Search PubMed⌕ Search

Biomedical subjects

D T Jones

Publications and source records attributed to D T Jones.

At least 91 records · Page 5Linked to original sources
PubMed1995

Taxonomy and phylogeny of industrial solvent-producing clostridia.

We performed a systematic study of 55 solvent-producing clostridial strains, the majority of which are currently classified as Clostridium acetobutylicum strains, by using a combination of biotyping and DNA fingerprint analysis. The biotyping procedures used included rifampin susceptibility testing, bacteriocin typing, and bacteriophage typing. The 55 strains examined exhibited a good correlation between their biotypes and DNA fingerprints, which allowed us to divide them into nine groups. The DNA fingerprints of the nine groups differed markedly, but within each group the DNA fingerprints exhibited a high level of similarity. To determine the phylogenetic relationships of the nine groups, we performed a 16S rRNA gene sequence analysis. The results of a comparative analysis of the partial sequence corresponding to positions 830 to 1383 (Escherichia coli numbering) of the 16S rRNA gene indicated that the nine biotype groups could be assembled into four taxonomic groups. The complete 16S rRNA sequences of strains representing these groups were determined. Our phylogenetic analysis revealed that the amylolytic type strain C. acetobutylicum ATCC 824 (taxonomic group I) was only distantly related to the saccharolytic strains belonging to taxonomic groups II, III, and IV (levels of sequence similarity, 90 to 90.5%). The strains belonging to taxonomic groups II, III, and IV, represented by C. acetobutylicum NCP 262, "Clostridium saccharoperbutylacetonicum" N1-4, and C. acetobutylicum NCIMB 8052T (T = type strain), respectively, were closely related (levels of sequence similarity, 98.2 to 98.9%). C. acetobutylicum NCIMB 8052T exhibited a level of similarity of 100% with the type strain of Clostridium beijerinckii. Reclassification of the saccharolytic solvent-producing strains is necessary, and possible names for the four taxonomic groups are discussed.

Bacterial Typing Techniques↗
PubMed1994

Protein superfamilies and domain superfolds.

As the protein sequence and structure databases expand rapidly a better understanding of the relationships between proteins is required. A classification is considered that extends the sequence-based superfamilies to include proteins with similar function and three-dimensional structures but no sequence similarity. So far there are only nine protein folds known to recur in proteins having neither sequence nor functional similarity. These folds dominate the structure database, representing more than 30 per cent of all determined structures. This observation has implications for protein-fold recognition.

Algorithms↗
PubMed1994

A model recognition approach to the prediction of all-helical membrane protein structure and topology.

This paper describes a new method for the prediction of the secondary structure and topology of integral membrane proteins based on the recognition of topological models. The method employs a set of statistical tables (log likelihoods) complied from well-characterized membrane protein data, and a novel dynamic programming algorithm to recognize membrane topology models by expectation maximization. The statistical tables show definite biases toward certain amino acid species on the inside, middle, and outside of a cellular membrane. Using a set of 83 integral membrane protein sequences taken from a variety of bacterial, plant, and animal species, and a strict jackknifing procedure, where each protein (along with any detectable homologues) is removed from the training set used to calculate the tables before prediction, the method successfully predicted 64 of the 83 topologies, and of the 37 complex multispanning topologies 34 were predicted correctly.

Animals↗
PubMed1994

A mutation data matrix for transmembrane proteins.

The widely used Mutation Data Matrix (MDM), is an amino acid comparison matrix calculated from a study of the exchange probabilities (or odds) derived from an analysis of the evolutionary changes seen in groups of very similar proteins. In this work, a mutation data matrix is calculated for membrane spanning segments. This new mutation data matrix is found to be very different from matrices calculated from general sequence sets which are biased towards water-soluble globular proteins, and the differences are discussed in the context of specific structural requirements of membrane spanning segments. This new matrix will help improve the accuracy of integral membrane protein sequence alignments, and could also be of use in the rational design of site directed mutagenesis experiments for this class of proteins.

Amino Acid Sequence↗
PubMed1994

De novo protein design using pairwise potentials and a genetic algorithm.

