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D R Davies

Publications and source records attributed to D R Davies.

At least 37 records · Page 2Linked to original sources
PubMed2000

Estimating the extent of degradation of ruminant feeds from a description of their gas production profiles observed in vitro: comparison of models.

An evaluation of general models that describe gas production profiles is presented. The models are derived from first principles by considering a simple three-pool scheme and permit the extent of ruminal degradation to be calculated, as described in the companion paper. The models evaluated were the generalized Mitscherlich, simple Mitscherlich, generalized Michaelis-Menten, simple Michaelis-Menten, Gompertz, and logistic. Five sets of gas production data consisting of 216 curves, obtained using a wide range of feeds (including straw, hay, silage, grain and various byproducts), were analysed to study the performance of these gas production models. Application of the non-sigmoidal models (simple Mitscherlich and Michaelis-Menten) to the data resulted in convergence problems and these models were found to be inadequate in many cases. Based on results of a pairwise comparison between models (variance ratio test), ranking of residual mean squares, lack-of-fit test, and of analyses of residuals, the generalized Mitscherlich and the generalized Michaelis-Menten models seemed particularly suited because of their flexibility to encompass sigmoidal and non-sigmoidal shapes of gas production profiles, whether symmetrical or not.

Animal Feed↗
PubMed2000

Acquisition and application of new technology skills: the influence of age.

This paper reviews the literature relating to the effects of ageing on the acquisition and application of new technology skills. Experiential, physiological, and cognitive factors are identified that place older adults at a disadvantage, relative to younger adults, when using new technologies. Consistent with this position, experimental evidence indicates an advantage for younger adults in speed of task performance, coupled with a tendency toward greater accuracy. The possibility that these differences can be overcome by means of training intervention is considered. However, it seems that age differences in performance persist, regardless of a training regime. Although some older adults are capable of high levels of performance, these tend to be individuals of high cognitive ability, relative to their peers. When age group means are considered, the only way that older adults are able to equal the performance of younger adults on new technology tasks is through additional practice.

Aged↗
PubMed2000

Crystallization and preliminary crystallographic study of triple-helical DNA.

Single crystals of d(CTCCT(S)CCGCGCG).d(CGCGCGGAG) have been grown by the vapor-diffusion method using 2-methyl-2,4-pentanediol as a precipitant. The crystals are tetragonal, space group P4(2), with unit-cell parameters a = b = 53.8, c = 43.1 A, and diffract to 1.8 A resolution at a synchrotron X-ray beamline. In the crystal, the asymmetric unit contains one copy of the construct. The two halves of the structure are related by non-crystallographic twofold symmetry. These observations are consistent with the conclusion that the sequences of the 12-mer and 9-mer oligonucleotides form a duplex DNA at one end and a triplex DNA at the other end.

Base Sequence↗
PubMed1999

Tn5: A molecular window on transposition.

DNA transposition is an underlying process involved in the remodeling of genomes in all types of organisms. We analyze the multiple steps in cut-and-paste transposition using the bacterial transposon Tn5 as a model. This system is particularly illuminating because of the existence of structural, genetic, and biochemical information regarding the two participating specific macromolecules: the transposase and the 19-bp sequences that define the ends of the transposon. However, most of the insights should be of general interest because of similarities to other transposition-like systems such as HIV-1 DNA integration into the host genome.

Base Sequence↗
PubMed1999

Structure of a triple helical DNA with a triplex-duplex junction.

