Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Deep phenotyping”

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 649 records · Page 36Linked to original sources

[A case of HNPP presenting with late onset of symptoms, chronic progressive course and sensory impairment in face and trunk].

A 69-year-old man was admitted with a chief complaint of progressive muscle weakness and tingling sensation in the distal portion of all extremities since the age of 55. On neurological examination, sensory impairment of all modalities was noted in the right side of face, segmental areas of the right Th4-10 and the distal portion of four extremities. Symmetrical muscle weakness and atrophy was also found over the distal portion of all extremities. All deep tendon reflexes except biceps brachii reflexes were absent. Neurophysiological studies, however, rather indicated mononeuritis multiplex in this case. The biopsied specimen of the sural nerve showed a significant decrease in large myelinated fibers and many tomaculous changes. The gene analysis revealed deletion in the CMT 1A locus on chromosome 17p11.2, providing evidence for the diagnosis of hereditary neuropathy with liability to pressure palsies (HNPP). The development of sensory impairment in face or thoracic nerves is quite rare in HNPP, indicating that there exists considerable phenotypic heterogeneity in the disease.

Aged↗

A standard strain of human ocular keratocytes.

The ability of an injured cornea to regenerate from deep tissue trauma is largely due to wound healing processes mediated by the surviving stromal keratocytes. Despite the importance of the wound healing process, and the ease with which keratocytes can be grown in tissue culture, a standardised strain of the cells has never been made available. Accordingly, this study reports a strain of human embryonic keratocytes, designated EK1.BR as a research tool for the ophthalmic community. EK1.BR has been characterised with respect to life-span, fraction of dividing cells and maintenance of a keratocyte phenotype in culture. It is hoped that these cells will prove useful in the in vitro study of stromal wound healing and the characterisation of keratocyte gene expression.

Aged↗

The role of the first postmitotic cortical cells in the development of thalamocortical innervation in the reeler mouse.

In the mutant mouse reeler, the tangential distribution of thalamocortical fibers is essentially normal, even though neurons of the cortical plate accumulate below the entire early-born preplate population (Caviness et al., 1998). This seems incompatible with the hypothesis that cells of the subplate (the lower component of the preplate in normal mammals) form an axonal scaffold that guides thalamic fibers and act as temporary targets for them (Blakemore and Molnár, 1990, Shatz et al., 1990). We used carbocyanine dyes to trace projections in wild-type and reeler mice between embryonic day 13 and postnatal day 3. Preplate formation and early extension of corticofugal fibers to form a topographic array are indistinguishable in the two phenotypes. So too are the emergence of thalamic axons in topographic order through the primitive internal capsule, their meeting with preplate axons, and their distribution over the preplate scaffold. Distinctive differences appear after the cortical plate begins to accumulate below the preplate of reeler, causing the preplate axons to form oblique fascicles, running through the cortical plate. Thalamic axons then pass through the plate within the same fascicles and accumulate in the "superplate" layer for approximately 2-3 d, before defasciculating and plunging down to terminate deep in the cortical plate, creating the curious "looping" pattern seen in the adult. Thus, thalamocortical innervation in reeler follows the same algorithm of development but in relation to the misplaced population of early-born neurons. Far from challenging the theory that preplate fibers guide thalamic axons, reeler provides strong evidence for it.

Animals↗

Ultrastructural and immunocytochemical analysis of the circumferential microfilament bundle in avian retinal pigmented epithelial cells in vitro.

The dedifferentiated phenotype of pigmented epithelial cells in vitro is bipotential and is effected by environmental alterations mediated by the cell surface and associated cytoskeleton. We have begun an investigation into the role that contractile microfilaments play in maintaining cell contact and cell shape in retinal pigmented epithelial cells in vitro. In this paper, we report a structural analysis of the intersection of the circumferential microfilament bundle with the cell membrane of cultured pigmented epithelial cells from chick retina. Techniques of electron microscopy, including freeze-fracturing and deep-etching, reveal that microfilaments of this bundle associate with a junctional complex in the apical cell compartment and with membrane domains which are not components of the junction. Microfilaments link with the cell membrane either at their termini or along the membrane-apposed surface of the circumferential bundle. Furthermore, we report the immunocytochemical localization of filamin (a high molecular weight actin-binding protein, which forms fiber bundles and sheet-like structures when bound with F-actin in solution) in the circumferential/microfilament bundle.

