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PubMed1999

Differential expression of c-kit in mouse undifferentiated and differentiating type A spermatogonia.

The proto-oncogene c-kit is encoded at the white-spotting locus and in the mouse mutations at this locus affect the precursor cells of melanocytes, hematopoietic cells, and germ cells. c-kit is expressed in type A spermatogonia, but whether or not c-kit is present both in undifferentiated and differentiating type A spermatogonia or only in the latter cell type is still a matter of debate. Using the vitamin A-deficient mouse model, we studied messenger RNA (mRNA) and protein expression in undifferentiated and differentiating type A spermatogonia. Furthermore, we quantified the immuno-positive type A spermatogonia in the epithelial stages VI, VII, IX/X, and XII in normal mice to correlate c-kit expression in type A spermatogonia with the differentiation of these cells. Our results show that in the VAD situation undifferentiated type A spermatogonia express little c-kit mRNA. The A spermatogonia with a larger nucleus expressed c-Kit protein, whereas the A spermatogonia with a smaller one did not. After induction of differentiation of these cells into type A1 spermatogonia, c-kit mRNA was enhanced. The percentage of A spermatogonia expressing c-Kit protein did not change during this process, suggesting that A spermatogonia, which are committed to differentiate express c-kit. Under normal circumstances in epithelial stage VI 16%+/-2% (mean +/- SD), in VII 45%+/-15%, in IX/X 78%+/-14% and in XII 90%+/-1.9% of the type A spermatogonia were c-kit positive, suggesting that Aaligned spermatogonia gradually change from c-Kit negative to c-Kit positive cells before their differentiation into A1 spermatogonia. It is concluded that c-kit can be used as a marker for differentiation of undifferentiated into differentiating type A spermatogonia.

Animals↗
PubMed2005

[The establishment of the two dimensional gel electrophoresis (2-DE) map of hypertrophic scar epidermal cells and the display of the differentially expressed proteins].

OBJECTIVE: To establish and optimize the two dimensional gel electrophoresis (2-DE) map of epidermal cells separated from the hypertrophic scar tissues so as to explore the function of the non cultured epidermal cells during the course of the formation of hypertrophic scar. METHODS: To separate the epidermal cells from the scar tissues, the scar epidermis was digested with Dispase II and trypsin. The total protein of the cells was then extracted and separated with 2-DE and visualized with silver stain. Spots detection and matching were performed with Melaine 3.0 gels analyzing software. The results were then compared with the normal epidermal cells' 2-DE map coming from the Danish Center for Human Genome Research' s 2-DE PAGE Databases. RESULTS: Nearly more than 600 protein spots were identified in the final optimized 2-DE map. We found out 24 differentially expressed proteins by comparing the difference in composition, shape or density of all the spots. In the 24 proteins, there are 8 up-regulated ones, 9 down-regulated ones, 4 disappeared ones and 3 newly founded ones. CONCLUSIONS: The method of digesting the epidermis with Dispase II and trypsin to separate the epidermal cells to establish the 2-DE map is feasible and it made the further study on hypertrophic scar proteomics possible. The 24 differentially expressed proteins revealed that epidermal cells might play a role in the formation of hypertrophic scar.

Cell Line↗
PubMed2005

Profiling of differentially expressed genes in wound margin biopsies of horses using suppression subtractive hybridization.

