Influence of liquid medium and surface morphology on the response of QCM during immobilization and hybridization of short oligonucleotides

With the goal of developing a quartz crystal microbalance (QCM)-based DNA sensor, we have conducted an in situ QCM study along with fluorescence measurements using oligonucleotides (15-mer) as a model single-stranded DNA (ss-DNA) in two different aqueous buffer solutions; the sequence of 15-mer is a part of iduronate-2-sulphate exon whose mutation is known to cause Hunter syndrome, and the 15-mer is thiolated to be immobilized on the Au-coated quartz substrate. The fluorescence data indicate that the initial immobilization as well as the subsequent hybridization with a complementary strand is hardly dependent on the kind of buffer solution. In contrast, the mass increases deducible from the decrease of QCM frequency via the Sauerbrey equation are 2.7-6.2 and 3.0-4.4 times larger than the actual mass increases, as reflected in the fluorescence measurements, for the immobilization and the subsequent hybridization processes, respectively. Such an overestimation is attributed to the trapping of solvent as well as the formation of quite a rigid hydration layer associated with the higher viscosities and/or densities of the buffer solutions. Another noteworthy observation is the excessively large frequency change that occurs when the gold electrode is deposited in advance with Au nanoparticles. This clearly illustrates that the QCM detection of DNA hybridization is also affected greatly by the surface morphology of the electrode. These enlarged signals are altogether presumed to be advantageous when using a QCM system as an in situ probing device in DNA sensors.     

Cr(VI) quantification using an amperometric enzyme-based sensor: interference and physical and chemical factors controlling the biosensor response in ground waters

The development of an amperometric enzyme-based sensor for chromate (CrO(4)(2-)) quantification in ground waters was investigated. Crucial physical and chemical factors characterising ground waters were tested for their influence or interference on chromate quantification: pH (7.6-8.5), temperature (9-25 degrees C), ionic strength (0-0.2M), oxygen, metals, bicarbonate and sulphate. The biosensor's response was dependent on temperature and pH as sensitivity increased with temperature and was higher at pH 7.6 than at pH 8.5. Sensitivity decreased with ionic strength until 0.1M, and was stable for higher values. Dissolved oxygen did not allow chromate quantification when it was present, but O(2) could be eliminated by adding Na(2)SO(3) or bubbling nitrogen gas into the solution. Bicarbonate did not interfere with chromate quantification by the biosensor. Sulphate was detected with a detection threshold 80 times higher than that of chromate and a lower sensitivity. Several metals (V(V), W(VI), Mn(VII), Mo(VI)) similar to chromate due to their oxidative properties and structure (oxyanions) were tested as possible interfering compounds. The sensitivity of the biosensor for these metals was low and the detection level was 30 times higher than that of chromate. These metal concentrations are usually weaker than chromate concentration in polluted ground waters so that dilution of the sample should allow chromate quantification by the biosensor. This study shows that the cytochrome c(3)-based sensor can detect compounds other than chromate but with a lower sensitivity. Although non-specific for the detection of chromate, it can however be adapted and used for the quantification of chromate in ground waters containing low sulphate concentration.     

Using control genes to correct for unwanted variation in microarray data

Microarray expression studies suffer from the problem of batch effects and other unwanted variation. Many methods have been proposed to adjust microarray data to mitigate the problems of unwanted variation. Several of these methods rely on factor analysis to infer the unwanted variation from the data. A central problem with this approach is the difficulty in discerning the unwanted variation from the biological variation that is of interest to the researcher. We present a new method, intended for use in differential expression studies, that attempts to overcome this problem by restricting the factor analysis to negative control genes. Negative control genes are genes known a priori not to be differentially expressed with respect to the biological factor of interest. Variation in the expression levels of these genes can therefore be assumed to be unwanted variation. We name this method "Remove Unwanted Variation, 2-step" (RUV-2). We discuss various techniques for assessing the performance of an adjustment method and compare the performance of RUV-2 with that of other commonly used adjustment methods such as Combat and Surrogate Variable Analysis (SVA). We present several example studies, each concerning genes differentially expressed with respect to gender in the brain and find that RUV-2 performs as well or better than other methods. Finally, we discuss the possibility of adapting RUV-2 for use in studies not concerned with differential expression and conclude that there may be promise but substantial challenges remain.     

Use of Bayes theorem to correct size-specific sampling bias in growth data

The bayesian decomposition of posterior distribution was used to develop a likelihood function to correct bias in the estimates of population parameters from data collected randomly with size-specific selectivity. Positive distributions with time as a parameter were used for parametrization of growth data. Numerical illustrations are provided. The alternative applications of the likelihood to estimate selectivity parameters are discussed.     

