Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae

The genome of Chlamydophila caviae (formerly Chlamydia psittaci, GPIC isolate) (1 173 390 nt with a plasmid of 7966 nt) was determined, representing the fourth species with a complete genome sequence from the Chlamydiaceae family of obligate intracellular bacterial pathogens. Of 1009 annotated genes, 798 were conserved in all three other completed Chlamydiaceae genomes. The C.caviae genome contains 68 genes that lack orthologs in any other completed chlamydial genomes, including tryptophan and thiamine biosynthesis determinants and a ribose-phosphate pyrophosphokinase, the product of the prsA gene. Notable amongst these was a novel member of the virulence-associated invasin/intimin family (IIF) of Gram-negative bacteria. Intriguingly, two authentic frameshift mutations in the ORF indicate that this gene is not functional. Many of the unique genes are found in the replication termination region (RTR or plasticity zone), an area of frequent symmetrical inversion events around the replication terminus shown to be a hotspot for genome variation in previous genome sequencing studies. In C.caviae, the RTR includes several loci of particular interest including a large toxin gene and evidence of ancestral insertion(s) of a bacteriophage. This toxin gene, not present in Chlamydia pneumoniae, is a member of the YopT effector family of type III-secreted cysteine proteases. One gene cluster (guaBA-add) in the RTR is much more similar to orthologs in Chlamydia muridarum than those in the phylogenetically closest species C.pneumoniae, suggesting the possibility of horizontal transfer of genes between the rodent-associated Chlamydiae. With most genes observed in the other chlamydial genomes represented, C.caviae provides a good model for the Chlamydiaceae and a point of comparison against the human atherosclerosis-associated C.pneumoniae. This crucial addition to the set of completed Chlamydiaceae genome sequences is enabling dissection of the roles played by niche-specific genes in these important bacterial pathogens.

Regulated expression of the X. tropicalis connexin43 promoter

The spatio-temporal expression pattern of the connexin43 gene during Xenopus development has been described (Van der Heyden et al. 2001). To further investigate the regulation and function of connexin43 (Cx43) in amphibians, we have isolated the gene from Xenopus tropicalis (Xt) and determined its structure. The X. tropicalis Cx43 gene displays the typical two exon-one intron connexin configuration, where the first exon is non-coding. The predicted amino acid sequence of the XtCx43 protein is highly homologous to that of X. laevis, chicken and mammals. Expression of XtCx43 cDNA in N2A cells results in gap-junction plaque formation. Promoter activity of a 3.5 kb upstream region of the X. tropicalis Cx43 gene, including exon 1, mimics endogenous timing of expression after injection of reporter constructs in X. laevis embryos.

Calcium supplementation on bone loss in postmenopausal women

BACKGROUND

Although calcium is one the simplest and least expensive strategies for preventing osteoporotic fractures calcium supplementation is nevertheless not without controversy (Kanis 1989; Nordin 1990). The Food and Drug Administration in the US has permitted a bone health claim for calcium-rich foods, and the NIH in its Consensus Development Process approved a statement that high calcium intake reduces the risk of osteoporosis.

OBJECTIVES

To assess the effects of calcium on bone density and fractures in postmenopausal women.

SEARCH STRATEGY

We searched Cochrane Controlled Register, MEDLINE and EMBASE up to 2001, and examined citations of relevant articles and proceedings of international meetings.

SELECTION CRITERIA

Trials that randomized postmenopausal women to calcium supplementation or usual calcium intake in the diet and reported bone mineral density of the total body, vertebral spine, hip, or forearm or recorded the number of fractures, and followed patients for at least one year were considered for inclusion.

DATA COLLECTION AND ANALYSIS

Three independent reviewers assessed the methodologic quality and extracted data for each trial. For each bone density site (lumbar spine, total body, combined hip and combined forearm), we calculated the weighted mean difference in bone density between treatment and control groups using the percentage change from baseline. We constructed regression models in which the independent variables were year and dose, and the dependent variable was the effect size. This regression was used to determine the years across which pooling was appropriate. Heterogeneity was assessed. For each fracture analysis we calculated a risk ratio.

