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C M Thomas

Publications and source records attributed to C M Thomas.

At least 91 records · Page 5Linked to original sources
PubMed1997

Characterization of the tomato Cf-4 gene for resistance to Cladosporium fulvum identifies sequences that determine recognitional specificity in Cf-4 and Cf-9.

In many interactions between plants and their pathogens, resistance to infection is specified by plant resistance (R) genes and corresponding pathogen avirulence (Avr) genes. In tomato, the Cf-4 and Cf-9 resistance genes map to the same location but confer resistance to Cladosporium fulvum through recognition of different avirulence determinants (AVR4 and AVR9) by a molecular mechanism that has yet to be determined. Here, we describe the cloning and characterization of Cf-4, which also encodes a membrane-anchored extracellular glycoprotein. Cf-4 contains 25 leucine-rich repeats, which is two fewer than Cf-9. The proteins have > 91% identical amino acids. DNA sequence comparison suggests that Cf-4 and Cf-9 are derived from a common progenitor sequence. Amino acid differences distinguishing Cf-4 and Cf-9 are confined to their N termini, delimiting a region that determines the recognitional specificity of ligand binding. The majority of these differences are in residues interstitial to those of the leucine-rich repeat consensus motif. Many of these residues are predicted to form a solvent-exposed surface that can interact with the cognate ligand. Both Cf-4 and Cf-9 are located within a 36-kb region comprising five tandemly duplicated homologous genes. These results provide further insight into the molecular basis of pathogen perception by plants and the organization of complex R gene loci.

Amino Acid Sequence↗
PubMed1997

Transcriptional and translational control of the genes for the mating pair formation apparatus of promiscuous IncP plasmids.

The trb operon of broad-host-range plasmid RK2 encodes most of the genes required for formation of mating-pair apparatus and is thus essential for the promiscuous spread of this plasmid. Only two promoters, lying upstream of trbA and trbB, have been identified for this operon. trbB encodes a protein belonging to a large family of proteins which function in the assembly of apparatuses associated with the cell surface. trbA encodes a repressor protein, one of whose targets is the trbB promoter. trbAp is arranged as a face-to-face divergent promoter with trfAp, the strongest of the three promoters in this region. trfAp completely inhibits trbAp unless it is repressed by the KorA protein, a key regulator encoded in the plasmid's central control operon. We show that when trfAp is firing constitutively, it also appears to interfere with trbBp, but that trbBp activity increases when trfAp activity is decreased by repression or mutation. A second global regulator encoded in the central control operon, KorB, represses trbBp, trfAp, and trbAp. The results presented here show that both KorB and TrbA are necessary for full repression of trbBp. The region between trbA and trbB encodes a large inverted repeat which has been proposed to modulate translation of trbB on transcripts which are initiated at trbAp but not trbBp. Using translational fusions to lacZ, we show that translation of trbB is completely blocked when transcripts incorporate the inverted repeat upstream of trbB but proceeds with reasonable efficiency when deletions remove the sequences predicted to sequester the ribosome binding site. Results from both transcriptional fusion and direct measurement of transcript size and intensity by Northern blot analysis show that most trbA transcripts are monocistronic and serve to express only trbA, although some transcription continues into trbB. The monocistronic trbA transcript appears to be the result of transcription termination downstream of trbA. Thus, trbAp and trbA appear to form an operon distinct from the trbB-trbP operon. Consequently, trbA and the switch that controls its expression help to provide the sequential steps which allow efficient expression of transfer genes during plasmid establishment but tight repression once the plasmid is established.

Bacterial Proteins↗
PubMed1997

Comparison of four 'second generation' immunoassay systems to determine CA 125 in serum by using a graphical approach to method comparison analysis.

