mechanisms underlying synergistic genetic regulation and may provide novel ideas for developing homeopathic therapies based on bioinformatics data.

Effects of β-catenin on Differentially Expressed Genes in Multiple Myeloma

Summary： This study aimed to identify the differentially expressed genes after silencing of β-catenin in multiple myeloma transduced with β-catenin shRNA. The DNA microarray dataset GSE17385 was downloaded from Gene Expression Omnibus, including 3 samples of MM1.S （human multiple mye- loma cell lines） cells transduced with control shRNA and 3 samples of MM1.S cells transduced with β-catenin shRNA. Then the differentially expressed genes （DEGs） were screened by using Limma. Their underlying functions were analyzed by employing Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. Moreover, DEGs annotation was conducted based on the databases of tumor associated genes, tumor suppressed genes and the transcriptional regulation from patterns to profiles. Furthermore, the protein-protein interaction （PPI） relationship was obtained from STRING and the protein-protein interaction network and the functional modules were visual- ized by Cytoscape. Then, the pathway enrichment for the DEGs in the functional module was per- formed. A total of 301 DEGs, including 124 up-regulated and 117 down-regulated DEGs, were screened. Functional enrichment showed that CCNB1 and CDK1 were significantly related to the function of cell proliferation. FOS and JUN were related to innate immune response-activating signal transduction. Pathway enrichment analysis indicated that CCNB 1 and CDK1 were most significantly enriched in the pathway of cell cycle. Besides, FOS and JUN were significantly enriched in the Toll-like receptor signaling pathway. FOXM1 was identified as a transcription factor. Moreover, there existed interactions among CCNB1, FOXM1 and CDK1 in PPI network. The expression of FOS, JUN, CCNB1, FOXM1 and CDK1 may be affected by β-catenin in multiple myeloma.

Identification of overlay differentially expressed genes in both rats and goats with blast lung injury through comparative transcriptomics

Purpose:To identify the potential target genes of blast lung injury(BLI)for the diagnosis and treatment.Methods:This is an experimental study.The BLI models in rats and goats were established by conducting a fuel-air explosive power test in an unobstructed environment,which was subsequently validated through hematoxylin-eosin staining.Transcriptome sequencing was performed on lung tissues from both goats and rats.Differentially expressed genes were identified using the criteria ofq≤0.05 and|log2 fold change|≥1.Following that,enrichment analyses were conducted for gene ontology and the Kyoto Encyclopedia of Genes and Genomes pathways.The potential target genes were further confirmed through quantitative real-time polymerase chain reaction and enzyme linked immunosorbent assay.Results:Observations through microscopy unveiled the presence of reddish edema fluid,erythrocytes,and instances of focal or patchy bleeding within the alveolar cavity.Transcriptome sequencing analysis identified a total of 83 differentially expressed genes in both rats and goats.Notably,49 genes exhibited a consistent expression pattern,with 38 genes displaying up-regulation and 11 genes demonstrating down-regulation.Enrichment analysis highlighted the potential involvement of the interleukin-17 signaling pathway and vascular smooth muscle contraction pathway in the underlying mechanism of BLI.Furthermore,the experimental findings in both goats and rats demonstrated a strong association between BLI and several key genes,including anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4,which exhibited up-regulation.Conclusions:Anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4 hold potential as target genes for the prognosis,diagnosis,and treatment of BLI.

Identification and Cloning of Differentially Expressed Genes Involved in the Interaction Between Potato and Phytophthora infestans using a Subtractive Hybridization and cDNA-AFLP Combinational Approach

