Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Data visualisation”

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 235 records · Page 13Linked to original sources
PubMed1996

GENOLYTE: a PC-based computer program for visualisation of genomic DNA sequences.

This paper describes the program "GENOLYTE" which has been developed for the visualisation and identification of the global and local patterns of long genomic DNA sequences quickly in a few minutes, with the aid of a microcomputer. Apart from global and local identification, GENOLYTE comparatively depicts the similarity of two or more than two genomic DNA sequences. The utility of the program has been demonstrated by analysing the complete mitochondrial DNA sequences (taken from EMBL databank) as an example and the results are discussed from therein. The program written in TURBO C++ has the following minimum requirements: (i) PC 386 AT, (ii) SVGA colour monitor, (iii) the [BGI] directory of TURBO C++ version 3.0.

Animals↗
PubMed1996

Baculovirus-mediated high level expression of a human thiopurine methyl transferase.

We have expressed the human thiopurine methyltransferase cDNA in a baculovirus vector in Sf21 (Spodoptera frugiperda) cells. This system expresses the enzyme at levels such that the thiopurine methyltransferase enzyme may be readily visualised by Coomassie blue stained sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The expressed enzyme catalysed the methylation of 6-mercaptopurine with an apparent Km of 892 microM, similar to that observed in human liver cytosol ie. 657 microM however, the Vmax was 13,500 pmole/mg/min, which is approximately 400 times higher than the Vmax observed in human liver cytosol ie. 33 pmole/mg/min. The thiopurine methyltransferase inhibitors 6-thioxanthine, p-methoxybenzoic acid and 3,5-dimethoxy benzoic acid were found to be potent inhibitors of the expressed enzyme.

Animals↗
PubMed1996

Visualising the dissociation of sequence selective ligands from individual binding sites on DNA.

We have used a modification of the footprinting technique to measure the dissociation of mithramycin, echinomycin and nogalamycin from their binding sites in a natural DNA fragment. Complexes with radiolabelled DNA were dissociated by addition of unlabelled DNA. Samples were removed at various times and subjected to DNase I digestion, and the rate of dissociation from each site was estimated from the time-dependent disappearance of the footprints. For echinomycin the slowest rate of dissociation is from ACGT, while the slowest site for mithramycin contains four contiguous guanines. The dissociation of nogalamycin is extremely slow, even from its weaker sites; the slowest rate was from ACGTA, which took longer than 4 h, even at 37 degrees C.

Base Sequence↗
PubMed1981

The role of two-dimensional echocardiography in the detection of potentially embolic intracardiac masses in patients with cerebral ischaemia.

The M-mode and two dimensional echocardiographic data of 62 consecutive cardiac patients referred from neurology centres were analysed retrospectively to establish the use of these techniques in detecting underlying cardiac pathology. All patients had presented initially to a neurologist with transient or permanent focal cerebral or retinal ischaemia, and had been referred for cardiac assessment after neurological investigations failed to establish the underlying cause of the neurological event. Patients were divided into two groups. In 30 patients the referring neurologist had found no evidence of cardiac disease (Group I); in the other 32 patients either heart disease or an arrhythmia had been diagnosed prior to cardiac referral (Group II). One of the patients in Group I had echocardiographic evidence of mitral valve prolapse not detected by the neurologist prior to referral; no cardiac pathology was recognised in the other 29 patients in this group. In seven of the 32 (22%) patients from Group II, a cardiac mass presumed responsible for the neurological manifestations was demonstrated echocardiographically, and in six of these histological confirmation was obtained following surgery or at necropsy. Two dimensional echocardiography was the only investigation which visualised the intracardiac pathology in four patients. In the remaining three patients, valve vegetations (two cases) and an atrial tumour (one case) were demonstrated by both echocardiographic methods. In patients with either clinical evidence of cardiac disease or an arrhythmia who have experienced one or more episodes of cerebral or retinal ischaemia, the presence of an intracardiac mass is not uncommon. Two dimensional echocardiography was the method of choice for detecting cardiac thrombus but the use of both methods of ultrasound should be considered as complementary techniques in the investigation of these cases. Routine echocardiography is unlikely to be of value in screening patients who have had a cerebrovascular event and who do not have clinical evidence of heart disease or an arrhythmia.