Clinical management of ovarian cancer patients is facilitated by CA 125 determinations in serum. Presently, several assay systems based on different concepts and different methodologies are available to measure CA 125. Method comparison analysis of such assay systems is usually performed through (linear) regression analysis, which requires assumptions about the distribution of experimental data and its measurement error. The aim of the present study was to compare four newly developed second generation assay systems for quantitation of CA 125 by utilizing an alternative simple approach to method comparison analysis. This alternative comprises the construction of relative difference plots and mountain plots, previously described by Krouwer et al. (Eur J Clin Chem Clin Biochem 1995; 33:525-7). In addition, the diagnostic value of the assays was illustrated through receiver-operating-characteristic (ROC) curves. Sera obtained from 300 women were assayed for CA 125 using the Abbott IMx CA 125 assay (Abbott), the Centocor CA 125 II RIA assay (Centocor), the Berilux Ov testing kit for CA 125 (Behringwerke), and the CA 125 TR-FIA assay (Wallac Oy). Both the relative difference plots and the mountain plots revealed higher serum concentrations with the Centocor RIA II (Median +33%, P2.5 to P97.5: -25% to 161%) and Berilux (Median +28%, P2.5 to P97.5: -17% to 108%) compared to the Abbott IMx system. The TR-FIA assay system showed lower serum concentrations (Median - 17%, P2.5 to P97.5: -74% to 229%). The combination of relative difference plots and mountain plots demonstrated clearly the wide range of differences between CA 125 assays measuring the same analyte. The relative difference plots provided insight into the distribution of the differences over the range of measurement as well as the identification of outliers. A simple quantitative assessment of the median differences could be made from the overlaying mountain plots. The close correspondence observed between the ROC curves illustrated that assay systems for CA 125 differing in design (type of antibodies used) and format can produce similar results on group level. However, the results of the clinical evaluation underline the importance of the application of assay specific cut-off values.

Adolescent↗
PubMed1996

Thiamine (vitamin B1) supplementation does not reduce fasting blood homocysteine concentration in most homozygotes for homocystinuria.

Homozygotes for homocystinuria due to cystathionine synthase (CS) deficiency accumulate homocysteine and methionine in their blood and tissues. High-dose pyridoxin, folic acid, vitamin B12, or betaine are therapeutical options to lower the elevated homocysteine concentration. These compounds stimulate the transsulfuration or remethylation of homocysteine. Despite such treatment, elevated blood homocysteine concentrations may persist in many homocystinurics. Therefore, it is warranted to study alternative regimen to reduce the blood homocysteine concentration in homocystinurics. Apart from entering the transsulfuration pathway, methionine can be catabolized via the transamination pathway, by conversion into 4-methylthio-2-oxobutyrate (MTOB), followed by oxidative decarboxylation of MTOB to 3-methylthiopropionate. Thiamine pyrophosphate, the active form of thiamine, is a cofactor of the supposed rate-limiting oxidative decarboxylation in the transamination of methionine. The effect of thiamine administered in 2 or 3 daily doses of 25 mg orally, was studied in nine homozygote CS deficient patients. Methionine levels decreased in 6 out of 9 patients. In 8 out of 9 patients, however, the levels of plasma homocysteine remained virtually unchanged, as did the serum transamination metabolites in all patients. We conclude that vitamin B1 cannot be used as an additional homocysteine-lowering treatment in most homozygotes for homocystinuria.

Cystathionine beta-Synthase↗
PubMed1996

Interaction of nucleotides with the NAD(H)-binding domain of the proton-translocating transhydrogenase of Rhodospirillum rubrum.

Transhydrogenase catalyzes the reduction of NADP+ by NADH coupled to the translocation of protons across a membrane. The polypeptide composition of the enzyme in Rhodospirillum rubrum is unique in that the NAD(H)-binding domain (called Ths) exists as a separate polypeptide. Ths was expressed in Escherichia coli and purified. The binding of nucleotide substrates and analogues to Ths was examined by one-dimensional proton nuclear magnetic resonance (NMR) spectroscopy and by measuring the quenching of fluorescence of its lone Trp residue. NADH and reduced acetylpyridine adenine dinucleotide bound tightly to Ths, whereas NAD+, oxidized acetylpyridine adenine dinucleotide, deamino-NADH, 5'-AMP and adenosine bound less tightly. Reduced nicotinamide mononucleotide, NADPH and 2'-AMP bound only very weakly to Ths. The difference in the binding affinity between NADH and NAD+ indicates that there may be an energy requirement for the transfer of reducing equivalents into this site in the complete enzyme under physiological conditions. Earlier results had revealed a mobile loop at the surface of Ths (Diggle, C., Cotton, N. P. J., Grimley, R. L., Quirk, P. G., Thomas, C. M., and Jackson, J. B. (1995) Eur. J. Biochem. 232, 315-326); the loop loses mobility when Ths binds nucleotide; the reaction involves two steps. This was more clearly evident, even for tight-binding nucleotides, when experiments were carried out at higher temperatures (37 degrees C), where the resonances of the mobile loop were substantially narrower. The binding of adenosine was sufficient to initiate loop closure; the presence of a reduced nicotinamide moiety in the dinucleotide apparently serves to tighten the binding. Two-dimensional 1H NMR spectroscopy of the Ths-5'-AMP complex revealed nuclear Overhauser effect interactions between protons of amino acid residues in the mobile loop (including those in a Tyr residue) and the nucleotide. This suggests that, in the complex, the loop has closed down to within 0.5 nm of the nucleotide.