Actin Cytoskeleton↗

Localization of types I, II and X collagen and osteocalcin in intramembranous, endochondral and chondroid bone of rats.

Chondroid bone is a unique calcified tissue intermediate between bone and cartilage. To clarify its characteristics, we examined the distributions of the ECMs associated with chondrogenic differentiation and matrix calcification in the chondroid bone of the rat glenoid fossa, and compared them to those in two typical bone tissues, alveolar bone of the maxilla (intramembranous bone) and the growth plate of long bone (endochrondral bone), using immunofluorescence techniques. Morphologically, the glenoid fossa consisted of the fibrous, progenitor and cartilaginous cell layers and the cartilaginous cell layer was further divided into the superficial non-hypertrophic layers (secondary cartilage) and the deep hypertrophic cell layers (chondroid bone). The co-distribution of type I and type II collagens was observed in secondary cartilage and chondroid bone, whereas type X collagen was restricted to the pericellular matrix of hypertrophied cells (chondroid bone). Osteocalcin, which was absent from the calcified cartilage of endochondral bone formation, was also present in the ECM of the chondroid bone, but not in cells. These results demonstrate that chondroid bone of rats, which is adjacent to secondary-type cartilage in the glenoid fossa, has phenotypic expressions associated with both hypertrophied chondrocytes and osteocytes.

Animals↗

Isolation and characterization of a Geobacillus thermoleovorans strain from an ultra-deep South African gold mine.

A thermophilic facultative bacterial isolate was recovered from 3.2km depth in a gold mine in South Africa. This isolate, designated GE-7, was cultivated from pH 8.0, 50 degrees C water from a dripping fracture near the top of an exploration tunnel. GE-7 grows optimally at 65 degrees C and pH 6.5 on a wide range of carbon substrates including cellobiose, hydrocarbons and lactate. In addition to O(2), GE-7 also utilizes nitrate as an electron acceptor. GE-7 is a long rod-shaped bacterium (4-6microm longx0.5microm wide) with terminal endospores and flagella. Phylogenetic analysis of GE-7 16S rDNA sequence revealed high sequence similarity with G. thermoleovorans DSM 5366(T) (99.6%), however, certain phenotypic characteristics of GE-7 were distinct from this and other previously described strains of G. thermoleovorans.

Bacillaceae↗

Expression of CD44 in human neoplastic and normal hyaline cartilage.

Although low-grade cartilage neoplasms typically consist of hyaline-like cartilage, most of them also contain some fibrocartilaginous regions. CD44, a cell surface receptor for hyaluronan, has been identified in cartilage. A family of alternatively spliced mRNA containing the variant 6 (v6) exon sequence of CD44 has been linked to several types of neoplasms. We hypothesized that expressions of v6-containing CD44 species are associated with fibrocartilaginous regions of low-grade cartilage neoplasms. To test this hypothesis we performed reverse transcriptase-polymerase chain reaction (RT-PCR) and immunohistochemical analysis on eight samples: four from normal articular cartilage, one from a synovial chondromatosis, and three chondrosarcomas which were graded as I and I/II. The standard CD44s and a unique v6-containing CD44 species (CD44v6-10) were identified in all tissue samples by RT-PCR analysis. Immunohistochemically, using an antibody that cross-reacted with all CD44 species, CD44 was localized to the cell surface, lacuna wall and intracellular compartment of the chondrocytes in the middle and deep zone of normal cartilage, as well as with cells throughout the neoplastic masses. Utilizing an antibody specific for v6-containing CD44 species, the variant species was identified throughout cells of the middle and deep zone of normal cartilage, and localized selectively to intracellular positions. In neoplastic masses, v6-containing CD44 species were found associated only with cells in the hyaline-like cartilage, but not in the fibrocartilaginous regions. Thus a differential expression of the v6-containing CD44 species in the neoplastic masses containing both hyaline-like cartilage and fibrocartilaginous regions was observed when compared to its homogenous expression in normal hyaline cartilage. An involvement between the lack of the variant CD44 (v6-containing) and altered tissue phenotype (e.g., fibrocartilaginous) is suggested.

