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Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment.

Seventy-four bacterial strains were freshly isolated from a mine gallery. Using these bacteria, we have investigated how a molecular identification based on the analysis of small subunit rDNA sequences would compare in terms of precision and reliability to a more classical comparison of phenotypical descriptions (100 morphological and physiological traits). Our data clearly showed that a phylogenetic analysis of small subunit rDNA sequences is more efficient than classical phenotypic methods for the identification of bacterial strains freshly isolated from a natural environment, because occurrences of misidentification are very much decreased by this method. The lack of rDNA sequences for many described species is probably the major cause of a few failures in molecular identification, as the completeness of the database of small subunit rDNA sequences holds much importance in the degree of uncertainty in such identifications.

Journal Article↗

The green non-sulfur bacteria: a deep branching in the eubacterial line of descent.

Ribosomal RNA sequence comparisons define a phylogenetic grouping, the green non-sulfur bacteria and relatives (GNS), known to contain the genera Chloroflexus, Herpetosiphon and Thermomicrobium--organisms that have little phenotypic similarity. The unit is phylogenetically deep, but entirely distinct from any other eubacterial division (phylum). It is also relatively ancient--branching from the common eubacterial stem earlier than any other group of eubacteria reported thus far. The group phenotype is predominantly thermophilic, and its thermophilic members, especially Thermomicrobium, are more slowly evolving than Herpetosiphon, a mesophile. The GNS unit appears significantly older than either the green sulfur bacteria or the cyanobacteria--making it likely that organisms such as Chloroflexus, not the cyanobacteria, generated the oldest stromatolites, which formed over three billion years ago.

Bacteria↗

Phylogenetic evidence for colour pattern convergence in toxic pitohuis: Müllerian mimicry in birds?

Bird species in the genus Pitohui are chemically defended by a potent neurotoxic alkaloid in their skin and feathers. The two most toxic pitohui species, the hooded pitohui (Pitohui dichrous) and the variable pitohui (Pitohui kirhocephalus), are sometimes strikingly patterned and, in certain portions of their geographical ranges, both species share a nearly identical colour pattern, whereas in other areas they do not. Müllerian mimicry (the mutual resemblance of two chemically defended prey species) is common in some other animal groups and Pitohui birds have been suggested as one of the most likely cases in birds. Here, we examine pitohui plumage evolution in the context of a well-supported molecular phylogeny and use a maximum likelihood approach to test for convergent evolution in coloration. We show that the 'mimetic' phenotype is ancestral to both species and that the resemblance in most races is better explained by a shared ancestry. One large clade of P. kirhocephalus lost this mimetic phenotype early in their evolution and one race nested deep within this clade appears to have re-evolved this phenotype. These latter findings are consistent with the hypothesis that Müllerian mimicry is driving the evolution for a similar colour pattern between P. dichrous, but only in this one clade of P. kirhocephalus

Animals↗

Periostin promotes atrioventricular mesenchyme matrix invasion and remodeling mediated by integrin signaling through Rho/PI 3-kinase.

Recent evidence suggests that extracellular matrix components may play a signaling role in embryonic valve development. We have previously identified the spatiotemporal expression patterns of periostin in developing valves, but its function during this process is largely unknown. To evaluate the functional role periostin plays during valvulogenesis, two separate three-dimensional culture assay systems, which model chick atrioventricular cushion development, were employed. These assays demonstrated that cushion mesenchymal cells adhered and spread on purified periostin in a dose-responsive manner, similar to collagen I and fibronectin via alpha(v)beta(3) and beta(1) integrin pairs. Periostin overexpression resulted in enhanced mesenchyme invasion through 3D collagen gels and increased matrix compaction. This invasion was dependent on alpha(v)beta(3) more than beta(1) integrin signaling, and was mediated differentially by Rho kinase and PI 3-kinase. Both matrix invasion and compaction were associated with a colocalization of periostin and beta(1) integrin expression to migratory cell phenotype in both surface and deep cells. The Rho/PI 3-kinase pathway also differentially mediated matrix compaction. Both Rho and PI 3-kinase were involved in normal cushion mesenchyme matrix compaction, but only PI 3-kinase was required for the enhanced matrix compaction due to periostin. Taken together, these results highlight periostin as a mediator of matrix remodeling by cushion mesenchyme towards a mature valve structure.

Adenoviridae↗

Potentially epileptogenic dysfunction of cortical NMDA- and GABA-mediated neurotransmission in Otx1-/- mice.

