Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “differential analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 577 records · Page 32Linked to original sources
PubMed2004

Microarray analysis of differentiation-specific gene expression during 3T3-L1 adipogenesis.

During cellular differentiation and development, it is recognized that many complex molecular mechanisms as well as precise patterns of differentially expressed genes occur in directing precursor cells toward a given lineage. Using microarray-based technology, we examined gene expression across the course of 3T3-L1 adipocyte differentiation. Total cellular RNA was isolated at times 0, 2, 8, 16, 24, 48, and 96 h following treatment with either standard hormonal inducers of differentiation; insulin, dexamethasone, isobutylmethylxanthine (IDX), or IDX plus trichostatin A (TsA), a histone deacetylase inhibitor and potent adipogenic inhibitor. cRNA was synthesized from cellular RNA and hybridized to high density Affymetrix MG_U74Av2 microarray gene chips containing 12,488 cDNA/Expressed Sequence Tags (ESTs) probe sets. From the IDX-only treated cells, all probe sets that were either unchanged or differentially expressed less than 2-fold throughout differentiation with respect to time 0 preadipocytes were excluded from further analyses. This selection resulted in a net of 1686 transcripts, 859 were increased in expression, and 827 were decreased in expression at least 2-fold across differentiation. To focus in on genes that were more specific to differentiation, the same analysis was performed on IDX plus TsA-treated non-differentiating cells and all probe sets from the IDX-only group that exhibited similar expression profiles in the non-differentiating TsA-treated group were excluded leaving a total of 1016 transcripts that were regulated only under differentiating conditions. Six hundred and thirty-six of these transcripts were elevated at least 2-fold and 380 exhibited a decrease in expression relative to time 0 preadipocytes. This group of genes was further analyzed using hierarchical clustering and self-organizing maps and resulted in the identification of numerous genes not previously known to be regulated during adipocyte differentiation. Many of these genes may well represent novel adipogenic mediators and markers of adipogenesis.

1-Methyl-3-isobutylxanthine↗
PubMed2006

Pharmacokinetic/pharmacodynamic insulin-glucose analysis for differentiation of beta-cell function: an 18 month follow-up study in pre-pubertal lean and obese children.

The objective of this study was to analyse the PK/PD of the insulin-glucose physiology for glucose stimulated insulin secretion from beta-cells between lean and obese pre-pubertal children in an 18 month study. The subjects were divided into two groups of six children according to their body mass index (BMI). Each subject was assessed on four occasions: on admission and at 6, 12 and 18 month follow-ups. Each time, 23 blood samples were obtained from the subjects according to the frequently sampled intravenous glucose tolerance test involving a bolus of 250 mg/kg dextrose. For the obese group, a significant difference (p <0.05) was found in the rate constant for the first phase secretion of insulin between the time of admission (1.73 +/- 0.372 min(-1)) and the 18 month follow-up (3.08 +/- 0.391 min(-1)). Additionally, the lean vs obese group comparisons showed a higher first phase insulin secretion rate constant (p <0.05) in the obese group on admission (1.73 +/- 0.372 vs 1.29 +/- 0.278 min(-1)), 6 months (1.96 +/- 0.317 vs 1.32 +/- 0.444 min(-1)), 12 months (2.33 +/- 0.621 vs 1.57 +/- 0.435 min(-1)) and 18 months (3.08 +/- 0.391 vs 1.83 +/- 0.587 min(-1)). The proposed PK/PD model for the insulin secretion from beta-cells is able to identify kinetic differences in first phase insulin secretion between lean and obese non-diabetic pre-pubertal children in this 18 month follow-up study.

Child↗
PubMed2006

Analysis of differential BRAF(V600E) mutational status in multifocal papillary thyroid carcinoma: evidence of independent clonal origin in distinct tumor foci.

