An absolute method for the determination of the persistence length of native DNA from electron micrographs.

Information on spatial correlation in the tangent direction along electron microscope images of filamentous molecule is shown to be obtainable by the analysis of statistical fluctuations in curvature, yielding an absolute measure of the persistence parameter a_micro. The relationship of a_micro, a local, microscopic parameter, to the persistence length introduced by Kratky and Porod is discussed. The hypotheses underlying the assumed theoretical model concern (1) the shape of the angle distribution, assumed to be Gaussian; (2) the passage from a three- to a two-dimensional situation, which is supposed to occur by deformation of the flexible chain in a manner that preserves the memory of the spatial correlation in orientation (except for the blocking of one degree of freedom); and (3) the adsorption conditions, which should meet the equilibrium requirement as closely as possible. The analytical method has been checked on computer simulated “Gaussian” molecules: the study of the simulated sample was essential in solving the problems connected with minimum statistics requirements and the effect of the reading error. Experimental images obtained for T2 DNA fragments at different ionic strengths by Kleinschmidt's adsorption technique have been analyzed by means of an automatic flying spot digitizer, the “Precision Encoder and Pattern Recognition.” The results show that adsorbed molecules do in fact “remember” the rigidity they possessed in solution and that the Gaussian hypothesis is well verified. Consequently, the slopes of log cosθ (l) or θ² (l) may be used indifferently in the estimate of a_micro. The dependence of this parameter on ionic strength in the range explored shows the expected behavior.     

Pretreatment Antibiotic Resistance in Helicobacter pylori Infection: Results of Three Randomized Controlled Studies

Background. Although combinations of antibiotics and antisecretory drugs are useful for treatment of Helicobacter pylori infection, treatment failure is common. The aim of this study was to evaluate the relation between pretreatment antibiotic resistance and outcome by using six different treatment regimens for H. pylori infection. Patients and Methods. Three hundred sixty-nine consecutive H. pylori–infected patients with dyspeptic symptoms were enrolled in three consecutive randomized, controlled, single-center clinical trials: trial A, 128 patients; trial B, 125 patients; trial C, 116 patients. Treatments consisted of (A) a 15-day course of dual therapy (omeprazole, 20 mg bid, and amoxicillin, 1 gm bid, or clarithromycin, 500 mg tid) (OA vs OC); (B) a 7-day triple therapy of omeprazole, 20 mg bid, plus metronidazole, 500 mg bid, and amoxicillin, 1,000 mg bid, or clarithromycin, 500 mg tid (OMA vs OMC); or (C) omeprazole, 20 mg bid, plus metronidazole, 500 mg bid, plus tetracycline, 500 mg qid, or doxycycline, 100 mg tid (OMT vs OMD). Diagnostic endoscopy was made in all patients before and 5 to 6 weeks after therapy. Six biopsies were taken from each patient for histology, rapid urease test, and H. pylori culture; antibiotic susceptibility testing was performed using the E-test method. Results. Overall cure rates were poor for both dual therapies OA and OC (38% and 37%, respectively) and for triple therapies OMA, OMC, and OMD (57%, 55%, and 58%, respectively). The OMT combination was successful in 91% (95% confidence interval [CI], 80.4%–97%). Metronidazole resistance was present in 29.7% (95% CI, 24%–35%), amoxicillin resistance was present in 26% (95% CI, 21%–32%), clarithromycin resistance was present in 23.1% (95% CI, 18%–29%), tetracycline resistance was present in 14% (95% CI, 10%–20%), and doxycycline resistance was present in 33.3% (95% CI, 21%–47%). Antibiotic resistance markedly reduced the cure rates and accounted for most of the poor results with the triple therapies: 89% versus 23%; 77% versus 26%; 100% versus 60%; and 67% versus 23% for OMC, OMA, OMT, and OMD, respectively. OMT appeared to be the best because of the high success rate with metronidazole-resistant H. pylori (71%) and in low-level tetracycline resistance. Conclusions. Pretreatment antibiotic-resistant H. pylori can, in part, explain the low cure rate of the infection and the variability in outcome in reported trials.     

Genetic characterization of clinical and agri-food isolates of multi drug resistant <Emphasis Type="Italic">Salmonella enterica</Emphasis> serovar Heidelberg from Canada

Background  

Salmonella enterica serovar Heidelberg ranks amongst the most prevalent causes of human salmonellosis in Canada and an increase in resistance to extended spectrum cephalosporins (ESC) has been observed by the Canadian Integrated Program for Antimicrobial Resistance Surveillance. This study examined the genetic relationship between S. Heidelberg isolates from livestock, abattoir, retail meat, and clinical human specimens to determine whether there was a link between the emergence of MDR S. Heidelberg in chicken agri-food sources and the simultaneous increase of MDR S. Heidelberg in human clinical samples.     

Stable isotopes track biogeochemical processes under seasonal ice cover in a shallow,productive lake

Biogeochemical dynamics under seasonal ice cover were investigated in the shallow (<10 m) water column of highly productive Georgetown Lake, western Montana, USA. This high altitude (1,800 m) reservoir is well-mixed in summer, but becomes strongly stratified under ice cover (mid-November–mid-May). A rapid drop in dissolved oxygen (DO) concentration and rise in dissolved inorganic carbon (DIC) concentration was observed after the onset of ice, with a corresponding increase in δ¹⁸O-DO and decrease in δ¹³C-DIC, likely caused by respiration (R) of organic carbon. Photosynthesis/respiration ratios (P/R) estimated from simultaneous measurement of DO and δ¹⁸O-DO were near unity prior to ice formation but then systematically decreased with time and depth in the lake under ice cover. P/R in the water column was higher at a shallower monitoring site compared to a deeper site near the dam outlet, which may have been important for over-winter survival of salmonids. By March, the bottom 3 m of the water column at both sites was anoxic, with the bottom 1 m being euxinic. Elevated concentrations of dissolved sulfide, ammonium, phosphate, Fe²⁺, and Mn²⁺ in deep water suggest coupling of organic carbon degradation with reduction of a number of electron acceptors (e.g., Fe³⁺, \({\text{NO}}_{3}^{ - } ,\;{\text{SO}}_{4}^{2 - }\) ). The concentrations and δ³⁴S values of H₂S in the deep water and \({\text{SO}}_{4}^{2 - }\) in the shallow water were similar, indicating near-complete reduction of sulfate in the euxinic zone. Late in the winter, an influx of isotopically heavy DIC was noted in the deep water coincident with a buildup of dissolved CH₄ to concentrations >1 mM. These trends are attributed to acetoclastic methanogenesis in the benthic sediments. This pool of dissolved CH₄ was likely released from the lake to the atmosphere during spring ice-off and lake turnover.     

Quantification of Bacterial Groups within Human Fecal Flora by Oligonucleotide Probe Hybridization

To investigate the population structure of the predominant phylogenetic groups within the human adult fecal microbiota, a new oligonucleotide probe designated S-G-Clept-1240-a-A-18 was designed, validated, and used with a set of five 16S rRNA-targeted oligonucleotide probes. Application of the six probes to fecal samples from 27 human adults showed additivity of 70% of the total 16S rRNA detected by the bacterial domain probe. The Bacteroides group-specific probe accounted for 37% ± 16% of the total rRNA, while the enteric group probe accounted for less than 1%. Clostridium leptum subgroup and Clostridium coccoides group-specific probes accounted for 16% ± 7% and 14% ± 6%, respectively, while Bifidobacterium and Lactobacillus groups made up less than 2%.