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At least 343 records · Page 19Linked to original sources
PubMed2006

Comprehensive analysis of differential gene expression profiles on D-galactosamine-induced acute mouse liver injury and regeneration.

Microarray analysis of RNA from d-galactosamine (GalN)-administered mouse livers was performed to establish a global gene expression profile during injury and regeneration stages at two different doses. A single dose of GalN at 266 or 26.6 mg/kg body weight was given intraperitoneally, and the liver samples were obtained after 6, 24, and 72 h. Histopathologic studies enabled the classification of the D-galactosamine effect into injury (6, 24 h) and regeneration (72 h) stages. By using the Applied Biosystems mouse genome survey microarray, a total of 7267 out of 33,315 (21.8%) genes were found to be statistically reliable at p<0.05 by two-way ANOVA, and 1469 (4.4%) probes at false discovery rate <5% by significance analysis of microarray. Among the statistically reliable clones by both analytical methods, 389 genes were differentially expressed when compared with non-treated control, with more than a 1.625-fold difference (which equals 0.7 in log(2) scale) at one or more GalN treatment conditions and with less than 1.625-fold difference at all three vehicle-treated conditions. Three hundred thirty six genes and 13 genes were identified as injury- and regeneration-specific genes, respectively, showing that most of the transcriptomic changes were seen during the injury stage. Furthermore, multiple genes involved in protein synthesis and degradation, mRNA processing and binding, and cell cycle regulation showed variable transcript levels upon acute GalN administration.

Acute Disease↗
PubMedDate not supplied

Molecular and cellular mechanisms of leukemic hemopoietic cell differentiation: an analysis of the Friend system.

Murine erythroleukemia (MEL or Friend) cells grown in culture and induced to differentiate into cells resembling orthochromatic normoblasts provide a suitable system for uncovering molecular and cellular mechanisms of hemopoiesis and for understanding globin gene regulation. Inducer-treated cells undergo an irreversible commitment to maturation and accumulate large amounts of hemoglobin. Clonal analysis of commitment of individual cells combined with biochemical measurements has revealed that MEL cell differentiation is a highly coordinated set of events (program) leading to the differentiated erythroid state. The developmental program of MEL cells consists of early and late processes. The early events appear to be membrane-mediated processes which operate independently of each other and lead to commitment to terminal maturation and hemoglobin synthesis. Inducer-treated cells express an ability to remember ("memory response") previous exposure to inducer and to continue their differentiation after discontinuous exposure to inducer; expression of "memory response" occurs early in differentiation and affects both the initiation of commitment and accumulation of globin mRNA in a similar manner in inducer-treated cells. Commitment to maturation appears to be the central process responsible for determining the pattern of gene expression, limitation of proliferative activity and nuclear condensation. Commitment, however, can occur independently of hemoglobin synthesis. Although initiation of commitment is associated with early membrane-mediated events (e.g., ion-transport), maintenance and completion of maturation erythroid state is a result of a number of cellular processes. These processes are discussed in relation to the molecular and cellular mechanisms of initiation and completion of MEL cell differentiation. The role of the MEL system as a model for studying mouse and human globin gene regulation is presented.

Animals↗
PubMed2002

Differential proteomic analysis of Bacillus subtilis nitrate respiration and fermentation in defined medium.

A comparative investigation of protein expression by two-dimensional gel electrophoresis was conducted between Bacillus subtilis cultures grown in defined medium under aerobic, anaerobic nitrate respiration, or fermentation conditions. Defined medium specific for either nitrate respiration or fermentation allowed distinction between proteins induced by each individual growth process. Our differential protein profiling analysis between aerobic and anaerobic conditions showed that anaerobic fermentation induced at least 44 proteins and nitrate respiration induced at least 19 proteins compared to aerobic controls. Certain proteins were specifically induced during nitrate respiration or fermentation, while others were induced by both anaerobic processes. Eleven proteins induced by nitrate respiration and/or fermentation were identified by peptide mass matching using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Proteins encoded by feuA, hmp, and ytkD were induced by nitrate respiration. Proteins encoded by pyrR, sucD, trpC, and ywjH were induced by fermentation. Proteins encoded by acuB, pdhC, ydjL, and yvyD were induced by nitrate respiration and fermentation. This proteomic analysis has provided a more complete characterization of B. subtilis anaerobic growth and increased our understanding of its metabolic pathways of nitrate respiration and fermentation.