Disturbed gene expression may disrupt the normal process of repair and lead to pathological situations resulting in excessive scarring. To prevent and treat impaired healing, it is necessary to first define baseline gene expression during normal repair. The objective of this study was to compare gene expression in normal intact skin (IS) and wound margin (WM) biopsies using suppression subtractive hybridization (SSH) to identify genes differentially expressed during wound repair in horses. Tissue samples included both normal IS and biopsies from 7-day-old wounds. IS cDNAs were subtracted from WM cDNAs to establish a subtracted (WM-IS) cDNA library; 226 nonredundant cDNAs were identified. Detection of genes previously shown to be expressed 7 days after trauma, including the pro-alpha(2)-chain of type 1 pro-collagen (COL1A2), annexin A(2), the pro-alpha(3)-chain of type 6 pro-collagen, beta-actin, fibroblast growth factor 7, laminin receptor 1, matrix metalloproteinase 1 (MMP1), secreted protein acidic cystein rich, and tissue inhibitor of metalloproteinase 2, supported the validity of the experimental design. A RT-PCR assay confirmed an increase or induction of the cDNAs of specific genes (COL1A2, MMP1, dermatan sulfate proteoglycan 2, cluster differentiation 68, cluster differentiation 163, and disintegrin and metalloproteinase domain 9) within wound biopsies. Among these, COL1A2 and MMP1 had previously been documented in horses; 68.8% of the cDNAs had not previously been attributed a role during wound repair, of which spermidine/spermine-N-acetyltransferase, serin proteinase inhibitor B10, and sorting nexin 9 were highly expressed and whose known functions in other processes made them potential candidates in regulating the proliferative response to wounding. In conclusion, we identified novel genes that are differentially expressed in equine wound biopsies and that may modulate repair. Future experiments must correlate changes in mRNA levels for precise molecules with spatiotemporal protein expression within tissues.

Animals↗
PubMed2002

Differential expression of desaturases and changes in fatty acid composition during sporangiospore germination and development in Mucor rouxii.

Polyunsaturated fatty acids (PUFAs), namely, oleic (C18:1), linoleic (C18:2), and gamma-linolenic acid (C18:3), constituted the majority in the total fatty acid content (44%) of sporangiospores of Mucor rouxii. At 30 degrees C, the germination begins within 1h at which time spore swelling occurs, followed by germ tube emergence within 3-4h. Throughout germination, an increase in gamma-linolenic acid (GLA) was observed and its content was highest at germ tube emergence. It took longer for sporangiospores of M. rouxii to germinate at sub-optimal temperatures (15 and 35 degrees C). However, the content of GLA was higher at the germ tube initiation than at the mycelial stage at all temperatures, suggesting the association of GLA and germination of sporangiospores. This finding was substantially confirmed by differential expression of delta9-, delta12-, and delta6-desaturase genes measured during spore germination. The expression of three desaturase genes parallels the pattern of GLA synthesis. By using RT-PCR techniques to follow gene expression, we found that mRNA of delta12- and delta6-desaturase genes were translated as soon as the spores were introduced into a fresh medium while the mRNA of delta9-desaturase gene could not be detected until 2h after introduction. A sharp increase in mRNA of delta6-desaturase genes correlated well with an increase in GLA content at germ tube emergence (4h). These results demonstrated that changes in fatty acid composition of sporangiospore of M. rouxii and differential expression of desaturase genes occurred during germination, and that extensive changes in GLA synthesis associated with some events in germination process.

Fatty Acid Desaturases↗
PubMed2001

Differential expression for tissue-specific isozymes in three species of Hypostomus Lacépède, 1803 (Teleostei: Loricariidae).

The expression patterns of 14 enzymatic systems in skeletal muscle, liver and heart tissues of three species of Hypostomus from the Iguaçu River basin (Brazil) were investigated. Although the patterns were similar for the three species, different tissues showed differential expressions, and the data showed that differential tissue expressions of isoperoxidases may be due to preferential combination or association of polypeptide subunits. The detected patterns for SOD isozymes showed that the quaternary structures of these enzymes were in disagreement with the subunit number reported for the majority of other vertebrate groups. Tissue-specific restriction on heterotetramer formation also were described in LDH and MDHP isozymes. Thus, these tissue-specific gene expression character in the species of Hypostomus have the greatest potential to be recognized and applied in systematic studies among species of Hypostomus.

Journal Article↗
PubMed2000

Cutting edge: Chandra, a novel four-transmembrane domain protein differentially expressed in helper type 1 lymphocytes.