Using a subtractive hybridization （SH）/cDNA-AFLP combinational approach, differentially expressed genes involved in the potato-Phytophthora infestans interaction were identified. These included genes potentially controlling pathogenesis or avr genes in P. infestans as well as those potentially involved in potato resistance or susceptibility to this pathogen. Forty-one differentially expressed transcript, derived fragments （TDFs）, resulting from the interaction, were cloned and sequenced. Two TDFs, suggested as potential pathogenicity factors, have sequence similarity to N-succinyl diaminopimelate aminotransferase and a transcriptional regulator, TetR family gene, respectively. Two other TDFs, suggested as potential avr genes, have sequence similarity to an EST sequence from Avr41Cf.41Avr91Cf- 9 and a P. infestans avirulence-associated gene, respectively. Genes＇ expression and origin were confirmed using Southern blots, Northern blots and qRT-PCR, he., potential resistance gene DL81 was induced at 12 hpi in the moderately resistant cultivar, whereas it was down-regulated as early as 6 hpi in the susceptible cultivar. On the other hand, DL21 was induced at 6 hpi （3.38-fold） in response to the highly aggressive isolate （US8） and strongly up-regulated thereafter （25.13-fold at 120 hpi.）, whereas it was only slightly up-regulated in response to the weakly aggressive isolate US11 （3.82-fold at 96 hpi）, suggesting its potential involvement as a susceptibility gene.

Identification of differentially expressed mRNAs as novel predictive biomarkers for gastric cancer diagnosis and prognosis

BACKGROUND Gastric cancer(GC)has a high mortality rate worldwide.Despite significant progress in GC diagnosis and treatment,the prognosis for affected patients still remains unfavorable.AIM To identify important candidate genes related to the development of GC and iden-tify potential pathogenic mechanisms through comprehensive bioinformatics analysis.METHODS The Gene Expression Omnibus database was used to obtain the GSE183136 dataset,which includes a total of 135 GC samples.The limma package in R software was employed to identify differentially expressed genes(DEGs).Thereafter,enrichment analyses of Gene Ontology(GO)terms and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways were performed for the gene modules using the clusterProfile package in R software.The protein-protein interaction(PPI)networks of target genes were constructed using STRING and visualized by Cytoscape software.The common hub genes that emerged in the cohort of DEGs that was retrieved from the GEPIA database were then screened using a Venn Diagram.The expression levels of these overlapping genes in stomach adenocarcinoma samples and non-tumor samples and their association with prognosis in GC patients were also obtained from the GEPIA database and Kaplan-Meier curves.Moreover,real-time quantitative polymerase chain reaction(RT-qPCR)and western blotting were performed to determine the mRNA and protein levels of glutamic-pyruvic transaminase(GPT)in GC and normal immortalized cell lines.In addition,cell viability,cell cycle distribution,migration and invasion were evaluated by cell counting kit-8,flow cytometry and transwell assays.Furthermore,we also conducted a retrospective analysis on 70 GC patients diagnosed and surgically treated in Wenzhou Central Hospital,Dingli Clinical College of Wenzhou Medical University,The Second Affiliated Hospital of Shanghai University between January 2017 to December 2020.The tumor and adjacent normal samples were collected from the patients to determine the potential association between the expression level of GPT and the clinical as well as pathological features of GC patients.RESULTS We selected 19214 genes from the GSE183136 dataset,among which there were 250 downregulated genes and 401 upregulated genes in the tumor samples of stage III-IV in comparison to those in tumor samples of stage I-II with a P-value<0.05.In addition,GO and KEGG results revealed that the various upregulated DEGs were mainly enriched in plasma membrane and neuroactive ligand-receptor interaction,whereas the downregulated DEGs were primarily enriched in cytosol and pancreatic secretion,vascular smooth muscle contraction and biosynthesis of the different cofactors.Furthermore,PPI networks were constructed based on the various upregulated and downregulated genes,and there were a total 15 upregulated and 10 downregulated hub genes.After a comprehensive analysis,several hub genes,including runt-related transcription factor 2(RUNX2),salmonella pathogenicity island 1(SPI1),lysyl oxidase(LOX),fibrillin 1(FBN1)and GPT,displayed prognostic values.Interestingly,it was observed that GPT was downregulated in GC cells and its upregulation could suppress the malignant phenotypes of GC cells.Furthermore,the expression level of GPT was found to be associated with age,lymph node metastasis,pathological staging and distant metastasis(P<0.05).CONCLUSION RUNX2,SPI1,LOX,FBN1 and GPT were identified key hub genes in GC by bioinformatics analysis.GPT was significantly associated with the prognosis of GC,and its upregulation can effectively inhibit the proliferative,migrative and invasive capabilities of GC cells.