Bacillus subtilis↗
PubMed1991

Multiple regression analysis of differential response to treatment in randomized controlled clinical trials.

A multiple regression model is presented for the analysis of the components of individual change in clinical trials. Of primary interest is the condition where treatment effects vary according to patient baseline level. The model differentiates the average effects of treatment from baseline-dependent treatment effects, as well as identifying regression toward the mean and temporal effects. This model is applied in the analysis of data from a clinical trial of nutritional supplementation.

Calcium↗
PubMed2024

Transcriptome analysis reveals that PRV XJ delgE/gI/TK protects against intestinal damage in nose-dropping-infected mice by regulating ECM-ITGA/ITGB-P-FAK.

Pseudorabies virus (PRV) is an ideal model for mechanistic investigations into &#x3b1;-herpesvirus. The neurotropism and latent infection of PRV have been extensively studied. Apart from neurological symptoms, diarrhea caused by PRV infection is also an essential cause of mortality in newborn and weaned piglets. However, little research has been done on PRV invasion of the gut. To fill this gap, a nasal drip PRV-infection mouse model was developed, consisting of three groups: the challenged group (Group A), the immunization-challenged group (Group B), and a mock group (Group C). The results showed that immunization with PRV XJ delgE/gI/TK successfully prevented intestinal damage caused by PRV drop-nose infection. Subsequently, intestines were collected for transcriptional analysis. Differentially expressed genes analysis revealed that PRV XJ delgE/gI/TK was effective in reducing the organismal intestinal transcriptional activity caused by PRV. The Group A vs Group C and Group A vs Group B had similar Kyoto Encyclopedia of Genes and Genomes (KEGG)-enriched signaling pathways and the differentially expressed genes were primarily enriched in pathways, such as cell adhesion molecules, focal adhesion kinase, and actin cytoskeleton regulation. Notably, transcriptome analysis indicated that genes associated with the focal adhesion kinase (FAK) signaling pathway (ECM-ITGA/ITGB-p-FAK) were significantly more highly expressed in Group A than in Group B and Group C. The results of quantitative real-time PCR (RT-qPCR) and western blotting were consistent with KEGG analysis. Therefore, we hypothesized that PRV promotes self-infection through activation of the ECM-ITGA/ITGB-p-FAK signaling pathway and that PRV XJ delgE/gI/TK immunization could attenuate the intestinal damage caused by PRV by inhibiting the activation of this pathway.IMPORTANCEPseudorabies virus (PRV) poses a significant threat to the swine industry and public health due to its ability to infect multiple species, including humans, leading to substantial economic losses and potential health risks. This study addresses a critical gap in understanding the impact of PRV infection on the gut, which has been less explored compared to its neurological effects. By developing a drip-nose PRV-infection mouse model, the research indicated that PRV might promote self-infection through activation of the ECM-ITGA/ITGB-p-FAK signaling pathway, and PRV XJ delgE/gI/TK immunization effectively prevents intestinal damage by significantly reducing the expression of genes in the ECM-ITGA/ITGB-p-FAK signaling pathway. The research has important implications for the swine industry and public health by contributing to the development of better vaccines and treatments, ultimately helping to control PRV and prevent its cross-species transmission.

Animals↗
PubMed1986

Platelet volume analysis for differential diagnosis of thrombocytosis.

The results of the Coulter counter S plus II platelet volume analysis were studied in 100 patients with reactive thrombocytosis (platelet count greater than 500 X 10(9)/l), in 30 patients with myeloproliferative thrombocytosis, and in 32 patients with chronic myeloproliferative disease and a platelet count less than 500 X 10(9)/l. Patients with reactive thrombocytosis had considerably lower mean platelet volumes than those with myeloproliferative thrombocytosis, or normal subjects. The opposite was true for the platelet distribution width. This index for platelet heterogeneity was normal in reactive, but increased in myeloproliferative thrombocytosis. There were no differences in mean platelet volume or platelet distribution width between patients with myeloproliferative disease and a high or normal platelet count. The increased platelet heterogeneity in myeloproliferative disease was caused by an increase of both small and large platelets. The platelet distribution width seemed to be the best variable for the differential diagnosis of thrombocytosis. A platelet distribution width greater than 17 was found in 26 of the 30 patients with myeloproliferative thrombocytosis but in only five of the 100 patients with reactive thrombocytosis. A normal platelet distribution width in a patient with a high platelet count strongly suggests reactive thrombocytosis.