Adolescent↗
PubMed1992

Immunocytochemical identification of oestrogen receptors in preoptic neurones containing calcitonin gene-related peptide in the male and female rat.

Using single- and double-labelling immunocytochemistry with antibodies specific for the oestrogen receptor and calcitonin gene-related peptide (CGRP), we have demonstrated oestrogen receptor immunoreactivity in the sexually dimorphic CGRP-immunoreactive (IR) population of the medial preoptic area (MPOA). In the short-term gonadectomised female approximately 80% of preoptic CGRP-IR neurones were immunoreactive for the oestrogen receptor. In short-term gonadectomised males, a small population of CGRP-IR cells was visualised in the MPOA only after colchicine treatment. Approximately 30% of CGRP-IR cells in the male were oestrogen receptor-IR, accounting for 2% of the total population of cells containing oestrogen receptors in this area. In the colchicine-treated female, it is estimated that 10-15% of preoptic oestrogen receptor-IR cells contain CGRP. These results indicate that CGRP is synthesised by preoptic neurones with oestrogen receptors. Furthermore, the identification of oestrogen receptors in the sexually dimorphic CGRP population suggests that these neurones may be directly linked with gonadal steroid-dependent, sex-specific functioning of the MPOA.

Animals↗
PubMed1993

Chitinolytic activities in Heligmosomoides polygyrus and their role in egg hatching.

The occurrence of chitin in the eggshell of Heligmosomoides polygyrus has been determined by histochemical and biochemical techniques. Approximately 5% of the egg dry weight was chitin. Staining with Calcofluor white showed the chitin in the eggshell to be more accessible to the stain after hatching or rupturing of the eggshell. Chitinolytic activity has been detected using fluorescent substrates in extracts of adult males (at low levels), females and eggs. Enzyme activity in situ, within the developing larvae, was visualised with the same substrates. It was localized in discrete granules about 1 micron in diameter which occurred as groups in areas of about 5 microns in diameter, in the posterior third of the larvae. The chitinolytic activity in the eggs increased with the age of the egg and was released into the medium when the eggs hatched. The chitinase activities were very sensitive to inhibition by allosamidin, a specific chitinase inhibitor, with an IC50 for the crude egg extract of 2.2 nM. However, treatment of eggs with 250 microM allosamidin resulted in a slowing but not cessation of egg hatching.

Acetylglucosamine↗
PubMed1994

A study of the interaction of DAPI with DNA containing AT and non-AT sequences--molecular specificity of minor groove binding drugs.

The binding specificity of DAPI to DNA has been probed by analysing its interactions with DNA octamers consisting of different base sequences, which include adenine, guanine, 2-amino adenine and inosine, using molecular mechanics methods. Presence of AT and non-AT base pairs in the immediate vicinity of the binding site, containing AT and non-AT base pairs is also investigated. Results show that DAPI most prefers to bind to homopolymer of AT, and least to the duplex containing alternating GC bases. DAPI interacts with homopolymeric duplexes in two possible orientations related by 180 degrees with nearly same affinity. Affinity of DAPI towards DNA comprising the modified bases, inosine and 2-amino adenine, is in between these extremities. The binding affinity is reduced to some extent by the occurrence of non AT bases flanking the four base paired binding region. An interesting revelation is that one can visualise DAPI to form a hydrogen bond with O2 of cytosine indicating that the 2-amino group of purines does not per se sterically preclude DAPI from residing in the minor groove of B-DNA helix. On the other hand, repulsive nature of electrostatic interactions that prevail at the minor groove consequent to the presence of these sequences contribute decisively in preventing further diffusion of the drug. Thus, electrostatics, rather than hydrogen bonding to bases, seemingly play an important role in determining the specificity of interaction. The retention of drug binders in the minor groove and therefore recognition, is governed by the combined effect of these various forces.

Base Sequence↗
PubMed1996

Localization of tobacco cytosolic glutamine synthetase enzymes and the corresponding transcripts shows organ- and cell-specific patterns of protein synthesis and gene expression.

