Automated nonparametric method for detection of step-like features in biological data sets.

Experimental data from single-molecule DNA-protein experiments, such as experiments using optical traps or magnetic tweezers, typically contain steps, plateaus, or dwell regions that are obscured by thermal and other noise sources. We present a nonparametric method for detecting step-like features in noisy biological data sets. Our algorithm does not assume that the steps can be modeled as Heaviside functions or any particular parametric form. No assumptions about the noise source, such as whether the noise is Gaussian or colored, are made either. Instead, for detection of plateaus, the algorithm uses the novel method of analyzing a probability distribution function of the data values. The vast majority of previously published methods for step detection rely on statistical fitting of step functions with the flat segments linked by vertical segments. Our approach is intended for use on data which cannot be modelled as a series of step functions but applies to step functions as a special case. These type of data traces have, so far, been difficult to characterize effectively. We examine the performance of the algorithm through systematic simulation studies and illustrate the use of our algorithm to analyze single molecule DNA-protein micromanipulation experiments carried out by our laboratory. The simulation results and experimental validation suggest that our method is very robust, avoids overfitting, and functions effectively in the presence of noise sources characteristic of single molecule experiments.

Characterization of Δ7/11, a functional prolactin-binding protein.

Prolactin is essential for normal mammary gland development and differentiation, and has been shown to promote tumor cell proliferation and chemotherapeutic resistance. Soluble isoforms of the prolactin receptor (PrlR) have been reported to regulate prolactin bioavailability by functioning as 'prolactin-binding proteins'. Included in this category is Δ7/11, a product of alternate splicing of the PrlR primary transcript. However, the direct interactions of prolactin with Δ7/11, and the resulting effect on cell behavior, have not been investigated. Herein, we demonstrate the ability of Δ7/11 to bind prolactin using a novel proximity ligation assay and traditional immunoprecipitation techniques. Biochemical analyses demonstrated that Δ7/11 was heavily glycosylated, similar to the extracellular domain of the primary PrlR, and that glycosylation regulated the cellular localization and secretion of Δ7/11. Low levels of Δ7/11 were detected in serum samples of healthy volunteers, but were undetectable in human milk samples. Expression of Δ7/11 was also detected in six of the 62 primary breast tumor biopsies analyzed; however, no correlation was found with Δ7/11 expression and tumor histotype or other patient demographics. Functional analysis demonstrated the ability of Δ7/11 to inhibit prolactin-induced cell proliferation as well as alter prolactin-induced rescue of cell cycle arrest/early senescence events in breast epithelial cells. Collectively, these data demonstrate that Δ7/11 is a novel regulatory mechanism of prolactin bioavailability and signaling.

Paraesthesiae during needle-through-needle combined spinal epidural versus single-shot spinal for elective caesarean section.

The aim of this study was to compare the incidence of paraesthesiae during spinal needle insertion in a needle-through-needle combined spinal-epidural (CSE) versus a single-shot spinal (SSS) technique. Eighty-nine women presenting for elective caesarean section at a tertiary referral obstetric unit were randomized to receive either needle-through-needle CSE or SSS. Equipment used was a 16 gauge/26 gauge combined spinal-epidural kit and a 26 gauge pencil-point spinal needle with introducer (both Sims Portex, Australia) The presence and distribution of paraesthesiae was recorded by an observer at spinal needle insertion and again on day one postoperatively. There were three failures to perform the intended block. One patient was lost to follow-up at postoperative day one. Seventeen of forty-six (37%) women in the needle-through-needle CSE group and four of forty-three (9%) in the SSS group had paraesthesiae upon spinal needle insertion (P < 0.05, Chi-squared test). No patient had persistent neurological symptoms at postoperative day one. We postulate that the higher incidence of paraesthesiae with needle-through-needle CSE may be related to deeper penetration of the subarachnoid space with this technique.