BACKGROUND: Papillary thyroid cancers often occur as multiple foci. Multifocal cancers have been considered to have a poor prognosis because they are thought to be the consequence of intrathyroidal spread of the papillary cancer. However, to the authors' knowledge there has been little investigation into whether multifocal thyroid papillary carcinomas arise from the intrathyroidal spread of a single carcinoma or from independent primary tumors. To answer this question, the BRAF(V600E) mutational status of individual tumor foci was examined. This approach was justified because in the Korean population a high proportion (65%) of papillary carcinomas harbor the BRAF mutation. METHODS: DNA was isolated from paraffin-embedded tissue samples of multifocal papillary thyroid carcinoma and the BRAF exon 15 was amplified by the polymerase chain reaction (PCR). The PCR product was digested with restriction endonuclease TspRI to test for the presence of the BRAF(V600E) (T1799A) mutation. RESULTS: In all, 140 cancers from 61 patients diagnosed with multifocal papillary carcinoma were examined. The BRAF mutation was found in all the individual cancers in 29 (47.5%) of the patients (all-positive group) and the mutation was absent in all the individual cancers in 8 (13.1%) patients (all-negative group). However, in 24 (39.3%) patients, some of the individual cancers contained the BRAF mutation, whereas others did not (mixed group). CONCLUSIONS: At least 39.3% of the multifocal papillary cancers in the Korean population that were examined could be attributed to independently arising papillary cancers rather than to intrathyroidal spread of single cancers.

Adult↗
PubMed2004

Proteomic analysis of differential protein expression in a human hepatoma revertant cell line by using an improved two-dimensional electrophoresis procedure combined with matrix assisted laser desorption/ionization-time of flight-mass spectrometry.

The proteomic profiles of a human hepatoma revertant, CL1, and its original cell line, SMMC7721, were compared by using an improved two-dimensional electrophoresis (2-DE) procedure, with multi-IPGstrips gels (length <or= 13 cm) run simultaneously on one sodium dodecyl sulfate (SDS) gel (shortened MSOG method). Nineteen proteins, showing significant difference in expression (P < 0.01), were selected and identified by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) and database search. In the revertant CL1 cells, compared to human hepatoma SMMC7721 cells, upregulated expression levels of some proteins related to tumor suppression, like maspin, were found, whereas some proteins related to tumor growth, like cathepsin D, were downregulated. These facts suggest that the phenotypic reversion of the CL1 cells was at least partially due to changes at the translational level of the proteins which favored the reconstruction of the normal phenotype of the cell.

Carcinoma, Hepatocellular↗
PubMed2003

Human oligodendrocyte precursor cells in vitro: phenotypic analysis and differential response to growth factors.

Following experimental demyelination in rodents, oligodendrocyte precursor cells (OPCs) proliferate and differentiate into myelin-producing oligodendrocytes which effect robust remyelination. In contrast, remyelination in multiple sclerosis, the major human demyelinating disease, is generally limited and transient. Rodent OPCs have been well characterized in vitro and their response to growth factors documented. Since there appear to be appreciable species differences in OPC growth factor responsiveness, and since human precursors have proven difficult to culture, the present study has investigated mitogenic growth factors for cultured fetal human OPCs. Moreover, because markers for cultured human OPCs are not well established, we also examined which of the extensively used rodent OPC markers also label human precursors. Using a culture system modified for fetal human oligodendroglia, we have shown for the first time that the platelet-derived growth factor alpha receptor (PDGFalphaR) and A2B5 antigen are expressed together on human OPCs. Human precursors also expressed NG2 chondroitin sulfate proteoglycan, as did a proportion of O4+ preoligodendrocytes. Several growth factors known to affect rodent OPCs were tested and found to have similar effects on human cells. PDGF, neurotrophin 3 (NT3), and glial growth factor 2 (GGF2) promoted proliferation, while insulin-like growth factor-1 (IGF-1), exerted a maturational effect.

Cell Differentiation↗
PubMed2006

Nanoparticles of poly(D,L-lactide)/methoxy poly(ethylene glycol)-poly(D,L-lactide) blends for controlled release of paclitaxel.