Biological Transport↗
PubMed1996

Mutation of Tyr235 in the NAD(H)-binding subunit of the proton-translocating nicotinamide nucleotide transhydrogenase of Rhodospirillum rubrum affects the conformational dynamics of a mobile loop and lowers the catalytic activity of the enzyme.

The Tyr residue in the mobile loop region of the soluble, domain I polypeptide (called Ths) of the proton-translocating transhydrogenase from Rhodospirillum rubrum has been substituted by Asn and by Phe. The recombinant proteins were expressed at high levels in Escherichia coli and purified to homogeneity. The two well defined resonances at 6.82 and 7.12ppm, observed in the one-dimensional proton NMR spectrum of wild-type protein, and previously attributed to the Tyr residue, were absent in both mutants. In the Tyr235 --> Phe mutant Ths, they were replaced by two new resonances at 7.26 and 7.33 ppm, characteristic of a Phe residue. In both mutants, narrow resonances attributable to Met residues (and in the Tyr235 --> Phe mutant, resonances attributable to Ala residues) were shifted relative to the wild type, but other features in the NMR spectra were unaffected. The conformational dynamics of the mobile loop closure in response to nucleotide binding by the protein were altered in the two mutants. The fluorescence emission from Trp72 was unaffected by both Tyr substitutions, and the fluorescence was still quenched by NADH. The mutant Ths proteins bound to chromatophore membranes depleted of their native Ths with undiminished affinity. In these reconstituted systems, the Km values for thio-NADP+ and NADH, during light-driven transhydrogenation, were similar to those of wild-type, but the kcat values were decreased about 2-fold. In reverse transhydrogenation, the Kmvalues for NADPH were slightly decreased in the mutants relative to wild-type, but those for acetyl pyridine adenine dinucleotide were increased about 10- and 13-fold, respectively, and the kcat values were decreased about 2- and 5-fold, respectively, in the Tyr235 --> Phe and Tyr235 --> Asn mutants. It is concluded that Tyr235 may contribute to the process of nucleotide binding and that substitution of this residue prevents proper functioning of the mobile loop in catalysis.

Asparagine↗
PubMed1996

The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins.

In plants, resistance to pathogens is frequently determined by dominant resistance genes, whose products are proposed to recognize pathogen-encoded avirulence gene (Avr) products. The tomato resistance locus Cf-2 was isolated by positional cloning and found to contain two almost identical genes, each conferring resistance to isolates of tomato leaf mould (C. fulvum) expressing the corresponding Avr2 gene. The two Cf-2 genes encode protein products that differ from each other by only three amino acids and contain 38 leucine-rich repeat (LRR) motifs. Of the LRRs, 20 show extremely conserved alternating repeats. The C-terminus of Cf-2 carries regions of pronounced homology to the protein encoded by the unlinked Cf-9 gene. We suggest that this conserved region interacts with other proteins involved in activating plant defense mechanisms.

Amino Acid Sequence↗
PubMed1996

Conservation of the genetic switch between replication and transfer genes of IncP plasmids but divergence of the replication functions which are major host-range determinants.