Bone Neoplasms↗

[Infiltration of the meninges or brain by a non-Hodgkin's lymphoma, diagnosed by flow cytometry in cerebrospinal fluid].

INTRODUCTION: Two forms of growth are reported in the neuroradiology of cerebral lymphomas: mass, single or multiple lesions, with homogeneous contrast enhancement, and diffuse infiltration. Flow cytometry enables us to diagnose non-Hodgkin's lymphoma, when clonality of B cells is detected. It is usually employed with peripheral blood or bone marrow samples but can be used with cerebrospinal fluid (CSF). CASE REPORT: We report the case of a 68-year-old female, who was admitted to hospital because of rapidly progressive onset of confusion and right-side hemiparesis that developed in a matter of days. Magnetic resonance imaging (MRI) of the head showed a diffuse infiltrative lesion, without contrast enhancement, which covered the left basal nuclei, the left frontal white matter, the genu of the corpus callosum and the right frontal white matter. The CSF showed slight pleocytosis (20 cells/mL) and a notable degree of hypoglycorrhachia (10 mg/dL). The cytological examination only revealed lymphocytes, with no data indicating atypicality. The flow cytometry assay detected large mononuclear B cells, with the CD19 + CD20 + CD10-lambda phenotype, which is characteristic of diffuse non-Hodgkin's lymphoma of large B cells. The clinical course ran quickly towards a fatal outcome; it progressed to left-side hemiplegia and coma, and the patient died two weeks after admission to hospital. CONCLUSIONS: In cases of cerebral lymphoma, especially when the neuroradiological pattern displays diffuse infiltration and there are anomalies involving CSF, the flow cytometry in CSF can be diagnostic, thus avoiding the need for other invasive brain procedures to deal with lesions that are usually located deep inside the brain at badly defined sites.

B-Lymphocytes↗

RecD function is required for high-pressure growth of a deep-sea bacterium.

A genomic library derived from the deep-sea bacterium Photobacterium profundum SS9 was conjugally delivered into a previously isolated pressure-sensitive SS9 mutant, designated EC1002 (E. Chi and D. H. Bartlett, J. Bacteriol. 175:7533-7540, 1993), and exconjugants were screened for the ability to grow at 280-atm hydrostatic pressure. Several clones were identified that had restored high-pressure growth. The complementing DNA was localized and in all cases found to possess strong homology to recD, a DNA recombination and repair gene. EC1002 was found to be deficient in plasmid stability, a phenotype also seen in Escherichia coli recD mutants. The defect in EC1002 was localized to a point mutation that created a stop codon within the recD gene. Two additional recD mutants were constructed by gene disruption and were both found to possess a pressure-sensitive growth phenotype, although the magnitude of the defect depended on the extent of 3' truncation of the recD coding sequence. Surprisingly, the introduction of the SS9 recD gene into an E. coli recD mutant had two dramatic effects. At high pressure, SS9 recD enabled growth in the E. coli mutant strain under conditions of plasmid antibiotic resistance selection and prevented cell filamentation. Both of these effects were recessive to wild-type E. coli recD. These results suggest that the SS9 recD gene plays an essential role in SS9 growth at high pressure and that it may be possible to identify additional aspects of RecD function through the characterization of this activity.

Escherichia coli↗

Terminal cytokinesis events uncovered after an RNAi screen.