Extended purine sequences on a DNA strand can lead to the formation of triplex DNA in which the third strand runs parallel to the purine strand. Triplex DNA structures have been proposed to play a role in gene expression and recombination and also have potential application as antisense inhibitors of gene expression. Triplex structures have been studied in solution by NMR, but have hitherto resisted attempts at crystallization. Here, we report a novel design of DNA sequences, which allows the first crystallographic study of DNA segment containing triplexes and its junction with a duplex. In the 1.8 A resolution structure, the sugar-phosphate backbone of the third strand is parallel to the purine-rich strand. The bases of the third strand associate with the Watson and Crick duplex via Hoogsteen-type interactions, resulting in three consecutive C(+).GC, BU.ABU (BU = 5-bromouracil), and C(+).GC triplets. The overall conformation of the DNA triplex has some similarity to the B-form, but is distinct from both A- and B-forms. There are large changes in the phosphate backbone torsion angles (particularly gamma) of the purine strand, probably due to the electrostatic interactions between the phosphate groups and the protonated cytosine. These changes narrow the minor groove width of the purine-Hoogsteen strands and may represent sequence-specific structural variations of the DNA triplex.

Base Pairing↗
PubMed1999

Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design.

HIV integrase, the enzyme that inserts the viral DNA into the host chromosome, has no mammalian counterpart, making it an attractive target for antiviral drug design. As one of the three enzymes produced by HIV, it can be expected that inhibitors of this enzyme will complement the therapeutic use of HIV protease and reverse transcriptase inhibitors. We have determined the structure of a complex of the HIV-1 integrase core domain with a novel inhibitor, 5ClTEP, 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-pro penone, to 2.1-A resolution. The inhibitor binds centrally in the active site of the integrase and makes a number of close contacts with the protein. Only minor changes in the protein accompany inhibitor binding. This inhibitor complex will provide a platform for structure-based design of an additional class of inhibitors for antiviral therapy.

Binding Sites↗
PubMed1999

Phosphorylation of phenylalanine ammonia-lyase: evidence for a novel protein kinase and identification of the phosphorylated residue.

The site of phosphorylation of phenylalanine ammonia-lyase (PAL) has been identified as a threonine residue. A Ca(2+)-stimulated protein kinase of approximately 55 kDa has been partially purified from elicited cells. The kinase can phosphorylate a synthetic peptide derived from PAL and a recombinant poplar PAL. PAL phosphorylation was associated with a decrease in Vmax in agreement with the suggestion that protein phosphorylation is involved in marking PAL subunits for turnover. The phosphorylation site in French bean PAL is most likely Thr545 in the sequence VAKRTLTT (539-546). Conservation of the phosphorylation site in PAL from diverse species suggests that phosphorylation of PAL may be a ubiquitous regulatory mechanism in higher plants.

Amino Acid Sequence↗
PubMed1999

The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution.

Transposon Tn5 employs a unique means of self-regulation by expressing a truncated version of the transposase enzyme that acts as an inhibitor. The inhibitor protein differs from the full-length transposase only by the absence of the first 55 N-terminal amino acid residues. It contains the catalytic active site of transposase and a C-terminal domain involved in protein-protein interactions. The three-dimensional structure of Tn5 inhibitor determined to 2.9-A resolution is reported here. A portion of the protein fold of the catalytic core domain is similar to the folds of human immunodeficiency virus-1 integrase, avian sarcoma virus integrase, and bacteriophage Mu transposase. The Tn5 inhibitor contains an insertion that extends the beta-sheet of the catalytic core from 5 to 9 strands. All three of the conserved residues that make up the "DDE" motif of the active site are visible in the structure. An arginine residue that is strictly conserved among the IS4 family of bacterial transposases is present at the center of the active site, suggesting a catalytic motif of "DDRE." A novel C-terminal domain forms a dimer interface across a crystallographic 2-fold axis. Although this dimer represents the structure of the inhibited complex, it provides insight into the structure of the synaptic complex.

Amino Acids↗
PubMed1999

Isolation of chloroform-resistant mutants of filamentous phage: localization in models of phage structure.