The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trb operon encodes most of the apparatus for mating pair formation, the first step in conjugative transfer. Comparison of the nucleotide sequence of the IncP beta plasmid R751 presented here with the equivalent IncP alpha sequence identifies conserved features of the organization and regulation of the trfA operon and the region controlling expression of the trb operon. As in IncP alpha plasmids, these operons are transcribed from a bidirectional promoter region consisting of trfAp for the trfA operon and trbAp and trbBp for the trb operon. The KorA-dependent switch between the trfA and trbA promoters is conserved as is the trbA gene encoding the third IncP global regulator. The intergenic region between trbA and trbB shows very little sequence identity between the two plasmids but the spacing, the KorB operator, the trbB promoter, and the existence of a hairpin loop (albeit of different actual sequence) which sequesters the trbB ribosome binding site are all conserved. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa. A TcR derivative of R751 was constructed and shown not to establish itself efficiently in P. aeruginosa at 37 degrees C, although it did establish itself inefficiently at lower temperatures, underlining the importance of this region in the adaptation of the plasmid to the host.

Amino Acid Sequence↗
PubMed1996

Two related rolling circle replication plasmids from salt-tolerant bacteria.

In a range of salt-tolerant bacteria isolated from soil, rhizosphere, and phyloplane, cross-hybridization tests revealed a group of seven plasmids which were chosen for further study. Two plasmids (pSH1418 and pSH1451) were picked as representative examples of the two related subgroups. Restriction mapping and Southern blotting identified a region common to the two plasmids which later was identified as encoding the replication functions. We were unable to join these plasmids to high-copy-number vectors but this was possible with low-copy-number IncP vectors. In Escherichia coli, cloned plasmids pSH1418 and pSH1451 conferred salt tolerance but the phenotype was unstable, with the loss of salt tolerance apparently being correlated with structural instability of the plasmid DNA. Plasmid pSH1451 was sequenced and shown to be closely related to RCR plasmids of Gram-positive bacteria. The host of this plasmid was classified as Bacillus pumilus by rDNA typing and lipid profiling by gas chromatography. A number of open reading frames (orfs) which could code for salt tolerance or other functions were identified in the plasmid sequence. Sequence similarity to previously sequenced genes suggested that the products of orf4 and orf5 may work together to transport a molecule such as aspartate ion that may promote osmotolerance.

Amino Acid Sequence↗
PubMed1996

Changes in androgens during treatment with four low-dose contraceptives.

The aim of the present study was to compare changes in the endogenous androgen environment in healthy women while on low-dose oral contraceptives (OCs). One-hundred healthy women were randomized to receive one of four OCs during six months: 21 tablets of Cilest, Femodeen, Marvelon, or Mercilon. During the luteal phase of the pretreatment cycle, body weight and blood pressure were recorded and the following parameters were measured: sex hormone-binding globulin (SHBG), corticosteroid-binding globulin (CBG), testosterone (T), free testosterone (FT), 5 alpha-dihydrotestosterone (DHT), androstenedione (A), dehydroepiandrosterone-sulphate (DHEA-S) and 17 alpha-hydroxyprogesterone (170HP) while also the free androgen index (FAI) was calculated. Measurements were repeated during the 3rd week of pill intake in the 4th and the 6th pill month. There were no differences on body mass and blood pressure with the use of the four OCs. The mean serum DHEA-S decreased significantly in all groups though less in the Mercilon group when compared to Cilest and Marvelon (approximately 20% vs 45%). Mean serum SHBG and CBG increased significantly in all four groups approximately 250% and 100%, respectively. In each group CBG also increased significantly but less in women taking Mercilon (-75%) as compared to the others (-100%). Current low-dose OCs were found to have similar impact on the endogenous androgen metabolism with significant decreases of serum testosterone, DHT, A, and DHEA-S. They may be equally beneficial in women with androgen related syndromes such as acne and hirsutism.

17-alpha-Hydroxyprogesterone↗
PubMed1996

Ovarian cancer incidence (1989-1991) and mortality (1954-1993) in The Netherlands.