Knockout Otx1 mice present a microcephalic phenotype mainly due to reduced deep neocortical layers and spontaneous recurrent seizures. We investigated the excitable properties of layer V pyramidal neurons in neocortical slices prepared from Otx1-/- mice and age-matched controls. The qualitative firing properties of the neurons of Otx1-/- mice were identical to those found in wild-type controls, but the proportion of intrinsically bursting (IB) neurons was significantly smaller. This is in line with the lack of the Otx1 gene contribution to the generation and differentiation of neurons destined for the deep neocortical layers, in which IB neurons are located selectively in wild-type rodents. The pyramidal neurons recorded in Otx1-/- mice responded to near-threshold electrical stimulation of the underlying white matter, with aberrant polysynaptic excitatory potentials often leading to late action potential generation. When the strength of the stimulus was increased, the great majority of the Otx1-/- neurons (78%) responded with a prominent biphasic inhibitory postsynaptic potential that was significantly larger than that observed in the wild-type mice, and was often followed by complex postinhibitory depolarizing events. Both late excitatory postsynaptic potentials and postinhibitory excitation were selectively suppressed by NMDA receptor antagonists, but not by AMPA antagonists. We conclude that the cortical abnormalities of Otx1-/- neocortex due to a selective loss of large projecting neurons lead to a complex rearrangement of local circuitry, which is characterized by an excess of N-methyl-d-aspartate-mediated polysynaptic excitation that is counteracted by GABA-mediated inhibition in only a limited range of stimulus intensity. Prominent postsynaptic inhibitory potentials may also act as a further pro-epileptogenic event by synchronizing abnormal excitatory potentials.

2-Amino-5-phosphonovalerate↗

Slow myosin in developing rat skeletal muscle.

Through S1 nuclease mapping using a specific cDNA probe, we demonstrate that the slow myosin heavy-chain (MHC) gene, characteristic of adult soleus, is expressed in bulk hind limb muscle obtained from the 18-d rat fetus. We support these results by use of a monoclonal antibody (mAb) which is highly specific to the adult slow MHC. Immunoblots of MHC peptide maps show the same peptides, uniquely recognized by this antibody in adult soleus, are also identified in 18-d fetal limb muscle. Thus synthesis of slow myosin is an early event in skeletal myogenesis and is expressed concurrently with embryonic myosin. By immunofluorescence we demonstrate that in the 16-d fetus all primary myotubes in future fast and future slow muscles homogeneously express slow as well as embryonic myosin. Fiber heterogeneity arises owing to a developmentally regulated inhibition of slow MHC accumulation as muscles are progressively assembled from successive orders of cells. Assembly involves addition of new, superficial areas of the anterior tibial muscle (AT) and extensor digitorum longus muscle (EDL) in which primary cells initially stain weakly or are unstained with the slow mAb. In the developing AT and EDL, expression of slow myosin is unstable and is progressively restricted as these muscles specialize more and more towards the fast phenotype. Slow fibers persisting in deep portions of the adult EDL and AT are interpreted as vestiges of the original muscle primordium. A comparable inhibition of slow MHC accumulation occurs in the developing soleus but involves secondary, not primary, cells. Our results show that the fate of secondary cells is flexible and is spatially determined. By RIA we show that the relative proportions of slow MHC are fivefold greater in the soleus than in the EDL or AT at birth. After neonatal denervation, concentrations of slow MHC in the soleus rapidly decline, and we hypothesize that, in this muscle, the nerve protects and amplifies initial programs of slow MHC synthesis. Conversely, the content of slow MHC rises in the neonatally denervated EDL. This suggests that as the nerve amplifies fast MHC accumulation in the developing EDL, accumulation of slow MHC is inhibited in an antithetic fashion. Studies with phenylthiouracil-induced hypothyroidism indicate that inhibition of slow MHC accumulation in the EDL and AT is not initially under thyroid regulation. At later stages, the development of thyroid function plays a role in inhibiting slow MHC accumulation in the differentiating EDL and AT.(ABSTRACT TRUNCATED AT 400 WORDS)

Aging↗

[Alagille's syndrome: a family case and its association with hepatocellular carcinoma].

