Precisely and Accurately Inferring Single-Molecule Rate Constants

The kinetics of biomolecular systems can be quantified by calculating the stochastic rate constants that govern the biomolecular state vs time trajectories (i.e., state trajectories) of individual biomolecules. To do so, the experimental signal vs time trajectories (i.e., signal trajectories) obtained from observing individual biomolecules are often idealized to generate state trajectories by methods such as thresholding or hidden Markov modeling. Here, we discuss approaches for idealizing signal trajectories and calculating stochastic rate constants from the resulting state trajectories. Importantly, we provide an analysis of how the finite length of signal trajectories restricts the precision of these approaches and demonstrate how Bayesian inference-based versions of these approaches allow rigorous determination of this precision. Similarly, we provide an analysis of how the finite lengths and limited time resolutions of signal trajectories restrict the accuracy of these approaches, and describe methods that, by accounting for the effects of the finite length and limited time resolution of signal trajectories, substantially improve this accuracy. Collectively, therefore, the methods we consider here enable a rigorous assessment of the precision, and a significant enhancement of the accuracy, with which stochastic rate constants can be calculated from single-molecule signal trajectories.

Tadalafil for Endometrial Growth in Clomiphene Citrate stimulated cycles in an IUI programma: A pilot study

AIM OF THE STUDY

The objective of this study was to assess the impact of tadalafil on endometrial growth, the uterine artery pulsatility index (PI) and the uterine artery resistance index (RI) in patients under clomiphene ovarian stimulation for intrauterine insemination (IUI).

METHODS

This randomized crossover study included 30 patients with a normal endometrium over 53 cycles, and 46 of those cycles in 23 patients were included in the analysis. In group A the patients were under 100 mg clomiphene daily for five days (2-6) and 5 mg tadalafil daily for 7 days (4-10). For Group B (control) the patients only received clomiphene. Measurements of the endometrium, PI, RI and estradiol determinations were taken on cycle days 4, 8 and 10.

RESULTS

We observed a better endometrial growth in Group A compared to Group B: 7.5 ± 2.1 mm vs 5.5 ± 1.2 mm, P < 0.0002 and 8.9 ± 1.8 mm vs 6.3 ± 1.8 mm, P < 0.0002 on days 8 and 10, respectively. Additionally, a progressive decrease in the RI was observed in Group A but not in Group B from day 8 (0.77 ± 0.15 vs 0.85 ± 0.18, P = 0.059) to day 10 (0.74 ± 0.20 vs 0.87 ± 0.14, P < 0.017). However, no differences were observed in PI or serum estradiol between Group A and Group B.

CONCLUSION

The use of tadalafil improved endometrial growth in patients under clomiphene ovarian stimulation with no significant effect on the uterine artery Pulsatility Index and serum estradiol.

Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot

Identification and characterization of a metal ion binding site in an RNA pseudoknot was accomplished using cobalt (III) hexammine, Co(NH3)63+, as a probe for magnesium (II) hexahydrate, Mg(H2O)62+, in nuclear magnetic resonance (NMR) structural studies. The pseudoknot causes efficient -1 ribosomal frameshifting in mouse mammary tumor virus. Divalent metal ions, such as Mg2+, are critical for RNA structure and function; Mg2+preferentially stabilizes the pseudoknot relative to its constituent hairpins. The use of Co(NH3)63+as a substitute for Mg2+was investigated by ultraviolet absorbance melting curves, NMR titrations of the imino protons, and analysis of NMR spectra in the presence of Mg2+or Co (NH3)63+. The structure of the pseudoknot-Co(NH3)63+complex reveals an ion-binding pocket formed by a short, two-nucleotide loop and the major groove of a stem. Co(NH3)63+stabilizes the sharp loop-to-stem turn and reduces the electrostatic repulsion of the phosphates in three proximal strands. Hydrogen bonds are identified between the Co(NH3)63+protons and non-bridging phosphate oxygen atoms, 2' hydroxyl groups, and nitrogen and oxygen acceptors on the bases. The binding site is significantly different from that previously characterized in the major groove surface of tandem G.U base-pairs, but is similar to those observed in crystal structures of a fragment of the 5 S rRNA and the P5c helix of the Tetrahymena thermophila group I intron. Changes in chemical shifts occurred at the same pseudoknot protons on addition of Mg2+as on addition of Co(NH3)63+, indicating that both ions bind at the same site. Ion binding dissociation constants of approximately 0.6 mM and 5 mM (in 200 mM Na+and a temperature of 15 degrees C) were obtained for Co(NH3)63+and Mg2+, respectively, from the change in chemical shift as a function of metal ion concentration. An extensive array of non-sequence-specific hydrogen bond acceptors coupled with conserved structural elements within the binding pocket suggest a general mode of divalent metal ion stabilization of this type of frameshifter pseudoknot. These results provide new thermodynamic and structural insights into the role divalent metal ions play in stabilizing RNA tertiary structural motifs such as pseudoknots.

Adjuvant immunotherapy with transfer factor in patients with melanoma metastatic to lung

Nine patients with resectable pulmonary metastases of malignant melanoma were treated with surgery and transfer factor. Twelve months after thoracotomy, all were alive. After a median follow-up of 20 months, only one patient had died. Historic, other-center controls treated with surgery alone had a significantly (p less than 0.025) lower survival rate. Recurrence rates tended to be lower in the transfer factor group, but the differences were not significant. These results suggest that transfer factor may prolong survival in patients with an immunologically responsive malignancy and a small residual tumor burden.

Altered regulation of mitogen responsiveness by suppressor cells in multiple sclerosis

Suppression of the lymphocyte response to concanavalin A (Con A), phytohaemagglutinin (PHA) and protein A from Staphylococcus aureus (SpA) by Con A-induced suppressor cells was measured in twenty-four patients with recently active-recovering multiple sclerosis (MS), twelve with inactive MS and twenty-three healthy controls. Patients with recently active disease displayed significantly greater suppression of the response to Con A. Suppression of the responses to PHA and SpA did not differ among the groups. Lymphocyte stimulation in cultures not showing suppression was similar in all three types of subjects. These results suggest a disturbance of lymphocyte regulation in patients with recently active-recovering MS and illustrate the potential usefulness of measuring the suppression of responsiveness to several mitogens.

Effect of levamisole as a surgical adjuvant therapy for malignant melanoma

The preliminary results of a trial in progress are reported. Two hundred patients have been enrolled in a randomized, double-blind, placebo-controlled trial of levamisole in malignant melanoma. A median followup of 20 months has been reached. Endpoints of the study include disease-free interval, interval free of visceral disease, and survival. Overall, there is a trend in favor of the levamisole group with regard to all three endpoints, but the difference is not significant. Significant differences between the control and levamisole groups are found at some, but not all, time intervals when the analysis includes only patients with stage II disease (positive lymph nodes at the initiation of the study). Although these preliminary results are encouraging, at the present time the overall curve for patients with stage II disease is not statistically significantly different when analyzed by the method of Mantel.