Evaluating Two Methods for Fingerprinting Genomes of Actinobacillus Actinomycetemcomitans

The arbitrary primer polymerase chain reaction (AP-PCR) and Southern blot restriction fragment length polymorphism (RFLP) were used to genotype the periodontal pathogen A. actinomycetemcomitans. Total genomic DNA from 73 strains was extracted by conventional methods. Three random-sequence 10-base oligonucleotide primers were chosen for AP-PCR. The amplified DNA products were separated electrophoretically in a 1% agarose gel containing ethidium bromide and the banding patterns were compared among different strains. For RFLP analysis, DNA was digested with EcoRI, separated on a 0.8% agarose gel and transferred to a nylon membrane. The membrane was probed with a previously characterized 5.2 kilobases (kb) DNA fragment cloned from A. actinomycetemcomitans strain Y4. The probe was labeled with digoxigenin, and hybridized fragments were detected with anti-digoxigenin antibody. AP-PCR produced 4–10 DNA bands in the 0.5–5 kb regions and distinguished 9, 13 or 17 genotypes, depending on the specific primer used. Southern blot RFLP analysis revealed 12 hybridization patterns consisting of 1 or 2 DNA fragments (2–23 kb). The addition of the Southern blot analysis to the AP-PCR analysis gave rise to a total of 30 DNA profiles among the 73 A. actinomycetemcomitans study strains. The results indicate that both AP-PCR and Southern blot analysis are useful in clonal analysis of A. actinomycetemcomitans

Comparison of Randomly Cloned and Whole Genomic DNA Probes for the Detection of Porphyromonas Gingivalis and Bacteroides Forsythus

Whole genomic and randomly-cloned DNA probes for two fastidious periodontal pathogens, Porphyromonas gingivalis and Bacteroides forsythus were labeled with digoxigenin and detected by a colorimetric method. The specificity and sensitivity of the whole genomic and cloned probes were compared. The cloned probes were highly specific compared to the whole genomic probes. A significant degree of cross-reactivity with Bacteroides species. Capnocytophaga sp. and Prevotella sp. was observed with the whole genomic probes. The cloned probes were less sensitive than the whole genomic probes and required at least 106 target cells or a minimum of 10 ng of target DNA to be detected during hybridization. Although a ten-fold increase in sensitivity was obtained with the whole genomic probes, cross-hybridization to closely related species limits their reliability in identifying target bacteria in subgingival plaque samples

Insertional Inactivation of Binding Determinants of Streptococcus Crista CC5A Using Tn916

Intermicrobial binding plays an important role in the ecology of the oral cavity because itrepresents one mechanism by which specific bacteria colonize dental plaque. The formation of“corncobs”, a morphologically distinct microbial unit composed of Streptococcus crista andFusobacterium nucleatum, is a highly specific binding interaction that depends on the presence ofpolar tufts of fimbriae on the streptococci. We have used a genetic approach to examine the role ofstreptococcal cell surface components involved in the binding of S. crista to F. nucleatum. Suchbinding may be an important component of corncob formation. A method for the genetictransformation of S. crista was used to transfer the broad host range transposon, Tn916, into thebacteria. Cells were grown to early log phase in brain heart infusion broth containing 10% fetalcalf serum. The competent cells were mixed with purified DNA from pDL916, a plasmidconstruct consisting of Tn916 and the streptococcal/Escherichia coli shuttle vector pDL278. Over300 transformants were screened for a reduction in binding to F. nucleatum. Five of thetransformants showed a change in binding ranging from 59% to 29% of the positive controlvalues. Southern blots revealed that the binding-deficient transformants contained the Tn916element integrated into one of 4 different sites in the chromosome. The transposon, integrated into4 different sites, appeared to be stable in the absence of selective pressure. Based on thesefindings, it appears that some strains of S. crista are naturally competent and that insertionalinactivation methods can be used to facilitate the study of binding receptors in this group of oralstreptococci

Direct estimation of the mutation rate at dinucleotide microsatellite loci in Arabidopsis thaliana (Brassicaceae)

This is the author's accepted manuscript, made available with the permission of the publisher.This research was supported by NIH grant GM073990 and NSF grant DEB-0543052 to J. K. Kelly, NSF grants DEB-9629457 and DEB-9981891 to R. G. Shaw, and NSF DEB-0108242 to M. Orive. M. E. Mort acknowledges DEB-0344883

Clinical deterioration during antituberculosis treatment in Africa: Incidence, causes and risk factors