MAIN RESULTS

Fifteen trials, representing 1806 participants, were included. Calcium was more effective than placebo in reducing rates of bone loss after two or more years of treatment. The pooled difference in percentage change from baseline was 2.05% (95% CI 0.24 to 3.86) for total body bone density, 1.66% (95% CI 0.92 to 2.39) for the lumbar spine at 2 years, 1.60% (95% CI 0.78 to 2.41) for the hip, and 1.91% (95% CI 0.33 to 3.50) for the distal radius. The relative risk of fractures of the vertebrae was 0.79 (95% CI 0.54 to 1.09); the relative risk for non-vertebral fractures was 0.86 (95% CI 0.43 to 1.72).

REVIEWER'S CONCLUSIONS

Calcium supplementation alone has a small positive effect on bone density. The data show a trend toward reduction in vertebral fractures, but it is unclear if calcium reduces the incidence of non vertebral fractures.

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.

Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains

Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.

Detection of hepatitis C core antigen in serum or plasma as a marker of hepatitis C viraemia in the serological window-phase

A new immunoassay for the detection of hepatitis C core antigen (HCVcoreAg) in peripheral blood during serological window-phase was evaluated among healthy blood donors, commercially available hepatitis C virus (HCV) seroconversion panels and in-house specimens from individuals undergoing seroconversion. Among 1964 low-risk blood donor samples, seven samples were initially reactive but only one was repeat reactive. Reactivity of this specimen was not confirmable by neutralization with specific anti-HCV core antibody, and the sample was negative for HCV RNA by polymerase chain reaction (PCR). The specificity of the HCVcoreAg enzyme-linked immunosorbent assay (ELISA) was 99.95%. In seven commercially available HCV seroconversion panels, HCVcoreAg appeared 23-46 days earlier than anti-HCV antibody by third generation assay. Additional testing with specimens from patients undergoing anti-HCV seroconversion indicated that HCVcoreAg becomes undetectable by the present test format soon after the onset of antibody. This test may be considered as an alternative to nucleic amplification techniques (NAT) for blood donor HCV screening. Additional development of technology for detecting HCVcoreAg may be useful for patient diagnosis and therapy monitoring.

Application of capillary zone electrophoresis to the separation and characterization of poly(amidoamine) dendrimers with an ethylenediamine core

Generations 0 through 5 of ethylenediamine-core poly(amidoamine) dendrimers were synthesized and capillary zone electrophoresis has been applied to the separation of different generations of synthesized dendrimers and for the characterization of individual generations.

Identification of a neuronal nitric oxide synthase in isolated cardiac mitochondria using electrochemical detection

Mitochondrial nitric oxide synthase (mtNOS), its cellular NOS isoform, and the effects of mitochondrially produced NO on bioenergetics have been controversial since mtNOS was first proposed in 1995. Here we functionally demonstrate the presence of a NOS in cardiac mitochondria. This was accomplished by direct porphyrinic microsensor measurement of Ca(2+)-dependent NO production in individual mitochondria isolated from wild-type mouse hearts. This NO production could be inhibited by NOS antagonists or protonophore collapse of the mitochondrial membrane potential. The similarity of mtNOS to the neuronal isoform was deduced by the absence of NO production in the mitochondria of knockout mice for the neuronal, but not the endothelial or inducible, isoforms. The effects of mitochondrially produced NO on bioenergetics were studied in intact cardiomyocytes isolated from dystrophin-deficient (mdx) mice. mdx cardiomyocytes are also deficient in cellular endothelial NOS, but overexpress mtNOS, which allowed us to study the mitochondrial enzyme in intact cells free of its cytosolic counterpart. In these cardiomyocytes, which produce NO beat-to-beat, inhibition of mtNOS increased myocyte shortening by approximately one-fourth. Beat-to-beat NO production and altered shortening by NOS inhibition were not observed in wild-type cells. A plausible mechanism for the reversible NO inhibition of contractility in these cells involves the reaction of NO with cytochrome c oxidase. This suggests a modulatory role for NO in oxidative phosphorylation and, in turn, myocardial contractility.

Airway management for the sports physician part 2: advanced techniques

Airway emergencies sometimes require techniques other than basic management methods. Advanced techniques are needed to manage laryngeal edema or fracture, upper-airway hemorrhage, or other injuries that make ventilation or intubation from above impossible. Placing various endotracheal devices and performing surgical techniques such as needle cricothyrotomy and tracheostomy can be done by physicians who have training and the necessary equipment. Surgical techniques can be performed with medical bag components, but commercial kits are available for those who are uncomfortable performing techniques using bag equipment.