Blood Platelets↗
PubMed2002

Microarray analysis of differentially expressed genes in placental tissue of pre-eclampsia: up-regulation of obesity-related genes.

Susceptibility genes present in both mother and fetus most likely contribute to the risk of pre-eclampsia. Placental biopsies were therefore investigated by high-density DNA microarray analysis to determine genes differentially regulated within chorionic villous tissue in pre-eclampsia and normal pregnancy. The pooled RNAs of pre-eclamptic and normotensive subjects were hybridized to the HuGeneFL array representing sequences from approximately 5600 full-length human cDNAs. The differentially expressed genes that were detected could be categorized into nine groups: adhesion molecules, obesity-related genes, transcription factors/signalling molecules, immunological factors, neuromediators, oncogenic factors, protease inhibitors, hormones and growth factor-binding proteins. Among those, the obesity-related genes included putative candidate genes associated with the pathogenesis of pre-eclampsia. One of the most up-regulated transcripts was the obese gene (43.6-fold change), and this was reflected by elevated leptin protein levels. In the case of feto-maternal contribution of polymorphic genes to pre-eclampsia, expression analysis of placental tissue has lead to numerous target genes waiting for large scale genetic linkage analyses.

Female↗
PubMed2004

Analysis of differential gene expression in the cochlea and kidney of mouse by cDNA microarrays.

Microarray hybridization analysis of gene expression in the cochlea and kidney suggest a relationship between these tissues at the genomic level, indicating the common gene expression, likely serving a common function in both the organs primarily maintaining ion transport, and implied previously from morphological, pharmaco-kinetic and teratogenic studies. The cDNAs of more than 100 genes listed on the hereditary hearing loss homepage were amplified as targets by RT-PCR and were hybridized with probes prepared from total RNA of the cochlea and the kidney. Thirteen of the genes analyzed showed altered fluorescence ratios of more than two logs. Of these, the expressions of 11 genes were over expressed and two were under expressed in the cochlea than in the kidney. Our data is the first report to corroborate the genomic similarities between these two important organs and may help to explain the somewhat similar response of these organs to certain therapeutic drugs.

Animals↗
PubMed2004

Comprehensive analysis of differential gene expression profiles on carbon tetrachloride-induced rat liver injury and regeneration.

Microarray analysis of RNA from carbon tetrachloride (CCl4)-administered rat livers was performed at various time points to establish a global gene expression profile during injury and regeneration stages. A single dose of 1 ml/kg of CCl4 was given by ip injection, and the liver samples were obtained after 6, 24, 48 h, and 2 weeks. Histopathologic, biochemical, and immunohistochemical studies enabled the classification of the CCl4 effect into injury (6 and 24 h) and regeneration (48 h and 2 weeks) stages. The expression levels of 5180 clones on a custom rat gene microarray were analyzed and 587 clones yielded changeable gene expression on at least single time point. One hundred seventy-nine clones were classified as injury-specific clones, while 38 clones as regeneration-specific clones. Characteristic gene expression profiles could be associated with CCl4-induced gene expression with the disruption of lipid metabolism, which is known to cause the fatty liver induced by CCl4 treatment. In addition, induction of the transcripts for many ribosomal proteins was detected during the injury stage, particularly at the 24-h time point, despite the previous report of decreased protein synthesis rate upon CCl4 treatment. Several genes with known functions were also identified as CCl4-regulated genes. In conclusion, we established a global gene expression profile utilizing microarray analysis in rat liver upon acute CCl4 administration with a full chronological profile that not only covers injury stage but also later points of regeneration stage.

