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Biomedical subjects

J O Thomas

Publications and source records attributed to J O Thomas.

At least 37 records · Page 2Linked to original sources
PubMed1999

Histone H1: location and role.

Recent experiments have shown directly that, in bulk chromatin, the globular domain of histone H1 is positioned close to the dyad axis and is asymmetrically disposed, consistent with a polar arrangement of H1 molecules along the nucleosome filament. In addition to a structural role, H1 may also have gene-specific effects on transcription. The positioning of a core particle relative to a transcription factor binding-site may favour either transcription factor binding or H1 binding, depending on the location of the site.

Amino Acid Sequence↗
PubMed1999

Fine needle aspiration (FNA) in the management of palpable masses in Ibadan: impact on the cost of care.

Fine needle aspiration cytology is a relatively new technique in the management of palpable lesions in Ibadan. In the University College Hospital (UCH) Ibadan, as in most centres in Nigeria, inadequate facilities, a heavy patient load, financial constraints and an unreliable supply of basic necessities like water, often delay definitive diagnosis and management. In order to alleviate the patient's problems and provide prompt and accurate diagnosis, an FNA Cytology Clinic was set up in the Pathology Department, UCH, Ibadan, managed by the pathology team. This report represents the results of our experience. The cost effectiveness and impact on cost of care are highlighted. FNA costs N250.00 (pounds sterling 2.00), whilst cost of biopsy can vary from N5000.00 to N10000.00 (pounds sterling 35.00 to pounds sterling 70.00). A total of 752 satisfactory smears was reviewed during the 3-year period 1995-97 from various sites including breast (n = 295), lymph node (n = 183) and thyroid (n = 143). Diagnostic accuracy varied with different sites, the accuracy rate for breast, lymph node and thyroid malignancy being approximately 100%, 80% and 93%, respectively.

Adolescent↗
PubMed1999

Highlights of extranodal lymphomas in Ibadan, Nigeria.

OBJECTIVE: To find out the pattern, trend and site distribution of extranodal lymphomas in Ibadan. DESIGN: Case series. SETTING: Department of Pathology, University College Hospital. SUBJECTS: All cases of malignant lymphomas with extranodal manifestations between 1981 and 1998. MAIN OUTCOME MEASURES: Frequency and distribution of primary extranodal lymphomas. RESULTS: Extranodal lymphomas constituted 9.8% of non-Hodgkin's lymphomas(NHLs) during the period, increasing from 8.5% of NHLs from 1980 to 1990 to 12.4% from 1991 to 1998. During the entire 18 year period the nasal/nasopharynx, gastro-intestinal tract (GIT), tonsils and skin were the most commonly affected sites constituting 20.2%, 19.3%, 14.3% and 13.4%, respectively of all extranodal lymphomas. However, between 1980 and 1991 the GIT was the most commonly affected site (26.1%) followed by the nasal/nasopharyngeal region (11.6%). The involvement of the nasopharyngeal area during the second period of the study accounted for 32.0%. CONCLUSION: The reasons for this changing trend are unknown and the significance of HIV infection in this regard is uncertain.

Adolescent↗
PubMed1998

Selection of a cDNA clone for chicken high-mobility-group 1 (HMG1) protein through its unusually conserved 3'-untranslated region, and improved expression of recombinant HMG1 in Escherichia coli.

Screening of cDNA libraries for the homologous vertebrate proteins high mobility group (HMG) 1 and 2 using DNA probes based on the coding sequences is likely to result in isolation of both HMG1 and HMG2 clones, as well as pseudogenes, which may be transcribed at low levels. However, the 3'-untranslated regions (UTRs) of HMG1 and 2 are quite distinct, and unusually conserved across species. We have used this property to select the true chicken HMG1 cDNA clone from a chicken lymphocyte cDNA library in lambdagt11, using a probe based on the 3'-UTR of rat HMG1 cDNA. The chicken HMG1 cDNA clone is very similar to all the complete HMG1 cDNA clones isolated so far. We suggest that the sequence designated chicken HMG1 in the GenBank Data Library (Accession number D14314) is, in fact, that of HMG2a [and moreover that the recently reported mouse clone (Accession number AF022465), proposed to encode a new HMG protein, HMG4, is also likely to encode an HMG2a, based on the translated amino-acid sequence and 3'-UTR]. We also report much improved expression of intact recombinant HMG1 in Escherichia coli by the use of chloramphenicol rather than ampicillin selection and conditions that limit cell growth. This should be general for all members of the HMG1 (and 2) family which may be toxic to cells (possibly because of the long acidic tail), and may also prove useful in the production of other such proteins.

