Nanopore detection of single molecule RNAP-DNA transcription complex.

In the past decade, a number of single-molecule methods have been developed with the aim of investigating single protein and nucleic acid interactions. For the first time we use solid-state nanopore sensing to detect a single E. coli RNAP-DNA transcription complex and single E. coli RNAP enzyme. On the basis of their specific conductance translocation signature, we can discriminate and identify between those two types of molecular translocations and translocations of bare DNA. This opens up a new perspectives for investigating transcription processes at the single-molecule level.

Influence of neuroblastoma stage on serum-based detection of MYCN amplification.

BACKGROUND: MYCN oncogene amplification has been defined as the most important prognostic factor for neuroblastoma (NB), the most common solid extracranial neoplasm in children. High copy numbers are strongly associated with rapid tumor progression and poor outcome, independently of tumor stage or patient age, and this has become an important factor in treatment stratification. PROCEDURE: By real-time quantitative PCR analysis, we evaluated the clinical relevance of circulating MYCN DNA of 267 patients with locoregional or metastatic NB in children less than 18 months of age. RESULTS: For patients in this age group with INSS stage 4 or 4S NB and stage 3 patients, serum-based determination of MYCN DNA sequences had good sensitivity (85%, 83%, and 75% respectively) and high specificity (100%) when compared to direct tumor gene determination. In contrast, the approach showed low sensitivity patients with stages 1 and 2 disease. CONCLUSION: Our results show that the sensitivity of the serum-based MYCN DNA sequence determination depends on the stage of the disease. However, this simple, reproducible assay may represent a reasonably sensitive and very specific tool to assess tumor MYCN status in cases with stage 3 and metastatic disease for whom a wait and see strategy is often recommended.

Integrating detection probabilities in species distribution models of amphibians breeding in Mediterranean temporary ponds

Aim  The imperfect detection of species may lead to erroneous conclusions about species-environment relationships. Accuracy in species detection usually requires temporal replication at sampling sites, a time-consuming and costly monitoring scheme. Here, we applied a lower-cost alternative based on a double-sampling approach to incorporate the reliability of species detection into regression-based species distribution modelling.Location  Doñana National Park (south-western Spain).Methods  Using species-specific monthly detection probabilities, we estimated the detection reliability as the probability of having detected the species given the species-specific survey time. Such reliability estimates were used to account explicitly for data uncertainty by weighting each absence. We illustrated how this novel framework can be used to evaluate four competing hypotheses as to what constitutes primary environmental control of amphibian distribution: breeding habitat, aestivating habitat, spatial distribution of surrounding habitats and/or major ecosystems zonation. The study was conducted on six pond-breeding amphibian species during a 4-year period.Results  Non-detections should not be considered equivalent to real absences, as their reliability varied considerably. The occurrence of Hyla meridionalis and Triturus pygmaeus was related to a particular major ecosystem of the study area, where suitable habitat for these species seemed to be widely available. Characteristics of the breeding habitat (area and hydroperiod) were of high importance for the occurrence of Pelobates cultripes and Pleurodeles waltl. Terrestrial characteristics were the most important predictors of the occurrence of Discoglossus galganoi and Lissotriton boscai, along with spatial distribution of breeding habitats for the last species.Main conclusions  We did not find a single best supported hypothesis valid for all species, which stresses the importance of multiscale and multifactor approaches. More importantly, this study shows that estimating the reliability of non-detection records, an exercise that had been previously seen as a naïve goal in species distribution modelling, is feasible and could be promoted in future studies, at least in comparable systems.

Short-term moderate hypocapnia augments detection of optimal cerebral perfusion pressure.