Animals↗
PubMedDate not supplied

An analysis of differential epidural spinal anesthesia and pentothal pain study in the differential diagnosis of back pain. Aids in avoiding unnecessary back surgery.

The selection of the proper patient for back surgery is of prime importance and is the topic of this report. An analysis of patients evaluated with differential epidural spinal anesthesia and the Pentothal pain study show these tests to be helpful in separating those patients with primarily organic pain who could benefit from surgery from those patients with primarily functional pain who should not be operated upon. These tests will help one determine whether a disability is related to the severity of pain, to the patient's emotional response to pain, or to a somatic manifestation of a gross emotional breakdown.

Affective Symptoms↗
PubMed1997

[Differential display analysis of human fetal brain mRNAs and isolation of brain-specific novel ESTs].

Using the differential display technique (DDRT-PCR) originally developed by Liang and Pardee, we tried to isolate the stage-specific or tissue-specific genes in the developing human neural system (brain). With about fifty sets of arbitrary primers and anchored primers, DDRT-PCR was carried out to analyze the differentially expressed mRNAs between human fetal brains of different developmental stage or different parts of human fetal brain at the same developmental stage. About one hundred bands containing cDNA fragments of differential interest were cut out from the polyacrylamide gel, thirty-four of which were cloned and sequenced. They were accepted as novel cDNA sequences by GeneBank. In order to check the feasibility of DDRT-PCR, three of the thirty-four cDNA sequences were randomly chosen as probes for further analysis by dot blot RNA hybridization, and two proved to be specifically expressed in human brain.

Brain Chemistry↗
PubMed2000

Goodness-of-Fit Analysis of Radial Velocity Surveys.

Using eigenmode expansion of the Mark III and SFI surveys of cosmological radial velocities, a goodness-of-fit analysis is applied on a mode-by-mode basis. This differential analysis complements the Bayesian maximum likelihood analysis that finds the most probable model given the data. Analyzing the surveys with their corresponding most likely models from the CMB-like family of models, as well as with the currently popular LambdaCDM model, reveals a systematic inconsistency of the data with these "best" models. There is a systematic trend of the cumulative chi(2) to increase with the mode number (where the modes are sorted by decreasing order of the eigenvalues). This corresponds to a decrease of the chi(2) with the variance associated with a mode and hence with its effective scale. It follows that the differential analysis finds that on small (large) scales the global analysis of all the modes "puts" less (more) power than actually required by the data. This observed trend might indicate one of the following: (1) the theoretical model (i.e., power spectrum) or the error model (or both) have an excess of power on large scales, (2) velocity bias, or (3) the velocity data suffers from systematic errors that have not yet been corrected.

Journal Article↗
PubMed1999

The use of non-linear analysis for differentiating the biomagnetic activity in ovarian lesions.

In this study we investigated the biomagnetic activity measured with the superconducting quantum interference device (SQUID) in benign and malignant ovarian lesions using non-linear analysis. We used a single channel biomagnetometer SQUID in order to measure the magnetic field emitted from benign and malignant ovarian lesions. We can differentiate such biomagnetic activities using non-linear analysis. Using the application of non-linear analysis in the ovarian lesions together with the use of dimensional calculations we have observed a clear saturation value for the dimension of malignant ovarian lesions and non-saturation for benign ovarian lesions. The biomagnetic measurements with the SQUID and the application of non-linear analysis in benign and malignant ovarian lesions, is a promising procedure in assessing and differentiating ovarian tumours.

Journal Article↗
PubMed1999

cDNA representational difference analysis of differentially expressed cDNA sequences in human nasopharyngeal carcinoma.

