Target choice and orientation preference of the insertion sequence IS903

We have examined the targeting preference of the bacterial insertion element IS903 by determining the sites of insertion of a large number of transposition events into the 55-kb conjugative plasmid pOX38. Despite the large target size, all the insertions were clustered in four small distinct regions associated with conjugal DNA transfer. Within these regions, many different sites were used for insertion; however, there were a few sites that IS903 inserted into more than once. Alignment of the insertion sites showed that there was no consensus sequence within the 9-bp target duplication but that there were preferred sequences located symmetrically on either side of the target. This is consistent with target recognition by a dimer or multimer of transposase, with either sequence-specific or structure-specific interactions on both sides of the target. We show further that when one of these preferred regions was cloned into a second conjugative plasmid, pUB307, it was still a preferred target, implying that all the sequences necessary for target selection are contained within this DNA segment. Also, we observed a very strong preference for insertion in a single orientation in pUB307. We examined the possibility that either DNA replication from the origin of vegetative replication, oriV, or the origin of transfer, oriT, might determine this orientation effect. We find that reversing the direction of vegetative replication had no effect on the orientation of transposon insertions; however, reversing the direction of DNA transfer abolished the orientation effect. This supports the idea that conjugal DNA transfer imparts a polarity on the target that is sensed by the transposon.     

Characterization of IS1515, a functional insertion sequence in Streptococcus pneumoniae

Several BRCA2 mutations are found to occur in geographically diverse breast and ovarian cancer families. To investigate both mutation origin and mutation-specific phenotypes due to BRCA2, we constructed a haplotype of 10 polymorphic short tandem-repeat (STR) markers flanking the BRCA2 locus, in a set of 111 breast or breast/ovarian cancer families selected for having one of nine recurrent BRCA2 mutations. Six of the individual mutations are estimated to have arisen 400-2,000 years ago. In particular, the 6174delT mutation, found in approximately 1% of individuals of Ashkenazi Jewish ancestry, was estimated to have arisen 29 generations ago (1-LOD support interval 22-38). This is substantially more recent than the estimated age of the BRCA1 185delAG mutation (46 generations), derived from our analogous study of BRCA1 mutations. In general, there was no evidence of multiple origins of identical BRCA2 mutations. Our study data were consistent with the previous report of a higher incidence of ovarian cancer in families with mutations in a 3.3-kb region of exon 11 (the ovarian cancer cluster region [OCCR]) (P=.10); but that higher incidence was not statistically significant. There was significant evidence that age at diagnosis of breast cancer varied by mutation (P<.001), although only 8% of the variance in age at diagnosis could be explained by the specific mutation, and there was no evidence of family-specific effects. When the age at diagnosis of the breast cancer cases was examined by OCCR, cases associated with mutations in the OCCR had a significantly older mean age at diagnosis than was seen in those outside this region (48 years vs. 42 years; P=.0005).     

Novel sequence organization and insertion specificity of IS605 and IS606: chimaeric transposable elements of Helicobacter pylori

We have used PKH26 dye, which is incorporated stably into the membrane of cells, to determine, using flow cytometry, lymphocyte proliferative responses to the antigen tetanus toxoid in fresh and cryopreserved samples. Measuring cell proliferation with this dye has advantages over either 3H-thymidine or Bromodeoxyuridine (BrdU). Whereas the existing methods measure proliferation at a single time point, PKH26 gives a cumulative measure of cell proliferation. As PKH26 is incorporated into the cell membrane, cells do not have to be permeabilised to allow dye incorporation into a cytoplasmic compartment. Most importantly, PKH26 can be used in combination with monoclonal antibodies to surface markers on mixed populations of cells, to determine the proliferation of individual subpopulations, without the need for prior cell fractionation. We also show that PKH26 can be used with similar efficacy in both fresh and cryopreserved samples. In addition since PKH26 is a cumulative measure of proliferative responses we were able to show that restimulation of the dividing population in vitro with fresh antigen presenting cells (APC) and antigen permits characterisation of a further proliferating cell population. The use of PKH26 dye in combination with cell phenotyping and measurement of cytokine production at the single cell level will prove a powerful tool for multiparameter analyses of cellular responses to antigen.     