Paclitaxel is one of the best antineoplastic drugs found in nature in the past decades, which has excellent therapeutic effects against a wide spectrum of cancers. Because of its high hydrophobicity, Cremophor EL has to be used as adjuvant in its clinical dosage form (Taxol), which has been found to cause serious side effects. Nanoparticles of biodegradable polymers may provide an ideal solution. In this research, paclitaxel-loaded nanoparticles of poly(D,L-lactide)/methoxy poly(ethylene glycol)-polylactide (PLA/MPEG-PLA) blends of various blend ratio 100/0, 75/25, 50/50, 25/75, and 0/100 were formulated by the nanoprecipitation method for controlled release of paclitaxel. It was found that increasing the proportion of MPEG-PLA component in the blend from 0 to 100% resulted in a progressive decrease of the particle size from 230.6+/-11.1 nm to 74.8+/-14.0 nm. The zeta potential of the drug-loaded nanoparticles was increased accordingly from -19.60+/-1.13 mV to a nearly neutral, that is, -0.33+/-0.28 mV, which indicates the gradual enrichment of PEG segments on the particle surface. The findings were further confirmed by X-Ray Photoelectron Spectroscopy (XPS) analysis. Differential scanning calorimetry (DSC) analysis showed that the glass transition temperature of PLA was significantly decreased from 58.7 to 52.1 degrees C with an increase of MPEG-PLA proportion from 0 to 75%, suggesting the miscibility of PLA and MPEG-PLA. The pure PLA nanoparticles (100/0) exhibited the slowest drug-release rate with 37.3% encapsulated drug released from the nanoparticles for 14 days while the MPEG-PLA nanoparticles (0/100) achieved the fastest drug release with 95.9% drug release in the same period.

Antineoplastic Agents, Phytogenic↗
PubMed2005

Proteomic analysis of differential protein expression in response to epidermal growth factor in neonatal porcine pancreatic cell monolayers.

We have proposed that porcine neonatal pancreatic cell clusters (NPCCs) may be a useful alternative source of cells for islet transplantation, and that monolayer cultures might provide an opportunity to manipulate the cells before transplantation. In addition we previously identified 10 genes up-regulated by epidermal growth factor (EGF) in cultured porcine NPCC monolayers. We have now analyzed the intracellular signaling pathways activated by EGF and searched for proteins differentially expressed following EGF treatment of the monolayers, using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). EGF treatment resulted in phosphorylation of both Erk 1/2 and Akt, as well as increased cell proliferation. Five unknown and 13 previously identified proteins were differentially expressed in response to EGF. EGF treatment increased the expression of several structural proteins of epithelial cells, such as cytokeratin 19 and plakoglobin, whereas vimentin, the intermediate filament protein of mesenchymal cells, and non-muscle myosin alkali chain isoform 1, decreased. Heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 factor, which promotes epithelial cell proliferation, and hemoglobin alpha I & II also increased, whereas cyclin A1, immunoglobulin heavy chain, apolipoprotein A1, 5,10-ethylenetetrahydrofolated reductase (5,10-MTHFR), angiotensin-converting enzyme 2 (ACE2), co-lipase II precursor, and NAD+ isocitrate dehydrogenase (NAD+ IDH) alpha chain proteins decreased. Our results show that EGF stimulates proliferation of pancreatic epithelial cells by simultaneously activating the MAPK and PI-3K pathways. HnRNP A2/B1, hemoglobin, cyclin A1, and ACE2 may play roles in the proliferation of epithelial cells in response to EGF.

Animals↗
PubMed1993

Analysis of differential HLA-DQB expression in autologous B cell lines.

Class II major histocompatibility complex genes are differentially expressed during cellular activation and differentiation, often in a locus-specific manner. We investigated the differential expression of the HLA-DQB gene, using B cell lines LAZ221 and LAZ388: LAZ221, derived from an early B cell leukemia, expresses HLA-DR but not HLA-DQ: LAZ388, the autologous Epstein-Barr virus-transformed B cell line, expresses both DR and DQ. Transfection experiments demonstrate differential function of class II gene upstream regulatory regions in the two lines, which correlates with differential class II gene expression. Using gel retardation and DNase I footprint assays, we demonstrate that absence of DQB gene expression is associated with characteristic nuclear protein-binding interactions in the proximal DQB gene upstream regulatory region. These interactions are visualized as DNA-protein complexes that are seen with nuclear proteins from the DQ-negative cell line, LAZ221, and involve consensus promoter Y box and W box elements, as well as novel upstream sites. Transcriptional regulatory proteins that differ in these autologous B cell lines may be stage-specific factors involved in the developmental regulation of HLA genes.

Animals↗
PubMed1978

A correlative microscopical analysis of differentiating ovarian follicles of mammals.