OBJECTIVE: To search differentially expressed sequences correlated with pathogenesis of human nasopharyngeal carcinoma (NPC), including the candidates of tumor suppressor genes. METHODS: Representational difference analysis (RDA) was performed to isolate differentially expressed sequences between cDNA from normal human primary cultures of nasopharyngeal epithelial cells and cDNA from NPC cell line HNE1. The source of differentially expressed products were proved by Southern blot, Northern blot and in situ hybridization. The fragments were cloned with pGEM-T easy kit and sequenced by the chain termination reaction. RESULTS: Four differentially expressed cDNA fragments were isolated in the fourth subtractive hybridization using cDNA from normal human nasopharyngeal epithelial cells as tester amplicon and cDNA from NPC cell line HNE1 as driver amplicon by cDNA RDA. These differential cDNA fragments revealed that they really came from the tester amplicon and were not expressed or down-regulated in the NPC HNE1 cells. Some of the genes were expressed only in human nasopharyngeal epithelial cells but deleted or down-regulated in the biopsies of NPC. Of these obtained clones, some were the sequences of the human known genes including house-keeping genes, the others represented novel gene sequences. CONCLUSION: The differentially expressed products including the candidates of tumor-suppressor genes may be associated with the initiation of the NPC.

DNA, Complementary↗
PubMed1999

A novel strategy for identifying differential gene expression: An improved method of differential display analysis.

We propose a novel alternative approach, an advanced method for recently developed strategies, for identifying differentially expressed genes. Firstly, double-stranded cDNAs were digested using Sau3AI and the 3'-end restriction fragments of the cDNA were ligated to a double-stranded adapter. Next, the restriction fragments were directly amplified using several combinations of adapter-specific primers and FITC-labeled oligo dT primers. The selected cDNA fragments were displayed on a polyacrylamide gel. Neither nested PCR nor purification of 3'-end fragments are necessary. We examined the validity of this approach by evaluating gene expression changes during granulocytic differentiation of HL-60 cells. This method can theoretically detect almost all gene expression changes more rapidly and through simpler manipulations than by any other approach.

Cell Differentiation↗
PubMed2004

Differential proteomic analysis of human hepatocellular carcinoma cell line metastasis-associated proteins.

PURPOSE: The comparative study of differentially expression of protein profiles of hepatocellular carcinoma cell lines with various metastasic potential and screening key molecules related to hepatocellular carcinoma metastasis and recurrence. METHODS: Using two-dimensional electrophoresis and liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS), we analyzed differentially displayed proteomics of human hepatocellular carcinoma cell lines Hep3B, MHCC97L, MHCC97H with different metastasic potential. RESULTS: Approximate 1,000 protein spots were detected on silver-stained gel by ImageMaster (977+/-113 spots in Hep3B, 1092+/-40 in MHCC97L, and 889+/-14 in MHCC97H). Fifty distinct different protein spots were analyzed with online LC-ESI-MS/MS. Only 26 protein spots had a positive result, including annexin1, S100A4, and so on. In comparison with nonmetastasis Hep3B cell lines, there were 16 proteins overexpressed in MHCC97H and MHCC97L, 10 proteins underexpressed in MHCC97H and MHCC97L. Applying cell immunohistochemistry and RT-PCR, we further validated two interesting and different proteins, annexin1 and S100A4. CONCLUSION: The protein profile of metastatic hepatocellular carcinoma cell lines displayed obvious differences compared with non-metastatic liver cancer cell lines. The results imply that various different proteins may lead to HCC metastasis together.

Carcinoma, Hepatocellular↗
PubMed2006

Identification and analysis of differentially expressed cDNAs during nonself-competitive interaction between Phlebiopsis gigantea and Heterobasidion parviporum.

The molecular factors regulating interspecific interaction between the saprotrophic biocontrol fungus Phlebiopsis gigantea and the conifer pathogen Heterobasidion parviporum were investigated. We constructed cDNA libraries and used expressed sequence tag analysis for the identification and characterization of genes expressed during the self and nonself-hyphal interaction. cDNA clones from either the pathogen or biocontrol agent were arrayed on nylon membrane filters and differentially screened with cDNA probes made from mycelia forming the barrage zone during nonself-interactions, mycelia growing outside the barrage zones or monocultures. BlastX analysis of the differentially expressed clones led to the identification of genes with diverse functions, including those with potential as virulence factors, such as hydrophobins. Because of the high sequence conservation (r2 = 0.81) between P. gigantea and H. parviporum, a selected number of genes from either fungus were used to monitor the expression profile under varying interaction conditions by virtual northern blot. The results are discussed with respect to the potential role of the induced genes during the nonself-competitive interaction for space and nutrients between P. gigantea and H. parviporum.

Basidiomycota↗