RNA-seq profiling reveals differentially expressed genes as potential markers for vital reaction in skin contusion: a pilot study

Detection of the vitality of wounds is essential in forensic practice.The present study used Illumina RNA-seq technology to determine gene expression profiles in contused mouse skin.In obtained high quality sequencing reads,the reads were mapped onto a reference transcriptome (Mus_musculus.GRCm38.83).The results revealed that there were 659 upregulated and 996 down-regulated differentially expressed genes (DEGs) in contused mouse skin.The DEGs were further analyzed using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases.Genes from different functional categories and signalling pathways were enriched,including the immune system process,immune response,defense response,cytokine-cytokine receptor interaction,complement and coagulation cascades and chemokine signalling pathway.Expression patterns of 11 DEGs were verified by RT-qPCR in mice skins.In addition,alterations of five DEGs were also analyzed in postmortem human wound samples.The results were in concordance with the results of RNA-seq.These findings suggest that RNA-seq is a powerful tool to reveal DEGs as potential markers for vital reaction in terms of forensic practices.

Identification and prioritization of differentially expressed genes for time-series gene expression data

Identification of differentially expressed genes （DEGs） in time course studies is very useful for understanding gene function, and can help determine key genes during specific stages of plant development. A few existing methods focus on the detection of DEGs within a single biological group, enabling to study temporal changes in gene expression. To utilize a rapidly increasing amount of single-group time-series expression data, we propose a two-step method that integrates the temporal characteristics of time-series data to obtain a B-spline curve fit. Firstly, a fiat gene filter based on the Ljung-Box test is used to filter out flat genes. Then, a B-spline model is used to identify DEGs. For use in biological experiments, these DEGs should be screened, to determine their biological importance. To identify high-confidence promising DEGs for specific biological processes, we propose a novel gene prioritization approach based on the partner evaluation principle. This novel gene prioritization ap- proach utilizes existing co-expression information to rank DEGs that are likely to be involved in a specific biological process/condition. The proposed method is validated on the Arabidopsis thaliana seed germination dataset and on the rice anther development expression dataset.

Differentially expressed genes identified by cross-species microarray in the blind cavefish Astyanax

Changes in gene expression were examined by microarray analysis during development of the eyed surface dwelling(surface fish)and blind cave-dwelling(cavefish)forms of the teleost Astyanax mexicanus De Filippi,1853.The cross-species microarray used surface and cavefish RNA hybridized to a DNA chip prepared from a closely related species,the zebrafish Danio rerio Hamilton,1822.We identified a total of 67 differentially ex-pressed probe sets at three days post-fertilization:six upregulated and 61 downregulated in cavefish relative to surface fish.Many of these genes function either in eye development and/or maintenance,or in programmed cell death.The upregulated probe set showing the highest mean fold change was similar to the human ubiquitin specific protease 53 gene.The downregulated probe sets showing some of the highest fold changes corresponded to genes with roles in eye development,including those encoding gamma crystallins,the guanine nucleotide binding pro-teins Gnat1 and Gant2,a BarH-like homeodomain transcription factor,and rhodopsin.Downregulation of gam-ma-crystallin and rhodopsin was confirmed by in situ hybridization and immunostaining with specific antibodies.Additional downregulated genes encode molecules that inhibit or activate programmed cell death.The results suggest that cross-species microarray can be used for identifying differentially expressed genes in cavefish,that many of these genes might be involved in eye degeneration via apoptotic processes,and that more genes are downregulated than upregulated in cavefish,consistent with the predominance of morphological losses over gains during regressive evolution.