3' Untranslated Regions↗
PubMed1998

DNA-binding properties of the tandem HMG boxes of high-mobility-group protein 1 (HMG1).

High-mobility-group protein 1 (HMG1) is a conserved chromosomal protein with two homologous DNA-binding HMG-box domains, A and B, linked by a short basic region to an acidic carboxy-terminal tail. NMR spectroscopy on the free didomain (AB) shows that the two HMG boxes do not interact. The didomain has a higher affinity for all DNA substrates tested than single HMG-box domains and has a significantly higher ability to distort DNA by bending and supercoiling. The interaction of the didomain with DNA is stabilized by the presence of the basic region (approximately 20 residues, 9 of which are Lys) that links the second HMG box to the acidic tail in intact HMG1; this may be, at least in part, why this region also enhances supercoiling of relaxed circular DNA by the didomain and circularization of short DNA fragments (in the presence of ligase). Competition assays suggest significantly different structure-specific preferences of single and tandem HMG boxes for four-way junction and supercoiled plasmid DNA. Binding to supercoiled DNA appears to be promoted by protein oligomerization, which is pronounced for the didomains. Electron microscopy suggests that the oligomers are globular aggregates, associated with DNA looping. One box versus two (or several) is likely to be an important determinant of the properties of (non-sequence specific) HMG-box proteins.

Binding Sites↗
PubMed1998

Acute appendicitis in Buraidah, Saudi Arabia.

OBJECTIVES: To compare the clinical diagnosis with the histopathological diagnosis; to highlight associated histological lesions and; to determine whether these provide additional useful information for management. DESIGN: Case series. SETTING: Pathology Department of the King Fahd Specialist Hospital in Buraidah, Saudi Arabia. SUBJECTS: 370 appendicectomy specimen reviewed within a 12 month period. MAIN OUTCOME MEASURES: Diagnostic accuracy of a clinical diagnosis of acute or chronic appendicitis. RESULTS: Acute appendicitis was found to be most common between ages 10 to 29 years (74.0%). The diagnostic accuracy was 81%. A higher rate of appendices without histological sign of inflammation was found in females. Incidental appendicectomy was commonly associated with cholecystectomy. Unsuspected but treatable parasitic and protozoal infections were detected in 3% of appendices. CONCLUSION: Routine examination of all appendicectomy specimens cannot be overemphasized, as unsuspected but treatable parasitic on protozoal infections may be detected.

Adolescent↗
PubMed1998

Fine needle aspiration cytology in the management of thyroid enlargement: Ibadan experience.

This report reviews our experience with fine needle aspiration (FNA) cytology in the assessment of thyroid enlargement in Ibadan between January 1995 and December 1997. The diagnostic accuracy of the procedure for malignancy was 80.6% with a sensitivity and specificity 83% and 80% respectively in this series. FNAC of thyroid enlargement is now a first line investigative procedure for thyroid enlargements in the University College Hospital, Ibadan.

Adolescent↗
PubMed1997

Carcinoma of the oesophagus in Ibadan.

This was a retrospective analysis of 177 histologically confirmed cases of oesophageal carcinoma seen in the University College Hospital, Ibadan, Nigeria over a period of 30 years. Oesophageal carcinoma constituted 0.6 per cent of all malignant neoplasms and 1.4 cases per 1000 surgical biopsies during the study period. Dysphagia and weight loss were the most common clinical manifestations. Ninety three patients presented within one year of onset of clinical symptoms. The peak age incidence occurred in the seventh decade of life. Sex distribution was equal. The middle third of the oesophagus was the most common location of the neoplasm and the vast majority (94.5%) were squamous cell carcinomas. Achalasia of the cardia and Barrett's oesophagus were not associated with oesophageal carcinoma in this study. Regional lymph nodes and lungs were the most common sites of metastasis. Surgical complications included mediastinitis and bronchopneumonia, both occurring within seven days postoperatively. Late clinical presentation and high postoperative mortality are responsible for the persistently poor prognosis of oesophageal carcinoma despite significant advances in the diagnosis and management of these neoplasms.

Adult↗
PubMed1996

Photoaffinity labelling of a DNA-binding site on the globular domain of histone H5.

We have labelled a DNA-binding site on the globular domain of histone H5 (GH5) by ultraviolet-activated cross-linking of a self-complementary 5-bromodeoxyuridine (5BrU)-substituted oligonucleotide with the sequence 5'-AGCGA5BrUATCGCT-3'. Cross-linking was to His62, mainly to the protein backbone. This observation provides further support for the mode of binding of GH5 to DNA proposed on the basis of the similarity between the X-ray crystal structure of GH5 and the DNA-bound structures of catabolite activator protein and hepatic nuclear factor 3 gamma [Ramakrishnan, V. (1994) Curr. Opin. Struct. Biol. 4. 44-50].

