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Biomedical subjects

T Brown

Publications and source records attributed to T Brown.

At least 109 records · Page 6Linked to original sources
PubMed1999

Crystal structure of a thwarted mismatch glycosylase DNA repair complex.

The bacterial mismatch-specific uracil-DNA glycosylase (MUG) and eukaryotic thymine-DNA glycosylase (TDG) enzymes form a homologous family of DNA glycosylases that initiate base-excision repair of G:U/T mismatches. Despite low sequence homology, the MUG/TDG enzymes are structurally related to the uracil-DNA glycosylase enzymes, but have a very different mechanism for substrate recognition. We have now determined the crystal structure of the Escherichia coli MUG enzyme complexed with an oligonucleotide containing a non-hydrolysable deoxyuridine analogue mismatched with guanine, providing the first structure of an intact substrate-nucleotide productively bound to a hydrolytic DNA glycosylase. The structure of this complex explains the preference for G:U over G:T mispairs, and reveals an essentially non-specific pyrimidine-binding pocket that allows MUG/TDG enzymes to excise the alkylated base, 3, N(4)-ethenocytosine. Together with structures for the free enzyme and for an abasic-DNA product complex, the MUG-substrate analogue complex reveals the conformational changes accompanying the catalytic cycle of substrate binding, base excision and product release.

Base Pair Mismatch↗
PubMed1999

DNA triple helix stabilisation by covalent attachment of a triplex-specific ligand.

We have prepared oligonucleotides with a naphthylquinoline triplex-binding ligand covalently tethered to the 5'-end and have used UV-melting and DNase I footprinting to examine the stability of intra- and inter-molecular triplexes containing this modification. We find that covalent attachment of the ligand increases the melting temperature of intramolecular 6-mer triplexes by about 14 K, and increases the binding of 9-mer oligonucleotides to their duplex target sites by about 60-fold.

Animals↗
PubMed1999

DNA triple helix formation at target sites containing several pyrimidine interruptions: stabilization by protonated cytosine or 5-(1-propargylamino)dU.

DNase I footprinting has been used to study the formation of parallel triplexes at oligopurine target sequences which are interrupted by pyrimidines at regular intervals. TA interruptions are targeted with third strand oligonucleotides containing guanine, generating G x TA triplets, while CG base pairs are targeted with thymine, forming T x CG triplets. We have attempted to optimize the stability of these complexes by varying the base composition and sequence arrangement of the target sites, and by replacing the third strand thymines with the positively charged analogue 5-(1-propargylamino)dU (U(P)). For the target sequence (AAAT)(5)AA, in which pyrimidines are positioned at every fourth residue, triplex formation with TG-containing oligonucleotides is only detected in the presence of a triplex-binding ligand, though stable triplexes were detected at the target site (AAAAAT)(3)AAAA. Triplex stability at targets containing pyrimidines at every fourth residue is increased by introducing guanines into the duplex repeat unit using the targets (AGAT)(5)AA and (ATGA)(5)AA. In contrast, placing C(+) x GC triplets on the 5'-side of G x TA, using the target (AGTA)(5)TT, produces complexes of lower stability. We have attempted further to increase the stability of these complexes by using the positively charged thymine base analogue U(P), and have shown that (TU(P)TG)(5)TT forms a more stable complex with target (AAAT)(5)AA than the unmodified third strand, generating a footprint in the absence of a triplex-binding ligand. Triplex formation at (AGTA)(5)AA is improved by using the modified oligonucleotide (TCGU(P))(5)TT, generating a complex in which the charged triplets C(+) x GC and U(P) x AT alternate with uncharged triplets. In contrast, placing U(P) x AT triplets adjacent to C(+) x GC, using the third strand oligonucleotide (U(P)CGT)(5)TT, reduces triplex formation, while the third strand with both substitutions, (U(P)CGU(P))(5)TT, produces a complex with intermediate stability. It appears that, although adjacent U(P) x AT triplets form stable triplexes, placing U(P) x AT adjacent to C(+) x GC is unfavorable. Similar results were obtained with fragments containing CG inversions within the oligopurine tract, though triplexes at (AAAAAC)(3)AA were only detected in the presence of a triplex-binding ligand. Placing C(+) x GC on the 5'-side of T x CG triplets also reduces triplex formation, while a 3'-C(+) x GC produces complexes with increased stability.

