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Biomedical subjects

D J Rose

Publications and source records attributed to D J Rose.

At least 19 recordsLinked to original sources
PubMed2003

Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T.

We determined the complete genome sequence of Shigella flexneri serotype 2a strain 2457T (4,599,354 bp). Shigella species cause >1 million deaths per year from dysentery and diarrhea and have a lifestyle that is markedly different from those of closely related bacteria, including Escherichia coli. The genome exhibits the backbone and island mosaic structure of E. coli pathogens, albeit with much less horizontally transferred DNA and lacking 357 genes present in E. coli. The strain is distinctive in its large complement of insertion sequences, with several genomic rearrangements mediated by insertion sequences, 12 cryptic prophages, 372 pseudogenes, and 195 S. flexneri-specific genes. The 2457T genome was also compared with that of a recently sequenced S. flexneri 2a strain, 301. Our data are consistent with Shigella being phylogenetically indistinguishable from E. coli. The S. flexneri-specific regions contain many genes that could encode proteins with roles in virulence. Analysis of these will reveal the genetic basis for aspects of this pathogenic organism's distinctive lifestyle that have yet to be explained.

Base Sequence↗
PubMed2002

Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.

We present the complete genome sequence of uropathogenic Escherichia coli, strain CFT073. A three-way genome comparison of the CFT073, enterohemorrhagic E. coli EDL933, and laboratory strain MG1655 reveals that, amazingly, only 39.2% of their combined (nonredundant) set of proteins actually are common to all three strains. The pathogen genomes are as different from each other as each pathogen is from the benign strain. The difference in disease potential between O157:H7 and CFT073 is reflected in the absence of genes for type III secretion system or phage- and plasmid-encoded toxins found in some classes of diarrheagenic E. coli. The CFT073 genome is particularly rich in genes that encode potential fimbrial adhesins, autotransporters, iron-sequestration systems, and phase-switch recombinases. Striking differences exist between the large pathogenicity islands of CFT073 and two other well-studied uropathogenic E. coli strains, J96 and 536. Comparisons indicate that extraintestinal pathogenic E. coli arose independently from multiple clonal lineages. The different E. coli pathotypes have maintained a remarkable synteny of common, vertically evolved genes, whereas many islands interrupting this common backbone have been acquired by different horizontal transfer events in each strain.

Acute Disease↗
PubMed2001

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.

The bacterium Escherichia coli O157:H7 is a worldwide threat to public health and has been implicated in many outbreaks of haemorrhagic colitis, some of which included fatalities caused by haemolytic uraemic syndrome. Close to 75,000 cases of O157:H7 infection are now estimated to occur annually in the United States. The severity of disease, the lack of effective treatment and the potential for large-scale outbreaks from contaminated food supplies have propelled intensive research on the pathogenesis and detection of E. coli O157:H7 (ref. 4). Here we have sequenced the genome of E. coli O157:H7 to identify candidate genes responsible for pathogenesis, to develop better methods of strain detection and to advance our understanding of the evolution of E. coli, through comparison with the genome of the non-pathogenic laboratory strain E. coli K-12 (ref. 5). We find that lateral gene transfer is far more extensive than previously anticipated. In fact, 1,387 new genes encoded in strain-specific clusters of diverse sizes were found in O157:H7. These include candidate virulence factors, alternative metabolic capacities, several prophages and other new functions--all of which could be targets for surveillance.

Base Sequence↗
PubMed2001

Desflurane or sevoflurane for gynaecological day-case anaesthesia with spontaneous respiration?

Sixty gynaecological day-case patients were anaesthetised with either desflurane or sevoflurane in oxygen/nitrous oxide, following intravenous induction. Mean end-tidal desflurane was 4.5% at 5 and 10 min post induction, whereas mean end-tidal sevoflurane was 1.7%. There were five untoward airway events (coughing, hiccoughs) in the desflurane group and three in the sevoflurane group, including one laryngospasm. Time to eye opening and orientation following anaesthesia were significantly faster in the desflurane group (2.8 min/4.8 min) than in the sevoflurane group (7.0 min/9.8 min; p < 0.0001). Time to being ready for discharge home was also significantly earlier in the desflurane group (3 h compared with 3.5 h). Telephone interview on the first postoperative day showed that in the desflurane group 29 of 31 were fully returned to normal activity compared with only 15 out of 29 in the sevoflurane group (p < 0.01).