One of the major goals of molecular biology is to understand how protein chains fold into a unique 3-dimensional structure. Given this knowledge, perhaps the most exciting prospect will be the possibility of designing new proteins to perform designated tasks, an application that could prove to be of great importance in medicine and biotechnology. It is possible that effective protein design may be achieved without the requirement for a full understanding of the protein folding process. In this paper a simple method is described for designing an amino acid sequence to fit a given 3-dimensional structure. The compatibility of a designed sequence with a given fold is assessed by means of a set of statistically determined potentials (including interresidue pairwise and solvation terms), which have been previously applied to the problem of protein fold recognition. In order to generate sequences that best fit the fold, a genetic algorithm is used, whereby the sequence is optimized by a stochastic search in the style of natural selection.

Algorithms↗
PubMed1994

A method for alpha-helical integral membrane protein fold prediction.

Integral membrane proteins (of the alpha-helical class) are of central importance in a wide variety of vital cellular functions. Despite considerable effort on methods to predict the location of the helices, little attention has been directed toward developing an automatic method to pack the helices together. In principle, the prediction of membrane proteins should be easier than the prediction of globular proteins: there is only one type of secondary structure and all helices pack with a common alignment across the membrane. This allows all possible structures to be represented on a simple lattice and exhaustively enumerated. Prediction success lies not in generating many possible folds but in recognizing which corresponds to the native. Our evaluation of each fold is based on how well the exposed surface predicted from a multiple sequence alignment fits its allocated position. Just as exposure to solvent in globular proteins can be predicted from sequence variation, so exposure to lipid can be recognized by variable-hydrophobic (variphobic) positions. Application to both bacteriorhodopsin and the eukaryotic rhodopsin/opsin families revealed that the angular size of the lipid-exposed faces must be predicted accurately to allow selection of the correct fold. With the inherent uncertainties in helix prediction and parameter choice, this accuracy could not be guaranteed but the correct fold was typically found in the top six candidates. Our method provides the first completely automatic method that can proceed from a scan of the protein sequence databanks to a predicted three-dimensional structure with no intervention required from the investigator. Within the limited domain of the seven helix bundle proteins, a good chance can be given of selecting the correct structure. However, the limited number of sequences available with a corresponding known structure makes further characterization of the method difficult.

Amino Acid Sequence↗
PubMed1994

Supplement to the code of practice for clinical proton dosimetry. ECHED (European Clinical Heavy Particle Dosimetry Group).

The 'Code of Practice for Clinical Proton Dosimetry' (Vynckier, S., Bonnett, D.E. and Jones, D.T.L. Code of practice for clinical proton dosimetry. Radiother. Oncol. 20: 53-63, 1991) was published in 1991, but since then new data for mass stopping powers have been reported and consideration has been given to the specification of absorbed dose in water instead of the original recommendation of absorbed dose in tissue. This supplement summarises the basic recommendations of the original Code of Practice and incorporates the new stopping power data for dose specification in water.

Absorption↗
PubMed1994

Effects of cadmium, copper, lead and zinc on growth, reproduction and survival of the earthworm Eisenia fetida (Savigny): Assessing the environmental impact of point-source metal contamination in terrestrial ecosystems.

The earthworm Eisenia fetida (Annelida: Oligochaeta) was exposed to a geometric series of concentrations of cadmium, copper, lead and zinc in artificial soil using the OECD recommended protocol. Mortality, growth and cocoon production were measured over 56 days to determine LC50 and EC50 values. No observed effect concentrations (NOECs) were also estimated. Furthermore, the percentage of viable cocoons and number of juveniles emerging per cocoon was recorded. Cocoon production was more sensitive than mortality for all the metals, particularly cadmium and copper for which NOEC reproduction values were an order of magnitude lower than those for NOEC mortality. However, there was no significant effect of metals on the viability of cocoons. The weights of earthworms declined in all treatments (including the controls) during the experiment. This was probably due to the lack of suitable food in the OECD standard soil medium used. It was concluded that future experiments should include animal manure in the test medium. The LC50, EC50 and NOEC values determined in this study were compared with concentrations of metals in soils in the vicinity of a smelting works at Avonmouth, southwest England. The 14-day LC50 for zinc in Eisenia fetida was exceeded in soils covering an area of 75 km2 around the works, compared to 4.2 km2 for copper and 4.7 km2 for lead. Soil values for cadmium did not exceed the LC50 value anywhere in the region. Similar estimates of relative effects on reproduction confirmed that zinc is most likely to be responsible for the absence of earthworms from sites close to the Avonmouth works. However, the OECD standard test overestimated the potential effects of metals on populations, since earthworms can be found as close as 1 km from the smelting works. The discrepancy between test and field observations was probably due to the greater availability of the metals in the artificial soil.