Do silicone breast implants cause rheumatologic disorders? A systematic review for a court-appointed national science panel

OBJECTIVE

To assist in evaluating expert testimony and scientific evidence presented in law suits brought against silicone breast implant manufacturers, a US District Court Order established a National Science Panel to assess whether existing studies provide scientific evidence of an association between silicone breast implants and systemic classic/accepted connective disease, atypical connective disease, and certain signs and symptoms identified by plaintiffs in the law suits. Local disorders potentially associated with these implants were not addressed in this review. Therefore, we performed a systematic review of published studies on the association between silicone breast implants and systemic connective tissue disorders.

METHODS

Data from relevant studies (human cohort, case-control, or cross-sectional studies with > or = 10 participants and appropriate controls) were identified through literature searches of Medline, Current Contents, HealthStar, Biological Abstracts, EMBase, Toxline, and Dissertation Abstracts. Two independent reviewers, using standard collection forms, extracted data from the included studies. Adjusted relative risks (RRs) in cohort studies and odds ratios (ORs) in case-control and cross-sectional studies were reported if provided; otherwise, unadjusted RRs and ORs were calculated.

RESULTS

Twenty-four studies meeting inclusion criteria were identified. No association was evident between breast implants and any established or atypical connective tissue disorder. There was discordance among studies in reports of arthralgias, lymphadenopathy, myalgias, sicca symptoms, skin changes, and stiffness.

CONCLUSION

The panel found no evidence to support expert testimony suggesting an association between silicone breast implants and connective diseases. Discordance for symptoms may reflect differences in symptoms included in various categories, the small number of cases, and the effect of having single subjects with > 1 symptom represented in analyses of each symptom reported. The process presented here is an early example of the use of independent scientific panels to help courts clarify scientific evidence in legal proceedings.

Airway management for the sports physician part 1: basic techniques

Airway emergencies are, fortunately, rare in sports medicine, but when they occur, they must be addressed quickly and effectively. Various techniques can be applied by a trained team physician to optimize oxygenation and ventilation for an acutely ill or injured athlete. Initial management of airway emergencies on the field can be guided using a simple algorithm. Basic maneuvers include methods to clear airways, place ventilation devices, and assist with breathing. More advanced techniques include placing various endotracheal tube devices and performing surgical techniques; these will be discussed in a subsequent article.

Feasibility of paramedic treatment and referral of minor illnesses and injuries

BACKGROUND

Approximately 40% of Hennepin County Medical Center's (HCMC's) ambulance runs are for minor medical conditions as defined by billing criteria ["ALS minor," i.e., no advanced life support (ALS) procedures done in the field]. Current metropolitan guidelines mandate that all such patients must be transported to a hospital unless they refuse this service. It has been proposed that some patients with minor medical conditions could be better served by treatment in the field by paramedics and referred to a clinic or hospital for early follow-up care. It is proposed that this approach would save costs and improve paramedic availability for patients with more serious conditions.

OBJECTIVE

To evaluate the feasibility and safety of implementing such a program by identifying high-volume, low-complexity groupings of cases. Such high-volume, low-complexity cases would serve as the topics for curriculum development for paramedic training in field treatment and referral.

METHODS

Data were obtained from ambulance run sheets and emergency department (ED) records for all patients transported by the HCMC ambulance service in 1996 who were covered by the Metropolitan Health Plan (MHP) and who were categorized for billing purposes as "ALS minor" transports. The data included demographic information, vital signs, presenting problem, diagnoses in the ED, and procedures, laboratory studies, or x-rays done in the ED. Patients were classified as "potentially treatable" in the field if they were treated and discharged from the ED without undergoing any procedures or diagnostic studies. Patients who required more extensive evaluation in the ED, or who were admitted, were classified as likely too "complex" to be treated at the scene and then referred for early follow-up. The data were analyzed to find the most common presenting problems and the numbers, characteristics, and dispositions of "potentially treatable" and "complex" patients in each group. This information was used to determine what, if any, types of patients could potentially be treated safely and effectively according to this scheme.