Genetic localization of the type I trimethoprim resistance gene and its dissemination in urinary tract isolates in Taiwan

In a total of 425 urinary isolates of E. coli, Enterobacter spp., and Klebsiella spp. selected, there were 169 (45.4%) isolates harbouring type I dihydrofolate reductase (DHFR) gene among 374 trimethoprim-resistant isolates. In these 169 isolates, only 17.2% hybridized with the Tn7 probe. According to another probe specific for the integrase gene of integron, 87.6% showed a positive reaction. Further analysis by restriction mapping proved that the type I DHFR gene was inserted into a integron-like structure. These results indicate that the type I DHFR gene that was initially observed in association with transposable element Tn7 is becoming associated with an integrase function similar to integrons in most instances. Further analysis of the distribution of Tn21-like integrase gene in clinical isolates indicated that the prevalence rates were 86.4%, 84.8%, and 76.7% respectively in E. coli, Enterobacter spp., and Klebsiella spp.. Furthermore, the integrase gene found in our clinical isolates proved to be mediated by a plasmid, demonstrated by Southern hybridization. Thus, the trimethoprim-resistant gene that developed under selective pressure from the double drug trimethoprim and sulphonamide was transmitted by insertion into integron-like structure and then mediated by plasmid transfer for dissemination.     

Stability of insertion sequence IS1245, a marker for differentiation of Mycobacterium avium strains

Recently a novel insertion element, IS1245, has been described and suggested for use as a probe in restriction fragment length polymorphism studies of Mycobacterium avium strains. An important issue in this context is the stability of the insertion element. We analyzed single colonies of M. avium cultures and found frequent small one- to two-band changes. However, following repeated in vitro passages over 1 year, similar one- to two-band changes were observed in the IS1245 patterns of only six M. avium strains investigated.     

Identification and characterisation of IS1383, a new insertion sequence isolated from Pseudomonas putida strain H

This is the first report of postcolumn amperometric reaction detection for capillary electrophoresis and dual-electrode detection. Bromide present in the run buffer is oxidized to bromine at the first electrode and subsequently detected at a second electrode downstream. Analytes that react with bromine cause a decrease in signal at the downstream electrode that is proportional to analyte concentration. Bromine is known to react with a variety of compounds, including thiols, thioethers, disulfides, amines, and unsaturated organic compounds. In this paper, the development of a new wire--wire on-capillary dual electrode that is well suited to bromine-based post-column reaction detection is described. System performance was evaluated using glutathione, cysteine, and methionine as test analytes. The final optimized system could be operated continuously for 24 h and was stable for day-to-day use for at least two weeks. The response for cysteine was linear from 0.5 to 20 microM with a limit of detection of approximately 80 nM.     

Distribution of insertion sequence IS200 among different clonal lines of the related Salmonella serotypes Livingstone and Eimsbuettel

The copy number and genetic location of IS200 have provided evidence of strain relatedness in many serotypes of Salmonella. In this study, 100 isolates of the related serotypes Livingstone (6,7:d:l,w) and Eimsbuettel (6,7,14:d:l,w), representing 10 ribotype/biotype (RT/BT) groups isolated from human and non-human sources in seven countries over a 26-year period, were examined for their IS200 profiles. The distribution of IS200 in strains of these serotypes was limited, being present in all 53 isolates of ribotype 1 (RT1) and its variant type RT6, in one of five isolates of RT5 but in none of 42 isolates of RTs 2, 3 or 4. Although the seven IS200 profiles identified in RT1 isolates were of little value for further discrimination within different biotype groups, they were extremely valuable for confirming serotype: isolates of RT1/BT8/IS200 profile A (or its variants) and those of RT1/BT3/IS200 profile B (or its variants) were almost invariably associated with serotypes Livingstone and Eimsbuettel, respectively.     

Immunological detection of sheep experimentally infected with strains of Mycobacterium avium subspecies containing insertion sequence IS901/IS902 and a 40 kDa protein

A monoclonal antibody raised against a 40 kDa protein present in certain M. avium strains (IS901/IS902 positive) was used for developing a blocking ELISA. Sera from experimentally infected sheep were evaluated by indirect ELISA, AGID and blocking ELISA. The blocking assay proved to be highly specific for differentiation of sheep infected with different subspecies of M. avium.     

High-frequency transposition of IS1373, the insertion sequence delimiting the amplifiable element AUD2 of Streptomyces lividans

IS1373 is the putative insertion sequence delimiting the amplifiable unit AUD2 of Streptomyces lividans. Two IS1373-derived thiostrepton-resistant transposons, Tn5492 and Tn5494, transposed into multiple sites of the S. lividans chromosome at frequencies as high as 0.4 and 1%, respectively. Hence, IS1373 is a functional insertion sequence and its unique open reading frame, insA, encodes the transposase.     

Current role of coagulase-negative staphylococci in urology

Coagulase-negative Staphylococci (CNS), considered for many years to be commensal bacteria of the skin are now recognized as major agents of nosocomial infection. Bacterial factors (increased resistance), host factors (immune status) and multiplication of the portals of entry (presence of foreign material) have contributed to the increased incidence of nosocomial infections. The importance of the role of NCS in urology is due to their great capacity to colonize catheters and most prostheses. The particular organization of these bacteria into a conglomerate called biofilm is responsible for prosthetic infections, which can impair renal function and can sometimes be life-threatening. The authors review the current increase of the number of CNS isolated in urology departments and describe the various therapeutic strategies that can be proposed to eradicate these bacteria.     