Much of our understanding of animal cell cytokinesis centers on the regulation of the equatorial acto-myosin contractile ring that drives the rapid ingression of a deep cleavage furrow. However, the central part of the mitotic spindle collapses to a dense structure that impedes the furrow and keeps the daughter cells connected via an intercellular bridge. Factors involved in the formation, maintenance, and resolution of this bridge are largely unknown. Using a library of 7,216 double-stranded RNAs (dsRNAs) representing the conserved genes of Drosophila, we performed an RNA interference (RNAi) screen for cytokinesis genes in Schneider's S2 cells. We identified both familiar and novel genes whose inactivation induced a multi-nucleate phenotype. Using live video microscopy, we show that three genes: anillin, citron-kinase (CG10522), and soluble N-ethylmaleimide sensitive factor (NSF) attachment protein (alpha-SNAP), are essential for the terminal (post-furrowing) events of cytokinesis. anillin RNAi caused gradual disruption of the intercellular bridge after furrowing; citron-kinase RNAi destabilized the bridge at a later stage; alpha-SNAP RNAi caused sister cells to fuse many hours later and by a different mechanism. We have shown that the stability of the intercellular bridge is essential for successful cytokinesis and have defined genes contributing to this stability.

Actins↗

Defective responses of transformed keratinocytes to terminal differentiation stimuli. Their role in epidermal tumour promotion by phorbol esters and by deep skin wounding.

Epidermal tumourigenesis can be achieved in rodents by the application of a single subthreshold dose of a carcinogen (initiation) followed by repeated applications of a tumour promoter such as 12-0-tetradecanoyl phorbol, 13-acetate (TPA). TPA induces terminal differentiation in the majority of epidermal keratinocytes in vitro. However, transformed keratinocytes respond weakly to this terminal differentiation signal, and it is suggested that this property allows initiated cells and their progeny to obtain a selective advantage over their normal counterparts during promotion of papilloma formation by TPA. New data are reviewed which suggest that a putative wound hormone TGF-beta has similar differential effects on normal and transformed epithelial cells to those of TPA. It is proposed that the release of TGF-beta from platelets following deep skin wounding may be an explanation as to why wounding is a promoting stimulus but milder forms of epidermal injury are not. Weakly promoting hyperplasiogenic agents are also discussed within the context of a selection theory of tumour promotion.

Animals↗

The delay phenomenon: the story unfolds.

Our previous studies have shown that when a flap is delayed, there is dilation of existing vessels within the flap not ingrowth of new vessels. The maximal anatomic effect on the arterial tree occurs at the level of the reduced-caliber "choke" anastomotic vessels that link adjacent vascular territories. To further investigate the sequence of anatomic changes that occurs during the delay phenomenon, a large series of 200 rabbits and 17 dogs underwent a flap delay procedure in either skin or muscle and the tissues were examined at postoperative periods between 1 hour and 1 year by using well-established fluorescein, angiographic, light microscopic, immunohistochemical, and electron microscopic techniques. These data in the rabbit skin consistently demonstrated an initial period of vasoconstriction that resolved within 3 hours postoperatively and was followed by an active and progressive dilation of choke vessels that was most dramatic between 48 and 72 hours. In vivo intravenous fluorescein dye testing revealed an interesting parallel in that there was a temporary barrier to the flow of fluorescein that occurred at the level of the choke vessels immediately after the flap was raised and that this temporary barrier-continued to impede the flow toward the flap tip in rabbits where flaps had been delayed for periods up to 72 hours. Thereafter, there was no obstruction to the flow of fluorescein along the flap. During this early delay period of 3 days, light microscopy revealed a decrease in vessel wall thickness associated with an increase in lumen diameter. Over the next 4 days, the luminal diameter continued to dilate to a lesser extent and the vessel wall thickened. Immunohistochemical analysis showed increased cell division, maximal between 24 and 72 hours, in all layers of the choke vessel wall. During this same postoperative interval, transmission electron microscopy revealed phenotypic changes in smooth muscle cells from contractile to synthetic cells. Hypertrophy of the smooth muscle cells was also observed. The vascular endothelium, which initially showed evidence of denudation, was restored to a healthy intact appearance within the first week after delay. When followed for longer periods, long-term studies of the delayed flap of up to 1 year demonstrated dramatically a permanent dilation of the choke vessel lumen and a thickening of the choke vessel wall. In canine studies, one rectus abdominis muscle was delayed by ligating the deep inferior epigastric artery. The time sequence of choke vessel dilation, studied by sequential angiograms in vivo, was comparable to that of the rabbit skin model. To ascertain the permanence and irreversibility of this dilation, the normal circulation of the delayed rectus abdominis muscle was restored by reanastomosing the deep inferior epigastric artery. Even after a recovery period of up to 3 months, the choke vessels remained dilated and tortuous instead of reverting to their original narrow diameters. From this work, it is suggested that the choke vessel dilation seen in the delay period is a permanent and irreversible event. It is an active process associated with both an increase (hyperplasia) and an enlargement (hypertrophy) of the cells in all layers of the choke artery wall and a resultant increase in caliber of these vessels. The time sequence for delay appears to be similar in different species and in different tissues, suggesting the possibility of a universal process for delay.