The subcellular localization of glutamine synthetase in tobacco and the differential expression of two genes encoding cytosolic enzyme was investigated using both immunocytochemistry and in situ hybridization. Two full length cDNA clones each encoding cytosolic GS (Gln 1-3 and Gln 1-5) were isolated from a tobacco seeding cDNA library. A strong homology was found in the coding region of the two clones whereas the 3'- and 5'-untranslated sequences were dissimilar. In order to determine the levels of transcription, specific sequences from Gln1-3 and Gln1-5 were used in an RNAse protection assay. This experiment clearly showed that the gene encoding Gln1-3 is expressed in roots and flowers whereas the gene encoding Gln1-5 is transcribed at a high level in stems and at a lower level in roots and flowers. Immunogold labelling was used to examine the subcellular and cellular distribution of glutamine synthetase in vegetative and reproductive organs of tobacco plants. In mature leaf tissue or petals and sepals, plastidic GS was visualised only in the stroma matrix of chloroplasts and plastids. Cytosolic GS was detected in a number of vegetative or reproductive organs including leaves and flowers. In leaves cytosolic GS was preferentially located in the vascular tissue. In situ hybridization was performed using sections of tobacco organs and specific antisense RNA probes to the genes encoding Gln1-3 and Gln1-5. Gln1-5 transcripts were localised in the vascular tissues of stems and roots whereas Gln1-3 transcripts were detected in all root cells and floral organs including petals, sepals and anthers.

Antisense Elements (Genetics)↗
PubMed1990

Visualisation of the gastrin receptor within rat mucosa using a biotinylated gastrin antagonist.

We have previously demonstrated that the peptide Boc-L-Trp-L-Leu-beta-Ala is a potent and specific antagonist of pentagastrin-stimulated acid secretion in both the rat and the dog. Using conventional solution phase methodology, the analogue biotinyl-L-Trp-L-Leu-beta-Ala was prepared in reasonable yield and purity and applied to cryostat sections of rat intestinal and other tissues. The sections were exposed to 5-10 micrograms of peptide and the bound analogue was visualised using streptavidin-fluorescein. The binding of the analogue was demonstrated in sections from fundus, duodenum, ileum, colon, and lung. However, the analogue failed to bind to tissue from the pancreas, heart, kidney, or liver. The binding of the probe was greatly reduced or completely inhibited by preincubation with Boc-L-Trp-L-Leu-beta-Ala, pentagastrin, or gastrin 1-17. The distribution of the cells recognised by the probe was consistent with the distribution of histamine-containing enterochromaffin-like cells. The results of this study may have some bearing on current theories of the mechanism of gastrin-stimulated acid release.

Amino Acid Sequence↗
PubMed1990

Structural analysis of plant ribosomal 5S RNAs. Visualisation of novel tertiary interactions by cleavage of lupin and wheat 5SrRNAs with ribonuclease H.

A model for the tertiary structure of plant 5S rRNA, previously proposed by our laboratory (Joachimiak, A. et al. (1990) Int. J. Biol. Macromol., in press) was tested by specific cleavage of the plant 5S rRNA in the presence of synthetic oligodeoxynucleotides. The hexanucleotides used in this study were complementary to different portions of loops C, D and E, the nucleotides of which have recently been proposed to be involved in tertiary hydrogen bonds. The results obtained strongly support the interaction of loops C and D by nucleotides C34, C35, C36, A37 and G85, G86, G87, U88, respectively. Digestion pattern of loop E (domain gamma, nucleotides 66-110) suggests a possible different arrangement of this part of the plant 5S rRNA molecule, when compared with other eukaryotes.

Base Sequence↗
PubMed1991

The glucocorticoid receptor in homodimeric and monomeric form visualised by electron microscopy.

The purified glucocorticoid receptor (GR) from rat liver has been visualised by electron microscopy. The specimens were prepared by spreading on thin carbon support and negatively stained using uranyl acetate. Two forms of GR, the monomeric and the dimeric forms, were identified based on size, chromatographic distribution, and DNA binding properties. The GR monomer consists of two globular domains of slightly different size with a thinner connecting domain in between. In the absence of DNA the dimeric GR has a characteristic four-leaf clover structure. The size and appearance of this structure is consistent with two GR subunits arranged in a side-by-side fashion. Monomeric and dimeric GR specifically bound to DNA are also shown.

Animals↗
PubMed1988

[Multiple neurologic manifestations of Borrelia burgdorferi infection].

