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W R Taylor

Publications and source records attributed to W R Taylor.

At least 55 records · Page 3Linked to original sources
PubMed2000

Assessing drug sensitivity of Plasmodium vivax to halofantrine or choroquine in southern, central Vietnam using an extended 28-day in vivo test and polymerase chain reaction genotyping.

Chloroquine-resistant Plasmodium vivax malaria is emerging in Oceania, Asia, and Latin America. We assessed the drug sensitivity of P. vivax to chloroquine or halofantrine in two villages in southern, central Vietnam. This area has chloroquine-resistant Plasmodium falciparum but no documented chloroquine-resistant P. vivax. Standard dose chloroquine (25 mg/kg, over 48 hours) or halofantrine (8 mg/kg, 3 doses) was administered to 29 and 25 patients, respectively. End points were parasite sensitivity or resistance determined at 28 days. Of the evaluable patients, 23/23 100% (95% confidence interval [CI] 85.1-100) chloroquine and 21/24 (87.5%) (95% CI 67.6-97.3) halofantrine-treated patients were sensitive. Three halofantrine recipients had initial clearance but subsequent recurrence of their parasitemias. Genotyping of the recurrent and Day 0 parasitemias differed, suggesting either new infections or relapses of liver hypnozoites from antecedent infections. Among these Vietnamese patients, P. vivax was sensitive to chloroquine and halofantrine. Genotyping was useful for differentiating the recurrent vivax parasitemias.

Adolescent↗
PubMed2000

Referral times of Vietnamese refugees with tuberculosis in camps in Hong Kong.

SETTING: Two closed camps in Hong Kong for Vietnamese refugees. OBJECTIVE: To determine the referral times by clinicians (doctor's delay) of cases of tuberculosis (TB) from refugee camp clinics to the hospital/chest clinic. DESIGN: Retrospective case-note study of 97 Vietnamese patients receiving treatment for tuberculosis. RESULTS: The sites of TB were pulmonary (n = 61), glandular (n = 15), pleural effusion (n = 15), and other (n = 6). The median referral time was 18 days (range 0-417). Median consultations numbered three (range 1-16). Fifty-three (54.6%) patients were prescribed antibiotics. Thirty-nine (40%) patients were referred within 10 days; of these, 18 were referred the same day. These 39 patients were less likely to have received antibiotics (9/39 [23.1%] vs 44/58 [75.9%], relative risk [RR] 0.3 95% confidence interval [CI] 0.17-0.55), but were equally likely to have been physically examined (RR 0.66, 95%CI 0.39-1.1). Sixteen (16.5%) patients were referred after 90 days. They attended the clinic more often (median attendances 6.5 vs 3, P = 0.0002), and were prescribed more antibiotic courses (mean antibiotic prescriptions 1.6 vs 0.7, P = 0.03). CONCLUSION: Referral times by these clinicians varied widely, with long delays for approximately 60% of patients. Guidelines pertinent to primary care clinicians are needed to heighten their awareness of tuberculosis to prevent referral delays and subsequent TB treatment.

Adolescent↗
PubMed1999

Induction of target cell apoptosis by channel catfish cytotoxic cells.

This study examines cytotoxic mechanisms used by channel catfish peripheral blood-derived effector cells. Transmission electron microscopy (TEM), coupled with [(3)H]thymidine DNA fragmentation (JAM) and terminal deoxynucleotidyl nick-end labeling (TUNEL) assays, provided the first evidence that catfish peripheral blood cytotoxic effectors killed allogeneic targets via an apoptotic pathway. TEM demonstrated that the effector cell population present within peripheral blood leukocytes (PBLs) was composed of agranular lymphocytes that formed conjugates with, and induced apoptosis in, allogeneic target cells. Both JAM and TUNEL assays showed that PBLs induced target cell DNA fragmentation within 1 h of coculture. In addition, fixed effectors did not induce target cell necrosis or apoptosis, and target cell lysis was completely inhibited by chelation of free Ca(2+) by EGTA. These results suggest that catfish peripheral blood-derived effector cells utilize a secretory mechanism rather than a ligand-based mechanism to trigger apoptosis.

Animals↗
PubMed1999

Iterated sequence databank search methods.