Two cases of Alagille syndrome are reported, father and son. This, a 6-year-old boy, presented with neonatal cholestasis but thereafter evolved with progressively decreasing jaundice and persisting pruritus. A liver biopsy confirmed the absence of intrahepatic bile ducts with preservation of hepatic architecture and no fibrosis. The patient had a characteristic phenotype: short stature, triangular face, deep eyes with hypertelorism, partial embryotoxon and data of peripheral pulmonary artery stenosis. His father died 43-year-old by a hepatocarcinoma. His liver biopsy showed also absence of intrahepatic bile ducts. In addition to the association Alagille's syndrome hepatocarcinoma (previously reported in six cases, three into the same family), it should be stressed in this case the long survival and the fact he had many children: the case with Alagille's syndrome, five children in good health, and one who died shortly after birth.

Abnormalities, Multiple↗

Barrett's oesophagus with predominant intestinal metaplasia correlates with superficial cyclo-oxygenase-2 expression, increased proliferation and reduced apoptosis: changes that are partially reversed by non-steroidal anti-inflammatory drugs usage.

BACKGROUND: Cyclo-oxygenase-2 expression has been reported to play an important role in the metaplasia-dysplasia-carcinoma sequence in Barrett's oesophagus. However, the existence of cyclo-oxygenase-2 expressing cells in Barrett's epithelium is still uncertain. AIM: To identify the cells that express cyclo-oxygenase-2 protein and to investigate the relationship between cyclo-oxygenase-2 expression and mucin-phenotype of Barrett's epithelium. METHODS: Sections from 466 biopsy samples of Barrett's epithelium from 358 non-medicated patients were immunohistochemically examined for the cyclo-oxygenase-2 expression, mucin-phenotype, cell proliferation and apoptosis. RESULTS: Cyclo-oxygenase-2 expression was detected in 71.0% of Barrett's epithelium biopsy samples. In Barrett's epithelium with the gastric predominant mucin-phenotype, cyclo-oxygenase-2 expression was mainly found in stromal and deep epithelial cells, whereas in intestinal predominant mucin-phenotype, it was mostly in superficial epithelial cell. A significant elevation of proliferating cell nuclear antigen index and suppression of apoptotic index was observed in Barrett's epithelium with superficial epithelial cyclo-oxygenase-2 expression. Neither such elevation of proliferating cell nuclear antigen index nor the suppression of apoptotic index could be found in chronic non-steroidal anti-inflammatory drugs users. CONCLUSIONS: Barrett's epithelium with intestinal mucin and superficial epithelial cyclo-oxygenase-2 expression possess a higher proliferation potential, but this risk may be thwarted by non-steroidal anti-inflammatory drugs administration.

Anti-Inflammatory Agents, Non-Steroidal↗

Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment.

Vol. 61, no. 9, p. 3406: the Acknowledgments should read as follows. "This work was supported by the CNRS and by grants of the European Community and ANDRA as part of the project Archimede-Argiles and of the Direction de la Recherche et des Etudes Doctorales. V.B. was a recipient of a CIFRE fellowship." [This corrects the article on p. 3400 in vol. 61.].

Journal Article↗

Differential effect of cyclosporin application on epithelial cells of the rat thymus. Immunohistochemical study.

Young adult male Wistar rats were given 30 mg per kg of cyclosporin (CS) for 21 consecutive days. A panel of monoclonal antibodies was used to study the phenotype of thymic epithelial cells. After treatment with CS, subcapsular epithelial cells, although phenotypically similar to medullary epithelial cells, were changed in a similar manner to phenotypically distinct epithelial cells of the deep cortex. These cells became enlarged, stockier and their cytoplasmic prolongations were thicker and coarser compared with control cells and their number was not decreased. In contrast, the number of medullary epithelial cells was markedly reduced, whereby the cells with the most mature phenotype (CK8+10-19- and CK8+10+19-) were the most prominently depleted. No proliferation of thymic epithelial cells was detected as monitored by incorporation of 5-bromodeoxyuridine.

Animals↗

Prognostic value of an assessment of ABH(0) isoantigens and Thomsen-Friedenreich (TF) antigen expression in patients with urinary bladder tumours.

The discriminating and prognostic value of the expression of ABH(0) and TF antigens in tumour cells of 76 patients with urinary bladder tumours was evaluated. In patients with superficial tumours the most frequently defined phenotype was ABH(-) TF(+) and in those with deep tumours ABH(-) TF(-). The lowest frequency of recurrences was seen in patients with TFCr(+) antigenic phenotype and no patient died in this group. The mean lifespan of patients with TF(-) tumours was shorter (21 months) than of those with TF(+) tumours. For detection of tumours with higher risk of recurrences an analysis of the combination of markers revealed to be more predictive than analysis of a single marker.