Animals↗

Selection of quiescent Escherichia coli with high metabolic activity.

Sustained metabolic activity in non-growing, quiescent cells can increase the operational life-span of bio-processes and improve process economics by decoupling production from cell growth. Because of the ill-defined molecular nature of this phenotype, we developed selection protocols for the evolution of quiescent Escherichia coli mutants that exhibit high metabolic activity in ammonium starvation-induced stationary phase. The best enrichment procedures were continuously or discontinuously fed ammonium-limited chemostat cultures with a very low dilution rate of 0.03 h(-1). After 40 generations of selection, improved mutants with up to doubled catabolic rates in stationary phase were isolated. The metabolically most active clones were identified by screening for high specific glucose uptake rates during ammonium starvation-induced stationary phase in deep-well microtiter plates.

Biological Evolution↗

Basal cell carcinoma: a dermatopathological and molecular biological update.

The ideal classification of basal cell carcinoma (BCC) should be able to identify subtypes which correlate with clinical behaviour and treatment requirements. Unfortunately, however, such a classification has yet to be defined. In the interim, the currently most favoured classification is one based predominantly on histological growth pattern. This classification contributes to the useful concept of low- and high-risk histological subtypes of BCC. The latter are characterized by an increased probability of subclinical extension and/or incomplete excision and/or aggressive local invasive behaviour and/or local recurrence. The Royal College of Pathologists has published a minimum dataset for the histopathological reporting of BCC and this has been written to be compatible with the British Association of Dermatologists' management guidelines. Growth patterns to be reported include nodular, superficial, infiltrative/morphoeic and micronodular types, together with differentiation when of severely atypical or malignant squamous type (basosquamous carcinoma). Deep and peripheral excision margins will be reported to be either involved or clear. The latter will include a comment of a clearance of less than 1 mm for close margins and a measured distance in whole millimetres for other excisions. Clinical assessment and histology remain the 'gold standard' for evaluating BCC and cancers in general. However, in the postgenomic era emphasis is changing from the gathering and archiving of genomic data to its analysis and use in guiding clinical practice. In this context, a current goal is to define cancer phenotype in terms of molecular abnormalities and use this as a new gold standard. One way to assess whether this goal is being achieved for BCC is to determine whether our knowledge of its molecular pathology has any relevance to the minimum dataset for histological reporting. Knowledge of BCC molecular pathology has been fuelled by the recent discovery that deregulation of the Hedgehog (Hh) signalling pathway, a key player in embryonic patterning, appears to be fundamental to tumour growth. But despite accrual of a large amount of data concerning Hh pathway molecular alterations in neoplasia, little is known about the functional consequences of these changes in BCC, how they lead to tumour development, or how they relate to non-Hh pathway alterations such as TP53 mutation. Recent work suggests that the cellular localization of beta-catenin gives a degree of credence to the growth pattern classification of BCC. Furthermore, it is possible that beta-catenin may have a pathogenetic role in the invasive behaviour of BCC. This review draws on current evidence to discuss these issues and assess whether they are relevant to the minimum dataset.

Basal Cell Carcinoma↗

[Exclusive nodular plexiform neurofibroma. An unusual case of neurofibromatosis type 1].