Iterated sequence databank search methods were assessed from the viewpoint of someone with the sequence of a novel gene product wishing to find distant relatives to their protein and, with the specific searches against the PDB, also hoping to find a relative of known structure. We examined three methods in detail, spanning a range from simple pattern-matching to sophisticated weighted profiles. Rather than apply these methods 'blindly' (with default parameters) to a large number of test queries, we have concentrated on the globins, so allowing a more detailed investigation of each method on different data subsets with different parameter settings. Despite their widespread use, regular-expression matching proved to be very limited-seldom extending beyond the sub-family from which the pattern was derived. To attain any generality, the patterns had to be 'stripped-down' to include only the most highly conserved parts. The QUEST program avoided these problems by introducing a more flexible (weighted) matching. On the PDB sequences this was highly effective, missing only a few globins with probes based on each sub-family or even a single representative from each sub-family. In addition, very few false-positives were encountered, and those that did match, often only did so for a few cycles before being lost again. On the larger sequence collection, however, QUEST encountered problems with maintaining (or achieving) the alignment of the full globin family. psi-BLAST also recognised almost all the globins when matching against the PDB sequences, typically, missing three or four of the most distantly related sequences while picking-up a few false-positives. In contrast to QUEST, psi-BLAST performed very well on the larger databank, getting almost a full collection of globins although still retaining the same proportion of false-positives. SAM applied to the PDB sequences performed reasonably well with the myoglobin and hemoglobin families as probes, missing, typically several of the more difficult proteins but performed poorly with the leghemoglobin probe. Only with the full family range as a probe did it produce results comparable to psi-BLAST and QUEST. With the larger databank, SAM produced a good result but, again, this was only achieved using the full range of sequence variation with the default regulariser and use of Dirichlet mixtures completely failed in this situation.

Amino Acid Sequence↗
PubMed1999

Coevolving protein residues: maximum likelihood identification and relationship to structure.

The identification of protein sites undergoing correlated evolution (coevolution) is of great interest due to the possibility that these pairs will tend to be adjacent in the three-dimensional structure. Identification of such pairs should provide useful information for understanding the evolutionary process, predicting the effects of site-directed substitution, and potentially for predicting protein structure. Here, we develop and apply a maximum likelihood method with the aim of improving detection of coevolution. Unlike previous methods which have had limited success, this method allows for correlations induced by phylogenetic relationships and for variation in rate of evolution along branches, and does not rely on accurate reconstruction of ancestral nodes. In order to reduce the complexity of coevolutionary relationships and identify the primary component of pairwise coevolution between two sites, we reduce the data to a two-state system at each site, regardless of the actual number of residues observed at that site. Simulations show that this strategy is good at identifying simple correlations and at recognizing cases in which the data are insufficient to distinguish between coevolution and spurious correlations. The new method was tested by using size and charge characteristics to group the residues at each site, and then evaluating coevolution in myoglobin sequences. Grouping based on physicochemical characteristics allows categorization of coevolving sites into positive and negative coevolution, depending on the correlation between equilibrium state frequencies. We detected a striking excess of negative coevolution (corresponding to charge) at sites brought into proximity by the periodicity of the alpha-helix, and there was also a tendency for sites with significant likelihood ratios to be close in the three-dimensional structure. Sites on the surface of the protein appear to coevolve both when they are close in the structure, and when they are distant, implying a role for folding and/or avoidance of quaternary structure in the coevolution process.

Computer Simulation↗
PubMed1999

Discovery of local packing motifs in protein structures.

We present a language for describing structural patterns of residues in protein structures and a method for the discovery of such patterns that recur in a set of protein structures. The patterns impose restrictions on the spatial position of each residue, their order along the amino acid chain, and which amino acids are allowed in each position. Unlike other methods for comparing sets of protein structures, our method is not based on the use of pairwise structure comparisons which is often time consuming and can produce inconsistent results. Instead, the method simultaneously takes into account information from all structures in the search for conserved structure patterns which are potential structure motifs. The method is based on describing the spatial neighborhoods of each residue in each structure as a string and applying a sequence pattern discovery method to find patterns common to subsets of these strings. Finally it is checked whether the similarities between the neighborhood strings correspond to spatially similar substructures. We apply the method to analyze sets of very disparate proteins from the four different protein families: serine proteases, cuprodoxins, cysteine proteinases, and ferredoxins. The motifs found by the method correspond well to the site and motif information given in the annotation of these proteins in PDB, Swiss-Prot, and PROSITE. Furthermore, the motifs are confirmed by using the motif data to constrain the structural alignment of the proteins obtained with the program SAP. This gave the best superposition/alignment of the proteins given the motif assignment.