Interaction of fd or M13 filamentous phage with a chloroform/water interface induces morphological change, contracting the filaments sequentially into shortened rods (I-forms), and then into spheroidal particles (S-forms). To further investigate this phage contraction, 34 and 26 chloroform-resistant isolates of fd and M13, respectively, were selected after chloroform treatment of wild-type phages at pH 8. 2 and 4 degrees C. DNA sequencing of gene VIII of the 34 fd isolates revealed five different mutants: these were D5H, M28L, V31L, I37T, and S50T. All 26 M13 isolates were I37T. These mutants exhibited variable sensitivity to chloroform, but all contracted much more slowly than wild-type phage during treatment at 4 degrees C. They all contracted like wild-type phage at 37 degrees C. Site-directed mutagenesis showed that the indicated single mutations carried the chloroform resistance. In structural models of the phage, the D5H locus is on the outside and the S50T locus is on the inside. The M28L and I37T loci are buried in a mostly hydrophobic region in the middle. Although these four mutants are spread out radially, they are localized in the axial direction into a thin disk in the model. The last mutant locus, V31L, is out of this disk, but this locus is proximal to the M28L and I37T loci and also in contact with the surface via a deep hydrophobic hole or depression. These five mutants, their locations, and their variable affects on contraction suggest that chloroform-induced contraction involves a specific mechanism rather than a generalized solvent-induced denaturation and that the critical structural changes occur in a localized level in the phage. These results add weight to suggestions that the sequential contraction of filaments-->I-forms-->S-forms mimic corresponding steps in phage penetration, and, in the reverse order, for phage assembly.

Bacteriophage M13↗
PubMed1999

Matrix metalloproteinase levels are elevated in inflammatory bowel disease.

BACKGROUND & AIMS: The expression of matrix metalloproteinases 1, 2, 3, and 9 was examined in biopsy specimens removed from adult and pediatric patients with ulcerative colitis and Crohn's disease. The aim of this study was to determine if the expression of these enzymes was altered between areas of actively inflamed vs. noninvolved mucosa in the same patient and between patients with diseased bowel vs. a control group of patients. METHODS: Proteolytic activity was quantified by zymography using image analysis. The identity of the matrix metalloproteinases was confirmed by using inhibitors, by comparison with purified standards, and by Western immunoblotting with specific antibodies. RESULTS: In patients with ulcerative colitis (n = 21), a significant increase (P = 0.0051) in metalloproteinase activity was found in inflamed areas of mucosa compared with noninvolved regions. The levels of activity also were significantly greater (P < 0.001) in noninvolved areas of the bowel (n = 21) compared with levels in control patients (n = 9). In Crohn's disease (n = 8), differences between ulcerated and nonulcerated sites were not significantly different but levels of protease activity at both of these sites were significantly elevated compared with levels in control patients (P < 0.03). Of the proteases detected, matrix metalloproteinase 9 was the most abundantly expressed in the inflamed bowel; neutrophils were confirmed as the likely origin of this protease. CONCLUSIONS: The abundance and activation of matrix metalloproteinases significantly increases in ulcerative colitis and Crohn's mucosa. Inhibitors of these proteolytic enzymes may therefore be of therapeutic value in the treatment of inflammatory bowel disease.

Adolescent↗
PubMed1999

Polycystin-1 expression in PKD1, early-onset PKD1, and TSC2/PKD1 cystic tissue.

BACKGROUND: The mutational mechanism responsible for cyst formation in polycystic kidney disease 1 gene (PKD1) remains controversial, with data indicating a two-hit mechanism, but also evidence of polycystin-1 expression in cystic tissue. METHODS: To investigate this apparent paradox, we analyzed polycystin-1 expression in cystic renal or liver tissue from 10 patients with truncating PKD1 mutations (including one early-onset case) and 2 patients with severe disease associated with contiguous deletions of TSC2 and PKD1, using monoclonal antibodies (mAbs) to both extreme N-(7e12) and C-terminal (PKS-A) regions of the protein. Truncation of the C-terminal epitope from the putative mutant proteins in each case allowed exclusive assessment of the nontruncated protein with PKS-A. RESULTS: In adult PKD1 tissue, the majority of cysts (approximately 80%) showed polycystin-1 expression, although staining was absent in a variable but significant minority (approximately 20%), in spite of the normal expression of marker proteins. Unlike adult PKD1, however, negative cysts were rarely found in infantile PKD1 or TSC2/PKD1 deletion cases. CONCLUSIONS: If a two-hit mutational mechanism is operational, these results suggest that the majority of somatic mutations in adult PKD1 are likely to be missense changes. The low level of polycystin-1-negative cysts in the three "early-onset" cases, however, suggests that a somatic PKD1 mutation may not always be required for cyst formation.

