Identification of signature and primers specific to genus <Emphasis Type="Italic">Pseudomonas</Emphasis> using mismatched patterns of 16S rDNA sequences

Background

Pseudomonas, a soil bacterium, has been observed as a dominant genus that survives in different habitats with wide hostile conditions. We had a basic assumption that the species level variation in 16S rDNA sequences of a bacterial genus is mainly due to substitutions rather than insertion or deletion of bases. Keeping this in view, the aim was to identify a region of 16S rDNA sequence and within that focus on substitution prone stretches indicating species level variation and to derive patterns from these stretches that are specific to the genus.

Results

Repeating elements that are highly conserved across different species of Pseudomonas were considered as guiding markers to locate a region within the 16S gene. Four repeating patterns showing more than 80% consistency across fifty different species of Pseudomonas were identified. The sub-sequences between the repeating patterns yielded a continuous region of 495 bases. The sub-sequences after alignment and using Shanon's entropy measure yielded a consensus pattern. A stretch of 24 base positions in this region, showing maximum variations across the sampled sequences was focused for possible genus specific patterns. Nine patterns in this stretch showed nearly 70% specificity to the target genus. These patterns were further used to obtain a signature that is highly specific to Pseudomonas. The signature region was used to design PCR primers, which yielded a PCR product of 150 bp whose specificity was validated through a sample experiment.

Conclusions

The developed approach was successfully applied to genus Pseudomonas. It could be tried in other bacterial genera to obtain respective signature patterns and thereby PCR primers, for their rapid tracking in the environmental samples.

     

Secretion of intracellular IL-1 receptor antagonist (type 1) is dependent on P2X7 receptor activation

Inflammatory mechanisms are critical in the arterial response to injury. Both IL-1 and the naturally occurring inhibitor of IL-1, IL-1R antagonist (IL-1ra), are expressed in the arterial wall, and in particular in the endothelium. Previous studies suggest that endothelial cells only make the intracellular type I isoform of IL-1ra (icIL-1ra1), an isoform known to lack a secretory signal peptide. It is unclear how icIL-1ra is released from the endothelial cell to act as an antagonist on cell surface IL-1 type I receptors. IL-1beta, which also lacks a secretory signal peptide, may be released by ATP stimulation of the P2X(7)R. Therefore, we examined whether icIL-1ra1 release occurs in an analogous manner, using both the mouse macrophage cell line RAW264.7 and HUVECs. P2X(7)R activation caused icIL-1ra1 release from LPS-primed RAW264.7 macrophages and from HUVECs. This release was inhibited in the absence of extracellular calcium, and attenuated by preincubation with oxidized ATP, KN62, and apyrase. Endogenous ATP release, which also facilitated release of icIL-1ra1, was detected during LPS treatment of both RAW264.7 macrophages and HUVECs. Annexin V assays showed that ATP stimulation resulted in a rapid phosphatidylserine (PS) exposure on the cell surface of RAW264.7 macrophages, and that PS-exposed microvesicles contained icIL-1ra1. However, PS flip and microvesicle shedding was not apparent in ATP-treated HUVECs. These data support a general role for the P2X(7)R in the release of leaderless cytokines into the extracellular medium, and indicate how icIL-1ra1 may act upon its extracellular target, the IL-1R.     

Risk factors for bacterial catheter colonization in regional anaesthesia

BACKGROUND: Although several potential risk factors have been discussed, risk factors associated with bacterial colonization or even infection of catheters used for regional anaesthesia are not very well investigated. METHODS: In this prospective observational trial, 198 catheters at several anatomical sites where placed using a standardized technique. The site of insertion was then monitored daily for signs of infection (secretion at the insertion site, redness, swelling, or local pain). The catheters were removed when clinically indicated (no or moderate postoperative pain) or when signs of potential infection occurred. After sterile removal they were prospectively analyzed for colonization, defined as > 15 colony forming units. RESULTS: 33 (16.7%) of all catheters were colonized, and 18 (9.1%) of these with additional signs of local inflammation. Two of these patients required antibiotic treatment due to superficial infections. Stepwise logistic regression analysis was used to identify factors associated with catheter colonization. Out of 26 potential factors, three came out as statistically significant. Catheter placement in the groin (odds-ratio and 95%-confidence interval: 3.4; 1.5-7.8), and repeated changing of the catheter dressing (odds-ratio: 2.1; 1.4-3.3 per removal) increased the risk for colonization, whereas systemic antibiotics administered postoperatively decreased it (odds ratio: 0.41; 0.12-1.0). CONCLUSION: Colonization of peripheral and epidural nerve catheter can only in part be predicted at the time of catheter insertion since two out of three relevant variables that significantly influence the risk can only be recorded postoperatively. Catheter localisation in the groin, removal of the dressing and omission of postoperative antibiotics were associated with, but were not necessarily causal for bacterial colonization. These factors might help to identify patients who are at increased risk for catheter colonization.     

A synthetic A tail rescues yeast nuclear accumulation of a ribozyme-terminated transcript

To investigate the role of 3' end formation in yeast mRNA export, we replaced the mRNA cleavage and polyadenylation signal with a self-cleaving hammerhead ribozyme element. The resulting RNA is unadenylated and accumulates near its site of synthesis. Nonetheless, a significant fraction of this RNA reaches the cytoplasm. Nuclear accumulation was relieved by insertion of a stretch of DNA-encoded adenosine residues immediately upstream of the ribozyme element (a synthetic A tail). This indicates that a 3' stretch of adenosines can promote export, independently of cleavage and polyadenylation. We further show that a synthetic A tail-containing RNA is unaffected in 3' end formation mutant strains, in which a normally cleaved and polyadenylated RNA accumulates within nuclei. Our results support a model in which a polyA tail contributes to efficient mRNA progression away from the gene, most likely through the action of the yeast polyA-tail binding protein Pab1p.     

