What do we learn from high-throughput protein interaction data?

The biological significance of protein interactions, their method of generation and reliability is briefly reviewed. Protein interaction networks adopt a scale-free topology that explains their error tolerance or vulnerability, depending on whether hubs or peripheral proteins are attacked. Networks also allow the prediction of protein function from their interaction partners and therefore, the formulation of analytical hypotheses. Comparative network analysis predicts interactions for distantly related species based on conserved interactions, even if sequences are only weakly conserved. Finally, the medical relevance of protein interaction analysis is discussed and the necessity for data integration is emphasized.     

PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data

The iCLIP and eCLIP techniques facilitate the detection of protein–RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP (https://github.com/skrakau/PureCLIP), a hidden Markov model based approach, which simultaneously performs peak-calling and individual crosslink site detection. It explicitly incorporates a non-specific background signal and, for the first time, non-specific sequence biases. On both simulated and real data, PureCLIP is more accurate in calling crosslink sites than other state-of-the-art methods and has a higher agreement across replicates.     

TGF-β enhances deposition of perlecan from COPD airway smooth muscle

Chronic obstructive pulmonary disease (COPD) and asthma are characterized by irreversible remodeling of the airway walls, including thickening of the airway smooth muscle layer. Perlecan is a large, multidomain, proteoglycan that is expressed in the lungs, and in other organ systems, and has been described to have a role in cell adhesion, angiogenesis, and proliferation. This study aimed to investigate functional properties of the different perlecan domains in relation to airway smooth muscle cells (ASMC). Primary human ASMC obtained from donors with asthma (n = 13), COPD (n = 12), or other lung disease (n = 20) were stimulated in vitro with 1 ng/ml transforming growth factor-β(1) (TGF-β(1)) before perlecan deposition and cytokine release were analyzed. In some experiments, inhibitors of signaling molecules were added. Perlecan domains I-V were seeded on tissue culture plates at 10 μg/ml with 1 μg/ml collagen I as a control. ASM was incubated on top of the peptides before being analyzed for attachment, proliferation, and wound healing. TGF-β(1) upregulated deposition of perlecan by ASMC from COPD subjects only. TGF-β(1) upregulated release of IL-6 into the supernatant of ASMC from all subjects. Inhibitors of SMAD and JNK signaling molecules decreased TGF-β(1)-induced perlecan deposition by COPD ASMC. Attachment of COPD ASMC was upregulated by collagen I and perlecan domains IV and V, while perlecan domain II upregulated attachment only of asthmatic ASMC. Seeding on perlecan domains did not increase proliferation of any ASMC type. TGF-β(1)-induced perlecan deposition may enhance attachment of migrating ASMC in vivo and thus may be a mechanism for ASMC layer hypertrophy in COPD.     

Facile measurement of polypeptide JHNHα coupling constants from HMQC-J spectra

A method, based on linewidth measurements, is described which permits the rapid and facile determination of J_HNH coupling constants from ¹⁵N labeled proteins. Using appropriately processed HMQC-J data, we have found that a simple linear relationship exists between the half-height linewidth (_1/2) of ¹⁵N–¹H cross peaks and their corresponding J_HNH coupling constants. Tests indicate that this technique permits the accurate measurement of up to 100 J_HNH coupling constants in less than 30 min. Furthermore, the J_HNH measurements can be done manually – without the need of any computer-based curve-fitting or minimization. Comparisons between J_HNH values predicted from high resolution X-ray structures and those determined using this technique indicate that the method is both accurate and precise (correlation coefficient = 0.90, rmsd = 0.75 Hz).     

Test of a pion range monitor using the radiative capture of pions on protonsπ −p→nγ

Summary The present paper demonstrates that neutron-photon pairs from radiative capture of stopped pions on chemically bound protons can be used to measure the range of negative pions within phantoms or a patient. Experimental results are given for a polyethylene and a water target of realistic size as well as for a Rando phantom. Monte-Carlo calculations were carried out in order to study the influence of various sizes of treatment volumes, detector geometries and neutron scattering within the targets upon the accuracy of the pion range determination. The results reveal clearly that a pion range monitor for the control of therapy plans and for actual patient irradiations can be designed according to the proposed principle. The absorbed dose required for a measurement is of the order of 0.1 Gy for a single pion beam if one aims at an accuracy of range determination of a few millimeters.     