Development of naive Th cells into Th1 and Th2 effector populations requires coordinated expression of a complex set of genes. In this study, we have identified a novel four-transmembrane domain protein, Chandra, that is differentially expressed in Th1 cells. Chandra expression is observed in STAT4- and IFN-gamma-deficient mice, indicating that Chandra is not an IL-12- or IFN-gamma-responsive gene. Interestingly, Chandra mRNA is detected in anti-CD3-activated T cells from STAT6-deficient mice in the absence of any differentiation conditions. Furthermore, neutralization of IL-4 signaling is sufficient to induce transcription of Chandra in anti-CD3-activated T cells from wild-type mice, demonstrating that STAT6 signaling is required to repress Chandra expression in activated T cells and Th2 subsets. This is the first demonstration of a differentially expressed four-transmembrane domain protein in Th1 cells.

Amino Acid Sequence↗
PubMed1988

Differential expression of phenotype by resting zone and growth region costochondral chondrocytes in vitro.

This study establishes an in vitro model for examining endochondral cartilage cell metabolism. Chondrocytes derived from the resting cell zone and adjacent growth zone of rat costochondral cartilage were compared for retention of phenotype in culture. At third passage confluence, two cell populations differ morphologically and biochemically. Resting zone cells are fibroblast-like, with smooth cell membranes and little rough endoplasmic reticulum. Growth zone cells are more polygonal, smaller in diameter, with numerous cytoplasmic extensions of the plasma membranes and abundant rough endoplasmic reticulum. Both cell populations produce matrix vesicles that are comparable morphologically to matrix vesicles isolated enzymatically from epiphyseal cartilage. While membrane vesicles are released into the media by cells derived from the resting zone as well as from the growth cartilage, alkaline phosphatase activity is enriched in media vesicles produced by growth cartilage cells. Alkaline phosphatase enriched vesicles appear to be preferentially incorporated into the extracellular matrix. Both the plasma membrane marker enzyme activity and the membrane phospholipid composition are differentially expressed in matrix vesicles and plasma membranes and are cell specific. Matrix vesicles produced by resting zone cells are enriched in alkaline phosphatase, 5'-nucleotidase, ouabain sensitive Na+/K+ ATPase and cardiolipin when compared to the cell membrane. In addition, the plasma membranes of these cells contain more phosphatidylcholine plus sphingomyelin than do growth cartilage plasma membranes. Resting zone cell matrix vesicles have less phosphatidylethanolamine than do vesicles from growth cartilage cultures. Matrix vesicles produced by growth cartilage cells contain one proteolipid at 43,000 Mr which comigrates with plasma membrane proteolipid and an additional proteolipid at approximately 3,000 Mr. These data indicate that both cells retain differential expression of phenotype in culture and that one expression of this phenotype is production of specific extracellular matrix vesicles.

Animals↗
PubMed1994

Subtractive hybridization cloning of novel genes differentially expressed during intestinal development.

Intestinal genes whose expression is regulated during development and differentiation were identified and cloned from a rat villi cDNA library using a subtracted cDNA probe. The isolated clones are transcribed in the fully differentiated intestinal epithelium 21 days after birth and absent or poorly expressed in the fetal gut at 15 days of gestation. Two of the DRI (differentially-expressed in rat intestine) genes are novel, while the others encode the microvillar protein ezrin and intracellular carrier proteins for retinol and fatty acids. Expression of the newly isolated DRI27 and DRI42 clones parallels epithelial differentiation during development and it is more pronounced in the distal portions of the small intestine. In situ hybridization experiments indicate that the DRI mRNAs are expressed in the differentiated cell types of the gut epithelium. Moreover, the expression of DRI27 and DRI42 is strongly related to the stage of epithelial differentiation during gut development. This relationship holds true also for the expression of DRI42 in other tissues. These clones will be a valuable tool to identify regulatory sequences and factors responsible for confining gene expression to the differentiated epithelial cell types in mammalian small intestine.

Animals↗
PubMed2001

Multiple procyclin isoforms are expressed differentially during the development of insect forms of Trypanosoma brucei.