ABO Blood-Group System↗

Epigenetic inheritance, genetic assimilation and speciation.

Epigenetic inheritance systems enable the environmentally induced phenotypes to be transmitted between generations. Jablonka and Lamb (1991, 1995) proposed that these systems have a substantial role during speciation. They argued that divergence of isolated populations may be first triggered by the accumulation of (heritable) phenotypic differences that are later followed and strengthened by genetic changes. The plausibility of this idea is examined in this paper. At first, we discuss the "exploratory" behaviour of an epigenetic inheritance system on a one peak adaptive landscape. If a quantitative trait is far from the optimum, then it is advantageous to induce heritable phenotypic variation. Conversely, if the genotypes get closer to the peak, it is more favorable to canalize the phenotypic expression of the character. This process would lead to genetic assimilation. Next we show that the divergence of heritable epigenetic marks acts to reduce or to eliminate the genetic barrier between two adaptive peaks. Therefore, an epigenetic inheritance system can increase the probability of transition from one adaptive state to another. Peak shift might be initiated by (i) slight changes in the inducing environment or by (ii) genetic drift of the genes controlling epigenetic variability. Remarkably, drift-induced transition is facilitated even if phenotypic variation is not heritable. A corollary of our thesis is that evolution can proceed through suboptimal phenotypic states, without passing through a deep adaptive valley of the genotype. We also consider the consequences of this finding on the dynamics and mode of reproductive isolation.

Animals↗

Expression of ets-1 transcription factor is correlated with penetrating tumor progression in patients with squamous cell carcinoma of the esophagus.

BACKGROUND: The Ets-1 transcription factor is proposed to play a role in tumor invasion. To evaluate the biologic significance of Ets-1 in the progression of squamous cell carcinoma of the esophagus, the authors investigated Ets-1 expression in tumors from 90 patients using immunohistochemical procedures. METHODS: The Ets-1 positive ratio (Ets-1 ratio) was determined in the center and deep margin areas of invasive sites and in the center and outer edge areas of intraepithelial spread contiguous with invasive disease. RESULTS: Ets-1 expression was heterogeneous within tumor tissue. The Ets-1 ratio was significantly higher at invasive sites compared with intraepithelial spread sites, and at deep margin areas compared with center areas (P < 0.0001 and P < 0.05, respectively, by two-way analysis of variance). No differences were noted in the Ets-1 ratio at the deep margin areas at each depth of invasion. Investigating the Ets-1 ratio at deep margin areas in each pathologic phenotype, the ratio of the small nest type was found to be higher than that of the large nest type (P < 0.0001). CONCLUSIONS: The authors propose that Ets-1 plays an important role in penetrating tumor progression, even very early in the invasive process (especially in the case of infiltrative invasive type tumors) at the deep margin areas of invasive sites in patients with squamous cell carcinoma of the esophagus.

Aged↗

Development of a Langerhans cell phenotype from peripheral blood monocytes.

Epidermal Langerhans cells (ELC) are definitively primed to differentiate into dendritic cells (DC). It is unknown at what stage of monocyte development this priming occurs. In a culture system characterized by low paracrine stimulation, i.e. Iscove's modified Dulbecco medium (IMDM) with 2% FCS, we tested the ability of peripheral blood monocytes to turn to the route of the LC-DC lineage. In this system monocytes did not develop significant yeast cell phagocytosis, although mannose receptors were available. However, they became strong stimulators of mannan specific T cell proliferation. Phenotype development was analysed by flow cytometry using the monoclonal antibodies OKT6 (CD1a), IOT2 (HLA-DR), IOM2 (CD14) and the ligand Man-BSA-FITC. CD1a was the first marker which distinguished cultured monocytes from developing macrophages, obtained by addition of 8% human serum. Like cord blood Langerhans cells (CBLC) they internalized OKT6 in deep coated pits. They maintained a phenotype of monocyte derived Langerhans cells (MoLC) during eight days of in vitro culture, expressing CD1a, mannose receptors and HLA-DR and decreasing CD14, if left in their own conditioned medium. MoLC could be converted into macrophages by addition of human serum only within the first four days in vitro. Our data suggest that monocytes acquire an LC phenotype by autocrine stimulation.

Antigens, CD↗

Discrimination of strains of Candida albicans isolated from deep and superficial sites by resistotyping.