The mammalian ovary has been studied by optical microscopy and by scanning and transmission electron microscopy with the purpose of presenting an integrated view of the differentiating mammalian follicle. During follicular development, changes in the granulosa cells are particularly noteworthy and include dramatic modifications in cell shape coincident with antrum formation. The cytoplasmic processes of those granulosa cells immediately surrounding the oocyte, as well as the more peripheral granulosa cells comprising a second and third layer, traverse the zona pellucida, infrequently interdigitate with the microvilli of the egg, and make both desmosomal and gap junction contacts with the oocyte. The zona pellucida is thus distinguished by numerous fenestrations of varying diameters. The membrana limitans (basal lamina) is a bipartite structure composed of (a) a homogenous stratum upon which the peripheral layer of granulosa cells rests, and (b) an outer region of collagen-like fibers. The specific advantages and limitations of the different methodologies utilized to study folliculo-genesis are discussed.

Animals↗
PubMed2004

Regulated expression of VP16CREB in neuroblastoma cells: analysis of differentiation and apoptosis.

Highly malignant neuroblastoma tumors generally have defects in differentiation and apoptotic pathways. For a better understanding of these events, we use a murine neuroblastoma cell line (NBP2) that terminally differentiates into mature neurons in response to elevated levels of cAMP. Because one of the main downstream effectors of the cAMP signaling pathway is cAMP-response element binding (CREB), we reasoned that it might affect the expression of genes associated with differentiation and apoptotic events in NBP2 cells. To investigate this, we established tetracycline-regulated expression (TetOff) of VP16CREB, which constitutively transactivates promoters containing the CRE sequence motif. Using this system, we found that inducible expression of VP16CREB in NBP2 cells results in 1) morphological differentiation that is characterized by the formation of neurites and growth cones, 2) reversible cell differentiation unlike cAMP-induced terminal differentiation, 3) cell cycle arrest at G1, 4) no apoptosis in the presence of partial inhibition of proteasome unlike an increase in cAMP levels, and 5) changes in the expression of many genes, including down-regulation of N-myc, cyclin B1, Dickkopf-1, and Mad-2 and up-regulation of tyrosine hydroxylase, c-fos, N10, and ICER genes. Although VP16CREB expression and activation of the cAMP pathway impart many similar effects in NBP2 cells, they also bear some distinct genetic and morphological differences. Our data suggest that increased levels of cAMP function through not only CREB but also other signaling pathways that account for the additional cAMP-induced effects, including irreversible differentiation and onset of apoptosis during partial inhibition of proteasome in NBP2 cells.

Animals↗
PubMed2004

Analysis of differential maternal mRNA expression in developmentally competent and incompetent bovine two-cell embryos.

The main objective of this study was to identify mRNA transcripts associated with embryonic developmental competence. In cattle, mRNA transcripts, ribosomes, and proteins accumulated during the growth phase are drawn on to sustain maturation, fertilization, and the initial cell cycle divisions up to the 8- to 16-cell stage. Early cleaving mammalian zygotes are more likely to develop to the blastocyst stage than their later cleaving counterparts, thus reflecting the intrinsic quality of the oocytes from which they originated. We describe the combination of this well-established model for the retrospective determination of developmental competence in mammalian oocytes with a technique for wide screening of differential gene expression in different biological populations. Immature cumulus oocyte complexes were recovered from surface visible follicles on abattoir ovaries, washed, and submitted to routine in vitro maturation and fertilization. Two-cell embryos were removed from culture at 3-hr intervals from 24 to 42 hr post insemination (pi). Two populations of two-cell embryos were identified; those that cleaved early (before 27 hpi) and those that cleaved late (after 33 hpi). Suppressive subtractive hybridization was carried out on cDNA from the two populations, following which, differentially expressed amplicons were subcloned and sequenced. The sequences were submitted to the nonredundant and expressed sequence tag (EST) databases at NCBI using the BLAST algorithm. The differential expression of three selected candidate genes that were identified as putatively upregulated in the early cleaving zygotes were chosen for further investigations; histone H3, cyclin B1, and GDF-9B. Using quantitative real time PCR we have shown that histone H3A is significantly more abundant in embryos that cleave earliest.

Animals↗