RESULTS

The study group comprised 1,103 patients, representing 127 different presenting medical problems. There were 523 (47%) "potentially treatable" patients and 580 (53%) "complex" patients. The 127 medical problems were grouped and the 15 most common presenting problem groups were identified. Within these groups there was no single medical problem with high volume. Each of these 15 most common problem groups contained a substantial proportion of "complex" patients, ranging from 24% to 100%.

CONCLUSIONS

None of the 15 most frequently encountered problem groups consisted of a high enough proportion of "potentially treatable" cases to serve as a high-volume, low-complexity category for paramedic treatment in the field with early follow-up. Without any identified high-volume, low-complexity categories, a treatment and referral program as proposed in this article would require a substantial investment in development of appropriate criteria and in training paramedics to apply the criteria for numerous clinical entities. This would limit any cost saving, and require great care to avoid compromising patient safety accompanied by substantial professional liability exposure.

Connexin43 expression during Xenopus development

The spatio-temporal expression of connexin43 in Xenopus laevis embryos was studied by in situ hybridization. Cx43 expression is first detected at stage 25 in the developing eye. In stage 32, expression was found in the margin of the lens placode, the cement gland, notochord, and in stage 37 in the branchial arches. Early limb buds show strong expression of Cx43 distally while later on expression is confined to sites of precartilage condensation.

Further refinement of the MYP2 locus for autosomal dominant high myopia by linkage disequilibrium analysis

INTRODUCTION

High myopia (>-6.00 diopters) is a complex common disorder that predisposes individuals to retinal detachment, glaucoma, macular degeneration, and premature cataracts. A recent linkage analysis of seven families with autosomal dominant high myopia has identified one locus (MYP2) for high myopia on chromosome 18p11.31 (Young et al.: Am J Hum Genet 1998;63:109-119). Haplotype analysis revealed an initial interval of 7.6 centimorgans (cM).

METHODS

Transmission disequilibrium tests (TDT) with both the Statistical Analysis for Genetic Epidemiology (SAGE) 3.1 TDTEX and GENEHUNTER 2 (GH2) programs were performed using chromosome 18p marker alleles for this interval.

RESULTS

Using SAGE analysis, the following p values were obtained for markers in marker order in this region: D18S1146 (p = 0.227), D18S481 (p = 0.001), D18S63 (p = 0.062), D18S1138 (p = 0.0004), D18S52 (p = 1.79 x 10(-6)), and D18S62 (p = 0.141). GH2 TDT analysis revealed the following p values for the best allele for the markers: D18S1146 (p = 0.083), D18S481 (p = 0.108), D18S63 (p = 0.034), D18S1138 (p = 0.011), D18S52 (p = 0.007), and D18S62 (p = 0.479).

CONCLUSION

These data suggest that the gene for 18p11.31-linked high myopia is most proximal to marker D18S52, with a likely interval of 0.8 cM between markers D18S63 and D18S52. Due to the contraction of the interval size by TDT, these results provide a basis for focused positional cloning and candidate gene analysis at the MYP2 locus.

Microbial genes in the human genome: lateral transfer or gene loss?

The human genome was analyzed for evidence that genes had been laterally transferred into the genome from prokaryotic organisms. Protein sequence comparisons of the proteomes of human, fruit fly, nematode worm, yeast, mustard weed, eukaryotic parasites, and all completed prokaryote genomes were performed, and all genes shared between human and each of the other groups of organisms were collected. About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates. Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation.

Setting system suitability criteria for detectability in high-performance liquid chromatography methods using signal-to-noise ratio statistical tolerance intervals

For pharmaceutical products, one approach developed to assure that different chromatographic systems are capable of generating valid results is the system suitability test. Typically, a system suitability test involves numerical limits for predefined chromatographic parameters such as theoretical plates, tailing factor, injector reproducibility, etc. An estimation of the ratio of signal compared to baseline is one way to measure system performance, according to a valid method, independent of the instrument. However, since this comparison relates the height of the signal to the height of the noise, it is difficult to relate to the peak area measurements that are typically used for quantification of samples. Additionally, although peak area and peak height may be highly correlated over a wide region, peak area at very low concentrations can be more sensitive to all components of noise due to peak shape. To establish a system suitability criterion, one can use the ratio of the area signal to the baseline noise for replicate injections for samples prepared at concentration equal to the limit of quantitation during the validation studies. A lower limit for this ratio can be derived using statistical tolerance intervals. This lower limit can be applied as a system suitability criterion to measure that any system is performing adequately for measuring low level components in the sample for all future use of the method.