Transmission of Trypanosoma brucei by the tsetse fly entails several rounds of differentiation as the parasite migrates through the digestive tract to the salivary glands of its vector. Differentiation of the bloodstream to the procyclic form in the fly midgut is accompanied by the synthesis of a new coat consisting of EP and GPEET procyclins. There are three closely related EP isoforms, two of which (EP1 and EP3) contain N-glycans. To identify the individual EP isoforms that are expressed early during synchronous differentiation in vitro, we exploited the selective extraction of GPI-anchored proteins and mass spectrometry. Unexpectedly, we found that GPEET and all isoforms of EP were coexpressed for a few hours at the onset of differentiation. At this time, the majority of EP1 and EP3 molecules were already glycosylated. Within 24 hours, GPEET became the major surface component, to be replaced in turn by glycosylated forms of EP, principally EP1, at a later phase of development. Transient transfection experiments using reporter genes revealed that each procyclin 3' untranslated region contributes to differential expression as the procyclic form develops. We postulate that programmed expression of other procyclin species will accompany further rounds of differentiation, enabling the parasite to progress through the fly.

3' Untranslated Regions↗
PubMed1996

Three forms of RPTP-beta are differentially expressed during gliogenesis in the developing rat brain and during glial cell differentiation in culture.

In situ hybridization and Northern analysis demonstrate that the three splicing variants of RPTP-beta have different spatial and temporal patterns of expression in the developing brain. The 9.5-kb and 6.4-kb transcripts, which encode transmembrane protein tyrosine phosphatases with different extracellular domains, are predominantly expressed in glial progenitors located in the subventricular zone (SVZ). The 8.4-kb transcript, which encodes a secreted chondroitin sulfate proteoglycan (phosphacan), is expressed at high levels by more mature glia that have migrated out of the SVZ. The three transcripts are also differentially expressed in glial cell cultures; O2A progenitors express high levels of the 9.5- and 8.4-kb transcript, whereas type 1 astrocyte progenitors predominantly express the 6.4-kb transcript. C6 gliomas also express high levels of the 6.4-kb transcript. Treating C6 cells with the differentiating agent dibutyryl cyclic-AMP (DBcAMP), induces a decrease in the 6.4-kb transcript and a corresponding increase in the 8.4-kb transcript. O2A cells grown in the presence of basic fibroblast growth factor (bFGF) and platelet-derived growth factor (PDGF) remain highly proliferative and undifferentiated, and continue to express high levels of RPTP-beta. However, when O2A cells are grown in conditions that induce oligodendrocyte differentiation, there is a marked decrease in the expression of the transmembrane forms of RPTP-beta, as determined by immunofluorescence. These results demonstrate that RPTP-beta expression is regulated during glial cell differentiation and suggest that the different forms of RPTP-beta perform distinct functions during brain development.

Animals↗
PubMed1998

Differential expression of the TEF family of transcription factors in the murine placenta and during differentiation of primary human trophoblasts in vitro.

We describe the molecular cloning of murine (m) Transcriptional Enhancer Factor (TEF)-5 belonging to the TEF family of transcription factors. We show that mTEF-5 is specifically expressed in trophoblast giant cells and other extra-embryonic structures at early stages of development. At later stages, mTEF-5 is specifically expressed in the labyrinthine region of the placenta and in several embryonic tissues. We further show that the other mTEFs are differentially expressed in extraembryonic structures and in the mature placenta. Interestingly, human (h)TEF-5 is specifically expressed in the differentiated syncytiotrophoblast of the human term placenta and its expression is upregulated during the differentiation of cytotrophoblasts to syncytiotrophoblast in vitro, whereas that of hTEF-1 is down-regulated. Together with previous results describing hTEF-binding sites in the human placental lactogen-B gene enhancer, these novel observations support a role for hTEF-5 in the regulation of this gene. We further propose that the hTEF factors may play a more general role in placental gene regulation and development.