Adult↗
PubMed1999

Recent advances in understanding the origin of the apoplastic oxidative burst in plant cells.

The origin of the oxidative burst during plant-pathogen interactions remains controversial. A number of possibilities have been identified, which involve the protoplast, plasmalemma or apoplast. The apoplastic production of H2O2 requires three components, an extracellular peroxidase, ion fluxes leading to extracellular alkalinisation and release of a substrate. Fatty acids are the major compounds that appear in the apoplast following elicitation, which can activate H2O2 production by peroxidases in vitro. However, the reaction with peroxidases appears to be novel and is uncharacterised at present. The apoplastic mechanism also cannot be readily distinguished from the operation of a plasma membrane NADPH oxidase system by the use of the inhibitors diphenylene iodonium and N,N diethyl-dithiocarbamate since it is also inhibited by these. These inhibitors have often in the past been used to define the involvement of the latter in the oxidative burst. In common with the NADPH oxidase system, the peroxidase responsible has been cloned but unlike the NADPH oxidase it has been shown to function in vitro to generate H2O2. In vivo studies of the oxidative burst have shown that the alkalinisation is essential and the underlying ion fluxes may be regulated by cAMP. Calcium fluxes are also essential. Although the oxidative activity of peroxidase requires calcium the fluxes have obvious other function. These may include activation of release of substrate and through the activation of a CDPK, regulation of enzymes involved in phytoalexin and cell wall phenolic production such as PAL.

Calcium↗
PubMed1999

An evaluation of the Banff classification of early renal allograft biopsies and correlation with outcome.

BACKGROUND: The Banff classification for assessment of renal allograft biopsies was introduced as a standardized international classification of renal allograft pathology and acute rejection. Subsequent debate and evaluation studies have attempted to develop and refine the classification. A recent alternative classification, known as the National Institutes of Health Collaborative Clinical Trials in Transplantation (NIH-CCTT) classification, proposed three distinct types of acute rejection. The 1997 Fourth Banff meeting appeared to move towards a consensus for describing transplant biopsies, which incorporated both approaches. Patients who received a renal allograft at the Oxford Transplant Centre were managed by a combination of protocol and clinically indicated biopsies. We have undertaken a retrospective analysis of the biopsies correlated with the clinical outcome to test the prognostic value of the original Banff (Banff 93-95) and NIH-CCTT classifications. METHODS: Three hundred and eighty-two patients received renal allografts between May 1985 and December 1989, and were immunosuppressed using a standard protocol of cyclosporine, azathioprine and steroid. Adequate 5-year follow-up data were available on 351 patients, and of these, 293 had at least one satisfactory biopsy taken between days 2 and 35 after transplantation, the latter patients forming the study group. The D2-35 biopsies taken from these patients, which were not originally reported according to the Banff classification, were re-examined and classified according to the Banff 93-95 protocols. For each patient the biopsy found to be the most severely abnormal was selected, and the Banff and NIH-CCTT grading compared with the clinical outcome. RESULTS: Seven hundred and forty-three biopsies taken from 293 patients between days 2 and 35 after transplantation were examined and the patients categorized on the basis of the 'worst' Banff grading as follows. Normal or non-rejection, 20%; borderline, 34%; acute rejection grade I (AR I), 18%; AR IIA, 6%; AR IIB, 14%; AR III, 1%; AR IIIC, 3%; widespread necrosis 3%. The clinical outcome for the last two groups combined was very poor with 18% of grafts functioning at 3 months and 6% at 5 years. The other groups with vascular rejection (AR IIB and AR III) had an intermediate outcome, graft survival being 78% at 3 months and 61% at 5 years. The remaining four groups (normal, borderline, cellular AR I and AR IIA) had the best outcome: graft survival 95% at 3 months and 78% at 5 years with virtually no difference between the four groups. Three forms of acute rejection, namely tubulo-interstitial, vascular and transmural vascular, were identified, but only the latter two categories were associated with a poor outcome. CONCLUSIONS: The eight sub-categories of the Banff classification of renal allograft biopsies are associated with three different prognoses with respect to graft survival in the medium term. These three prognostic groups correspond to the three NIH-CCTT types. The data provide support for the consensus developed at Banff 97 separating tubulo-interstitial, vascular and transmural vascular rejection (types I, II and III acute rejection).