An autoregulation-oriented strategy has been proposed to guide neurocritical therapy toward the optimal cerebral perfusion pressure (CPPOPT). The influence of ventilation changes is, however, unclear. We sought to find out whether short-term moderate hypocapnia (HC) shifts the CPPOPT or affects its detection. Thirty patients with traumatic brain injury (TBI), who required sedation and mechanical ventilation, were studied during 20 min of normocapnia (5.1±0.4 kPa) and 30 min of moderate HC (4.4±3.0 kPa). Monitoring included bilateral transcranial Doppler of the middle cerebral arteries (MCA), invasive arterial blood pressure (ABP), and intracranial pressure (ICP). Mx -autoregulatory index provided a measure for the CPP responsiveness of MCA flow velocity. CPPOPT was assessed as the CPP at which autoregulation (Mx) was working with the maximal efficiency. During normocapnia, CPPOPT (left: 80.65±6.18; right: 79.11±5.84 mm Hg) was detectable in 12 of 30 patients. Moderate HC did not shift this CPPOPT but enabled its detection in another 17 patients (CPPOPT left: 83.94±14.82; right: 85.28±14.73 mm Hg). The detection of CPPOPT was achieved via significantly improved Mx-autoregulatory index and an increase of CPP mean. It appeared that short-term moderate HC augmented the detection of an optimum CPP, and may therefore usefully support CPP-guided therapy in patients with TBI.

Efficient T cell activation requires an optimal dwell-time of interaction between the TCR and the pMHC complex.

Cytotoxic T cell (CTL) activation by antigen requires the specific detection of peptide-major histocompatibility class I (pMHC) molecules on the target-cell surface by the T cell receptor (TCR). We examined the effect of mutations in the antigen-binding site of a Kb-restricted TCR on T cell activation, antigen binding and dissociation from antigen.These parameters were also examined for variants derived from a Kd-restricted peptide that was recognized by a CTL clone. Using these two independent systems, we show that T cell activation can be impaired by mutations that either decrease or increase the binding half-life of the TCR-pMHC interaction. Our data indicate that efficient T cell activation occurs within an optimal dwell-time range of TCR-pMHC interaction. This restricted dwell-time range is consistent with the exclusion of either extremely low or high affinity T cells from the expanded population during immune responses.

Small scale underwater change detection

In this paper, we present a method to deal with the constraints of the underwater medium for finding changes between sequences of underwater images. One of the main problems of underwater medium for automatically detecting changes is the low altitude of the camera when taking pictures. This emphasise the parallax effect between the images as they are not taken exactly at the same position. In order to solve this problem, we are geometrically registering the images together taking into account the relief of the scene

Diagnostic value of vestibulo-ocular reflex parameters in the detection and characterization of labyrinthine lesions.

OBJECTIVE: To evaluate the power of various parameters of the vestibulo-ocular reflex (VOR) in detecting unilateral peripheral vestibular dysfunction and in characterizing certain inner ear pathologies. STUDY DESIGN: Prospective study of consecutive ambulatory patients presenting with acute onset of peripheral vertigo and spontaneous nystagmus. SETTING: Tertiary referral center. PATIENTS: Seventy-four patients (40 females, 34 males) and 22 normal subjects (11 females, 11 males) were included in the study. Patients were classified in three main diagnoses: vestibular neuritis: 40; viral labyrinthitis: 22; Meniere's disease: 12. METHODS: The VOR function was evaluated by standard caloric and impulse rotary tests (velocity step). A mathematical model of vestibular function was used to characterize the VOR response to rotational stimulation. The diagnostic value of the different VOR parameters was assessed by uni- and multivariable logistic regression. RESULTS: In univariable analysis, caloric asymmetry emerged as the most powerful VOR parameter in identifying unilateral vestibular deficit, with a boundary limit set at 20%. In multivariable analysis, the combination of caloric asymmetry and rotational time constant asymmetry significantly improved the discriminatory power over caloric alone (p<0.0001) and produced a detection score with a correct classification of 92.4%. In discriminating labyrinthine diseases, different combinations of the VOR parameters were obtained for each diagnosis (p<0.003) supporting that the VOR characteristics differ between the three inner ear disorders. However, the clinical usefulness of these characteristics in separating the pathologies was limited. CONCLUSION: We propose a powerful logistic model combining the indices of caloric and time constant asymmetries to detect a peripheral vestibular loss, with an accuracy of 92.4%. Based on vestibular data only, the discrimination between the different inner ear diseases is statistically possible, which supports different pathophysiologic changes in labyrinthine pathologies.