Adenine↗
PubMed1999

5-(1-propargylamino)-2'-deoxyuridine (UP): a novel thymidine analogue for generating DNA triplexes with increased stability.

We have used quantitative DNase I footprinting and UV-melting studies to examine the formation of DNA triplexes in which the third strand thymines have been replaced by 5-propargylamino-dU (UP). The intra-molecular triplex A6-L-T6-L-(UP)5T (L = two octanediol residues) shows a single UV-melting transition which is >20 degrees higher than that of the parent triplex A6-L-T6-L-T6at pH 5.5. Although a single transition is observed at all pHs, the melting temperature (Tm) of the modified oligonucleotide decreases at higher pHs, consistent with the requirement for protonation of the amino group. A similar intramolecular triplex with a longer overhanging duplex shows two melting transitions, the lower of which is stabilised by substitution of T by UP, in a pH dependent fashion. Triplex stability increases by approximately 12 K for each T to UP substitution. Quantitative footprinting studies have examined the interaction of three UP-containing 9mer oligonucleotides with the different portions of the 17mer sequence 5'-AGGAAGAGAAAAAAGAA. At pH 5.0, the UP-containing oligo-nucleotides footprint to much lower concentrations than their T-containing counterparts. In particular (UP)6CUPT binds approximately 1000-fold more tightly than the unmodified oligonucleotide T6CTT. Oligonucleotides containing fewer UP residues are stabilised to a lesser extent. The affinity of these modified third strands decreases at higher pHs. These results demonstrate that the stability of DNA triplexes can be dramatically increased by using positively charged analogues of thymine.

DNA↗
PubMed1999

Solution conformation of a parallel DNA triple helix with 5' and 3' triplex-duplex junctions.

BACKGROUND: Polypurine x polypyrimidine sequences of DNA can form parallel triple helices via Hoogsteen hydrogen bonds with a third DNA strand that is complementary to the purine strand. The triplex prevents transcription and could therefore potentially be used to regulate specific genes. The determination of the structures of triplex-duplex junctions can help us to understand the structural basis of specificity, and aid in the design of optimal antigene oligonucleotides. RESULTS: The solution structures of the junction triplexes d(GAGAGACGTA)-X-(TACGTCTCTC)-X-(CTCTCT) and d(CTCTCT)-X-(TCTCTCAGTC)-X-(GACTGAGAGA) (where X is bis(octylphosphate) and nucleotides in the triplex regions are underlined) have been solved using nuclear magnetic resonance (NMR) spectroscopy. The structure is characterised by significant changes in the conformation of the purine residues, asymmetry of the 5' and 3' junctions, and variations in groove widths associated with the positive charge of the protonated cytosine residues in the third strand. The thermodynamic stability of triplexes with either a 5' or a 3'CH+ is higher than those with a terminal thymidine. CONCLUSIONS: The observed sequence dependence of the triplex structure, and the distortions of the DNA at the 5' and 3' termini has implications for the design of optimal triplex-forming sequences, both in terms of the terminal bases and the importance of including positive charges in the third strand. Thus, triplex-stabilising ligands might be designed that can discriminate between TA x T-rich and CG x C+-rich sequences that depend not only on charge, but also on local groove widths. This could improve the stabilisation and specificity of antigene triplex formation.

Base Composition↗
PubMed1999

The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) shows significant differences to that found in solution.