Shoreline displacement of Lake Ladoga — new data from Kilpolansaari

Dating of sediments sampled from small lakes in the Kilpolansaari region, in the NW part of Lake Ladoga, indicate that the River Neva, which is the present outlet of Lake Ladoga, originated at 3,100 radiocarbon years BP This is in agreement with some earlier estimations but no consensus concerning the age of the River Neva has previously been reached. New diatom data provide information concerning salinity and nutrient conditions in northern Lake Ladoga prior to the formation of the River Neva, when the Litorina Sea occupied the Baltic basin and approached the level of the ancient Lake Ladoga. Some slightly brackish water diatom species may indicate occasional saline water incursions into the Ladoga basin but, on the other hand, slightly brackish water species also occur in the present Lake Ladoga.     

Nitrogen deposition and reduction of terrestrial biodiversity:Evidence from temperate grasslands

Biodiversity is thought to be essential for ecosystem stability, function and long-term sustainability. Since nitrogen is the limiting nutrient for plant growth in many terrestrial ecosystems, reactive nitrogen has the potential to reduce the diversity of terrestrial vegetation and associated biota through favouring species adapted to quickly exploiting available nutrients. Although the potential has long been recognised, only recently has enough evidence come together to show beyond reasonable doubt that these changes are already occurring. Linked together, experimental, regional/empirical, and time-series research provide a powerful argument that enhanced deposition of reactive nitrogen across Great Britain, and potentially the rest of Europe, has resulted in a significant and ongoing decline in grassland species richness and diversity.     

Infrared and Raman spectra and vibrational analyses calculated with Moeller–Plesset perturbation theory of second order of nitrosoethylene and its chloro-derivatives

The conformational and structural stabilities of nitrosoethylene CH₂=CH–N=O, chloronitrosoethylene CH₂=CCl–N=O, and Dichloronitrosoethylene CCl₂=CH–N=O were investigated by ab initio Moeller–Plesset perturbation theory of second order (MP2) calculations using the 6−311+G^** basis set to include electron correlation. From the calculations all three were predicted to exist predominantly in the planar trans structure (C=C and N=O bonds are trans to each other) with high trans-cis rotational barriers of about 9 kcal mol⁻¹ as a result of pronounced conjugation between C=C and N=O bonds. The vibrational frequencies were computed for the three molecules, and also the d ₁ and d ₂ deuterated variants for the parent molecule at the MP2 level. Normal coordinate analyses were carried out and the potential energy distributions (PED), among the symmetry coordinates of the normal modes of the molecule were computed. Complete vibrational assignments were made on the basis of normal coordinate analyses for the molecules. The two chlorinated derivatives of nitrosoethylene were also investigated in the same way. As expected, we then find high Raman and infrared intensities in all modes that contain a high content of chlorine movements because vibrations of C–Cl bonds lead to large changes in polarizability, as well as to a large change in dipole moment. However, modes involving double bonds also have quite large intensities. An appreciable number of modes in these molecules are more or less pure symmetry coordinates.     

Does clinical data quality affect fluid-structure interaction simulations of patient-specific stenotic aortic valve models?

Numerical models are increasingly used in the cardiovascular field to reproduce, study and improve devices and clinical treatments. The recent literature involves a number of patient-specific models replicating the transcatheter aortic valve implantation procedure, a minimally invasive treatment for high-risk patients with aortic diseases. The representation of the actual patient’s condition with truthful anatomy, materials and working conditions is the first step toward the simulation of the clinical procedure.The aim of this work is to quantify how the quality of routine clinical data, from which the patient-specific models are built, affects the outputs of the numerical models representing the pathological condition of stenotic aortic valve.Seven fluid–structure interaction (FSI) simulations were performed, completed with a sensitivity analysis on patient-specific reconstructed geometries and boundary conditions. The structural parts of the models consisted of the aortic root, native tri-leaflets valve and calcifications. Ventricular and aortic pressure curves were applied to the fluid domain.The differences between clinical data and numerical results for the aortic valve area were less than 2% but reached 12% when boundary conditions and geometries were changed. The difference in the aortic stenosis jet velocity between measured and simulated values was less than 11% reaching 27% when the geometry was changed. The CT slice thickness was found to be the most sensitive parameter on the presented FSI numerical model.In conclusion, the results showed that the segmentation and reconstruction phases need to be carefully performed to obtain a truthful patient-specific domain to be used in FSI analyses.     