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

We introduce a statistical model for microarray gene expression data that comprises data calibration, the quantification of differential expression, and the quantification of measurement error. In particular, we derive a transformation h for intensity measurements, and a difference statistic Deltah whose variance is approximately constant along the whole intensity range. This forms a basis for statistical inference from microarray data, and provides a rational data pre-processing strategy for multivariate analyses. For the transformation h, the parametric form h(x)=arsinh(a+bx) is derived from a model of the variance-versus-mean dependence for microarray intensity data, using the method of variance stabilizing transformations. For large intensities, h coincides with the logarithmic transformation, and Deltah with the log-ratio. The parameters of h together with those of the calibration between experiments are estimated with a robust variant of maximum-likelihood estimation. We demonstrate our approach on data sets from different experimental platforms, including two-colour cDNA arrays and a series of Affymetrix oligonucleotide arrays.     

The ratio of germanium to silicon in plant phytoliths: quantification of biological discrimination under controlled experimental conditions

Slight differences in the chemical behavior of germanium (Ge) and silicon (Si) during soil weathering enable Ge/Si ratios to be used as a tracer of Si pathways. Mineral weathering and biogenic silicon cycling are the primary modifiers of Ge/Si ratios, but knowledge of the biogenic cycling component is based on relatively few studies. We conducted two sets of greenhouse experiments in order to better quantify the range and variability in Ge discrimination by plants. Graminoid species commonly found in North American grassland systems, Agropyron smithii, Schizachyrium scoparium, and Andropogon gerardii were grown under controlled hydroponic environmental conditions. Silicon leaf contents were positively correlated with solution Si and ambient temperature but not with nutrient solution pH, electrical conductivity, or species. The Ge/Si ratio incorporated into phytoliths shows a distribution coefficient [(Ge/Si)_phytolith/(Ge/Si)_solution] of about 0.2 and is remarkably invariant between species, photosynthetic pathway, and solution temperature. Ge seems to be discriminated against during the uptake and translocation of Si to the opal deposition sites by about a factor of five. In the second experiment, a wider range of graminoid species (Agropyron smithii, Bouteloua gracilis, Buchloe dactyloides, Oryzopsis hymenoides, Schizachyrium scoparium and Andropogon gerardii) were grown in two different soil mediums. Plant phytoliths showed a distribution factor of about 0.4 for field grown grasses, and 0.6 for potting soil grown grasses with no clear trends among the species. Evidence of the direction and degree of biological Ge discrimination during plant uptake provides a geochemical finger print for plants and improves the utility of Ge/Si ratios in studies of terrestrial weathering and links between Si cycles in terrestrial and marine systems.     

Protein turnover quantification in a multilabeling approach: from data calculation to evaluation

Liquid chromatography coupled to tandem mass spectrometry in combination with stable-isotope labeling is an established and widely spread method to measure gene expression on the protein level. However, it is often not considered that two opposing processes are responsible for the amount of a protein in a cell--the synthesis as well as the degradation. With this work, we provide an integrative, high-throughput method--from the experimental setup to the bioinformatics analysis--to measure synthesis and degradation rates of an organism's proteome. Applicability of the approach is demonstrated with an investigation of heat shock response, a well-understood regulatory mechanism in bacteria, on the biotechnologically relevant Corynebacterium glutamicum. Utilizing a multilabeling approach using both heavy stable nitrogen as well as carbon isotopes cells are metabolically labeled in a pulse-chase experiment to trace the labels' incorporation in newly synthesized proteins and its loss during protein degradation. Our work aims not only at the calculation of protein turnover rates but also at their statistical evaluation, including variance and hierarchical cluster analysis using the rich internet application QuPE.     

Temperature response in electrosensors and thermal voltages in electrolytes

Temperature sensation is increasingly well understood in several model organisms. One of the most sensitive organs to temperature changes is the functional electrosensor of sharks and their relatives; its extreme thermal responsiveness, in excised preparations, has not been mechanistically described. In recent years, conflicting reports have appeared concerning the properties of a hydrogel that fills the ampullae of Lorenzini. The appearance of a thermoelectric effect in the gel (or, using different methods, a reported lack thereof) suggested a link between the exquisite electrosense and the thermal response of the electroreceptors (or, alternately, denied that link). I review available electrophysiology evidence of the organ’s temperature response, calculate a theoretical gel signal prediction using physical chemistry, analyze the strengths and weaknesses of the existing gel measurements, and discuss broader implications for the ampullae and temperature sensation.     