The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) has been solved and refined at 2.5 A resolution. The refinement procedure converged at R = 0.181 for all reflections in the range 20.0-2.5 A. In the crystal, the RNA/DNA hybrid duplex has an A' conformation with all but one of the nucleotide sugar moieties adopting a C3'- endo (N) conformation. Both strands in the double helix adopt a global conformation close to the A-form and the width of the minor groove is typical of that found in the crystal structures of other A-form duplexes. However, differences are observed between the RNA and DNA strands that make up the hybrid at the local level. In the central portion of the duplex, the RNA strand has backbone alpha, beta and gamma torsion angles that alternate between the normal gauche -/ trans / gauche + conformation and an unusual trans / trans / trans conformation. Coupled with this so-called 'alpha/gamma flipping' of the backbone torsion angles, the distance between adjacent phosphorous atoms on the RNA strand systematically varies. Neither of these phenomena are observed on the DNA strand. The structure of the RNA/DNA hybrid presented here differs significantly from that found in solution for this and other sequences. Possible reasons for these differences and their implications for the current model of RNase H activity are discussed.

Circular Dichroism↗
PubMed1999

Outcome after surgical repair of junctional epidermolysis bullosa-pyloric atresia syndrome: a report of 3 cases and review of the literature.

BACKGROUND: Junctional epidermolysis bullosa-pyloric atresia syndrome is recognized as a distinct autosomal recessive entity. Affected infants present with skin fragility and inability to feed due to intestinal obstruction. Despite successful surgical repair of the anatomical defect, the outcome is poor owing to poor feeding, malabsorption, failure to thrive, and sepsis. OBSERVATIONS: In 70 cases of intestinal obstruction and epidermolysis bullosa reported in the medical literature and the 3 reported here, surgical intervention was attempted 51 times. In all except 16 infants, death occurred before age 11 months (mean age, 70 days). Renal involvement and continued failure to thrive accompanied the skin disease in survivors, who ranged in age from 30 days to 16 years (mean age, 4.0 years). CONCLUSIONS: The poor prognosis of this condition must be considered when decisions are made regarding surgical correction. Attempting surgical correction may be warranted in individual circumstances, but withholding surgical intervention and providing palliative support is an acceptable alternative.

Epidermolysis Bullosa, Junctional↗
PubMed1999

Simplified sample preparation for the analysis of oligonucleotides by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry.

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) for the analyses of oligonucleotides has generally been carried out using negative ionisation conditions, usually following ammonium ion-exchange chromatography and the addition of ammonium buffers to the MALDI matrix. The molecular ion region is complex, due to the varying degrees of ammoniation of the phosphate backbone of the oligonucleotide. This gives rise to an overall decrease in sensitivity compared with similar size peptides and can cause ambiguity of assignment of the relative molecular mass of the sample. This study describes the use of H(+) ion exchange resin in situ as the means of removing alkali metal ions from the phosphate backbone of the oligonucleotide. An increase in resolution, sensitivity and identification of the molecular species is reported, with little or no difference in sensitivity observed between positive or negative ionisation spectra. This method is now used for routine screening of synthetic oligonucleotides with a gain in sensitivity of 1-2 orders of magnitude compared with previous methods, and mass assignment errors of +/-0.1% are routinely recorded for externally calibrated data.

Ion Exchange Resins↗
PubMed1999

The keratinocyte-derived cytokine IL-7 increases adhesion of the epidermal T cell subset to the skin basement membrane protein laminin-5.

Human epidermis contains a subset of epidermal T cells that can mount an immune response by migrating through the skin and into the peripheral lymphnodes to proliferate before re-entering the epidermis. The cytokine IL-7 is shown to be localized to the basement membrane of normal human skin. Furthermore, culturing in the presence of IL-7 causes increased adhesion of epidermal T cells but not peripheral blood T cells to the major epidermal basement membrane protein, laminin-5. The mechanism for increased T cell adhesion to laminin-5 is due, at least in part, to an increase in the cell surface expression of the integrin alpha3beta1. Epidermal T cells cultured in IL-7 that are strongly adherent to laminin-5 are shown by flow cytometry to consist of a variety of subsets; therefore, the increase in cell adhesion is not due to an outgrowth of one T cell subset during culturing. We hypothesize that in vivo, exposure to IL-7 is required for epidermal T cell adhesion to laminin-5.