Resistotyping was used to characterise 106 strains of Candida albicans classified as to whether they came from deep or superficial infections. The data were analysed by logistic regression analysis. There was a statistically significant difference between the two groups of strains. After removal of variables by the log-likelihood method four resistotyping agents were found to predict source of strain: boric acid, benzalkonium chloride, malachite green and mercurochrome. Whilst there were phenotypic differences between strains isolated from deep and superficial sites it is not clear whether this strain represents different strain types or strain histories.

Candida albicans↗

Cytokine and growth factor mRNA expression patterns associated with the hypercontracted, hyperpigmented healing phenotype of red duroc pigs: a model of abnormal human scar development?

BACKGROUND: Skin wounds in red Duroc pigs heal with the formation of hypercontractile, hyperpigmented scars, similar in some respects to human hypertrophic scars. OBJECTIVE: The goal of this study was to characterize the mRNA expression patterns for a subset of relevant cytokines, growth factors, receptors, and transcription factors involved in the red Duroc scarring phenotype. METHODS: Full-thickness and deep dermal wounds were created on the backs of juvenile female red Duroc pigs. Samples were taken every two weeks postwounding and total RNA and DNA were extracted and quantified. RT-PCR was performed using porcine gene-specific primers for 15 relevant molecules. RESULTS: The majority of molecules examined exhibited a biphasic pattern of expression, with peaks of expression at days 14 and 56 postinjury. CONCLUSIONS: The molecular expression pattern observed correlates well with the gross healing phenotype and matrix molecule expression patterns previously reported in red Duroc pigs. These findings enhance our understanding of the processes associated with fibroproliferative scar-formation.

Animals↗

Taxonomy and biotransformation activities of some deep-sea actinomycetes.

Deep-sea soft sediments from trench systems and depths in the northwestern Pacific Ocean ranging from less than 300 to 10,897 m in depth have been analyzed for three target genera of actinomycetes: Micromonospora, Rhodococcus, and Streptomyces. Only culturable strains, recovered at atmospheric pressure on selective isolation media, have been examined to date. Maximum recoveries of culturable bacteria were greater that 10(7)/ml wet g sediment, but actinomycetes comprised a small proportion of this population (usually less than 1%). The target actinomycetes were isolated at all depths except from the Mariana Trench sediments. Actinomycete colonies were defined initially on the basis of colony morphologies, and preliminary identification then was made by chemotaxonomic tests. Pyrolysis mass spectrometry (PyMS) of deep-sea mycolic acid-containing actinomycetes gave excellent correspondence with numerical (phenetic) taxonomic analyses and subsequently was adopted as a rapid procedure for assessing taxonomic diversity. PyMS analysis enabled several clusters of deep-sea rhodococci to be distinguished that are quite distinct from all type strains. 16S rRNA gene sequence analysis has revealed that several of these marine rhodococci have sequences that are very similar to certain terrestrial species of Rhodococcus and to Dietzia. There is evidence for the intrusion of terrestrial runoff into these deep trench systems, and the inconsistency of the phenotypic and molecular taxonomies may reflect recent speciatiion events in actinomycetes under the high-pressure conditions of the deep sea. The results of DNA-DNA pairing experiments point to the novelty of Rhodococcus strains recovered from hadal depths in the Izu Bonin Trench. Biotransformation studies of deep-sea bacteria have focused on nitrile compounds. Nitrile-metabolizing bacteria, closely related to rhodococci, have been isolated that grow well at low temperature, high salt concentrations, and high pressures, suggesting that they are of marine origin or have adapted to the deep-sea environment.

Actinomycetales↗

Investigation of sexual dimorphism in the rabbit masseter muscle showing different effects of androgen deprivation in adult and young adult animals.

To evaluate the role played by androgens in the development and maintenance of sex differences in the proportion of muscle fibres of different phenotypes, the effects of castration in adult (>6 months old) and in young adult (2-3 months old) male rabbits was examined. Immunohistochemical methods were used to evaluate the proportion of muscle fibres containing different myosin heavy-chain isoforms in 10 different neuromuscular compartments of the masseter. In young adult animals of both sexes, the proportion of fibres of different phenotypes in different compartments was not significantly different from that of normal adult females. In animals castrated as young adults, the development of adult male phenotype proportions was completely blocked in most compartments. In animals castrated as adults, proportions were not significantly different from those of the intact males. For most masseter compartments, androgens produced permanent changes in muscle fibre phenotype during a critical period of postnatal development. However, in the posterior deep compartment, androgen deprivation in young adults had no effect on phenotype proportions, but castration of adults resulted in a striking increase in the proportion of fibres containing the IIa myosin heavy-chain isoform.

Age Factors↗