Anthropogenic N deposition and the fate of 15NO 3 − in a northern hardwood ecosystem

Human activity has substantially increased atmospheric NO ₃ ^– deposition in many regions of the Earth, which could lead to the N saturation of terrestrial ecosystems. Sugar maple (Acer saccharum Marsh.) dominated northern hardwood forests in the Upper Great Lakes region may be particularly sensitive to chronic NO ₃ ^– deposition, because relatively moderate experimental increases (three times ambient) have resulted in substantial N leaching over a relatively short duration (5–7 years). Although microbial immobilization is an initial sink (i.e., within 1–2 days) for anthropogenic NO ₃ ^– in this ecosystem, we have an incomplete understanding of the processes controlling the longer-term (i.e., after 1 year) retention and flow of anthropogenic N. Our objectives were to determine: (i) whether chronic NO ₃ ^– additions have altered the N content of major ecosystem pools, and (ii) the longer-term fate of ¹⁵NO ₃ ^– in plots receiving chronic NO ₃ ^– addition. We addressed these objectives using a field experiment in which three northern hardwood plots receive ambient atmospheric N deposition (ca. 0.9 g N m^–2 year^–1) and three plots which receive ambient plus experimental N deposition (3.0 g NO₃ ^–-N m^–2 year^–1). Chronic NO ₃ ^– deposition significantly increased the N concentration and content (g N/m²) of canopy leaves, which contained 72% more N than the control treatment. However, chronic NO ₃ ^– deposition did not significantly alter the biomass, N concentration or N content of any other ecosystem pool. The largest portion of ¹⁵N recovered after 1 year occurred in overstory leaves and branches (10%). In contrast, we recovered virtually none of the isotope in soil organic matter (SOM), indicating that SOM was not a sink for anthropogenic NO ₃ ^– over a 1 year duration. Our results indicate that anthropogenic NO ₃ ^– initially assimilated by the microbial community is released into soil solution where it is subsequently taken up by overstory trees and allocated to the canopy. Anthropogenic N appears to be incorporated into SOM only after it is returned to the forest floor and soil via leaf litter fall. Short- and long-term isotope tracing studies provided very different results and illustrate the need to understand the physiological processes controlling the flow of anthropogenic N in terrestrial ecosystems and the specific time steps over which they operate.     

An ab initio and DFT study of structure and vibrational spectra of γ form of Oleic acid: Comparison to experimental data

Oleic acid (cis-9-octadecenoic acid) is the most abundant cis-unsaturated fatty acid in nature; it is distributed in almost all organisms. In this work, we present a detailed vibrational spectroscopy investigation of Oleic acid by using infrared and Raman spectroscopies. These data are supported by quantum mechanical calculations, which allow us to characterize completely the vibrational spectra of this compound. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311G(d, p) basis set. After a proper scaling the calculated wavenumbers show a very good agreement with the observed values. A complete vibrational assignment is provided for the observed Raman and infrared spectra of Oleic acid. In this work, we also investigate the deviation of vibrational wavenumbers computed with two quantum chemical methods (HF and B3LYP).     

Standardisation of data from real-time quantitative PCR methods – evaluation of outliers and comparison of calibration curves

Background  

As real-time quantitative PCR (RT-QPCR) is increasingly being relied upon for the enforcement of legislation and regulations dependent upon the trace detection of DNA, focus has increased on the quality issues related to the technique. Recent work has focused on the identification of factors that contribute towards significant measurement uncertainty in the real-time quantitative PCR technique, through investigation of the experimental design and operating procedure. However, measurement uncertainty contributions made during the data analysis procedure have not been studied in detail. This paper presents two additional approaches for standardising data analysis through the novel application of statistical methods to RT-QPCR, in order to minimise potential uncertainty in results.     