Evaluation Studies as Topic↗
PubMed1999

Pupil abnormality in amyloidosis with autonomic neuropathy.

Darkness pupil diameters, light reflexes, and redilatation times have been recorded with infrared TV pupillometry in 12 consecutive patients with systemic amyloidosis associated with sensory motor and autonomic neuropathy. Nine of the patients had AL amyloidosis, two had familial amyloidosis associated with a transthyretin abnormality, and one was untyped. The pupils were abnormal in all 12 patients. On the basis of redilatation lag without pupillotonia, six patients had bilateral Horner's syndrome and in one of them amyloid deposits were found in a sympathetic ganglion and in the attached sympathetic chain obtained at necropsy. Four patients had bilateral tonic pupils with light-near dissociation and two had abnormally small pupils with reduced light reactions which could not be characterised. It seems that in patients with systemic amyloidosis generalised autonomic neuropathy is strongly associated with pupil abnormality as shown by tonic reactions with light-near dissociation, by redilatation lag, or by reduced size in darkness.

Adult↗
PubMed1999

Correcting the calculation of extent of degradation to account for particulate matter loss at zero time when applying the polyester bag method.

The established calculation of ruminal extent of degradation using the polyester bag method overestimates extent. The wash fraction, at least in part, is subject to losses from the rumen due to passage. Four formulae are proposed to minimize this risk of overestimation. Four options are considered: 1) passage losses for particulate matter escaping from the bag at zero time are according to the particulate fractional passage rate, 2) the liquid rate, and 3) the average of the two, and additionally 4) there is no instantly degradable fraction. The established and proposed formulae were examined using polyester bag data for six forages: grass silage, fresh ryegrass, fresh white clover, alfalfa hay, mixed grasses hay, and hay from a permanent mountain meadow. The established formula gave appreciably higher estimates of extent of degradation in all cases. Overestimation was at least 6.9, 4.9, 2.9, 2.1, 2.4, and 4.5%, respectively, for the six forages.

Animal Feed↗
PubMed1999

Evidence of a role for plant proteases in the degradation of herbage proteins in the rumen of grazing cattle.

Protein breakdown in the rumen is generally regarded as a two-stage process in which proteases produced by rumen microorganisms cleave plant protein into peptides and amino acids. However, many of the fiber-degrading cellulolytic species in the rumen are not in fact proteolytic, and the proteolytic activity of the entire rumen microbial population is only moderate when compared to the gastric and pancreatic secretions in the abomasum. Moreover, plant cell walls remain largely intact after initial chewing (particularly in cattle), presenting a physical barrier that must be breached prior to their effective colonization. The present study considers the hypothesis that the plant enzymes are at least partly responsible for herbage protein degradation in grazing ruminants. Ryegrass, red clover, white clover, and bird's-foot trefoil were incubated in the presence and absence of rumen microorganisms. The production of volatile fatty acids indicated the level of microbial activity, whereas the relative disappearance of the large subunit of ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco LSU) indicated proteolytic activity. In all incubations, the relative abundance of the Rubisco LSU decreased as the incubation progressed. When rumen microorganisms were absent, low molecular weight peptides (below 20 kDa) accumulated as the incubation progressed. This accumulation was not observed in the presence of rumen microorganisms. Therefore we suggest that the intrinsic plant proteases contribute to the initial stages of proteolysis of grazed herbage.

Animal Feed↗