Biomedical subjects

David T Jones

Publications and source records attributed to David T Jones.

25 records · Page 2Linked to original sources

PubMed2003

Assembling novel protein folds from super-secondary structural fragments.

The results of applying a fragment-based protein tertiary structure prediction method to the prediction of 14 CASP5 target domains are described. The method is based on the assembly of supersecondary structural fragments taken from highly resolved protein structures using a simulated annealing algorithm. A number of good predictions for proteins with novel folds were produced, although not always as the first model. For two fold recognition targets, FRAGFOLD produced the most accurate model in both cases, despite the fact that the predictions were not based on a template structure. Although clear progress has been made in improving FRAGFOLD since CASP4, the ranking of final models still seems to be the main problem that needs to be addressed before the next CASP experiment.

Algorithms↗

PubMed2002

Targeting novel folds for structural genomics.

The ultimate goal of structural genomics is to obtain the structure of each protein coded by each gene within a genome to determine gene function. Because of cost and time limitations, it remains impractical to solve the structure for every gene product experimentally. Up to a point, reasonably accurate three-dimensional structures can be deduced for proteins with homologous sequences by using comparative modeling. Beyond this, fold recognition or threading methods can be used for proteins showing little homology to any known fold, although this is relatively time-consuming and limited by the library of template folds currently available. Therefore, it is appropriate to develop methods that can increase our knowledge base, expanding our fold libraries by earmarking potentially "novel" folds for experimental structure determination. How can we sift through proteomic data rapidly and yet reliably identify novel folds as targets for structural genomics? We have analyzed a number of simple methods that discriminate between "novel" and "known" folds. We propose that simple alignments of secondary structure elements using predicted secondary structure could potentially be a more selective method than both a simple fold recognition method (GenTHREADER) and standard sequence alignment at finding novel folds when sequences show no detectable homology to proteins with known structures.

Animals↗

PubMed2002

Identification of the sources of fecal coliforms in an urban watershed using antibiotic resistance analysis.

Bacteria such as fecal coliforms are used as indicators of fecal pollution in natural waters. These bacteria are found in the feces of most wild and domestic animals and thus provide no information as to the source of fecal contamination, yet identification of indicator bacteria sources allows improved risk assessment, remediation, and total daily maximum load (TDML) assessment of environmental waters. This bacterial source tracking study was initiated in order to identify the dominant source(s) of fecal contamination in the urban watershed of Stevenson Creek in Clearwater, Florida. Five sites that represent areas where routine monitoring has previously shown high levels of fecal coliforms were sampled over 7 months. Fecal coliforms were enumerated by membrane filtration, and antibiotic resistance analysis was used to "fingerprint" a subset of randomly selected isolates and statistically match them to fingerprints of fecal coliforms from known sources (the library). A field test of the classification accuracy of the library was carried out by isolating fecal coliforms from the soil and waters surrounding a failing onsite wastewater treatment and disposal system (OSTDS). The vast majority of the isolates were classified into the human category. The major sources of fecal pollution in Stevenson Creek over the course of the study were wild animal, human, and, to a lesser extent, dog. Overall, wild animal feces were identified as the dominant source when fecal coliform levels were high, but when fecal coliform levels were low, the dominant source was identified as human. The results of this study demonstrate that the sources of fecal indicator bacteria within one urban watershed can vary substantially over temporal and spatial distances.

Animals↗

PubMed2002

Getting the most from PSI-BLAST.

Most biologists now conduct sequence searches as a matter of course. But how do we know that a relationship predicted by a homology search is a true, rather than false, hit with the same score? Many biologists design their own experiments with exquisite care yet still assume that results from programs with more than 20 adjustable parameters are 100% reliable. This article explains some of the key steps in getting the most from PSI-Blast, one of the most popular and powerful homology search programs currently available.

Algorithms↗

PubMed2002

Rapid protein domain assignment from amino acid sequence using predicted secondary structure.

The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (+/-20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed.

Amino Acid Sequence↗

PubMed2001

Physical and genetic map of the Clostridium saccharobutylicum (formerly Clostridium acetobutylicum) NCP 262 chromosome.

A physical and genetic map of the Clostridium saccharobutylicum NCP 262 chromosome was constructed. The order of macrorestriction fragments was determined by analysing fragments generated after single and double digestion with the restriction enzymes BssHII, I-CeuI, Sse8387I, RsrII and SfiI and separation by PFGE. The I-CeuI backbone of C. saccharobutylicum was constructed by indirect end-labelling with rrs- and 3' rrl-specific probes located on either side of the I-CeuI site in the rrn operon, and reciprocal separation of BssHII and I-CeuI digestion products by two-dimensional PFGE. The positions of BssHII fragments on the physical map were determined using a library of linking clones containing BssHII cleavage sites. The size of the circular genome was estimated to be 5.3 Mb with a mean resolution of approximately 140 kb. The chromosome of C. saccharobutylicum contains 12 rrn operons, located on 46% of the chromosome, which are transcribed divergently from the deduced origin of replication. The genetic map was constructed by determining the location of 28 genes involved in house-keeping, heat-shock response, sporulation, electron transfer and acid- and solvent-formation. Comparison of the C. saccharobutylicum genetic map with those of the spore-forming bacteria Bacillus subtilis, Clostridium acetobutylicum, Clostridium perfringens and Clostridium beijerinckii indicated C. saccharobutylicum to be most similar to the latter two Clostridium species, with the order of the genes within the gyrAB and recA loci being conserved.

Blotting, Southern↗

PubMed1988

Cloning and Expression of a Clostridium acetobutylicum Alcohol Dehydrogenase Gene in Escherichia coli.

An alcohol dehydrogenase (ADH) gene from Clostridium acetobutylicum was cloned on a recombinant plasmid, pCADH100. Escherichia coli HB101, and an allyl alcohol-resistant mutant, HB101-adh1, containing this plasmid were unable to grow aerobically or anaerobically on agar media containing sublethal concentrations of allyl alcohol. E. coli HB101 and HB101-adh1 transformed with the plasmid pCADH100 produced increased levels of ethanol when grown anaerobically under alkaline conditions in the absence of nitrate. Cell extracts from aerobically and anaerobically grown E. coli HB101(pCADH100) and HB101-adhl(pCADH100) cells exhibited increased levels of NADP-dependent ADH activity with either ethanol or butanol as the substrate. The inability of E. coli HB101(pCADH100) to grow in the presence of allyl alcohol correlated with the appearance of an NADP-dependent ADH activity band on nondenaturing polyacrylamide gel electrophoresis with either ethanol or butanol as the substrate. The position of the cloned NADP-dependent ADH activity bands in E. coli HB101(pCADH100) cell extracts with either ethanol or butanol as the substrate coincided with the position of a single NADP-dependent ADH activity band in extracts of C. acetobutylicum cells. E. coli HB101(pCADH100) cell extracts prepared from both aerobically and anaerobically grown cells exhibited an additional protein band with an apparent M(r) of approximately 33,000 on sodium dodecyl sulfate-polyacryl-amide gel electrophoresis which was absent in cell extracts of E. coli HB101. A protein band with a similar apparent M(r) was observed in cell extracts of C. acetobutylicum, and in vitro transcription and translation experiments with pCADH100 produced a major protein product with a similar apparent M(r).

Journal Article↗