An error model for protein quantification

MOTIVATION

Quantitative experimental data is the critical bottleneck in the modeling of dynamic cellular processes in systems biology. Here, we present statistical approaches improving reproducibility of protein quantification by immunoprecipitation and immunoblotting.

RESULTS

Based on a large data set with more than 3600 data points, we unravel that the main sources of biological variability and experimental noise are multiplicative and log-normally distributed. Therefore, we suggest a log-transformation of the data to obtain additive normally distributed noise. After this transformation, common statistical procedures can be applied to analyze the data. An error model is introduced to account for technical as well as biological variability. Elimination of these systematic errors decrease variability of measurements and allow for a more precise estimation of underlying dynamics of protein concentrations in cellular signaling. The proposed error model is relevant for simulation studies, parameter estimation and model selection, basic tools of systems biology.

AVAILABILITY

Matlab and R code is available from the authors on request. The data can be downloaded from our website www.fdm.uni-freiburg.de/~ckreutz/data.

Impact of the AEP-Monitor/2-derived composite auditory-evoked potential index on propofol consumption and emergence times during total intravenous anaesthesia with propofol and remifentanil in children

BACKGROUND

The composite auditory evoked potential index (cAAI), derived from the AEP Monitor/2 (version 1.6; Danmeter A/S, Odense, Denmark) is a measure of the hypnotic component of general anaesthesia. The purpose of this study was to evaluate the impact of cAAI guidance on propofol consumption and emergence times in children receiving total intravenous anaesthesia (TIVA) with propofol and remifentanil.

METHODS

Twenty children, aged 3-11 years, scheduled for strabismus repair under TIVA with propofol and remifentanil were enrolled. Remifentanil was given to all patients at a constant infusion rate of 0.3 microg kg(-1) min(-1) throughout the anaesthesia. Patients were randomly allocated to receive a continuous propofol infusion adjusted either according to a conventional clinical practice (Group C, n = 10) or guided by cAAI-monitoring (Group G, n = 10, target cAAI 25-35). All patients were connected to the AEP Monitor/2, but in group C the anaesthetist was blinded to cAAI values. Propofol consumption (mgkg(-1)h(-1)) and emergence times (min) were the primary and secondary outcome measures.

RESULTS

Propofol consumption and emergence times (mean +/- SD) were significantly lower in group G compared to group C (Propofol: G: 4.2 +/- 1.7 vs. C 6.4 +/- 1.3 mg kg(-1) h(-1); P < 0.01; emergence times: G: 5.1 +/- 3.7 vs. C 13.2 +/- 8.2 min; P < 0.01). Intraoperative cAAI values (median [interquartile range]) were significantly higher in group G (23.9 [18-29.7]) than in group C (18.4 [16.0-22.1]; P < 0.01). Haemodynamic variables remained stable within age-related limits, and there were no observations of adverse events, especially no clinical signs of intraoperative awareness in any patient.

CONCLUSION

Composite auditory evoked potential index monitoring during propofol/remifentanil-TIVA in children results in reduced propofol consumption and faster emergence.

Control of oxygen transport in the microcrustacean Daphnia: regulation of haemoglobin expression as central mechanism of adaptation to different oxygen and temperature conditions

The pathway for oxygen, the control of oxygen transport and the role of haemoglobin expression for the physiological adaptation to different oxygen and temperature conditions were studied in the ecological model organism Daphnia magna. Ventilation of the inner walls of the carapace as the main gas exchange area as well as of the embryos in the brood pouch are controlled, oxygen-dependent processes. The P(O2)-dependent increase of heart rate as well as perfusion rate during short-term, progressive hypoxia improves the circulatory oxygen transport within the body. The regulation of haemoglobin (Hb) expression is the central mechanism for a medium-term adaptation to hypoxia. Genetic control elements and oxygen conditions near the two Hb synthesis sites (fat cells, epipodite epithelial cells) determine, which types of Hb subunits and, accordingly, hetero-multimeric Hb macromolecules are produced. One synthesis site may respond mainly to internal, the other one to external oxygen conditions. Depending on environmental condition, either higher quantities of macromolecules of unchanged functionality (P50) or increasing amounts of macromolecules with higher oxygen affinity are synthesized. The Hb subunit DmHbA is probably of considerable importance for this functional change. The physiological benefits of haemoglobin in Daphnia are discussed. Physiological adaptation of Daphnia to different temperatures is also related to the control of oxygen transport processes with the regulation of haemoglobin expression again as a central mechanism.

Simulation of all-order density-functional perturbation theory, using the second order and the strong-correlation limit

To boost the accuracy of electronic structure calculations, the exchange-correlation energy may be constructed from the Kohn-Sham orbitals. A formally exact construction is the density-functional perturbation series, which appears to diverge for many real systems. We predict the radius of convergence and resum this series, using only exact exchange and second-order correlation plus explicit density functionals for the strong-interaction limit. Our new correlation functional, along with exact exchange, predicts atomization energies with competitive accuracy and without the usual error cancellation.

Toxicity of combined sewer overflows on river phytoplankton: the role of heavy metals

The toxic effect of a combined sewer overflow (CSO) on the phytoplankton community of the river Seine has been studied by means of short-term primary production measurements. As the discharged solids usually do not remain in the water column, only filtered or centrifugated fractions were tested. The collected phytoplankton were grown in the laboratory for 2 days, after addition of N, P and EDTA. Stock cultures in exponential growth were directly tested with heavy metals, but resuspended algal cells were used for effluent testing. The results show an increase of EC50 value for the single metal species in the order Cu<<Zn</=Pb. Free metal contents were calculated with the chemical speciation model Mineql+. The EC50 dilution of the tested CSOs effluent was 50%. This value increased by 30% after addition of 5 10(-6) M EDTA, indicating that the effluent toxicity is only partially due to its metallic compounds.