Algorithms↗
PubMed1999

p53 inhibits entry into mitosis when DNA synthesis is blocked.

Human and mouse fibroblasts with normal p53 fail to enter mitosis when DNA synthesis is blocked by aphidicolin or hydroxyurea. Isogenic p53-null fibroblasts do enter mitosis with incompletely replicated DNA, revealing that p53 contributes to a checkpoint that ensures that mitosis does not occur until DNA synthesis is complete. When treated with N-(phosphonacetyl)-L-aspartate (PALA), which inhibits pyrimidine nucleotide synthesis, leading to synthesis of damaged DNA from highly unbalanced dNTP pools, p53-null cells enter mitosis after they have completed DNA replication, but cells with wild-type p53 do not, revealing that p53 also mediates a checkpoint that monitors the quality of newly replicated DNA.

Animals↗
PubMed1999

Role of NFkappaB in the regulation of macrophage colony stimulating factor by tumor necrosis factor-alpha in ST2 bone stromal cells.

Expression of MCSF in bone is important to the regulation of osteoclastogenesis. We show here that tumor necrosis factor-alpha (TNFalpha) increases the production of both soluble (sMCSF) and membrane-bound (mMCSF) macrophage colony stimulating factor by ST2 bone stromal cells. Treatment of ST2 cells with TNFalpha caused sMCSF levels to increase by 394+/-5% from basal; mMCSF rose by 316+/-66% from 30+/-10 per 100,000 cells in the same time. These increases were consistent with increased expression of mRNAs encoding both isoforms. Increases in MCSF mRNA are also seen after stimulation with dexamethasone. To investigate the potential role of NFkappaB in this TNFalpha effect, we treated cells with sodium salicylate (NaS), an inhibitor of NFkappaB translocation. NaS decreased TNFalpha-stimulated NFkappaB activation by 50% as assessed by EMSA. Despite inhibition of NFkappaB signaling, NaS enhanced TNFalpha-stimulated MCSF secretion and did not prevent TNFalpha-stimulated increases in sMCSF mRNA, suggesting that NFkappaB was not involved in TNFalpha effect on the gene. TNFalpha failed to stimulate transcription of a 774 nucleotide MCSF promoter-luciferase reporter transfected into ST2 cells which contained the NFkappaB consensus sequence. Deletion of the seven nucleotides containing the NFkappaB homology response sequence from the MCSF promoter increased basal gene transcription by twofold. TNFalpha thus contributes to an osteoclastogenic environment through upregulation of bone expression of both MCSF isoforms. Our data suggests that NFkappaB is not the major signaling pathway through which this occurs.

Bone and Bones↗
PubMed1999

Osteoclastogenesis is repressed by mechanical strain in an in vitro model.

Functional loading provides a site-specific signal for the regulation of bone mass and morphology. To determine if strain can inhibit the resorptive component of bone remodeling, osteoclast formation was assessed in marrow cultures plated on flexible membranes subjected to 5% strain for 10 cycles/minute, 24 hours per day. Cultures strained during days 2 through 7 inhibited osteoclast formation to 61+/-7% of control cultures (p < 0.05), a degree of inhibition similar to that observed when the cultures were subjected to strains during only days 2 through 4 but also evaluated on day 7 (67+/-4% of control; p < 0.05). In contrast, straining of cultures during days 5 through 7 had little influence on inhibiting the formation of osteoclasts (94+/-5% of control; no significant difference). The nonuniformly strained substrate was subdivided into three concentric rings. and cultures were used to examine the site-specificity of the inhibition caused by strain. Osteoclast formation in the outermost boundary, which was distended from 3.6 to 5%, was 41+/-7% of that observed in outer regions of control wells. The inhibitory potential of mechanical strain was reduced within the middle ring (73+/-6% of control osteoclasts: p < 0.01), where the strain ranged from 0.2 to 3.6%. The central region, which experienced strains equivalent to those in the middle ring (0.2 to -4% strain), showed inhibition of osteoclast formation to a similar degree (75+/-6% of control). Media harvested from strained cultures failed to inhibit osteoclast formation in unstrained cultures; this implies that the inhibitory effect of strain depended on the direct interaction of the cell with the substrate rather than by a humoral factor. A second device, where a uniform strain was delivered at 1.8% throughout the entire plate, inhibited osteoclast recruitment to 48+/-3.6%, emphasizing that uniform strain in the absence of shear stress constrains osteoclast recruitment. These in vitro experiments can but model the complex environment generated by in vivo mechanical strains: however, they provide the first direct evidence that strain must be considered as inhibitory to osteoclast recruitment.