Review of health consequences from high-, intermediate- and low-level exposure to organophosphorus nerve agents

Short and long-term health effects from exposure to organophosphorus (OP) military and insecticidal nerve agents are evaluated based on the abundant scientific literature published over five decades on health effects in humans (from human experimentation and occupational exposures) and in laboratory animals. Four distinct health effects are identified: acute cholinergic toxicity; organophosphate-induced delayed neuropathy (OPIDN); subtle long-term neuropsychological and neurophysiological effects; and a reversible muscular weakness called 'intermediate syndrome'. Some effects are subtle and difficult to differentiate from health effects caused by other diseases or occupational exposures. Each effect has data suggesting threshold exposure levels below which it is unlikely to be clinically detectable. Therefore, meaningful interpretation of human and animal studies requires rigid exposure characterization. Because precise exposure levels are often difficult to reconstruct, a system for characterizing exposure is proposed based upon observed initial acute signs and symptoms, as high-level (definitive cholinergic poisoning); intermediate-level (threshold cholinergic effects including miosis, rhinorrhea or clinically measurable depression of cholinesterase); and low-level (no immediate clinical signs or symptoms) exposure. Threshold exposure levels for known long-term effects from OP nerve agent are at or above intermediate-level exposure. Long-term health effects seen at intermediate-level exposures or in many survivors of high-level exposure are subtle, detectable in exposed populations but not individuals, and not reported in individuals experiencing low-level exposure alone. Co-exposure to other pharmaceutical agents may promote or protect against health effects from OP nerve agents, but qualitatively they are the same effects seen with OP nerve agents alone. Thus, the system for characterizing exposure based on initial acute effects is also useful for evaluating health outcomes from co-exposure to OP nerve and other agents.     

Identification and characterization of IS1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in Pseudomonas putida

A new insertion sequence (IS element), IS1411, was identified downstream of the phenol degradation genes pheBA that originated from plasmid DNA of Pseudomonas sp. strain EST1001. According to sequence analysis, IS1411 belongs to a new family of IS elements that has recently been named the ISL3 family (J. Mahillon and M. Chandler, Microbiol. Mol. Biol. Rev. 62:725-774, 1998). IS1411 generates 8-bp duplication of the target DNA and carries 24-bp inverted repeats (IRs), highly homologous to the IRs of other IS elements belonging to this family. IS1411 was discovered as a result of insertional activation of promoterless pheBA genes in Pseudomonas putida due to the presence of outward-directed promoters at the left end of IS1411. Both promoters located on the IS element have sequences that are similar to the consensus sequence of Escherichia coli sigma70. IS1411 can produce IS circles, and the circle formation is enhanced when two copies of the element are present in the same plasmid.     

Surveillance for the emergence and dissemination of antimicrobial resistance in bacteria

Effective surveillance of antimicrobial-resistant bacteria is important for developing rational empiric therapy guidelines and for guiding public health efforts to control and prevent the spread of infective agents. Surveillance must include a timely and thorough review of the test results generated in clinical microbiology laboratories because this data serves as the core of surveillance activities. Besides ensuring data accuracy and optimizing detection of emerging resistance, the role of clinical microbiology also includes supporting the production of informative surveillance reports, providing laboratory resources for outbreak investigations, and monitoring the performance of commonly used susceptibility testing methods. Once the accuracy of susceptibility results has been validated, the data are used by public health agencies and professional societies to monitor resistance trends on a local, state, national, and international level. This information is also used to develop policies for prudent antimicrobial use locally and nationally.     

Differences in the prevalence of IS6110 insertion sites in Mycobacterium tuberculosis strains: low and high copy number of IS6110

The elaboration of new operative procedures established in the last decade has led to an improved prognosis in patients with renal cell carcinoma with vena caval extension. We report on our personal operative experience in over 100 patients and present the current analysis of 76 patients with renal carcinoma with vena caval extension seen in our institution between 1985 and 1996. Sixty-six patients underwent nephrectomy and removal of vena caval tumor thrombi. Actuarial 5-year survival for patients without metastasis was 38%. For patients with tumor stages between I and III, 5-year survival was between 40 and 50% and was not significantly related to the rostral extent of the tumor thrombus. The relatively poor outcome for patients with tumor thrombi invading the right atrium was caused by a high perioperative mortality (50%). For patients with distant metastases, medium survival time was 10.5 months, implying that radical surgery is useless in cases of distant metastases.     