1H, 51V and 15N nuclear magnetic resonance studies of structure and properties of vanadia supported on TiO chi/SiO2

1H magic-angle spinning nuclear magnetic resonance (MAS NMR) spectra of TiO chi/SiO2 catalysts suggest the interaction of surface TiO chi species with Si-OH groups of the silica. Simultaneously, Ti-OH groups from surface titania species appear. The distribution of TiO chi species over SiO2 is non-uniform, since a considerable part of surface OH groups remains unreacted with supported titania. Supported vanadia species interact both with Si-OH and Ti-OH groups. 51V NMR spectra suggest the interaction of vanadia with supported titania species and show the non-uniform distribution of titania over the SiO2 surface. Deposition of titania as well as vanadia produces strong electron-accepting (Lewis) sites which interact with the terminal N atom of adsorbed N2O molecules, resulting in a downfield shift of the resonance in 15N NMR spectra. The acid strength of electron-accepting sites is similar in both cases. Only about 10% of the total amount of supported titania and vanadia create Lewis sites.

Induction of stress fibres and intercellular gaps in human vascular endothelium by shock-waves

Human umbilical cords were exposed to high amplitude focussed ultrasonic pulses with focal energy densities 0.6 and 0.4 mJ mm-2. The endothelium of the exposed vessel (vein) was examined by means of confocal laser scanning microscopy and scanning electron microscopy. The degree of tissue change ranged from the induction of stress fibres and intercellular gaps to the complete detachment of endothelial cells combined with damage of the basement membrane. An increased number of stress fibres may indicate an increased vessel wall permeability. This might explain the enhanced effects in experimental tumour therapy that have been found by other authors when combining shock-waves with drugs.

Shock wave induced endothelial damage--in situ analysis by confocal laser scanning microscopy

For more than a decade, extracorporal shock wave lithotripsy has been a standard clinical method for the treatment of urinary stones. However, side effects that are likely to be correlated to vessel damage can often be observed using noninvasive diagnostic techniques, e.g., magnetic resonance imaging. To avoid side effects it is useful to understand the interaction between shock waves and the vascular system. In particular, this is important in view of new applications like gallstone lithothripsy. In the present study, we exposed human umbilical vessels to electromagnetically generated ultrasound shock waves to analyze subsequent alterations of their endothelial layer. Following en face preparation and fluorescent staining, the endothelium was examined in a confocal laser scanning microscope. Endothelial cells of the shock wave exposed vessels revealed permeabilization of plasma membranes and mitochondrial alterations as potentially lethal damage. An increase in the number of stress fibres may indicate functional changes possibly influencing vessel wall permeability.

Testosterone metabolism in the medial basal hypothalamus of the starved male rat

The conversion of testosterone to estradiol by aromatase and to dihydrotestosterone by 5 alpha-reductase was measured in the medial basal hypothalamus of starved and control male rats. Activities of both enzymes were significantly reduced in starved animals. Aromatase activity was 18.2 +/- 2.3 versus 29.8 +/- 5.7 fmol E2/mg protein/90 min (mean +/- SEM, P less than 0.02) and 5 alpha-reductase was 4.95 +/- 0.35 versus 5.96 +/- 0.30 pmol DHT/mg protein/90 min (P less than 0.02) for starved and control animals respectively. The results indicate that hypothalamic metabolism of testosterone is decreased during starvation. Therefore the increased sensitivity of the T-LH feedback described earlier in starved rats [4] cannot be explained by changes in central testosterone metabolism.

Location of heparin-binding sites of fibronectin. Detection of a hitherto unrecognized transamidase sensitive site

Resolution of a cathepsin D digest of plasma fibronectin on heparin-Sepharose yielded, in addition to non-bound and weakly retained material (Fraction I and II), various fragments which were not eluted until 0.25M NaCl (Fraction III) and 0.5M NaCl (Fraction IV) was applied. Fraction III contained predominantly a peptide of Mr 70 000 originating from the N-terminus of the fibronectin subunits as well as high molecular weight precursors yielding the Mr 70 000 peptide by further digestion. All those peptides were retained by immobilized denatured collagen, type I, indicating the presence of the known gelatin-binding domain. In addition, they contained a transamidase-sensitive site as revealed from a digest of fibronectin previously labelled with [14C]putrescine by a transamidase-mediated reaction. Plasminolysis of the fragment of Mr 70 000 resulted in two peptides of Mr 30 000 and 40 000, only the former being retained by heparin-Sepharose. Fraction IV contained a fragment of Mr 140 000 which, after reduction, dissociated into two peptides of Mr 75 000 and 65 000. Apparently, it included the disulfide bond(s) connecting the two fibronectin subunits close to their C-terminal ends. Partial digestion of the two electrophoretically separated peptide chains with protease of Staphylococcus aureus V8 yielded for each chain a number of peptides with equal electrophoretic migration rate. In addition, however, some peptides were different in the two digests. The results were consistent with an identical or homologous structure of the two peptide chains with an additional sequence in the longer chain. The latter (Mr 75 000) uniquely contained a transamidase susceptible site as demonstrated by processing of [14C]putrescine-labelled fibronectin.