Amino Acid Sequence↗
PubMed2001

[Relationship between differential expression patterns of multigene families and heterosis in a wheat diallel crosses].

In order to understand molecular basis of heterosis, the patterns of differential gene expression of multigene families between wheat hybrids and their parents in seedling leaves were analyzed by using mRNA differential display. Relationships between differential gene expression patterns, heterosis and F1 hybrid performance were determined. Four patterns of differential gene expression were observed, which include: (1) bands observed in both parents but not in the F1; (2) bands occurring in only one parent but not in the F1 or the other parent; (3) bands detected in only the F1 but neither of the parents; (4) bands present in one parent and F1 but absent in the other parent. The analysis showed that patterns of differential gene expression were not correlated with the F1 hybrid performance for all the eight agronomic traits. However, differentially expressed fragments that occurred only in the F1 but neither of the parents were found to be positively correlated with heterosis. On the contrary, fragments observed in both parents but not in the F1 were negatively correlated with heterosis. It is concluded that the differential expression of regulatory genes plays an important role in heterosis.

Crosses, Genetic↗
PubMed2000

Differential expression of lymphoid and myeloid markers on differentiating hematopoietic stem cells in normal and tumor-bearing adult human liver.

The presence and phenotype of lineage-committed hematopoietic progenitors in the normal adult human liver (AHL) were investigated and compared with the profiles of differentiating hematopoietic precursor populations detected in liver bearing metastases of colonic origin. Levels of hematopoietic stem cells (HSCs) (CD34(+)CD45(+)) detected in hepatic mononuclear cell (HMNC) populations were increased 6-fold when compared with matched peripheral blood samples. In normal liver, less than 5% of HSCs expressed the myeloid-associated antigen, CD33, whereas considerable proportions expressed lymphoid-associated markers (T cell, 33.39%; B cell, 17.39%; and natural killer [NK] cell, 37.17%). Significant increases were observed in the relative proportions of hepatic HSCs coexpressing CD33 (20.53%; P =.001), and the T-cell marker (CD7, 58. 13%; P =.02) in tumor-bearing liver compared with normal liver. HSCs with B-cell progenitor phenotype (CD19(+)) were significantly decreased in tumor-bearing liver (0.06%; P =.02). Despite these differences, the activation status of hematopoiesis, as measured by the coexpression of the differentiation and activation markers, CD38 and CD45RA, did not differ significantly between normal and tumor-bearing liver. These results indicate that the normal AHL harbors lineage-committed hematopoietic progenitors, and the vast majority of these progenitors express lymphoid-associated antigens with changes occurring in both the myeloid and lymphoid compartments of the hepatic hematopoietic pathway on tumor challenge. While tumor-bearing livers are enriched for intrahepatic myeloid precursors and T-cell progenitor cells, further studies are required to establish the origin and in situ development potential of hepatic HSCs in the adult human and their role in tumor immunity.

Adolescent↗
PubMed2004

Differential expression of osteogenic factors associated with osteoinductivity of human osteosarcoma cell lines.

Differential expression of multiple osteogenic factors may be responsible for the different osteoinductivity of osteosarcoma cell lines. We compared in vivo osteoinductivity of human osteosarcoma cell lines (Saos-2 vs. U-2 OS) in nude mice, and their in vitro expression of various osteogenic factors of protein level by quantitative immunocytochemistry and mRNA level by RT-PCR and/or in situ hybridization. Saos-2 cells, but not U-2 OS, were osteoinductive in vivo. Significantly higher expression (independent t-test, all p < 0.005) of osteogenic factors were observed in Saos-2 cells compared with U-2 OS, which included bone morphogenetic proteins (particularly BMPs-2, 3, 4, and 7), transforming growth factor-beta (TGF-beta), BMP receptor (BMPR)-1A, receptor-regulated Smads (R-Smads), Smads 1, 2, and 5, and common-mediator Smad (Co-Smad), Smad 4. In contrast, U-2 OS cells expressed higher levels of inhibitory Smad 6 (I-Smad) protein than Saos-2 cells (p < 0.001). These results suggest that a combination of osteogenic factors (BMPs, TGF-beta, BMPRs, and R/Co-Smads) against I-Smad may play important roles in the Saos-2 cell osteoinductivity. This may have a clinical implication in selecting key osteogenic factors for combined therapy for bone defect diseases. The characterized cell lines can be used as positive and negative controls for the assessments of both in vitro and in vivo bone formation capabilities of designed tissues or biomaterials.