OBJECTIVE: To examine ovarian cancer incidence and mortality in the Netherlands, and to relate trends in mortality to changes in parity and use of oral contraceptives. METHODS: Age-standardized and age-specific incidence and mortality rates are presented using incidence data from the Netherlands Cancer Registry, 1989-1991, and mortality data from the Netherlands Central Bureau of Statistics, 1954-1993. RESULTS: In the period 1989-1991, age-standardized incidence of ovarian cancer was 14.9 per 10(5) woman-years. The majority (89%) of these tumors had an epithelial origin. Two-thirds of all newly diagnosed ovarian cancers already showed extension to the pelvis or beyond at diagnosis. From the period 1954-1958 to 1969-1973, age-standardized mortality rates increased from 10.6 to 13.1 per 10(5) woman-years. Thereafter, a decline was noted to 11.4 per 10(5) woman-years in the period 1989-1993. Age-specific mortality rates showed a pattern of rising mortality in the elderly, whereas mortality in the younger age categories was declining. The number of live births has declined gradually, and oral contraceptive use has increased. CONCLUSION: Incidence of ovarian cancer is high in the Netherlands, but comparable to other countries in north-western Europe and North America. Mortality rates are rising in the elderly and declining in the young. Further research is needed concerning the effects of oral contraceptives, fertility drugs, and hormone replacement therapy on the incidence and mortality of ovarian cancer.

Adult↗
PubMed1996

Clinical implications of the rise and fall of prostate specific antigen after laser prostatectomy.

OBJECTIVE: To characterize the serum kinetics of prostate specific antigen (PSA) after visual laser ablation of the prostate (VLAP). PATIENTS AND METHODS: The PSA values of 45 patients were measured at 24 h and at 1, 4, 12, 26 and 52 weeks after VLAP and the changes assessed in relation to symptom scores, urinary flow rates and prostate size. RESULTS: After an initial rise immediately after VLAP, the serum PSA level declined. At 24 h, the PSA value reached a mean level 23 times higher than the PSA level before VLAP and then took a mean of 78 days to reach a new baseline. The mean decrease of the subsequent baseline value relative to that before treatment was 1.7 ng/mL. The prostatic size and energy applied correlated positively with the rise in PSA 24 h after VLAP. The rise in maximal urinary flow after VLAP, the decrease in the symptom score and residual urine volume did not correlate with the rise in PSA level 24 h after VLAP or with the time to reach a value halfway between the level at 24 h and the new baseline value. CONCLUSIONS: The pattern of the increase in serum PSA level and decline after VLAP was not predictive of the clinical outcome of therapy.

Humans↗
PubMed1996

The use of 'ultrasensitive' prostate-specific antigen assays in the detection of biochemical recurrence after radical prostatectomy.

OBJECTIVE: To determine the gain in lead time obtained when using ultrasensitive prostate-specific antigen (PSA) assays in the diagnosis of biochemical progression after radical prostatectomy. PATIENTS AND METHODS: The post-operative PSA serum concentrations of 137 patients who had undergone radical prostatectomy were evaluated retrospectively. From these patients, 12 were selected who showed biochemical recurrence, as measured by the Hybritech Tandem-E Singlepoint PSA assay. Samples of the serum frozen at the time of the initial analysis were thawed and PSA values were remeasured by the Abbott IMx PSA assay and the Tandem-E Multipoint PSA assay. Analytical thresholds (zero-dose + 3 SD) for the Tandem-E Singlepoint, IMx and Tandem-E Multipoint assay were 1.0, 0.04 and 0.04 ng/mL, respectively. The lead time to the detection of a recurrence obtained when using the IMx and the Tandem-E Multipoint PSA assay was compared with that attained using the Tandem-E Singlepoint PSA assay. As a control, PSA values were determined in 58 serum specimens of nine patients having no evidence of recurrence after radical prostatectomy. RESULTS: All 58 control specimens had PSA levels below the analytical thresholds of the three assays, except one which had a PSA serum concentration of 0.08 ng/mL, estimated by the IMx assay. When compared with the lead time obtained with the Tandem-E Singlepoint assay, the 12 patients with a biochemical recurrence had a median gain in lead time of 327 days (range 60-627) with the IMx assay and of 369 days (range 60-639) with the Tandem-E Multipoint assay. CONCLUSION: A PSA value > 0.04 ng/mL after radical prostatectomy heralds further biochemical progression. The use of the ultrasensitive IMx and the Tandem-E Multipoint assays provided more lead time, but there is no clear evidence that this gain is necessarily of benefit to the patient.