The outcome of endodontic resurgery: a systematic review

AIM

The aim of this paper is to establish an outcome standard for the assessment of healing radiographically after resurgery of persistent periradicular lesions by systematically reviewing the results from published studies.

METHODOLOGY

The systematic review process requires the definition of predetermined criteria delineating the inclusion parameters of studies reviewed. Of 42 papers that were reviewed, eight qualified for inclusion. A weighted-average was calculated from the results taken from the eight eligible, peer-reviewed studies, published between 1970 and 1997.

RESULTS

Three hundred and thirty patients out of 2375 (14%) from the included studies underwent resurgery for failure of healing as determined radiographically. Of this population, 35.7% healed successfully after resurgery, 26.3% healed with uncertain results and 38% did not heal at the one-year follow-up.

CONCLUSIONS

Although there is nearly equal distribution of results between all categories, a 35.7% rate of healing as assessed radiographically is essentially equivalent to the 38% failure rate. This paper will allow an evaluation of current research results to establish an outcome standard and enable techniques and filling materials to be evaluated and compared. Furthermore, the outcome standard can assist in defining demographic and aetiological factors that contribute to the potential outcome of resurgery cases.

Identification of respiratory complexes I and III as mitochondrial sites of damage following exposure to ionizing radiation and nitric oxide

In 32D cl 3 hematopoietic progenitor cells, the overexpression of manganese superoxide dismutase (MnSOD, SOD2), the enzyme normally found in mitochondria, protects against the damaging effects of ionizing radiation. In the presence of a nitric oxide donor, which exacerbates the damage, inhibition of mitochondrial function can be demonstrated to be associated with respiratory complexes I (NADH dehydrogenase) and III (cytochrome c reductase), but not II (succinate dehydrogenase), IV (cytochrome c oxidase), or V (ATP synthase). The same pattern of inhibition is observed in the case of isolated bovine heart mitochondria exposed to ionizing radiation and the nitric oxide donor. The addition of authentic peroxynitrite (ONO2(-)) to isolated mitochondria also results in damage to complexes I and III (but not II, IV, and V), as shown by assays of electron-transfer activities and electron paramagnetic resonance (EPR) spectroscopic measurements, suggesting ONO2(-) to be responsible for most of the observed radiation damage in both the cultured cell lines and isolated mitochondria. It is argued that, in general, production of ONO2(-) is an important contributor to radiation damage in biological systems and the implications of these findings in relation to possible mechanisms of oxidant-linked apoptosis are briefly considered.

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Double-chambered right ventricle in an adult patient

A 65-year-old male was referred for to our facility for right and left heart catheterization and coronary angiography for evaluation of a ventricular septal defect and to rule out significant coronary artery disease. During the procedure, the patient was diagnosed with a double-chambered right ventricle (DCRV). Most DCRV cases are diagnosed at a young age; presentation in an adult is extremely rare.

Efficacy of a hepatitis C virus core antigen enzyme-linked immunosorbent assay for the identification of 'window-phase' blood donations

BACKGROUND AND OBJECTIVES

Recent studies have suggested that potentially infectious donations provided during the antibody-negative 'window' phase of hepatitis C virus (HCV) infection may be identified by testing for viral RNA or HCV core protein. We therefore evaluated the performance of an HCV antigen enzyme-linked immunosorbent assay (ELISA) for identification of window-phase donations and for prospective screening of blood donors.

MATERIALS AND METHODS

One-hundred and twenty-eight archived plasma donations containing HCV RNA, but lacking antibody to HCV (anti-HCV), were tested by using the HCV antigen ELISA, together with 9951 freshly collected serum and plasma specimens from blood donors.

RESULTS

HCV core antigen was detected in 94% (120/128) of window-phase plasma donations. Overall specificity in freshly collected blood donor specimens was 99.74%. Two putative window-phase donations containing HCV core protein and viral RNA were identified from paid plasma donors by prospective testing with the HCV antigen ELISA.

CONCLUSION

These results indicate that an HCV antigen ELISA can identify almost all (94%) of viraemic donations given during the seronegative window phase of infection. The performance of the HCV antigen ELISA appears to be suitable for large-scale screening of blood donations.