INTRODUCTION: Type 1 neurofibromatous tumours (NF) are benign skin tumours which include cutaneous, subcutaneous and plexiform neurofibromas. Plexiform neurofibromas are either diffuse or nodular, the latter form being much more frequent. CASE REPORT: We observed a particular form of neurofibroma in an 18-year-old patient who developed large deep subcutaneous which histology examination revealed to be exclusively nodular plexiform neurofibromas. The patient also had 6 café au lait spots leading to the diagnosis of sporadic NF 1. He did not have acoustic neuronoma, schwannoma or posterior cataract, eliminating NF 2. COMMENTS: In NF 1, subcutaneous neurofibromas develop in 5 p. 100 of the patients. These lesions are termed nodular plexiform neurofibromas when they form long formations along nerve branches. The exclusive nature of the nodular plexiform neurofibromas in our case was exceptional. It could be hypothesized that the particular phenotype in our patient might correspond to a particular anomaly of the NF 1 gene.

Adolescent↗

Brachytelephalangy with mental retardation, peculiar face and short stature in two sibs. A new MCA/MR syndrome?

A new MCA/MR syndrome?: Two sibs are described who shares as clinical features microcephaly, short stature, deep set eyes, thick eyebrow, straight long nose with prominent bridge, septum extending below alae nasi, short philtrum, small mouth, high palate, prominent everted lower lip, and brachytelephalangy. To the best of our knowledge, this association has not been reported before.

Abnormalities, Multiple↗

Phylogenetic analysis of ecomorphological divergence, community structure, and diversification rates in dusky salamanders (Plethodontidae: Desmognathus).

An important dimension of adaptive radiation is the degree to which diversification rates fluctuate or remain constant through time. Focusing on plethodontid salamanders of the genus Desmognathus, we present a novel synthetic analysis of phylogeographic history, rates of ecomorphological evolution and species accumulation, and community assembly in an adaptive radiation. Dusky salamanders are highly variable in life history, body size, and ecology, with many endemic lineages in the southern Appalachian Highlands of eastern North America. Our results show that life-history evolution had important consequences for the buildup of plethodontid-salamander species richness and phenotypic disparity in eastern North America, a global hot spot of salamander biodiversity. The origin of Desmognathus species with aquatic larvae was followed by a high rate of lineage accumulation, which then gradually decreased toward the present time. The peak period of lineage accumulation in the group coincides with evolutionary partitioning of lineages with aquatic larvae into seepage, stream-edge, and stream microhabitats. Phylogenetic simulations demonstrate a strong correlation between morphology and microhabitat ecology independent of phylogenetic effects and suggest that ecomorphological changes are concentrated early in the radiation of Desmognathus. Deep phylogeographic fragmentation within many codistributed ecomorph clades suggests long-term persistence of ecomorphological features and stability of endemic lineages and communities through multiple climatic cycles. Phylogenetic analyses of community structure show that ecomorphological divergence promotes the coexistence of lineages and that repeated, independent evolution of microhabitat-associated ecomorphs has a limited role in the evolutionary assembly of Desmognathus communities. Comparing and contrasting our results to other adaptive radiations having different biogeographic histories, our results suggest that rates of diversification during adaptive radiation are intimately linked to the degree to which community structure persists over evolutionary time.

Adaptation, Biological↗

Update on cluster headache.

PURPOSE OF REVIEW: Although cluster headache has traditionally been thought of as a vascular headache disorder, its periodicity suggests an involvement of central areas such as the hypothalamus. This review covers the past 3 years, which have seen remarkable progress in understanding the pathophysiology of circadian headache syndromes and have brought exciting news. RECENT FINDINGS: As more cluster headache patients are seen by headache specialists, new forms of this well-defined primary headache syndrome are being identified. In addition, we discuss recent findings with regard to abnormalities in the secretion of hormones, genetic influences, neuroimaging of cluster headache attacks, and the use of newer substances as preventive therapy in cluster headache. SUMMARY: We have entered a new diagnostic and therapeutic era in primary headache disorders. In recent reports, the use of deep brain stimulation of the hypothalamus has enabled intractable chronic cluster headache patients to be successfully operated upon. Further research in this field is urgently needed and the recent possibility of combining deep brain stimulation with positron emission tomography will certainly help to unravel the brain circuitry implicated in stimulation-produced analgesia. The time has come to use the evidence for a disorder of circadian rhythm in cluster headache to further the development of chronobiotics in the treatment of this disorder.

Cluster Headache↗