Adolescent↗
PubMed2001

Evaluation of dynamic balance among community-dwelling older adult fallers: a generalizability study of the limits of stability test.

OBJECTIVE: To establish reliability estimates of the 75% Limits of Stability Test (75% LOS test) when administered to community-dwelling older adults with a history of falls. DESIGN: Generalizability theory was used to estimate both the relative contribution of identified error sources to the total measurement error and generalizability coefficients. A random effects repeated-measures analysis of variance (ANOVA) was used to assess consistency of LOS test movement variables across both days and targets. SETTING: A motor control research laboratory in a university setting. PARTICIPANTS: Fifty community-dwelling older adults with 2 or more falls in the previous year. MAIN OUTCOME MEASURES: Spatial and temporal measures of dynamic balance derived from the 75% LOS test included average movement velocity, maximum center of gravity (COG) excursion, end-point COG excursion, and directional control. RESULTS: Estimated generalizability coefficients for 2 testing days ranged from.58 to.87. Total variance in LOS test measures attributable to inconsistencies in day-to-day test performance (Day and Subject x Day facets) ranged from 2.5% to 8.4%. The ANOVA results indicated that no significant differences were observed in the LOS test variables across the 2 testing days. CONCLUSIONS: The 75% LOS test administered to older adult fallers on 2 consecutive days provides consistent and reliable measures of dynamic balance.

Accidental Falls↗
PubMed2001

Arthroscopic treatment of an intra-articular lipoma of the knee joint.

Intra-articular lipoma is an exceedingly rare diagnosis. There have been less than 15 documented cases of an intra-articular lipoma of the knee joint. This report presents the first description of an intra-articular knee lipoma treated entirely by arthroscopic methods. Preoperative history, examination, and imaging studies are reviewed. Intraoperative findings, treatment, and postoperative evaluation are discussed as well. Symptomatic intra-articular lipoma of the knee joint can be successfully treated by arthroscopic resection. Differentiating intra-articular lipoma from lipoma arborescens, a similar but more common condition, is important with regards to optimal treatment.

Adult↗
PubMed2001

Arthroscopic diagnosis and management of ochronotic arthropathy of the knee.

Ochronotic arthropathy is a progressive joint disorder resulting from the deposition of a derivative of homogentisic acid into connective tissues, especially meniscal and articular cartilage. Patients may present with symptoms, physical examination results, and radiographic changes consistent with degenerative joint disease. We present a case in which an operative arthroscopy of the knee was highly suggestive of ochronotic arthropathy. The definitive diagnosis of ochronosis was subsequently confirmed by laboratory and pathologic evaluation.

Arthralgia↗
PubMed2001

Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri.

The complete sequence analysis of the 210-kb Shigella flexneri 5a virulence plasmid was determined. Shigella spp. cause dysentery and diarrhea by invasion and spread through the colonic mucosa. Most of the known Shigella virulence determinants are encoded on a large plasmid that is unique to virulent strains of Shigella and enteroinvasive Escherichia coli; these known genes account for approximately 30 to 35% of the virulence plasmid. In the complete sequence of the virulence plasmid, 286 open reading frames (ORFs) were identified. An astonishing 153 (53%) of these were related to known and putative insertion sequence (IS) elements; no known bacterial plasmid has previously been described with such a high proportion of IS elements. Four new IS elements were identified. Fifty putative proteins show no significant homology to proteins of known function; of these, 18 have a G+C content of less than 40%, typical of known virulence genes on the plasmid. These 18 constitute potentially unknown virulence genes. Two alleles of shet2 and five alleles of ipaH were also identified on the plasmid. Thus, the plasmid sequence suggests a remarkable history of IS-mediated acquisition of DNA across bacterial species. The complete sequence will permit targeted characterization of potential new Shigella virulence determinants.

Amino Acid Sequence↗
PubMed2000

The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer.

Salmonella typhi, the causative agent of typhoid fever, annually infects 16 million people and kills 600 000 world wide. Plasmid-encoded multiple drug resistance in S. typhi is always encoded by plasmids of incompatibility group H (IncH). The complete DNA sequence of the large temperature-sensitive conjugative plasmid R27, the prototype for the IncHI1 family of plasmids, has been compiled and analyzed. This 180 kb plasmid contains 210 open reading frames (ORFs), of which 14 have been previously identified and 56 exhibit similarity to other plasmid and prokaryotic ORFs. A number of insertion elements were found, including the full Tn 10 transposon, which carries tetracycline resistance genes. Two transfer regions, Tra1 and Tra2, are present, which are separated by a minimum of 64 kb. Homologs of the DNA-binding proteins TlpA and H-NS that act as temperature-regulated repressors in other systems have been located in R27. Sequence analysis of transfer and replication regions supports a mosaic-like structure for R27. The genes responsible for conjugation and plasmid maintenance have been identified and mechanisms responsible for thermosensitive transfer are discussed.