Development of bioreporter assays for the detection of bioavailability of long-chain alkanes based on the marine bacterium Alcanivorax borkumensis strain SK2.

Long-chain alkanes are a major component of crude oil and therefore potentially good indicators of hydrocarbon spills. Here we present a set of new bacterial bioreporters and assays that allow to detect long-chain alkanes. These reporters are based on the regulatory protein AlkS and the alkB1 promoter from Alcanivorax borkumensis SK2, a widespread alkane degrader in marine habitats. Escherichia coli cells with the reporter construct reacted strongly to octane in short-term (6 h) aqueous suspension assays but very slightly only to tetradecane, in line with what is expected from its low water solubility. In contrast, long-term assays (up to 5 days) with A. borkumensis bioreporters showed strong induction with tetradecane and crude oil. Gel-immobilized A. borkumensis reporter cells were used to demonstrate tetradecane and crude oil bioavailability at a distance from a source. Alcanivorax borkumensis bioreporters induced fivefold more rapid and more strongly when allowed physical contact with the oil phase in standing flask assays, suggesting a major contribution of adhered cells to the overall reporter signal. Using the flask assays we further demonstrated the effect of oleophilic nutrients and biosurfactants on oil availability and degradation by A. borkumensis. The fluorescence signal from flask assays could easily be captured with a normal digital camera, making such tests feasible to be carried out on, e.g. marine oil responder vessels in case of oil accidents.

Detection of bovine foetal DNA from amniotic fluid using the polymerase chain reaction

Selostus: Sikiön DNA:n tunnistaminen naudan sikiövedestä polymeraasiketjureaktion avulla

Detection of moving groups among early type stars

Our procedure to detect moving groups in the solar neighbourhood (Chen et al., 1997) in the four-dimensional space of the stellar velocity components and age has been improved. The method, which takes advantadge of non-parametric estimators of density distribution to avoid any a priori knowledge of the kinematic properties of these stellar groups, now includes the effect of observational errors on the process to select moving group stars, uses a better estimation of the density distribution of the total sample and field stars, and classifies moving group stars using all the available information. It is applied here to an accurately selected sample of early-type stars with known radial velocities and Strömgren photometry. Astrometric data are taken from the HIPPARCOS catalogue (ESA, 1997), which results in an important decrease in the observational errors with respect to ground-based data, and ensures the uniformity of the observed data. Both the improvement of our method and the use of precise astrometric data have allowed us not only to confirm the existence of classical moving groups, but also to detect finer structures that in several cases can be related to kinematic properties of nearby open clusters or associations.

Agonist-induced internalization and recycling of the glucagon-like peptide-1 receptor in transfected fibroblasts and in insulinomas.

Glucagon-like peptide-1 (GLP-1) is the most potent stimulator of glucose-induced insulin secretion and its pancreatic beta-cell receptor is a member of a new subfamily of G-protein-coupled receptors which includes the receptors for vasoactive intestinal polypeptide, secretin and glucagon. Here we studied agonist-induced GLP-1 receptor internalization in receptor-transfected Chinese hamster lung fibroblasts using three different approaches. First, iodinated GLP-1 bound at 4 degrees C to transfected cells was internalized with a t 1/2 of 2-3 min following warming up of the cells to 37 degrees C. Secondly, exposure to GLP-1 induced a shift in the distribution of the receptors from plasma membrane-enriched to endosomes-enriched membrane fractions, as assessed by Western blot detection of the receptors using specific antibodies. Thirdly, continuous exposure of GLP-1 receptor-expressing cells to iodinated GLP-1 led to a linear accumulation of peptide degradation products in the medium following a lag time of 20-30 min, indicating a continuous cycling of the receptor between the plasma membrane and endosomal compartments. Potassium depletion and hypertonicity inhibited transferrin endocytosis, a process known to occur via coated pit formation, as well as GLP-1 receptor endocytosis. In contrast to GLP-1, the antagonist exendin-(9-39) did not lead to receptor endocytosis. Surface re-expression following one round of GLP-1 receptor endocytosis occurred with a half-time of about 15 min. The difference in internalization and surface re-expression rates led to a progressive redistribution of the receptor in intracellular compartments upon continuous exposure to GLP-1. Finally, endogenous GLP-1 receptors expressed by insulinoma cells were also found to be internalized upon agonist binding. Together our data demonstrate that the GLP-1 receptor is internalized upon agonist binding by a route similar to that taken by single transmembrane segment receptors. The characterization of the pathway and kinetics of GLP-1-induced receptor endocytosis will be helpful towards understanding the role of internalization and recycling in the control of signal transduction by this receptor.