Animals↗
PubMed1999

Demonstration of the presence of lipid peroxide-modified proteins in human atherosclerotic lesions using a novel lipid peroxide-modified anti-peptide antibody.

Immunohistochemical demonstration of oxidation-specific epitopes using antibodies developed against oxidized low density lipoprotein (Ox-LDL), LDL modified by products of lipid peroxidation (e.g. malondialdehyde-modified LDL), and lipid peroxide-modified albumin has been considered as strong evidence for the presence of oxidatively modified proteins in atherosclerotic lesions. However, the antigens used in the development of these antibodies were derived from lipoproteins and other proteins that are constituents of both normal and atherosclerotic arteries. In order to demonstrate the unequivocal presence of oxidatively modified proteins, we have used a 15 amino acid synthetic peptide derived from the sequence of human glycodelin. Using an antibody developed against this peptide and the second antibody developed against the lipid peroxide-modified peptide, we immunostained progressive human atherosclerotic lesions. Antibody to the unmodified peptide did not react with antigenic epitopes present in mild, moderate, or severe human atherosclerotic lesions. In contrast, the antibody developed against lipid peroxide-modified peptide highly reacted with tissue samples and provided strong evidence for the presence of lipid peroxide-modified proteins. This study suggests the presence of lipid peroxide-modified proteins in the lesion and that these epitopes are derived by direct interaction of lysine residues with lipid peroxides.

Antibodies, Monoclonal↗
PubMed1999

Measles in Vietnamese refugee children in Hong Kong.

From September 1991-January 1992, there was a measles epidemic in an established refugee camp for 7000 Vietnamese 'Boat People' living in Hong Kong. This 16 week outbreak occurred against a backdrop of poor uptake of measles vaccination and overcrowded living conditions. Two hundred and sixty-two children were affected (155 boys, 107 girls); 235 children (89.7 %) were < 2 years old, age range 5-39 months. Children age 6-11 months had the highest crude attack rate (AR) of 54.3%. The highest age specific crude AR was 83.8% in children aged 14 months. Measles complications affected 234 (89.3%) children. Sixty-six children (25.2%) were admitted to hospital. There were two deaths from pneumonia, giving a case fatality rate of 0.76%. Measles control in refugee camps continues to be a public health challenge.

Age Distribution↗
PubMed1999

Malaria prophylaxis using azithromycin: a double-blind, placebo-controlled trial in Irian Jaya, Indonesia.

New drugs are needed for preventing drug-resistant Plasmodium falciparum malaria. The prophylactic efficacy of azithromycin against P. falciparum in malaria-immune Kenyans was 83%. We conducted a double-blind, placebo-controlled trial to determine the prophylactic efficacy of azithromycin against multidrug-resistant P. falciparum malaria and chloroquine-resistant Plasmodium vivax malaria in Indonesian adults with limited immunity. After radical cure therapy, 300 randomized subjects received azithromycin (148 subjects, 750-mg loading dose followed by 250 mg/d), placebo (77), or doxycycline (75, 100 mg/d). The end point was slide-proven parasitemia. There were 58 P. falciparum and 29 P. vivax prophylaxis failures over 20 weeks. Using incidence rates, the protective efficacy of azithromycin relative to placebo was 71.6% (95% confidence interval [CI], 50.3-83.8) against P. falciparum malaria and 98.9% (95% CI, 93.1-99.9) against P. vivax malaria. Corresponding figures for doxycycline were 96.3% (95% CI, 85.4-99.6) and 98% (95% CI, 88.0-99.9), respectively. Daily azithromycin offered excellent protection against P. vivax malaria but modest protection against P. falciparum malaria.

Adolescent↗
PubMed1999

Mechanisms of G2 arrest in response to overexpression of p53.