BACKGROUND:HIV-1 and Mycobacterium tuberculosis cause substantial morbidity and mortality. Despite the availability of antiretroviral and antituberculosis treatment in Africa, clinical deterioration during antituberculosis treatment remains a frequent reason for hospital admission. We therefore determined the incidence, causes and risk factors for clinical deterioration. METHODS: Prospective cohort study of 292 adults who initiated antituberculosis treatment during a 3-month period. We evaluated those with clinical deterioration over the following 24 weeks of treatment. RESULTS: Seventy-one percent (209/292) of patients were HIV-1 infected (median CD4+: 129 cells/muL [IQR:62-277]). At tuberculosis diagnosis, 23% (34/145) of HIV-1 infected patients qualifying for antiretroviral treatment (ART) were receiving ART; 6 months later, 75% (109/145) had received ART. Within 24 weeks of initiating antituberculosis treatment, 40% (117/292) of patients experienced clinical deterioration due to co-morbid illness (n = 70), tuberculosis related illness (n = 47), non AIDS-defining HIV-1 related infection (n = 25) and AIDS-defining illness (n = 21). Using HIV-1 uninfected patients as the referent group, HIV-1 infected patients had an increasing risk of clinical deterioration as CD4+ counts decreased [CD4+>350 cells/muL: RR = 1.4, 95% CI = 0.7-2.9; CD4+:200-350 cells/muL: RR = 2.0, 95% CI = 1.1-3.6; CD4+<200 cells/muL: RR = 3.0, 95% CI = 1.9-4.7]. During follow-up, 26% (30/117) of patients with clinical deterioration required hospital admission and 15% (17/117) died. Fifteen deaths were in HIV-1 infected patients with a CD4+<200 cells/muL. CONCLUSIONS: In multivariate analysis, HIV-1 infection and a low CD4+ count at tuberculosis diagnosis were significant risk factors for clinical deterioration and death. The initiation of ART at a CD4+ count of <350 cells/muL will likely reduce the high burden of clinical deterioration

Plasma Dynamics

Contains table of contents for Section 2 and reports on four research projects.Lawrence Livermore National Laboratory (Subcontract 6264005)National Science Foundation (Grant ECS 84-13173)National Science Foundation (Grant ECS 85-14517)U.S. Air Force - Office of Scientifc Research (Contract AFOSR 84-0026)U.S. Army - Harry Diamond Laboratories (Contract DAAL02-86-C-0050)U.S. Navy - Office of Naval Research (Contract N00014-87-K-2001)U.S. Department of Energy (Contract DE-AC02-78-ET-51013)National Science Foundation (Grant ECS 85-1 5032

Plasma Dynamics

Contains table of contents for Section 2 and reports on four research projects.Lawrence Livermore National Laboratory Subcontract 6264005National Science Foundation Grant ECS 84-13173National Science Foundation Grant ECS 85-14517U.S. Air Force - Office of Scientific Research Contract AFOSR 89-0082-AU.S. Army - Harry Diamond Laboratories Contract DAAL02-86-C-0050U.S. Navy - Office of Naval Research Contract N00014-87-K-2001Lawrence Livermore National Laboratory Subcontract B108472National Science Foundation Grant ECS 88-22475U.S. Department of Energy Contract DE-FG02-91-ER-54109National Aeronautics and Space Administration Grant NAGW-2048U.S. Department of Energy Contract DE-AC02-ET-51013U.S. Department of Energy Contract DE-AC02-78-ET-5101

Plasma Dynamics

Contains table of contents for Section 2 and reports on four research projects.Lawrence Livermore National Laboratory Subcontract 6264005National Science Foundation Grant ECS 84-13173National Science Foundation Grant ECS 85-14517U.S. Air Force - Office of Scientific Research Contract AFOSR 84-0026U.S. Army - Harry Diamond Laboratories Contract DAAL02-86-C-0050U.S. Navy - Office of Naval Research Contract N00014-87-K-2001National Science Foundation Grant ECS 85-15032National Science Foundation Grant ECS 88-22475U.S. Department of Energy Contract DE-AC02-ET-5101

Identification of the Pangenome and Its Components in 14 Distinct Aggregatibacter actinomycetemcomitans Strains by Comparative Genomic Analysis

Aggregatibacter actinomycetemcomitans is genetically heterogeneous and comprises distinct clonal lineages that may have different virulence potentials. However, limited information of the strain-to-strain genomic variations is available.The genome sequences of 11 A. actinomycetemcomitans strains (serotypes a-f) were generated de novo, annotated and combined with three previously sequenced genomes (serotypes a-c) for comparative genomic analysis. Two major groups were identified; serotypes a, d, e, and f, and serotypes b and c. A serotype e strain was found to be distinct from both groups. The size of the pangenome was 3,301 genes, which included 2,034 core genes and 1,267 flexible genes. The number of core genes is estimated to stabilize at 2,060, while the size of the pangenome is estimated to increase by 16 genes with every additional strain sequenced in the future. Within each strain 16.7-29.4% of the genome belonged to the flexible gene pool. Between any two strains 0.4-19.5% of the genomes were different. The genomic differences were occasionally greater for strains of the same serotypes than strains of different serotypes. Furthermore, 171 genomic islands were identified. Cumulatively, 777 strain-specific genes were found on these islands and represented 61% of the flexible gene pool.Substantial genomic differences were detected among A. actinomycetemcomitans strains. Genomic islands account for more than half of the flexible genes. The phenotype and virulence of A. actinomycetemcomitans may not be defined by any single strain. Moreover, the genomic variation within each clonal lineage of A. actinomycetemcomitans (as defined by serotype grouping) may be greater than between clonal lineages. The large genomic data set in this study will be useful to further examine the molecular basis of variable virulence among A. actinomycetemcomitans strains