Adult↗
PubMed1999

Preliminary assessment of extrastriatal dopamine D-2 receptor binding in the rodent and nonhuman primate brains using the high affinity radioligand, 18F-fallypride.

We have identified the value of 18F-fallypride [(S)-N-[(1-allyl-2-pyrrolidinyl)methyl]-5-(3-[18F]fluoropropyl)-2, 3-dimethoxybenzamide], as a dopamine D-2 receptor radiotracer for the study of striatal and extrastriatal receptors. Fallypride exhibits high affinities for D-2 and D-3 subtypes and low affinity for D-4 (3H-spiperone IC50s: D-2 = 0.05 nM [rat striata], D-3 = 0.30 nM [SF9 cell lines, rat recombinant], and D-4 = 240 nM [CHO cell lines, human recombinant]). Biodistribution in the rat brain showed localization of 18F-fallypride in striata and extrastriatal regions such as the frontal cortex, parietal cortex, amygdala, hippocampus, thalamus, and hypothalamus. In vitro autoradiographic studies in sagittal slices of the rat brain showed localization of 18F-fallypride in striatal and several extrastriatal regions, including the medulla. Positron emission tomography (PET) experiments with 18F-fallypride in male rhesus monkeys were carried out in a PET VI scanner. In several PET experiments, apart from the specific binding seen in the striatum, specific binding of 18F-fallypride was also identified in extracellular regions (in a lower brain slice, possibly the thalamus). Specific binding in the extrastriata was, however, significantly lower compared with that observed in the striata of the monkeys (extrastriata/cerebellum = 2, striata/cerebellum = 10). Postmortem analysis of the monkey brain revealed significant 18F-fallypride binding in the striata, whereas binding was also observed in extrastriatal regions such as the thalamus, cortical areas, and brain stem.

Animals↗
PubMed1999

Detection of PCR products using self-probing amplicons and fluorescence.

Molecular diagnostics is progressing from low-throughput, heterogeneous, mostly manual technologies to higher throughput, closed-tube, and automated methods. Fluorescence is the favored signaling technology for such assays, and a number of techniques rely on energy transfer between a fluorophore and a proximal quencher molecule. In these methods, dual-labeled probes hybridize to an amplicon and changes in the quenching of the fluorophore are detected. We describe a new technology that is simple to use, gives highly specific information, and avoids the major difficulties of the alternative methods. It uses a primer with an integral tail that is used to probe an extension product of the primer. The probing of a target sequence is thereby converted into a unimolecular event, which has substantial benefits in terms of kinetics, thermodynamics, assay design, and probe reliability.

BRCA2 Protein↗
PubMed1999

Comparison of the functional potencies of ropinirole and other dopamine receptor agonists at human D2(long), D3 and D4.4 receptors expressed in Chinese hamster ovary cells.

1. The aim of the present study was to characterize functional responses to ropinirole, its major metabolites in man (SKF-104557 (4-[2-(propylamino)ethyl]-2-(3H) indolone), SKF-97930 (4-carboxy-2-(3H) indolone)) and other dopamine receptor agonists at human dopamine D2(long) (hD2), D3 (hD3) and D4.4 (hD4) receptors separately expressed in Chinese hamster ovary cells using microphysiometry. 2. All the receptor agonists tested (ropinirole, SKF-104557, SKF-97930, bromocriptine, lisuride, pergolide, pramipexole, talipexole, dopamine) increased extracellular acidification rate in Chinese hamster ovary clones expressing the human D2, D3 or D4 receptor. The pEC50s of ropinirole at hD2, hD3 and hD4 receptors were 7.4, 8.4 and 6.8, respectively. Ropinirole is therefore at least 10 fold selective for the human dopamine D3 receptor over the other D2 receptor family members. 3. At the hD2 and hD3 dopamine receptors all the compounds tested were full agonists as compared to quinpirole. Talipexole and the ropinirole metabolite, SKF-104557, were partial agonists at the hD4 receptor. 4. Bromocriptine and lisuride had a slow onset of agonist action which precluded determination of EC50s. 5. The rank order of agonist potencies was dissimilar to the rank order of radioligand binding affinities at each of the dopamine receptor subtypes. Functional selectivities of the dopamine receptor agonists, as measured in the microphysiometer, were less than radioligand binding selectivities. 6. The results show that ropinirole is a full agonist at human D2, D3 and D4 dopamine receptors. SKF-104557 the major human metabolite of ropinirole, had similar radioligand binding affinities to, but lower functional potencies than, the parent compound.