Feedback control and quantification of the response of EEG alpha to visual stimulation

The response of the posterior EEG alpha rhythms to visual stimulation is so variable that it is difficult to obtain reliable on-line measurement of it. Feedback between the EEG alpha and the visual stimulus (1) reduces random variation in the response and (2) facilitates on-line quantification. With feedback EEG, the response to visual stimulation is measured as a series of time durations of alpha and of no-alpha intervals in the EEG. This time series occurs in two stages: an initial disturbance followed by a recovery. The quantification of the series of time durations is achieved by fitting curves to the series of alpha time intervals and of no-alpha time intervals. These functions, computed in each trial of 30 stimulations, are an objective, quantitative definition of EEG response. The utility of the method was demonstrated by testing it with reference to well-known effects. Habituation to a repeated stimulus, dishabituation, habituation to a class of stimuli, dishabituation by changing the class of stimuli, and differences among brain-lesioned, psychiatric patients and normals were shown with a detailed quantification. It was concluded that biofeedback is the method of choice for quantitative research on the EEG component of the human orienting response.     

d'plus: A program to calculate accuracy and bias measures from detection and discrimination data

The program d'plus calculates accuracy (sensitivity) and response-bias parameters using Signal Detection Theory. Choice Theory, and 'nonparametric' models. is is appropriate for data from one-interval, two- and three-interval forced-choice, same different, ABX, and oddity experimental paradigms.     

Anti-rabbit immunoglobulin G detection in complex medium by PM-RAIRS and QCM Influence of the antibody immobilisation method

Two antibody immobilisation procedures were compared to set up an immunosensor for goat anti-rabbit immunoglobulin (anti-rIgG), i.e. rIgG covalently bound or immobilised via affinity to protein A (PrA). In both cases, the first layer of protein was covalently bound to a mixed self-assembled monolayer (SAM) of mercaptoundecanoic acid (MUA) and mercaptohexanol (C6OH) on a gold surface. The elaboration of the sensitive surfaces, as well as their selectivity and sensitivity were studied step by step by polarization modulation-reflection absorption infra-red spectroscopy (PM-RAIRS) and quartz crystal microbalance (QCM) with impedance measurement. QCM measurements showed that the viscoelastic properties of the antibody layer were markedly modified during the antigen recognition when the antibody was bound by affinity to PrA. The specific detection of antigen within a complex medium was assessed by PM-RAIRS thanks to the grafting of cobalt-carbonyl probes. Affinity constants between the immobilised rIgG and the anti-rIgG were determined from PM-RAIRS analysis.     

RNA interference: PCR strategies for the quantification of stable degradation-fragments derived from siRNA-targeted mRNAs

mRNA targeted by siRNA is endogeneously cleaved into a 5'- and a 3'-fragment and finally degraded in cells. Little is known about the relative stability and degradation kinetics of these 5'- and 3'-fragments after the siRNA mediated first cut. We present a qRT-PCR protocol which allows the determination of the optimal time point for mRNA analyses, helping to avoid the generation of false positive effects in downstream experiments, such as microarray analysis, which may be caused by undegraded fragments of a siRNA-targeted mRNA.     

Electrophysiological response of honey bee labial palp contact chemoreceptors to sugars and electrolytes

ABSTRACT. The sensilla chaetica on segments II, III and IV of honey-bee labial palps were investigated electrophysiologically. The responses (spikes/s) correlated with the log of the concentrations of sucrose, glucose, fructose, NaCl, KCl and LiCl, but not with CaCl₂ or MgCl₂, which gave inconsistent responses. The firing rates were higher and thresholds lower to the sugars than to the electrolytes. The sensitivity of the segments fell in the order: III > II > IV for most of the stimulants, which elicited responses in the order: sucrose > glucose = fructose' KCl > LiCl > NaCl. The sensilla adapted logarithmically with time. No synergism of response was noted when mixed-sugar solutions were applied, but inhibition of response was seen when glucose–sucrose, fructose–sucrose, and glucose–fructose–sucrose mixtures were applied. None of the sensilla tested responded to water.     

Thiol oxidation in signaling and response to stress: detection and quantification of physiological and pathophysiological thiol modifications

Cysteine thiol modifications are increasingly recognized to occur under both physiological and pathophysiological conditions, making their accurate detection, identification, and quantification of growing importance. Among free cysteines, the bulk of modifications occurs on a subset of cysteines that are more reactive. These exist as thiolate anions at physiological pH because of their surrounding electrostatic environment. Reagents with iodoacetamide-active groups can be used to selectively label these reactive thiols with a high degree of selectivity. Thiol adducts can be detected by the failure to label with iodoacetamide or other reagents; restoration of labeling by specific reducing agents (e.g., ascorbate or glutaredoxin) can be used to detect reversible S-nitroso and S-glutathione adducts. These adducts also may be detected with radiolabels and antibodies. S-Glutathiolation in response to physiological stimuli may be detected in cells and tissues with glutathione ester labeled with biotin. Mass spectrometry can identify thiol modifications with precision, and with isotope-coded affinity tags, used to quantify modification of specific thiols. Combinations of these methods increase sensitivity and specificity, and enable quantification and precise identification of thiol modifications that occur under physiological and pathological conditions.