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PubMed1988

Description and analysis of differential sensitivity to glucocorticoids in Fao cells.

This study shows that the derived hepatoma cell line Fao displays different sensitivities for glucocorticoid induction of tyrosine aminotransferase (TAT), alanine aminotransferase (AAT) and gamma-glutamyltransferase (GGT). This was seen in the different behaviors of nine steroids with respect to these three effects: (1) in the presence of full agonists (dexamethasone or deacylcortivazol), half-maximal induction of GGT occurred at approx 5- to 6-fold higher agonist concentrations than those required for half-maximal induction of AAT and TAT; (2) in the presence of full antagonists (RU 486, R5020, or progesterone) the GGT response induced by an equal agonist concentration was inhibited at concentrations approx 4- to 5-fold lower than those required for an equivalent inhibition of TAT response; (3) in the presence of cortexolone, deoxycorticosterone, 11 beta-hydroxyprogesterone and dexamethasone-3'-oxetanone, there was a partial agonistic effect (30-50%) on TAT and AAT responses, whereas there was a mainly antagonistic effect (very weak agonistic effect: 0-10%) on GGT response; (4) regardless of the steroid or its full or partial agonist activity, a given TAT induction level (50%, for example) always corresponded to the same AAT and GGT induction levels (50 and 10% respectively). We provide evidence showing that the three above-mentioned biological responses are mediated via the same type of glucocorticoid receptor binding site. Consequently, this differential behavior probably originates from a phenomenon occurring after the common steps (activation, translocation) that follow the formation of the steroid-receptor complex. This leads us to propose a model in which this phenomenon is assumed to originate from a difference in the affinities of the activated receptor for the nuclear acceptor sites of the TAT and GGT genes.

Alanine Transaminase↗
PubMed1996

A duplicated sequence in sugarbeet mitochondrial transcripts is differentially edited: analysis of orfB and its derivative orf324 mRNAs.

RNA editing of the duplicated sequences was investigated in the transcripts of orfB and orf324 genes from sugarbeet mitochondria. The orf324 shares the first 59 bp of the reading frame and 321 bp upstream sequence with orfB. Two cytidine-to-uridine editing sites were found in orfB, but the corresponding cytidine residues remained unchanged in the transcripts of orf324. In the vicinity of the non-edited cytidine residues within the shared sequence element of orf324 were identified three point mutations that may abolish orf324 editing. Our results also suggest that selection of editing sites depends on primary sequence.

Amino Acid Sequence↗
PubMed1987

Dynamic analysis of differential scanning calorimetry data.

The apparent heat capacity function measured by high-sensitivity differential scanning calorimetry contains dynamic components of two different origins: (1) an intrinsic component arising from the finite instrument time response; and (2) a sample component arising from the kinetics of the thermal transition under study. The intrinsic instrumental component is always present and its effect on the shape of the experimental curve depends on the magnitude of the calorimeter response time. Usually, high-sensitivity instruments exhibit characteristic time constants varying from 10 to 100 s. This slow response introduces distortions in the shape of the heat capacity function especially at fast scanning rates. In addition to this instrumental component, dynamic effects due to sample relaxation processes also contribute to the shape of the experimental heat capacity profile. Since the nature and magnitude of these effects are a function of the kinetic parameters of the transition, they can be used to obtain kinetic information. This communication presents a dynamic deconvolution technique directed to remove artificial distortions in the shape of the heat capacity function measured at any scanning rate, and to obtain a kinetic characterization of a thermally induced transition. The kinetic characterization obtained by this method allows the researcher to obtain transition relaxation times as a continuous function of temperature. This technique has been applied to the thermal unfolding of ribonuclease A and the pretransition of dipalmitoylphosphatidylcholine (DPPC). In both systems the transition relaxation times are temperature dependent. For the protein system the relaxation time is very slow below the transition temperature (approximately 30 s) and very fast above Tm (less than 1 s) in agreement with direct kinetic measurements. For the pretransition of DPPC, the relaxation time is maximal at the transition midpoint and of the order of approx. 40 s.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1993

Human ribosomal protein L37a: cloning of the cDNA and analysis of differential gene expression in tissues and cell lines.