Journal Article↗
PubMed1994

Sheepskins and bedding in childhood, and the risk of development of bronchial asthma.

BACKGROUND: Sheepskin bedding might increase house dust mite exposure and so explain some of the increasing prevalence of severity of childhood asthma. METHODS: Relationships between use of different types of bedding, and diagnoses of asthma, symptoms of wheezing, skin prick test evidence of house dust mite sensitivity, and airway responsiveness to methacholine, were examined retrospectively in a birth cohort of children followed longitudinally to age 15 years. RESULTS: In the whole cohort, no associations were identified to suggest a causal relationship between use of any type of bedding and development of features of asthma. Although not an a priori hypothesis, we noted that among children with a family history of atopic disease, those who were house dust mite sensitive were more likely to have used an innerspring mattress (29.6% vs 10.2% who had not used an innerspring mattress, p = 0.005). CONCLUSION: In this subgroup, increased airway responsiveness and mite sensitivity were significantly associated with use of innerspring mattresses, although whether this is a causal or secondary association is not certain. Use of a sheepskin in the bed in early childhood was not an additional risk factor for the development of asthma.

Allergens↗
PubMed1994

Interferon alfa-2a therapy for airway hemangiomas.

Hemangioma is a well-recognized cause of airway obstruction in the infant with stridor. Corticosteroid and laser therapy are effective in stabilizing the airway in most cases. There are, however, some extensive airway lesions that are not adequately managed by these modalities. This report describes the use of recombinant interferon alfa-2a in 15 patients with life-threatening airway hemangiomas. All patients had failed corticosteroid and/or laser therapy. Multiple upper airway sites were involved, including the base of the tongue, supraglottis, subglottis, trachea, and mediastinum. Eleven patients have completed therapy and are doing well. Four patients have resolving lesions on the drug regimen. Life-threatening airway lesions unresponsive to conventional treatment should be considered for a trial of interferon alfa-2a.

Adrenal Cortex Hormones↗
PubMed1994

Innominate artery compression of the trachea in infants.

Innominate artery compression of the trachea in infants can cause severe biphasic stridor, cyanosis, and respiratory arrest. These episodes are sometimes referred to as "dying spells." In the past, aortopexy has been used for the treatment of this problem, but since many have questioned its success, its use has not been popularized or generally accepted. Over the past 4 years, 12 children have been successfully treated for innominate artery compression of the trachea with aortopexy. These children all initially presented with significant respiratory and/or feeding difficulties. Preoperative and postoperative videos were obtained to document the degree of tracheal compression and/or lumen size before and after surgery. Since treatment, all patients have been without further feeding problems or cyanosis. When performed in selected patients, aortopexy is successful in relieving tracheal obstruction from innominate artery compression. This article discusses proper patient selection, operative technique, and follow-up care. The management of compression in patients with less severe symptoms will also be addressed.

Airway Obstruction↗
PubMed1994

Sjögren's syndrome: cytokine and Epstein-Barr viral gene expression within the conjunctival epithelium.