Aged↗
PubMed1996

Review on the simultaneous determination of total prostate-specific antigen and free prostate-specific antigen.

BACKGROUND: The total prostate-specific antigen (t-PSA) in serum measured by PSA assays represents the sum of free (f-PSA) and PSA complexed with alpha 1-antichymotrypsin. The f-PSA/t-PSA (F/T) ratio in prostate cancer (PCA) patients is lower than in patients suffering from benign prostatic hyperplasia (BPH). This review summarizes the current literature on the clinical relevance of measurement of the F/T PSA ratio. METHODS: Discussed are: physiology of PSA, assays for t-PSA and F/T ratio, factors which bias the F/T PSA ratio, use of F/T PSA ratio in the detection of PCA, correlation with histological features, and pathological stage. RESULTS: Using the F/T ratio in the intermediate t-PSA range, a reduction of approximately 30% in biopsies can be accomplished in the detection of prostate cancer. CONCLUSIONS: The F/T PSA ratio could become a valuable tool in the differentiation of BPH from PCA. To accomplish this goal, an international standardization not only for the t-PSA measurement but also for the F/T PSA ratio must be a priority for manufacturers of PSA assays.

Biopsy↗
PubMed1995

Sodium arsenite and heat shock induce stress proteins in precision-cut rat liver slices.

The present study was undertaken to investigate the usefulness of stress proteins as early, sensitive indicators of hepatotoxicity. Induction of stress protein synthesis in precision-cut rat liver slices was examined following in vitro exposure to sodium arsenite or heat shock. Precision-cut rat liver slices were incubated with 10(-5) or 10(-6) M sodium arsenite for 2, 4 or 8 h in the presence of 35S-methionine or exposed to hyperthermia (42.5 +/- 0.5 degrees C) for 45 min and then incubated with 35S-methionine for 2, 4 or 8 h. Fluorographic analysis indicated an increase in the synthesis of HSP 70 and HSP 90 family of proteins by both treatments. Immunoblot analysis demonstrated that there was a specific induction of HSP 72 and HSP 90. Induction of HSP 70 was greater than that of HSP 90 by both treatments. Stress protein induction occurred at earlier times by concentrations of arsenite which did not alter other viability parameters such as leakage of intracellular K+ or total protein synthesis. The results indicated that induction of stress proteins has the potential usefulness as an early biomarker of arsenite toxicity.

Animals↗
PubMed1995

Dissection of the core and auxiliary sequences in the vegetative replication origin of promiscuous plasmid RK2.

The vegetative replication origin (oriV) of promiscuous IncP plasmid RK2 can function in many Gram-negative bacterial species when supplied with the plasmid-encoded replication protein TrfA and host-encoded replication proteins including DnaA. Nine TrfA binding sites (iterons) are known, and also two DnaA binding sites, box 1, between TrfA iterons 4 and 5, and box 2, downstream of repeat 9. The deletion analysis presented here shows that the core oriV requires DnaA box 1 for function in Escherichia coli and Pseudomonas putida. This DnA box is not essential in Pseudomonas aeruginosa, although its deletion does reduce plasmid copy number in this species. A putative IHF binding site is located upstream of DnaA box 1, but IHF deficiency in E. coli seems not to alter replication efficiency or copy number control. Cloned oriV can interfere with maintenance of an independent RK2 replicon. Analysis of replication inhibition functions associated with oriV showed that a short putative orf between TrfA iterons 1 and 2 is not necessary for replication inhibition, the presence of repeats 5 to 9 in target and inhibitor plasmid are not sufficient for efficient inhibition and inhibition does not correlate directly with the number of direct repeats present. Rather, the results showed that the isolated repeats 1 and 2 to 4, potentiate replication inhibition disproportionately to their effect on the number of TrfA binding sites. The results are consistent with the idea that repeats 1 to 4, arranged as a single copy and as an irregular group of three, potentiate the ability of the oriV region to form complexes which inhibit replication. We suggest that TrfA bound at these iterons may be more susceptible to forming pairs between oriV sequences on different plasmids.

Bacterial Proteins↗