Amino Acid Sequence↗
PubMed2000

Can the control of bodily orientation be significantly improved in a group of older adults with a history of falls?

OBJECTIVE: To determine the short-term effectiveness of a biofeedback-based, computerized intervention that applied the principles of the ecological theory of perception and control of bodily orientation to the rehabilitation of older adults with a history of falling. PARTICIPANTS: Forty-five older adults (X = 78.5 years) with a history of falls were assigned to either a control (n = 21) or intervention group (n = 24). DESIGN: A 2 x 2 (Group x Time) mixed factorial design with repeated measures on the second factor. SETTING: A motor control research laboratory in a university setting. MEASUREMENT: Impairments in multiple dimensions of balance (i.e., dynamic postural control and sensory organization) were measured before and after an 8-week balance intervention using the 100% Limits of Stability Test and Sensory Organization Test. More functional limitations in balance and/or mobility were measured using two clinical tests: Berg Balance Scale and Timed Up and Go test. MAIN RESULTS: Repeated measures multivariate analyses and follow-up testing indicated significant improvements in the dynamic balance and sensory integration capabilities in the case of the intervention group only (P < .03). Significant improvements were also observed in the two clinical measures of balance and mobility evaluated before and after the intervention for the intervention group only. CONCLUSIONS: Theory-driven rehabilitation programs that focus on manipulating individual, task, and environmental constraints concurrently can significantly improve the control of bodily orientation of older adults with a previous history of falls in both static and dynamic action environments. Moreover, the significant improvements in functional performance observed for the intervention group suggest that interventions emphasizing task-specific practice are not the only means by which an older adult's ability to perform daily activities requiring postural control can be improved.

Accidental Falls↗
PubMed1999

Lethal kinesin mutations reveal amino acids important for ATPase activation and structural coupling.

To study the relationship between conventional kinesin's structure and function, we identified 13 lethal mutations in the Drosophila kinesin heavy chain motor domain and tested a subset for effects on mechanochemistry. S246F is a moderate mutation that occurs in loop 11 between the ATP- and microtubule-binding sites. While ATP and microtubule binding appear normal, there is a 3-fold decrease in the rate of ATP turnover. This is consistent with the hypothesis that loop 11 provides a structural link that is important for the activation of ATP turnover by microtubule binding. T291M is a severe mutation that occurs in alpha-helix 5 near the center of the microtubule-binding surface. It impairs the microtubule-kinesin interaction and directly effects the ATP-binding pocket, allowing an increase in ATP turnover in the absence of microtubules. The T291M mutation may mimic the structure of a microtubule-bound, partially activated state. E164K is a moderate mutation that occurs at the beta-sheet 5a/loop 8b junction, remote from the ATP pocket. Surprisingly, it causes both tighter ATP-binding and a 2-fold decrease in ATP turnover. We propose that E164 forms an ionic bridge with alpha-helix 5 and speculate that it helps coordinate the alternating site catalysis of dimerized kinesin heavy chain motor domains.

Adenosine Triphosphatases↗
PubMed1999

Arthroscopic removal of bullet fragments from the subtalar joint.

A case of arthroscopic removal of a bullet fragment from the subtalar joint and the calcaneus is presented. The bullet fragments impinged on the fibula, limiting eversion and causing pain. The fragments were removed both arthroscopically and through open incision. The patient noted complete relief of pain and improved range of motion within 1 week, and complete recovery soon thereafter.

Adult↗
PubMed1999

Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product.