A cDNA corresponding to human ribosomal protein L37a (hL37a) was obtained by screening a SHSY5Y neuroblastoma library. The full-length cDNA contained 366 nucleotides (nt) in addition to a poly(A) tail. The pyrimidine-rich sequence, CTTTCT, that is common to many ribosomal protein-encoding cDNAs was present at the 5' terminus. The nt sequence displayed 85% identity with rat L37a (rL37a) cDNA. The predicted protein contains 92 amino acids with a M(r) of 10,277, is highly basic, and has 100% sequence identity with rL37a. A putative zinc-finger domain is present in the central region of the protein. Human lymphocytes and several human cell lines express hL37a mRNA at significantly higher levels than the rat cell lines and rat tissues tested. The hL37a gene does not contain introns.

Amino Acid Sequence↗
PubMed2005

Bacterial response to eukaryotic cells. Analysis of differentially expressed proteins using nano liquid chromatography-electrospray ionization tandem mass spectrometry.

Host-bacteria interactions have mostly been investigated with regard to the host response or to activities of pathogenic bacteria. In contrast, we aim to identify reactions of non-pathogenic bacteria that result from their contact with host cells of the gastrointestinal tract. In a proteomic approach, the response of non-pathogenic human Escherichia coli bacteria on gut epithelial cells (rat IEC-6) was investigated in an in vitro co-culture model. For this purpose, a sensitive analytical procedure was developed based on the identification of two-dimensional polyacrylamide gel electrophoresis separated proteins by online nanoLC-electrospray ionization MS/MS using a quadrupole time-of-flight tandem mass spectrometer for accurate mass determination. We demonstrate here the efficiency of this technique by the identification of a total of 43 differentially expressed proteins, out of which 25 were up-regulated and 18 were down-regulated. They represent a wide range of molecular weight and different metabolic and physiological functions.

Animals↗
PubMed2006

Differential proteomic analysis of the anti-proliferative effect of glucocorticoid hormones in ST1 rat glioma cells.

Glucocorticoid hormones (GCs) exert a potent anti-proliferative activity on several cell types. The classic molecular mechanism of GCs involves modulation of the activity of the glucocorticoids receptor, a transcriptional regulator. However, the anti-proliferative effect of GCs may also involve modulation of processes such as translation, subcellular localization and post-translational modifications, which are not reflected at the mRNA level. To investigate these potential effects of GCs, we employed the proteomic approach (two-dimensional electrophoresis and mass spectrometry) and the ST1 cells, obtained from the C6 rat glioma cell line, as a model. GC treatment leads ST1 cells to a complete transformed-to-normal phenotypic reversion and loss of their tumorigenic potential. By comparing sets of 2D nuclear protein profiles of ST1 cells treated (or not) with hydrocortisone (Hy), 13 polypeptides displaying >or=two-fold difference in abundance upon Hy treatment were found. Five of these polypeptides were identified by peptide mass fingerprinting, including Annexin 2 (ANX2), hnRNP A3 and Ubiquitin. Evidence obtained by Western blot analysis indicates that ANX2 is present in the nucleus and has its subcellular localization modulated by GC-treatment of ST1 cells. Our findings indicate complementary mechanisms contributing to the regulation of gene expression associated with ST1 cells' response to GCs.

Animals↗
PubMed2005

Quantitative proteomics analysis of differential protein expression and oxidative modification of specific proteins in the brains of old mice.

The brain is susceptible to oxidative stress, which is associated with age-related brain dysfunction, because of its high content of peroxidizable unsaturated fatty acids, high oxygen consumption per unit weight, high content of key components for oxidative damage, and the relative scarcity of antioxidant defense systems. Protein oxidation, which results in functional disruption, is not random but appears to be associated with increased oxidation in specific proteins. By using a proteomics approach, we have compared the protein levels and specific protein carbonyl levels, an index of oxidative damage in the brains of old mice, to these parameters in the brains of young mice and have identified specific proteins that are altered as a function of aging. We show here that the expression levels of dihydropyrimidinase-like 2 (DRP2), alpha-enolase (ENO1), dynamin-1 (DNM1), and lactate dehydrogenase 2 (LDH2) were significantly increased in the brains of old versus young mice; the expression levels of three unidentified proteins were significantly decreased. The specific carbonyl levels of beta-actin (ACTB), glutamine synthase (GS), and neurofilament 66 (NF-66) as well as a novel protein were significantly increased, indicating protein oxidation, in the brains of old versus young mice. These results were validated by immunochemistry. In addition, enzyme activity assays demonstrated that oxidation was associated with decreased GS activity, while the activity of lactate dehydrogenase was unchanged in spite of an up-regulation of LDH2 levels. Several of the up-regulated and oxidized proteins in the brains of old mice identified in this report are known to be oxidized in neurodegenerative diseases as well, suggesting that these proteins may be particularly susceptible to processes associated with neurodegeneration. Our results establish an initial basis for understanding protein alterations that may lead to age-related cellular dysfunction in the brain.