Overexpression of p53 causes G2 arrest, attributable in part to the loss of CDC2 activity. Transcription of cdc2 and cyclin B1, determined using reporter constructs driven by the two promoters, was suppressed in response to the induction of p53. Suppression requires the regions -287 to -123 of the cyclin B1 promoter and -104 to -74 of the cdc2 promoter. p53 did not affect the inhibitory phosphorylations of CDC2 at threonine 14 or tyrosine 15 or the activity of the cyclin-dependent kinase that activates CDC2 by phosphorylating it at threonine 161. Overexpression of p53 may also interfere with the accumulation of CDC2/cyclin B1 in the nucleus, required for cells to enter mitosis. Constitutive expression of cyclin B1, alone or in combination with the constitutively active CDC2 protein T14A Y15F, did not reverse p53-dependent G2 arrest. However, targeting cyclin B1 to the nucleus in cells also expressing CDC2 T14A Y15F did overcome this arrest. It is likely that several distinct pathways contribute to p53-dependent G2 arrest.

Apoptosis↗
PubMed1999

Protein structural domain identification.

A simple method for the definition of protein structural domains is described that requires only alpha-carbon coordinate data. The basic method, which encodes no specific aspects of protein structure, captures the essence of most domains but does not give high enough priority to the integrity of beta-sheet structure. This aspect was encouraged both by a bias toward attaining intact beta-sheets and also as an acceptance condition on the final result. The method has only one variable parameter, reflecting the granularity level of the domains, and an attempt was made to set this level automatically for each protein based on the best agreement attained between the domains predicted on the native structure and a set of smoothed coordinates. While not perfect, this feature allowed some tightly packed domains to be separated that would have remained undivided had the best fixed granularity level been used. The quality of the results was high and, when compared with a large collection of accepted domain definitions, only a few could be said to be clearly incorrect. The simplicity of the method allowed its easy extension to the simultaneous definition of domains across related structures in a way that does not involve loss of detail through averaging the structures. This was found to be a useful approach to reconciling differences among structural family members. The method is fast, taking less than 1 s per 100 residues for medium-sized proteins.

Models, Chemical↗
PubMed1999

Protein structure comparison using iterated double dynamic programming.

A protein structure comparison method is described that allows the generation of large populations of high-scoring alternate alignments. This was achieved by incorporating a random element into an iterative double dynamic programming algorithm. The maximum scores from repeated comparisons of a pair of structures converged on a value that was taken as the global maximum. This lay 15% over the score obtained from the single fixed (unrandomized) calculation. The effect of the gap penalty was observed through the shift of the alignment populations, characterized by their alignment length and root-mean-square deviation (RMSD). The best (lowest RMSD) values found in these populations provided a base-line against which other methods were compared.

Protein Conformation↗
PubMed1999

Plasmodium falciparum mdr1 mutations and in vivo chloroquine resistance in Indonesia.

Mutations in the Pfmdr1 gene are reported to be associated with chloroquine resistance in some Plasmodium falciparum isolates. A polymerase chain reaction/restriction fragment length polymorphism method was used for the detection of Pfmdr1 mutations in chloroquine-resistant field isolates of P. falciparum collected in Irian Jaya. The frequency of Pfmdr1 mutations was significantly higher in chloroquine-resistant P. falciparum parasites than background frequencies observed in the same location. The 7G8 mutation was identified in some parasites although always in a mixed genotype status. Chloroquine-resistant P. falciparum specimens were characterized using the World Health Organization 28-day criteria, supplemented by demonstrating adequate chloroquine absorption and genetic analysis.

ATP-Binding Cassette Transporters↗
PubMed1998

A p53-dependent S-phase checkpoint helps to protect cells from DNA damage in response to starvation for pyrimidine nucleotides.

Normal mammalian cells arrest primarily in G1 in response to N-(phosphonacetyl)-L-aspartate (PALA), which starves them for pyrimidine nucleotides, and do not generate or tolerate amplification of the CAD gene, which confers resistance to PALA. Loss of p53, accompanied by loss of G1 arrest, permits CAD gene amplification and the consequent formation of PALA-resistant colonies. We have found rat and human cell lines that retain wild-type p53 but have lost the ability to arrest in G1 in response to PALA. However, these cells still fail to give PALA-resistant colonies and are protected from DNA damage through the operation of a second checkpoint that arrests them reversibly within S-phase. This S-phase arrest, unmasked in the absence of the G1 checkpoint, is dependent on p53 and independent of p21/waf1.

Animals↗