Lysogenic bacteriophages are major vehicles for the transfer of genetic information between bacteria, including pathogenicity and/or virulence determinants. In the enteric pathogen Escherichia coli O157:H7, which causes hemorrhagic colitis and hemolytic-uremic syndrome, Shiga toxins 1 and 2 (Stx1 and Stx2) are phage encoded. The sequence and analysis of the Stx2 phage 933W is presented here. We find evidence that the toxin genes are part of a late-phage transcript, suggesting that toxin production may be coupled with, if not dependent upon, phage release during lytic growth. Another phage gene, stk, encodes a product resembling eukaryotic serine/threonine protein kinases. Based on its position in the sequence, Stk may be produced by the prophage in the lysogenic state, and, like the YpkA protein of Yersinia species, it may interfere with the signal transduction pathway of the mammalian host. Three novel tRNA genes present in the phage genome may serve to increase the availability of rare tRNA species associated with efficient expression of pathogenicity determinants: both the Shiga toxin and serine/threonine kinase genes contain rare isoleucine and arginine codons. 933W also has homology to lom, encoding a member of a family of outer membrane proteins associated with virulence by conferring the ability to survive in macrophages, and bor, implicated in serum resistance.

Attachment Sites, Microbiological↗
PubMed1998

Subdivision of the Escherichia coli K-12 genome for sequencing: manipulation and DNA sequence of transposable elements introducing unique restriction sites.

A transposon-based method of introducing unique restriction sites was used for subdivision of the Escherichia coli genome into a contiguous series of large non-overlapping segments spanning 2.5Mb. The segments, sizes ranging from 150 to 250kb, were isolated from the chromosome using the inserted restriction sites and shotgun cloned into an M13 vector for DNA sequencing. These shotgun sizes proved easily manageable, allowing the genomic sequence of E. coli to be completed more efficiently and rapidly than was possible by previously available methods. The 9bp duplication generated during transposition was used as a tag for accurate splicing of the segments; no further sequence redundancy at the junction sites was needed. The system is applicable to larger genomes even if they are not already well-characterized. We present the technology for segment sequencing, results of applying this method to E. coli, and the sequences of the transposon cassettes.

Chromosomes, Bacterial↗
PubMed1998

Inkjet dispensing technology: applications in drug discovery.

The past year has seen significant advances in the reduction to practice of inkjet dispensing technology in drug discovery applications. Although much of the work in this area has been done by relatively few 'early innovators', broader acceptance of the feasibility of the use of inkjet dispensing is on the rise. Of the three main areas of drug discovery - genomics, high-throughput screening, and combinatorial chemistry - high-throughput screening has had the most applications to date. The burgeoning field of genomics has seen rapid incorporation of technologies that enable miniaturization of gene expression experiments. Inkjet dispensing has a clear role in this effort. Finally, as the miniaturization needs of combinatorial chemistry become more clear, inkjet dispensing technology will potentially play a role.

Biotechnology↗
PubMed1998

DNA sequencing and analysis of the low-Ca2+-response plasmid pCD1 of Yersinia pestis KIM5.

The low-Ca2+-response (LCR) plasmid pCD1 of the plague agent Yersinia pestis KIM5 was sequenced and analyzed for its genetic structure. pCD1 (70,509 bp) has an IncFIIA-like replicon and a SopABC-like partition region. We have assigned 60 apparently intact open reading frames (ORFs) that are not contained within transposable elements. Of these, 47 are proven or possible members of the LCR, a major virulence property of human-pathogenic Yersinia spp., that had been identified previously in one or more of Y. pestis or the enteropathogenic yersiniae Yersinia enterocolitica and Yersinia pseudotuberculosis. Of these 47 LCR-related ORFs, 35 constitute a continuous LCR cluster. The other LCR-related ORFs are interspersed among three intact insertion sequence (IS) elements (IS100 and two new IS elements, IS1616 and IS1617) and numerous defective or partial transposable elements. Regional variations in percent GC content and among ORFs encoding effector proteins of the LCR are additional evidence of a complex history for this plasmid. Our analysis suggested the possible addition of a new Syc- and Yop-encoding operon to the LCR-related pCD1 genes and gave no support for the existence of YopL. YadA likely is not expressed, as was the case for Y. pestis EV76, and the gene for the lipoprotein YlpA found in Y. enterocolitica likely is a pseudogene in Y. pestis. The yopM gene is longer than previously thought (by a sequence encoding two leucine-rich repeats), the ORF upstream of ypkA-yopJ is discussed as a potential Syc gene, and a previously undescribed ORF downstream of yopE was identified as being potentially significant. Eight other ORFs not associated with IS elements were identified and deserve future investigation into their functions.

Calcium↗
PubMed1997

The complete genome sequence of Escherichia coli K-12.

The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.

Bacterial Proteins↗