Actins↗
PubMed2006

In vitro analysis of differential expression of collagens, integrins, and growth factors in cultured human chondrocytes.

OBJECTIVES: Tissue engineering represents a promising method for the construction of autologous chondrogenic grafts for reconstructive surgery. In cultured chondrocytes, the dedifferentiation and proliferation of the cells are critical factors that influence the generation of transplants. The aim of our study was to find and characterize markers for cell proliferation and dedifferentiation in cultured chondrocytes. STUDY DESIGN AND SETTING: Human chondrocytes were isolated from septal cartilage and held in primary cell culture. Cells were harvested after 1, 6, and 21 days. The differentiation of the cells was investigated with bright-field microscopy, the expression patterns of various proteins using immunohistochemistry, and the expression of distinct genes with the microarray technique. RESULTS: The chondrocytes showed a strong proliferation. After 6 and 21 days, collagen 9 and 10 were downregulated; collagen 11 was activated. Collagen 1 and 2 were downregulated after 6 days but were reactivated after 21 days. Tumor growth factor beta (TGF-beta)1 was strongly expressed on days 1, 6, and 21, TGF-beta2 was never expressed, and TGF-beta3 and -beta4 were upregulated from day 1 to day 21. The TGF-beta receptor III was expressed on days 1, 6, and 21. Integrin beta1, beta5, and alpha5 were upregulated from day 1 to day 21; integrin beta3 was downregulated. CONCLUSION AND SIGNIFICANCE: Collagens 3, 4, 8, 9, and 11 might be new markers for the dedifferentiation of chondrocytes. Collagen 2 might be a marker for the synthetic activity of the cells rather than the dedifferentiation. TGF-beta3 and -beta4 might influence the dedifferentiation, which is fortified by the expression of TGF-beta receptor III. Integrin beta1, beta5, and alpha5 might be involved in signal transmission for the dedifferentiation.

Biomarkers↗
PubMed2006

Psammomatoid ossifying fibromas: immunohistochemical analysis and differential diagnosis with psammomatous meningiomas of craniofacial bones.

OBJECTIVE: To clarify the role of immunohistochemistry in the diagnosis of psammomatoid ossifying fibroma (PSOF), conventional cemento-ossifying fibroma (COF), and psammomatous meningioma (PM) of the craniofacial skeleton. STUDY DESIGN: The histology and immunohistochemistry of 4 PSOFs, 6 COFs, and 7 PMs was studied. Antibodies included EMA, cytokeratins, smooth muscle actin (SMA), desmin, vimentin, CD34, CD10, S-100 protein, and glial fibrillary acidic protein (GFAP). RESULTS: All PSOFs showed multiple round ossicles homogeneously distributed within a fibroblastic stroma. Psammomatous meningiomas had meningothelial features. All tumors, except 1 COF, were positive for EMA. All of them expressed vimentin, and none showed cytokeratins. Staining for SMA and S-100 protein was variable. CD10 was positive in all cases except 2 meningiomas. CD34 and GFAP stained only 1 case of meningioma each. CONCLUSIONS: The diagnosis of PSOF should rest on histologic features. An incorrect diagnosis of meningioma based on the expression of EMA should be avoided.

Actins↗
PubMed2004

Comprehensive transcriptome analysis of differentiation of embryonic stem cells into midbrain and hindbrain neurons.