The neurological spectrum of Borrelia burgdorferi infections is still enlarging. We review epidemiological, pathological and serological data of Lyme disease. The course of the disease is divided in three stages: stage 1 during the first month is characterised by erythema chronicum migrans and associated manifestations; stage 2 includes not only the classical European meningoradiculitis but also less specific neurological symptoms: isolated lymphocytic meningitis with an acute or even relapsing course, apparently idiopathic facial palsy, neuritis of other cranial nerves, polyneuritis cranialis, Argyll-Robertson sign, peripheral nerve involvement, acute transverse myelitis, severe encephalitis, myositis. During stage 3, three to five months or longer after the onset of the disease, chronic arthritis, acrodermatitis chronica atrophicans and various neurological symptoms can be observed: chronic neuropathy with mainly sensory or motor signs, recurrent strokes due to cerebral angiopathy and progressive encephalomyelitis; this third stage the central nervous system involvement is characterised by slowly progressive or fluctuating course during months or years, ataxic or spastic gait disorder, bladder disturbances, cranial nerve dysfunction including optic atrophy and hypoacusia, dysarthria, focal and diffuse encephalopathy. This chronic central nervous system disease can mimic multiple sclerosis, anorexia nervosa, psychic disorders or subacute presenile dementia. It is often associated with pleiocytosis, abnormal EEG and evoked potentials, sometimes multifocal and mainly periventricular white matter lesions visualised by CT or MRI, and as a rule high antibody titers against Borrelia burgdorferi. High doses of penicillin can halt the disease, sometimes induce spectacular regression of symptoms or sometimes be inefficient; ceftriaxone could be a more powerful therapy. Similarities between syphilis and Borreliosis are multiple: both of these spirochetes contain plasmids, can be transmitted through the placenta and progress for many years through successive stages, with multiorgan symptoms, including parenchymatous and vascular lesions of the central nervous system. Borrelia burgdorferi is the new great imitator.

Animals↗
PubMed1996

Application of novel vectors for GFP-tagging of proteins to study microtubule-associated proteins.

We describe the construction of pBact-NGFP and pBact-CGFP, two expression vectors that incorporate green fluorescent protein (GFP) as a fluorescent tag at the N- or C terminus of the produced protein. When transfected into recipient cells, GFP-tagged proteins can be visualised in the living cells using standard fluorescence microscopy techniques. Using these expression vectors, we have produced GFP-tagged versions of the neuronal microtubule-associated proteins (MAP), MAP2c and Tau34, in a number of different cell types. Both GFP-MAP2c and GFP-Tau34 were fluorescent and retained their ability to bind to microtubules. The pBact-NGFP and pBact-CGFP expression vectors represent a fast and convenient way to produce fluorescently tagged polypeptides of selected sequences encoding whole proteins or fragments for the analysis of function and dynamic events in living cells.

Animals↗
PubMed1988

Passive smoking and lung cancer: a publication bias?

To assess the likelihood of publication bias in a recent review of the effect of passive smoking on lung cancer the evidence from the reviewed papers was visualised on a "funnel" plot. In such a plot if the relative risks from various studies are plotted according to sample size they should scatter round some underlying true value, the scatter being greatest where the studies have the lowest statistical power--thus showing a "funnel" pattern. If there is publication bias and studies with non-significant results are not being published there should be a "gap" in the plot. The logarithm of the relative risks was plotted against the standard error of the logarithm of the relative risk (which was used instead of sample size as a measure of statistical uncertainty). The resulting plot was compatible with a publication bias but only in studies on men. Further studies of passive smoking and lung cancer in men seem to be warranted.

Data Interpretation, Statistical↗
PubMed1995

Detection of Epstein-Barr virus and human papillomavirus in nasopharyngeal carcinoma by the polymerase chain reaction technique.

We used the PCR technique to detect the Epstein-Barr virus (EBV) and human papillomavirus (HPV) DNA in paraffin-embedded tissues from Greek patients with nasopharyngeal carcinoma (NPC). The oligonucleotide primers used for the detection of EBV amplify a 375-bp long sequence from the EcoRI B fragment of the viral genome, whereas for HPV the primers amplify a 151-bp long sequence of the viral genome. The PCR products were analysed by agarose gel electrophoresis and visualised by UV illumination after staining with ethidium bromide. Sixty-three specimens were examined. EBV specific sequence was amplified in 20 (32%) and HPV in 12 (19%) out of the 63 samples. There was no co-infection with EBV and HPV. Although there is a high correlation of EBV infection with poorly differentiated NPC in patients from Southern China and South-East Asia, the restricted distribution suggests genetic or environmental cofactors in the development of the neoplasm. Our results confirm this suggestion since there was only a 32% correlation of EBV with NPC in Greece. HPV may also be involved in the carcinogenesis of EBV-negative squamous cell nasopharyngeal carcinomas.