PURPOSE: In primary Sjögren's syndrome (SS), ocular surface changes within the conjunctival epithelium include lymphocytic infiltration, squamous cell metaplasia, and a reduction in goblet cell number. These changes may be the simple result of increased mechanical abrasion secondary to dryness. Alternatively, they may represent a local response to ocular and/or systemic inflammatory processes, perhaps in response to Epstein-Barr viral (EBV) infection, an agent recently implicated in the etiology of SS. To determine whether inflammatory processes or local infection by EBV contribute to the ocular surface pathology of SS, we examined the expression of inflammatory cell surface markers, cytokines, and EBV gene products within the ocular conjunctiva of patients with SS. METHODS: Ocular conjunctival tissue was isolated from patients with primary SS and nondry eye control patients by impression cytology or direct biopsy. These specimens were examined by immunofluorescence microscopy and reverse-transcriptase polymerase chain reaction (RT-PCR) for the expression of various markers. RESULTS: The authors found the frequency of expression of HLA-DR (P < 0.0001), ICAM-1 (P < 0.035), and IL-6 (P < 0.0001) to be significantly elevated in patients with primary SS versus nondry eye control patients. The IL-2 receptor and cytokines IL-1 beta and IL-8 were each found to be expressed with relatively high frequency in both patient populations, whereas mRNAs encoding cytokines IL-2, IFN-gamma, GM-CSF, and TGF-beta were not reproducibly detectable in either population. Messenger RNA encoding a marker for passive-latent EBV infection (EBNA-1) was detected with high frequency in both SS and normal populations. The EBV IL-10 analog BCRF-1 was expressed with low frequency in the SS population; however, these levels were not significantly different from the control population. The expression of two other markers of EBV infection, latent membrane protein (LMP, a lytic and latent marker), and BZLF-1 (putative latent-lytic switch gene) was undetectable in either study population. CONCLUSION: Based on the increased expression of the cell surface molecules HLA-DR and ICAM-1, and the inflammatory cytokine IL-6, the authors propose that local inflammatory processes contribute to the ocular surface changes and ocular surface dryness associated with primary SS.

Base Sequence↗
PubMed1993

Deriving an amino acid distance matrix.

Various methods were investigated to convert an amino acid similarity matrix into a low-dimensional, metric distance matrix. Using projection techniques, no unique transformation was found and of the many inversion forms investigated, simple negation normalized by the diagonal elements produced a good fit to the original data. An inter-row distance also gave a comparable fit and when evaluated by weighted least-squares minimization was found to be preferable. A rank-ordered form of the matrices was also derived by constraining neighbours to be equidistant in 3D-space. This produced a network configuration not unlike that produced in a previous analysis of amino acid physicochemical properties. The derived forms might find applications in sequence alignment, including pattern-matching algorithms, and the construction of phylogenetic trees.

Amino Acid Sequence↗
PubMed1993

A structural model for the nucleotide binding domains of the flavocytochrome b-245 beta-chain.

NADPH is a system in phagocytic cells that generates O2- and hydrogen peroxide in the endocytic vacuole, both of which are important for killing of the engulfed microbe. Dysfunction of this oxidase results in the syndrome of chronic granulomatous disease, characterized by a profound predisposition to bacterial and fungal infections. A flavocytochrome b is the site of most of the mutations causing this syndrome. The FAD and NADPH binding sites have been located on the beta subunit of this molecule, the C-terminal half of which showed weak sequence similarity to other reductases, including the ferredoxin-NADP reductase (FNR) of known structure. This enabled us to build a model of the nucleotide binding domains of the flavocytochrome using this structure as a template. The model was built initially using a novel automatic modeling method based on distance-matrix projection and then refined using energy minimization with appropriate side-chain torsional constraints. The resulting model rationalized much of the observed sequence conservation and identified a large insertion as a potential regulatory domain. It confirms the inclusion of the neutrophil flavocytochrome b-245 (Cb-245) as a member of the FNR family of reductases and strongly supports its function as the proximal electron transporting component of the NADPH oxidase.

Amino Acid Sequence↗
PubMed1993

Recurring structural motifs in proteins with different functions.

BACKGROUND: Structures that have diverged from a common ancestor often retain functional and sequence similarity, although the latter may be very reduced. Even so, the overall fold of the structure is generally highly conserved. Now however, several have been identified of proteins that have been identified that have different functions but which have converged to a similar fold. These proteins will also have low sequence identities. RESULTS: By comparing the complete structure databank against itself, using sequence and structure alignment techniques, we have been able to identify six new examples of structurally related folds that have no apparent sequence or functional similarity. These related proteins include a family of crambin-like folds and a family of ferredoxin II folds. We found that all the similarities between structures are present in small proteins and occur as motifs within the core of a larger protein. CONCLUSION: The low sequence similarity and the lack of any obvious functional relationship between proteins with similar structures suggest that the proteins have diverged from independent ancestors. The similarities may therefore be of interest for understanding the various stereochemical and physical criteria that operate to generate a favourable fold.

Journal Article↗