Neurogenesis is one of the most complex events in embryonic development. However, little information is available regarding the molecular events that occur during neurogenesis. To identify regulatory genes and underlying mechanisms involved in the differentiation of embryonic stem (ES) cells to neurons, gene expression profiling was performed using cDNA microarrays. In mouse ES cells, we compared the gene expression of each differentiated cell stage using a five-stage lineage selection method. Of 10,368 genes, 1633 (16%) known regulatory genes were differentially expressed at least 2-fold or greater at one or more stages. At stage 3, during which ES cells differentiate into neural stem cells, modulation of nearly 1000 genes was observed. Most of transcription factors (Otx2, Ebf-3, Ptx3, Sox4, 13, 18, engrailed, Irx2, Pax8, and Lim3), signaling molecules (Wnt, TGF, and Shh family members), and extracellular matrix/adhesion molecules (collagens, MAPs, and NCAM) were up-regulated. However, some genes which may play important roles in maintaining the pluripotency of ES cells (Kruppel-like factor 2, 4, 5, 9, myeloblast oncogene like2, ZFP 57, and Esg-1) were down-regulated. The many genes identified with this approach that are modulated during neurogenesis will facilitate studies of the mechanisms underlying ES cell differentiation, neural induction, and neurogenesis.

Animals↗
PubMed2007

Porcine kallikrein gene family: genomic structure, mapping, and differential expression analysis.

Kallikreins belong to a family of serine proteases that are widespread throughout living organisms, expressed in diverse tissue-specific patterns, and known to have highly diverse physiological functions. The 15 human and 24 mouse kallikreins have been implicated in pathophysiology of brain, kidney, and respiratory and reproductive systems and often are used as cancer biomarkers. To better elucidate the structure and evolutionary origin of this important gene family in the pig, we have constructed a contiguous BAC clone-derived physical map of the porcine kallikrein gene region and have fully sequenced a BAC clone containing 13 kallikrein genes, 11 of which are novel. Radiation hybrid mapping assigns this kallikrein-gene-rich region to porcine chromosome 6. Phylogenetic and percent identity plot-based analyses revealed strong structure and order conservation of kallikreins among four mammalian species. Reverse transcriptase-polymerase chain reaction-based expression analysis of porcine kallikreins showed a complex expression pattern across different tissues with the thymus being the only tissue expressing all 13 kallikrein genes. [The sequence data described in this paper has been submitted to GenBank under Accession No. AC149292].

Animals↗
PubMed2026

Comprehensive analysis of differentially expressed mRNAs, lncRNAs, and miRNAs involved in ovarian differentiation and development in Qihe gibel carp (Carassius gibelio var. Qihe).

Qihe gibel carp (Carassius gibelio var. Qihe) exhibits diverse reproductive modes including gynogenesis and sexual reproduction, yet the molecular mechanisms of ovarian differentiation remain poorly understood. Ovarian tissues at 20, 30, and 60 days after hatching (dah), representing key stages covering early ovarian differentiation and primary oocyte growth, were subjected to whole-transcriptome sequencing. A total of 27,259 mRNAs, 2622 lncRNAs, and 2467 miRNAs were differentially expressed. Cell cycle, transcription, translation, and DNA replication pathways were significantly upregulated from 20 to 60 dah. Oocyte meiosis was enriched from 20 and 30 dah, whereas metabolic pathways (lipid, carbohydrate, and nucleotide metabolism) were enriched from 30 to 60 dah, indicating sequential progression from meiosis initiation to primary oocyte growth with nutrient synthesis. Hub lncRNAs and key ceRNA networks (e.g., MSTRG.28669.5-miR-221-ccnb2) were identified. This study provides the first comprehensive characterization of ncRNA-mediated regulation and ceRNA networks during ovarian development in Qihe gibel carp, establishing a foundation for understanding ovarian differentiation in this species.

Animals↗
PubMedDate not supplied

Analysis of differential clinical profiles of different antipsychotic molecules in the first psychotic episode: a retrospective study.