Animals↗
PubMed1999

Anti-G in a pregnant patient.

BACKGROUND: Anti-G is a red cell (RBC) antibody of the Rh system. It has been described in pregnant women only in association with anti-D or anti-C; therefore, the ability of this antibody alone to cause hemolytic disease of the newborn is uncertain. One case in which this antibody caused no clinical sequelae is reported. CASE REPORT: The patient was a 35-year-old primigravida with type O, D-, C-, E-, c+ RBCs who was given 4 units of type O, D- allogeneic RBCs and 2 units of autologous RBCs 2 years antepartum. She was found to have anti-D and anti-C by an outside laboratory as part of a routine prenatal work-up. Further evaluation by our laboratory revealed the presence of anti-G and possible anti-C without anti-D. Titers at 22 weeks' gestation were 64 against r'r RBCs and 16 against R2R2 RBCs; these remained unchanged throughout the pregnancy. Amniocentesis performed at Weeks 28 and 32 showed no evidence of hemolytic disease of the newborn. A healthy 3.3-kg infant was delivered at 36 weeks' gestation. Prophylactic Rh immune globulin was administered antepartum and postpartum. The infant's RBCs were type O, D+, c+ C-, E-, and the direct antiglobulin test was positive. An acid eluate prepared from the baby's RBCs revealed anti-G. The total bilirubin was 5.5 mg per dL at birth, and the hematocrit was 66 percent. Total bilirubin peaked on Day 5 at 11.9 mg per dL, and no therapeutic intervention was required. CONCLUSIONS: Anti-G alone caused little if any fetal or neonatal hemolysis in this case. Although further study is needed, invasive fetal monitoring may be unnecessary if anti-G is the sole cause of fetomaternal RBC incompatibility.

Adult↗
PubMed1999

Severe delayed hemolytic transfusion reaction secondary to anti-At(a).

BACKGROUND: Anti-At(a) is a rare red cell (RBC) alloantibody found in the black population. It has been described as causing one case of mild hemolytic disease of the newborn, but its ability to cause hemolytic transfusion reactions is uncertain. CASE REPORT: The patient was a 60-year-old black female with a history of three uneventful pregnancies but no transfusions. On admission, her direct and indirect antiglobulin tests were negative, total bilirubin was 0.5 mg per dL, and lactate dehydrogenase was 224 IU per L. She received nine units of compatible RBCs in the perioperative period of a hemicolectomy. Her hemoglobin rose appropriately and stabilized at 12.6 g per dL by the 6th postoperative day. By Day 10 after surgery her hemoglobin had dropped to 6.8 g per dL, and her total bilirubin and lactate dehydrogenase had risen to 1.4 mg per dL and 783 IU per L, respectively. The direct and indirect antiglobulin tests were now newly positive with strengths of 3+. A warm hemolytic autoantibody was suspected. She was transfused two units of incompatible RBCs for a rapidly falling hemoglobin and symptomatic anemia. On Day 11, the total bilirubin rose to 3.5 mg per dL, and the lactate dehydrogenase was 1154 IU per L with a hemoglobin of 7.6 g per dL. Corticosteroids were begun. Studies of serum and an acid eluate revealed anti-At(a), but no other RBC antibodies. The patient stabilized, and further transfusion was avoided. CONCLUSION: Although anti-At(a) was previously described as being of uncertain clinical significance, this patient demonstrated the ability of the antibody to cause a severe delayed hemolytic transfusion reaction.