Base Sequence↗
PubMed1993

Visualising the kinetics of dissociation of actinomycin from individual sites in mixed sequence DNA by DNase I footprinting.

We have investigated the kinetics of dissociation of actinomycin D from DNA by a variation of the footprinting technique. Complexes of actinomycin with a radiolabelled DNA fragment (tyrT) were dissociated by addition of a large excess of unlabelled calf thymus DNA and the mixture subjected to DNase I footprinting at subsequent intervals. The rates at which the footprints disappeared varied between the different binding sites. The dissociation was temperature dependent with average time constants of 30 s, 10 mins and 2 hours at temperatures of 37 degrees C, 20 degrees C and 4 degrees C respectively. The dissociation from a DNA fragment containing the synthetic insert T9GCA9 was significantly faster, with a half-life of about 1 min at 20 degrees C. In contrast, the dissociation of distamycin was too fast to measure (< 5 s) even at 4 degrees C.

Base Sequence↗
PubMedDate not supplied

In situ hybridization and cytofluorometric analysis of cytokine mRNA during in vitro activation of human T cells.

We present an original method for in situ hybridization (ISH) using non isotopic probes and flow cytometry analysis that permits rapid detection of lymphokine transcripts at single cell level in an in vitro activated human Jurkat T cell line and in peripheral blood T cell subsets. After PMA and either ionomycin or ConA stimulation, cells were fixed and hybridized with digoxigenin (DIG)-labelled RNA antisense or sense probes specific for IL-2 and IFN-gamma. The level of cytokine gene expression in individual cells was visualised using FITC-conjugated anti-DIG antibody, and the resultant signal was analysed by flow cytometry. IL-2 mRNA was first detected in activated Jurkat T cells. Addition of cycloheximide 4 hours after the beginning of stimulation increased both the frequency of labelled cells and the amount of mRNA per cell, as determined by the mean fluorescence intensity. The specificity and sensitivity of IL-2 mRNA detection were tested by comparison with Northern blot analysis and in situ hybridization (ISH) with immuno-cytochemical staining. IL-2 and IFN-gamma mRNA were detectable in PBMC as early as 3 hours after in vitro stimulation with PMA and ionomycin. The frequency of positive cells and the amount of mRNA per cell peaked at 6-8 hours, when the percentages of IL-2 and IFN-gamma mRNA-containing cells reached 30-40% and 15-20%, respectively. The two lymphokines were expressed in both CD4+ and CD8+ T cells, but the frequency of IL-2 expressing cells and the amount of IL-2 mRNA per cell were higher in CD4+ (60%) than in CD8+ T cells (25%), whereas IFN-gamma were preferentially transcribed by CD8+ T cells (40%). The results obtained by this method were in accordance with the data obtained by Northern blot analysis, with cellular protein content estimated by immuno-fluorescence staining, and with IL-2 titration by bioassay. We compared the performance of this method with ISH using radioactive probes.

Animals↗
PubMed1996

Dynamics of insulin-stimulated translocation of GLUT4 in single living cells visualised using green fluorescent protein.

Insulin increases glucose uptake by promoting the translocation of the GLUT4 isoform of glucose transporters to the plasma membrane. We have studied this process in living single cells by fusing green fluorescent protein (GFP) to the N-terminus (GFP-GLUT4) or C-terminus (GLUT4-GFP), of GLUT4. Both chimeras were expressed in a perinuclear compartment of CHO cells, and in a vesicular distribution through the cytosol. Insulin promoted an increase in plasma membrane fluorescence as a result of net translocation of the chimeras to the cell surface. GLUT4-GFP, but not GFP-GLUT4, was re-internalised upon the removal of insulin suggesting that a critical internalisation signal sequence exists in the N-terminus of GLUT4. The use of GFP thus allows an analysis of GLUT4 trafficking in single living cells.

Animals↗