Our study starts from the supposition that the ideal pharmacological treatment should improve the patient's global behaviour, as a consequence of the therapeutic activity on positive, negative, behavioural, affective and cognitive symptoms. It should have few secondary effects, both in the short and long term, thus assuring a good life-quality, the fundamental condition for the patient's compliance and adherence. Currently only few studies have been published evaluating atypical antipsychotic effects vs. typical ones in the first psychotic episode, particularly studying different profile evaluations and different molecule rating standards. Our aim has been the therapeutic profile evaluation of atypical anti-psychotic molecules vs. typical ones, using "Liège's star" parameters (anti- manic, anti-autistic, anti-delusional, extra-pyramidal, ataraxic-sedative and adrenolitic). We added 2 complex scales, the first for loss in affectiveness, the second for cognitive and behavioural disorganization. We utilized Aosta's Psychiatric Service data-base, evaluating patients in their first psychotic episode diagnosed with various schizophrenic disorders per DSM IV criteria. We considered everyone who received, as monotherapy, or a typical molecule or an atypical one and who had been tested, at the beginning and at the end of the psychotic episode, with MMPI and PANSS Rating Scale. We evaluated 107 patients, 68 men and 39 women, whose mean age was 25,04 years (SD=3,789): 21 schizo-affective, 27 schizophreniform, 23 brief reactive psychosis and 36 paranoid- type schizophrenic disorders. The mean observation time was 117,18 days. Monotherapy was with olanzapine (23), quetiapine (8), risperidon (19), haloperidol (20), clopentixol (9), chlorpromazine (10), pimozide (8) and sulpiride (10). For the evaluation of adrenolitic, sedative and extrapyramidal effects we utilized clinical data and specific drugs administrations. We based our estimate for anti-delusional activity on P1, p3, p4, p5, p6, p7, g9 and g12 PANSS items score, correlated with Se and Pa MMPI results; for anti- autistic activity 2,3 and 4 PANSS items score related with MMPI Si Scale; for activity on behavioural and cognitive symptoms p2, n5, n6, n7 PANSS items score; for activity on negative symptoms PANSS negative global score. From the MMPI score we evaluated aggressiveness, hypochondria, negative symptoms, depression and psychasthenia. Our trial results hypothesise that neuroleptic anti-deficitary activity develops itself on different, qualitative and chronological levels: a continuous pathway from the original stimulus, through a dis-inhibiting effect to a final anti-autistic effect it would cause a deficit reduction. We haven't seen considerable differences between typical or atypical molecules perform inhibiting activity on D2 receptors. It seems that atypical molecules specific activity on D1, D3 and D4 receptors (affinity) and on 5HT2 receptors (inhibition) comes out as negative symptoms improve. We can say, too, that, according to compliance, adherence and concordance parameters, atypical molecules improve patient's life-quality through a good treatment and a real therapeutic alliance. Finally, we have seen that therapies with atypical molecules increase the family's satisfaction and compliance.

Adult↗
PubMed2000

Iron overload and gene expression in HepG2 cells: analysis by differential display.

The aim of the present study was to evaluate the effect of iron overload on gene expression in HepG2 cells by differential display. Iron-treated cells showed a 50% decrease in apolipoprotein B100 (Apo B100) and a 2- and 3-fold increase in semaphorin cd100 and aldose reductase mRNA, respectively, with parallel variations in Apo B100 and aldose reductase proteins. These effects were time-dependent. Vitamin E prevented the increase in aldose reductase expression, but had no effect on Apo B100 and semaphorin cd100. Treatment with hydrogen peroxide and 4-hydroxy-2,3-nonenal increased only aldose reductase mRNA. These data suggest that iron can affect mRNA levels by lipid peroxidation-dependent and -independent pathways.

Aldehyde Reductase↗
PubMed1998

Differential genome analysis applied to the species-specific features of Helicobacter pylori.

We introduce a simple and rapid strategy to identify genes that are responsible for species-specific phenotypes. The genome of a species that has a specific phenotype is compared with at least one, closely related, species that lacks this phenotype. Homologous genes that are shared among the species compared are identified and discarded from the list of candidates for species-specific genes. The process is automated and rapidly yields a small subset of the genome that likely contains genes responsible for the species-specific features. Functions are assigned to the genes, and dubious annotations are filtered out. Information is extracted not only from the presence of genes, but also from their absence with respect to known phenotypes. We have applied the technique to identify a set of species-specific genes in Helicobacter pylori by comparing it with its closest relatives for which complete genome sequences are available, Haemophilus influenzae and Escherichia coli. Of the genes of this set for which functional features can be obtained, a large fraction (63%, 123 proteins) is (potentially) involved in H. pylori's interaction with its host. We hypothesize that a family of outer membrane proteins is critical for the ability of H. pylori to colonize host cells in highly acidic environments.

Amino Acid Sequence↗