Black People↗
PubMed1999

Comparison of cervicovertebral dimensions in Australian Aborigines and Caucasians.

Cervicovertebral dimensions were compared in a group of 30 male and 30 female young adult Australian Aborigines from the Northern Territory, and a control sample consisting of 60 Caucasian dental students from Adelaide, matched for sex and age. Thirty-six variables, 22 cervical and 14 craniofacial, were derived from standardized lateral roentgenograms with the use of a computerized cephalometric system. Vertebral body height and length were significantly greater in Aboriginal males than females for C3 to C7, while dorsal arch height of C1 and C2 displayed the greatest dimensional variability in both sexes. The antero-posterior length of C1, dens height, and body heights of C3 and C4 were significantly shorter in Aborigines than Caucasians for both males and females. Total length of the column from C2 to C6 was approximately 12 per cent shorter in the Aborigines compared with Caucasians. The height of the posterior arch of C1 was significantly correlated with one or both posterior cranial base lengths in Aborigines and Caucasians. Associations were also noted between mandibular lengths and posterior arch heights of the upper two vertebrae. The results confirm and clarify several previous observations on the relative shortness of the cervical spine in Australian Aboriginals. They also indicate some associations between dimensions of the cervical vertebrae and craniofacial lengths, particularly those representing the posterior cranial base and the mandible.

Adolescent↗
PubMed1999

Gap junctions regulate responses of tendon cells ex vivo to mechanical loading.

Avian digital flexor tendons were used with a device to apply load ex vivo to study the effects on deoxyribonucleic acid and collagen synthesis when cell to cell communication is blocked. Flexor digitorum profundus tendons from the middle toe of 52-day-old White Leghorn chickens were excised and used as nonloaded controls, or clamped in the jaws of a displacement controlled tissue loading device and mechanically loaded for 3 days at a nominal 0.65% elongation at 1 Hz for 8 hours per day with 16 hours rest. Tendon samples were radiolabeled during the last 16 hours with 3H-thymidine to monitor deoxyribonucleic acid synthesis or with 3H-proline to radiolabel newly synthesized collagen. Cyclic loading of whole avian flexor tendons stimulated deoxyribonucleic acid and collagen synthesis, which could be blocked with octanol, a reversible gap junction blocker. Cells from human digital flexor tendon were used to populate a rectangular, three-dimensional, porous, polyester foam that could be deformed cyclically in vitro. Together, these results support the hypothesis that tendon cells must communicate to sustain growth and matrix expression and that an engineered three-dimensional construct can be used to study responses to mechanical load in vitro.

Animals↗
PubMed1999

Species, interindividual, and tissue specificity in endocrine signaling.

The activity of endocrine-active agents exhibits specificity at many levels. Differential responsiveness to these agents has been observed between different species and extends to interindividual differences within a species and between different tissues as well. In cases where they have been identified, the biologic and molecular mechanisms underlying this specificity are quite diverse. Determinants of species specificity include differences that exist in receptor binding, gene transcription, and cellular responses to endocrine-active compounds between species. Interindividual differences in responsiveness may be determined at the level of genetic polymorphisms in hormone-metabolizing enzymes, hormone receptors, and in those genes that are transactivated by these receptors, as well as during changing windows of susceptibility that occur as a function of age, such as prenatal and postmenopausal exposures. Extrinsic factors such as diet can also impact individual susceptibility to endocrine-active agents. Tissue-specific determinants of susceptibility are well documented, but little is known regarding the mechanisms underlying these different responses. Differences in the expression of accessory proteins for steroid hormone receptors and different patterns of receptor expression, estrogen receptor alpha and estrogen receptor beta; for example, may contribute to tissue specificity, as may differences in the pattern of expression of other genes such as hormone-metabolizing enzymes. The use of animal model systems and development of appropriate mathematical models has the potential to yield additional valuable information for elucidating the role of these determinants of specificity at low-dose exposures and for improved risk assessments for the adverse health effects of endocrine-active compounds.

Age Factors↗