Factors influencing preoperative stress response in coronary artery bypass graft patients

BACKGROUND: In many studies investigating measures to attenuate the hemodynamic and humoral stress response during induction of anaesthesia, primary attention was paid to the period of endotracheal intubation since it has been shown that even short-lasting sympathetic cardiovascular stimulation may have detrimental effects on patients with coronary artery disease. The aim of this analysis was, however, to identify the influencing factors on high catecholamine levels before induction of anaesthesia. METHODS: Various potential risk factors that could impact the humoral stress response before induction of anaesthesia were recorded in 84 males undergoing coronary aortic bypass surgery, and were entered into a stepwise linear regression analysis. The plasma level of norepinephrine measured immediately after radial artery canulation was chosen as a surrogate marker for the humoral stress response, and it was used as the dependent variable in the regression model. Accordingly, the mean arterial blood pressure, heart rate and the calculated pressure-rate product were taken as parameters of the hemodynamic situation. RESULTS: Stepwise regression analysis revealed that the oral administration of low-dose clonidine (mean dose 1.75 μg.kg-1) on the morning of surgery was the only significant predictor (p = 0.004) of the high variation in preoperative norepinephrine plasma levels. This intervention decreased norepinephrine levels by more than 40% compared to no clonidine administration, from 1.26 to 0.75 nmol.l-1. There was no evidence for dose-responsiveness of clonidine. All other potential predictors were removed from the model as insignificant (p > 0.05). The use of beta-blocker, ace-inhibitors, ejection fraction, and body mass index were significant determinants for the hemodynamic situation (heart rate, mean arterial pressure, pressure rate product) of the patient during the pre-induction period. CONCLUSION: The oral administration of clonidine is the only significant predictor for the observed variation of norepinephrine levels during the preoperative period. Lack of significant dose responsiveness suggests that even a low dose of the drug can attenuate the preoperative stress response and thus is recommended in cardiovascular high risk patients.     

Coronary pressure and FFR predict long-term outcome after PTCA

Although coronary stents have been the most important improvement in percutaneous coronary interventions in the last 10 years, it is well known to interventionalists that many patients after percutaneous transluminal coronary angioplasty (PTCA) have a favourable outcome without stenting. Coronary angiography, however, is not sensitive enough to identify those particular patients and it has been suggested that a combination of angiographic and functional criteria would be more suitable to distinguish patients with a low restenosis chance after plain balloon angioplasty. In the present study, the authors investigated the value of coronary pressure measurement for conditional stenting in 85 patients. It was demonstrated that in patients in whom a high fractional flow reserve (FFR) was present (> 0.90), the incidence of coronary events at two-year follow-up was almost three times lower than in those patients with an FFR below 0.90. Such high FFRs could be obtained in approximately 45% of all patients. In an additional group of patients, it was demonstrated by intravascular ultrasound (IVUS) studies that the mechanism of a high FFR after plain balloon angioplasty is most likely the result of a larger lumen compared with patients with a suboptimal FFR. This means that, in patients in whom both the angiographic and the functional result after PTCA is optimal, a restenosis rate is achieved similar to that achieved by stenting. Obviously, in such patients, additional stenting and a number of problems in the long-term possibly related to stenting can be avoided. Therefore, coronary angiography and coronary pressure measurement have a complementary value in the evaluation of PTCA results and such information can be easily obtained by using a pressure wire instead of a regular guidewire.     

Interaction of monoclonal antibodies with MHC class I antigens on mouse spleen cells. II. Levels of expression of H-2K, H-2D, and H-2L in different mouse strains

The numbers of MHC class I molecules expressed by spleen cells from various mouse strains were determined by using MHC-specific monoclonal antibodies and a radioactive binding assay. Although small differences were found to exist in some cases, our general conclusion is that different mice of the same strain, congenic mice of different haplotypes, and syngeneic mice of varying background all express similar numbers of class I antigens. B10.A mice (8 to 10 wk old), for example, express 5.3 X 10(4) Kk molecules/cell, 5.4 X 10(4) Dd molecules/cell, and 2.2 X 10(4) Ld molecules/cell. Some of the differences observed in class I antigen expression included: 1) the level of Kk expression increased to a small but significant extent with age in B10.A mice; 2) female B10.A mice expressed slightly higher amounts of Kk than male mice; and 3) B10.A(2R) and B10.A(4R) recombinant strains expressed elevated levels of K-end antigens and slightly decreased levels of D-end antigens when compared with the unrecombinant B10.A strain. In several strains, F1 mice express approximately 50% as many copies of each parental antigen as do the homozygous parents. B10 mice, which are negative for the L antigen, nevertheless express the same total number of D-end molecules as do B10.A mice. The data suggest that the levels of expression of MHC class I molecules are controlled by at least two factors: gene dosage and another factor(s) that gives rise to the small variations in class I antigen expression seen with age, sex, and strain, and to the low expression of Ld relative to Dd and Kk.