Affinity Labels↗
PubMed1996

Identification of two DNA-binding sites on the globular domain of histone H5.

The nature of the complexes of histones H1 and H5 and their globular domains (GH1 and GH5) with DNA suggested two DNA-binding sites which are likely to be the basis of the preference of H1 and H5 for the nucleosome, compared with free DNA. More recently the X-ray and NMR structures of GH5 and GH1, respectively, have identified two basic clusters on opposite sides of the domains as candidates for these sites. Removal of the positive charge at either location by mutagenesis impairs or abolishes the ability of GH5 to assemble cooperatively in 'tramline' complexes containing two DNA duplexes, suggesting impairment or loss of its ability to bind two DNA duplexes. The mutant forms of GH5 also fail to protect the additional 20 bp of nucleosomal DNA that are characteristically protected by H1, H5 and wild-type recombinant GH5. They still bind to H1/H5-depleted chromatin, but evidently inappropriately. These results confirm the existence of, and identify the major components of, two DNA-binding sites on the globular domain of histone H5, and they strongly suggest that both binding sites are required to position the globular domain correctly on the nucleosome.

Amino Acid Sequence↗
PubMed1996

A preference of histone H1 for methylated DNA.

We have identified a clear preference of histone H1 for CpG-methylated DNA, irrespective of DNA sequence. The conditions under which this preference is observed allowed cooperative binding of H1; the H1-DNA complexes formed were shown earlier to be 'tramlines' of two DNA duplexes bridged by an array of H1 molecules, and multiples of these. The preference for methylated DNA is clear in sedimentation assays, which also show that the preference is greater with increased methylation level, and in gel retardation assays with an oligonucleotide containing a single methyl-CpG pair; it is shared by the globular domain which also binds cooperatively to DNA. A small intrinsic preference of H1 for methylated DNA is also apparent in Southwestern assays where the immobilized H1 presumably cannot bind cooperatively. Methylated DNA in H1-DNA complexes was partially protected (relative to unmethylated DNA) against digestion by MspI but not by enzymes whose cutting sites were not methylated, consistent with a direct interaction of H1 with methylated nucleotides; this was also true of GH1-DNA complexes. H1 variants (spH1 and H5) from transcriptionally repressed nuclei have a stronger preference than H1 for methylated DNA, suggesting that this may be relevant to the stabilization of chromatin higher order structure and transcriptional repression.

Animals↗
PubMed1995

Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy.

HMG1 has two homologous, folded DNA-binding domains ("HMG boxes"), A and B, linked by a short basic region to an acidic C-terminal domain. Like the whole protein, which may perform an architectural role in chromatin, the individual boxes bind to DNA without sequence specificity, have a preference for distorted or prebent DNA, and are able to bend DNA and constrain negative superhelical turns. They show qualitatively similar properties with quantitative differences. We have previously determined the structure of the HMG box from the central B-domain (77 residues) by two-dimensional NMR spectroscopy, which showed that it contains a novel fold [Weir et al. (1993) EMBO J. 12, 1311-1319]. We have now determined the structure of the A-domain (as a Cys-->Ser mutant at position 22 to avoid oxidation, without effect on its DNA-binding properties or structure) using heteronuclear three- and four-dimensional NMR spectroscopy. The A-domain has a very similar global fold to the B-domain and the Drosophila protein HMG-D [Jones et al. (1994) Structure 2, 609-627]. There are small differences between A and B, in particular in the orientation of helix I, where the B-domain is more similar to HMG-D than it is to the A-domain; these differences may turn out to be related to the subtle differences in functional properties between the two domains [Teo et al. (1995) Eur. J. Biochem. 230, 943-950] and will be the subject of further investigation. NMR studies of the interaction of the A-domain of HMG1 with a short double-stranded oligonucleotide support the notion that the protein binds via the concave face of the L-shaped structure; extensive contacts with the DNA are made by the N-terminal extended strand, the N-terminus of helix I, and the C-terminus of helix II. These contacts are very similar to those seen in the LEF-1 and SRY-DNA complexes [Love et al. (1995) Nature 376, 791-795; Werner et al. (1995) Cell 81, 705-714].

Animals↗
PubMed1995

Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy.