Feasibility of in vivo 15N MRS detection of hyperpolarized 15N labeled choline in rats.

The increase of total choline in tumors has become an important biomarker in cancer diagnosis. Choline and choline metabolites can be measured in vivo and in vitro using multinuclear MRS. Recent in vivo(13)C MRS studies using labeled substrates enhanced via dynamic nuclear polarization demonstrated the tremendous potential of hyperpolarization for real-time metabolic studies. The present study demonstrates the feasibility of detecting hyperpolarized (15)N labeled choline in vivo in a rat head at 9.4 T. We furthermore report the in vitro (172 +/- 16 s) and in vivo (126 +/- 15 s) longitudinal relaxation times. We conclude that with appropriate infusion protocols it is feasible to detect hyperpolarized (15)N labeled choline in live animals.

Diabetische Neuropathien: Klinische Manifestationsformen, Früherkennung und Zuweisung zu einem Neurologen [Diabetic Neuropathies: Clinical sub-Types, Early Detection, and Asking Help from Neurologist].

In diabetes mellitus, it is expected to see a common, mainly sensitive, distal symmetrical polyneuropathy (DPN) involving a large proportion of diabetic patients according to known risk factors. Several other diabetic peripheral neuropathies are recognized, such as dysautonomia and multifocal neuropathies including lumbosacral radiculoplexus and oculomotor palsies. In this review, general aspects of DPN and other diabetic neuropathies are examined, and it is discussed why and how the general practionner has to perform a yearly examination. At the present time, some consensuses emerge to ask help from neurologist when faced to other forms of peripheral neuropathies than distal symmetrical DPN.

Diagnostic value of MRI for the detection of suspected placental invasion: Does it depend on observers' experience?

Purpose: To evaluate the diagnostic value of specific MR features for detection of suspected placental invasion according to observers' experience.Methods and Materials: Our study population included 25 pregnant women (mean age 35.16) investigated by prenatal MRI. In twelve out of them placental invasion was histopathologically proven, the 13 other women (52%) without placental invasion served as control group. Multiplanar T1- and T2-weighted sequences had been performed mostly without IV contrast injection (1.5 T). MR examinations of the two groups were rendered anonymous, mixed, then independently and retrospectively reviewed by two senior and two junior radiologists in view of 8 MR features indicating placentar invasion including the degree. Results were compared with surgical diagnosis (placenta normal/increta/accreta/percreta). Interobserver agrement between senior and junior readers were calculated. Stepwise logistic regression and receiver operating (ROC) curvers were performed.Results: Demographics between the two groups were not statistically different. Overall sensitivity and specificity for detecting placentar invasion was 90.9% and 75.0% for senior readers, and 81.8% and 61.8% for junior readers respectively. The most significant MR features indicating placentar invasion were T2 hypointense placental bands, followed by placenta praevia, focally interrupted myometrial border, posterior placental insertion, and heterogeneous placental signal. For each of the evaluated MR features the interobserver agreement kappa between the two senior readers was superior than that between the junior readers, ranging from bad (<0.4) to good (0.4-0.75).Conclusions: MRI can be a reliable and reproducible tool for detection of suspected placentar invasion, however very variable according to the observers' experience.