IS481 and IS1002 of Bordetella pertussis create a 6-base-pair duplication upon insertion at a consensus target site

The insertion sequence IS481 and its isoform IS1002 have been observed to transpose into the bvgAS locus of Bordetella pertussis, for which the DNA sequence has previously been determined. Upon insertion of IS481 at three different sites and IS1002 at one site, a 6-bp sequence originally present was found at the junction of bvg and insertion sequence DNA. This indicates that, contrary to prior reports, IS481 and IS1002 do create a duplication upon insertion. In this light, examination of these and other examples of IS481 and IS1002 reported in the literature leads to the observation that the 6-bp recognition sequence usually fits the consensus NCTAGN. The near-palindromic nature of this sequence, when directly repeated at the ends of IS481 or IS1002, apparently led to the interpretation that 5 of these base pairs were part of the terminal inverted repeats flanking these elements.     

Plasmid profile and antibiotic resistance in coagulase-negative staphylococci isolated from polluted water

(1) Submitochondrial particles prepared from beef liver mitochondria were immobilized on Fractosil, a porous form of silica, in order to stabilize their enzymatic activity. (2) The catalytic activity of succinate-cytochrome c reductase, an enzyme complex of the inner mitochondrial membrane, was followed in this study. Adsorption resulted in significant stabilization with a lowering of K(m) (app.) for succinate, in spite of mass transfer and diffusion limitations expected to occur in such a complex and heterogeneous system. An increase in catalytic potential was also observed upon immobilization. These observations, taken together, suggest that substantial degree of conversation of substrates to their respective products may be achieved by such immobilized preparations. (3) Positive cooperative interactions for binding of submitochondrial particles to the matrix was observed, apparently with two sets of sites, the second set indicating a much greater hill coefficient. (4) The present report indicates that adsorption with the use of a porous inorganic support such as Fractosil may provide a simple and efficient method of immobilization. Such preparations containing membrane enzymes in their native microenvironments would be useful for continuous catalytic transformations and also for construction of biosensors.     

A race-specific insertion of transposable element IS801 in Pseudomonas syringae pv. phaseolicola

To detect free zinc ions in the rat testes four rats were transcardially perfused with Na2S, and the seminiferous tubules from two other rats were incubated in Na2S. Sections from the two sources were autometallographically (AMG) developed, whereby zinc sulphide crystal lattices created in the tissue by the sulphide treatment were silver enhanced. Light microscopical analysis showed zinc ions in primary spermatogonia until the zygotene primary spermatocytes (stage I), in late pachytene spermatocytes (stages XII and XIII), and in late spermatids from step 15 to step 19 (stages I-VIII). The highest intensity of AMG grains was detected in the residual bodies and tails of step 19 spermatids. Grains were occasionally found in the cytoplasm of Leydig cells. Sections from animals treated with the chelator diethyldithiocarbamate prior to sulphide treatment showed a complete lack of AMG staining. At ultrastructural levels the AMG grains were found in smooth-surfaced endoplasmic reticulum of all spermatogonial stages, and in the acrosome, midpiece, and tail of late spermatids. The presence of zinc ions in preleptotene spermatocytes and cytoplasmic lobes of late spermatids suggests a specific role of free zinc at the onset of meiosis and at spermiation.     

Examination of methicillin-resistant and methicillin-susceptible Staphylococcus aureus mutants with low-level fluoroquinolone resistance

For Staphylococcus aureus, stepwise mutations result in high-level quinolone resistance. Methicillin-resistant and -susceptible quinolone-resistant, first-step mutants generated in vitro were obtained and found to be no different than those recovered from murine abscesses. Approximately 10% of all first-step mutants were resistant to ethidium bromide, and selected strains had mutations that mapped to flqB. NorA-mediated resistance among first-step mutants may be more prevalent than previously reported.     

The transcriptional activator HlyU of Vibrio cholerae: nucleotide sequence and role in virulence gene expression

HlyU upregulates expression of the haemolysin, HlyA, of Vibrio cholerae. DNA sequence analysis indicates that HlyU is an 11.9 kDa protein containing a putative helix-turn-helix motif and belonging to a family of small regulatory proteins, including NoIR (Rhizobium meliloti), SmtB (Synechococcus PCC 7942) and ArsR (plasmids R773, Escherichia coli; pI258, Staphylococcus aureus; and pSX267, Staphylococcus xylosus). An hlyU mutant was constructed by insertional inactivation, and found to be deficient in the production of both the haemolysin and a 28 kDa secreted protein. The mutant was assessed for virulence in the infant mouse cholera model, revealing a 100-fold increase in the LD50. This suggests that HlyU promotes expression of virulence determinant(s) in vivo.