The HMG-box sequence motif (approximately 80 residues) occurs in a number of abundant eukaryotic chromosomal proteins such as HMG1, which binds DNA without sequence specificity, but with "structure specificity", as well as in several sequence-specific transcription factors. HMG1 has two such boxes, A and B, which show approximately 30% sequence identity, and an acidic C-terminal tail. The boxes are responsible for the ability of the protein to bend DNA and bind to bent or distorted DNA. The structure of the HMG box has been determined by NMR spectroscopy for the B-domain of HMG1 [Weir et al. (1993) EMBO J. 12, 1311-1319; Read et al. (1993) Nucleic Acids Res. 21, 3427-3436) and for Drosophila HMG-D (Jones et al. (1994) Structure 2, 609-627]. It has an unusual twisted L-shape, suggesting that the protein might tumble anisotropically in solution. In this paper we report studies of the A-domain from HMG1 using 15N NMR spectroscopy which show that the backbone dynamics of the protein can be described by two different rotational correlation times of 9.0 +/- 0.5 and 10.8 +/- 0.5 ns. We show that the relaxation data can be analyzed by assuming that the protein is a rigid, axially symmetric ellipsoid undergoing anisotropic rotational diffusion; the global rotational diffusion constants, D parallel and D perpendicular, were estimated as 2.47 x 10(7) and 1.49 x 10(7) s-1, respectively. By estimating the angle between the amide bond vectors and the major axis of the rotational diffusion tensor from the family of structures determined by NMR spectroscopy [see accompanying paper, Hardman et al. (1995) Biochemistry 34, 16596-16607], we were able to show that the ellipsoid spectral density equation can reproduce the major features of the 15N T1 and T2 profiles of the three helices in the HMG1 A-domain. The backbone dynamics of the A-domain were then compared with those of the B-domain and the HMG box from HMG-D. This comparison strongly supported the differences observed in the orientation of helix I in the three structures, where the B-domain appears to be more similar to HMG-D than it is to the A-domain. These differences may turn out to be related to subtle differences in the DNA-binding properties of the A- and B-domains of HMG1.

Animals↗
PubMed1995

Two mutations in the HMG-box with very different structural consequences provide insights into the nature of binding to four-way junction DNA.

Mutation of the highly conserved tryptophan residue in the A-domain HMG-box of HMG1 largely, but not completely, destroys the protein tertiary structure and abolishes its supercoiling ability, but does not abolish structure-specific DNA binding to four-way junctions. Circular dichroism shows that the protein has some residual alpha-helix (< 10%) and does not re-fold in the presence of DNA. Structure-specific DNA binding might therefore be a property of some primary structure element, for example the N-terminal extended strand, which even in the unfolded protein would be held in a restricted conformation by two, largely trans, X-Pro peptide bonds. However, mutation of P5 or P8 of the A-domain to alanine does not abolish the formation of the (first) complex in a gel retardation assay, which probably arises from binding to the junction cross-over, although the P8 mutation does affect the formation of higher complexes which may arise from binding to the junction arms. Since mutation of P8 in the W49R mutant has no effect on structure-specific junction binding, we propose that some residual alpha-helix in the protein might be involved, implicating this element in the interactions of HMG-boxes generally with DNA.

Amino Acid Sequence↗
PubMed1995

Differences in the DNA-binding properties of the HMG-box domains of HMG1 and the sex-determining factor SRY.

High-mobility-group protein 1 (HMG1) is an abundant, non-sequence-specific, chromosomal protein with two homologous, HMG-box, DNA-binding domains, A and B, and an acidic tail. The HMG-box motif also occurs, as a single copy, in some sequence-specific transcription factors, e.g. the sex-determining factor, SRY. We have investigated whether or not there are differences in the DNA-binding properties of the isolated A and B HMG-box domains of HMG1 and SRY and whether, in the case of A and B, there might also be differences due to different sequence contexts within the native protein. The basic regions that flank the HMG1 B box, giving B', enhance its DNA-binding, supercoiling and DNA-bending activities, and promote the self-association of the DNA-bound B-box. All the HMG-box domains bind with structure specificity to four-way junctions, but the structure selectivity is significantly greater for A and the SRY box than for the HMG1 B or B' domains, as judged by competition with excess plasmid DNA. The domains self-associate to different extents on supercoiled DNA and this may explain differences in the ability to discriminate between four-way junctions and supercoiled DNA. The HMG1 A, B and B' domains constrain negative superhelical turns in DNA, but the SRY HMG box does not. Only the full B domain (B') bends DNA in a ligase-mediated circularisation assay; the minimal B box, the A domain and the SRY box do not. Thus, despite a common global fold, the HMG box appears to have been adapted to various functions in different protein contexts.

Amino Acid Sequence↗