Differentially Expressed Genes Associated with Primordial Follicle Formation and Transformation to Primary Follicles

Objective: Primordial follicle assembly and the transition from primordial follicle to primary follicle are critical processes in ovarian biology.These processes determine the size of the primordial follicle pool, which may limit the reproductive lifespan of a female. When the follicle pool is depleted, reproduction ceases and females enter menopause. In this study, we aimed to explore the role of differentially expressed genes(DEGs) in the processes of primordial follicle assembly and the transformation from primordial to primary follicle.Methods: The gene chip GSE9300 was downloaded from the Gene Expression Omnibus database. DEGs between ovaries on postnatal day0 and ovaries on postnatal day 4, as well as ovaries on postnatal day 4 and ovaries cultured for 7 days from postnatal day 0 were identified.Gene ontology(GO), pathway enrichment analysis, and protein-protein interaction network construction were performed.Results: In total, 99 upregulated genes and 123 downregulated genes were identified in the process of primordial follicle assembly, and 101 upregulated genes and 98 downregulated genes were identified in the process of transformation from primordial to primary follicle. The GO analysis showed that response to estradiol was associated with two of the processes of assembly and subsequent development of primordial follicle, but the genes involved in response to estradiol between the two processes were significantly different. Furthermore, the two groups of DEGs were all associated with metabolic pathways.Conclusions: DEGs may provide new insights into the exploration of mechanisms related to primordial follicle assembly and subsequent development.

Screening of differentially expressed genes in the hypothalamus of a rat neuropathic pain model following sciatic nerve injury

Background Neuropathic pain is induced by injury or disease of the nervous system. Most studies have so far focused only on a few known molecules and signaling pathways among neurons. However, all signal transmissions involved in neuropathic pain appear to be an integral system at different molecular levels. This study was designed to screen the differentially expressed genes of the hypothalamus in chronic constriction injury （CCI） rats and analyze their functions in developing neuropathic pain. Methods Ten adult female Sprague-Dawley rats （（200±10） g） were used in experimental group and sham group （n=-5 in each group）. Mechanical allodynia tests were performed to ensure that the CCI rat model was constructed successfully. Total hypothalamus RNAs were isolated from each group. Forward suppression subtractive hybridization （SSH） library of rat hypothalamus was constructed and up-regulated cDNA clones at neuropathic pain states were obtained via suppressed subtractive hybridization technique and the functions of these genes were analyzed bioinformatically. Results Mechanical allodynia tests showed that the experimental rats had a significantly reduced mechanical allodynia threshold 3 to 13 days after CCI vs sham surgery rats （P 〈0.01）, indicating that the model was successful. Forward SSH library of the rat hypothalamus was constructed successfully and 26 over-expressed expression sequence tags （ESTs） were obtained from these up-regulated cDNA clones. Conclusion Twenty-six up-regulated genes, involved in the regulation of cell cycle and apoptosis, signal transduction, and neuroprotection, may play key roles in decreasing mechanical withdraw thresholds in CCI rats, which implicates a multidimensional and integrated molecular mechanism at gene level in developing neuropathic pain with the supraspinal contributions.

Analysis of Growth Characteristics and Differentially Expressed Homologous Genes in Rhodobacter sphaeroides under Normal and Simulated Microgravity Conditions

The term “microgravity” is used to describe the “weightlessness” or “zero-g” circumstances that can only be found in space beyond earth’s atmosphere. Rhodobacter sphaeroides is a gram-negative purple phototroph, used as a model organism for this study due to its genomic complexity and metabolic versatility. Its genome has been completely sequenced, and profiles of the differential gene expression under aerobic, semi-aerobic, and photosynthetic conditions were examined. In this study, we hypothesized that R. sphaeroides will show altered growth characteristics, morphological properties, and gene expression patterns when grown under simulated microgravity. To test that, we measured the optical density and colony-forming units of cell cultures grown under both microgravity and normal gravity conditions. Differences in the cell morphology were observed using scanning electron microscopy (SEM) images by measuring the length and the surface area of the cells under both conditions. Furthermore, we also identified homologous genes of R. spheroides using the differential gene expression study of Acidovorax under microgravity in our laboratory. Growth kinetics results showed that R. sphaeroides cells grown under microgravity experience a shorter log phase and early stationary phase compared to the cells growing under normal gravity conditions. The length and surface area of the cells under microgravity were significantly higher confirming that bacterial cells experience altered morphological features when grown under microgravity conditions. Differentially expressed homologous gene analysis indicated that genes coding for several COG and GO functions, such as metabolism, signal-transduction, transcription, translation, chemotaxis, and cell motility are differentially expressed to adapt and survive microgravity.