Animals↗
PubMed1995

Identification of proteins differentially expressed in quiescent and proliferatively senescent fibroblast cultures.

We have examined the differential expression of proteins in quiescent (nongrowing) early versus late population doubling level (PDL) WI-38 human diploid fibroblasts. Age-associated changes in gene expression at the level of both secreted and total cellular protein were identified using high-resolution, two-dimensional gel electrophoresis followed by N-terminal sequencing or Western blot analysis. A comparison of secreted proteins revealed the senescence-specific absence of all forms of EPC-1, a protein associated with early PDL cells in the G0 state. This comparison also revealed the absence of a processed (cleaved) form of alpha I (type III) procollagen in senescent cells, suggesting a distinctive remodeling of the extracellular matrix. A comparison of total cellular protein between early passage and proliferatively aged fibroblasts identified an altered form of the enzyme ubiquitin carboxyl-terminal hydrolase in senescent cells, a result that could explain the increase in ubiquitinated proteins in these cells. These findings further elucidate the phenotype of fibroblasts aged in vitro and support the concept that senescent cells are arrested in a state fundamentally different from that of G0 early PDL cells.

Amino Acid Sequence↗
PubMed1993

Differential expression of the cellular retinaldehyde-binding protein in bovine ciliary epithelium.

Differential expression of the cellular retinaldehyde-binding protein (CRALBP), a likely component of the visual cycle, has been observed in the ocular ciliary epithelium, a bilayer of neurepithelial cells involved in the active transport of aqueous humor. Antibody probes raised to bovine ciliary epithelium were used to isolate a cDNA encoding CRALBP from a bovine ciliary epithelium cDNA expression library. Northern analysis of poly A+RNA isolated from three different regions of the neonate ciliary epithelium revealed a three-fold higher level of CRALBP expression in the most anterior portion of the pars plicata region relative to the posterior pars plana region. Western blot analysis using CRALBP-specific antibodies also demonstrated that the level of CRALBP expression was higher in the most anterior portion of the ciliary epithelium and gradually decreases toward the posterior region in both neonate and adult bovine eyes. Using indirect immunofluorescence and frozen-sectioned bovine ciliary epithelium, CRALBP was localized to the pigmented ciliary epithelial cell layer along the entire ciliary epithelium. In the nonpigmented ciliary epithelial cell layer, CRALBP was only detected in the pars plana region. Pigmented ciliary epithelial cells have also been cultured and CRALBP expression demonstrated for several continuous passages by Northern and Western analysis. These results raise questions regarding the physiological role of CRALBP in the ciliary epithelium and the involvement of the protein in the defining regional and functional boundaries with this tissue.

Animals↗
PubMed2004

Finding differentially expressed genes for pattern generation.

MOTIVATION: It is important to consider finding differentially expressed genes in a dataset of microarray experiments for pattern generation. RESULTS: We developed two methods which are mainly based on the q-values approach; the first is a direct extension of the q-values approach, while the second uses two approaches: q-values and maximum-likelihood. We present two algorithms for the second method, one for error minimization and the other for confidence bounding. Also, we show how the method called Patterns from Gene Expression (PaGE) (Grant et al., 2000) can benefit from q-values. Finally, we conducted some experiments to demonstrate the effectiveness of the proposed methods; experimental results on a selected dataset (BRCA1 vs BRCA2 tumor types) are provided. CONTACT: alhajj@cpsc.ucalgary.ca.

Algorithms↗