Species–area relationships arise from interaction of habitat heterogeneity and species pool

Species–area relationships (SARs) represent a ubiquitous and useful empirical regularity characterizing biodiversity. The rate of species accumulation, captured by the value of the exponent, z, varies substantially and for many reasons. We hypothesized that one of the major contributors to this variation is heterogeneity and its change with scale. To test this hypothesis, we used an array of natural microcosms for which we had invertebrate species composition and physical properties of habitat. Using GIS and cluster analysis, we organized the species data into four sets: communities grouped by spatial proximity in the field, randomly, by similarity of their physical habitat and by dissimilarity of their physical habitat. These groupings produced varying levels of heterogeneity at different scales. We fitted species–area and species–volume relationships to the four groups of communities, and obtained z-values for each group or a portion of the group if the slope of the relationship varied. As predicted, we recovered a number of properties reported by others. More interestingly, we found that small- and large-scale habitat heterogeneity produced scale-dependent z-values while the random grouping of pool habitats produced z-values more robust across scales but also susceptible to initial values of habitat richness. Habitat area affected rate at which species accumulated much less than the mean degree of inter-habitat differences: increasing area that is heterogeneous at broader scales produces higher z-values than increasing an area that shows heterogeneity at small scale only. Our results, while from a microcosm system, rely on logic transferable to larger scale data sets.     

Energy transfer from retinal to amino acids — a time-resolved study of the ultraviolet emission of bacteriorhodopsin

Two-step excitation of retinal in bacteriorhodopsin by visible light is followed by an energy transfer to amino acids that is seen as fluorescent emission around 350 nm. The fluorescence spectrum obtained after two-step excitation (2 × 527 nm) differs from the fluorescence spectrum obtained after one-step ultraviolet excitation (263.5 nm) by a strongly quenched emission with a fluorescence lifetime of 10 ± 5 ps and a smaller spectral width. The two-step absorption process presumably selects tryptophan residues which strongly couple to the retinal chromophore.     

Lack of interaction between α2 and dopamine D2-receptors in mediating their inhibitory effects on [3H]dopamine release from rat nucleus accumbens slices

The ₂-adrenoceptor agonist, UK14304, dose-dependently inhibited the electrically stimulated release of dopamine (DA) from rat nucleus accumbens slices. This effect was antagonized by idazoxan, confirming that it was an ₂-adrenoceptor mediated effect. There was no evidence of endogenous activation of noradrenergic receptors suggesting that the ₂-adrenoceptor agonist was not acting presynaptically to inhibit noradrenaline release. An in vitro superfusion technique was used to investigate wheher there was any interaction between ₂-adrenoceptors and DA D₂-receptors in mediating their inhibitory effects on [³H]DA release from rat nucleus accumbens slices. ₂-Adrenoceptor and DA D₂-receptors interact with similar second messenger systems and it was considered that they may compete for a common pool of G-proteins. The inhibitory effects of the ₂-adrenoceptor agonist, UK14304, and the DA receptor agonists, quinpirole, apomorphine and pergolide were not independent. However, there was no evidence of any interaction between UK14304 and the DA D₂-receptor antagonists, sulpiride or haloperidol, suggesting that the two receptors do not compete for a common pool of G-proteins in mediating their inhibitory effects on DA release.     

Mechanism of interaction of the cyanine dye DiS−C3-(5) with renal brush-border vesicles

Summary The equilibrium binding mechanism and kinetics of binding of diS–C₃-(5) (3,3-dipropylthiodicarbocyanine iodide) to rabbit renal brush-border membrane vesicles (BBMV) were examined using steady-state and time-resolved fluorescence, and fluorescence stopped-flow methods. In aqueous solution, diS–C₃-(5) exists as a monomer at concentrations <5 m with fluorescence emission peak at 670 nm (excitation 622 nm), anisotropyr=0.102, and lifetime =1.2 nsec (23°C). Upon addition of increasing BBMV (voltage clamped to 0 mV using K⁺/valinomycin), the 670 nm emission peak decreases, corresponding to formation of a nonfluorescent membrane dimer, and subsequently a new emission peak at 695 nm increases, corresponding to membrane monomer. Dynamic depolarization studies show that aqueous diS–C₃-(5) rotation is unhindered with a rotational rateR=0.57 nsec^–1 while membrane monomer is hindered with steady-state anisotropyr=0.190, lifetime =2.1 nsec,R=0.58 nsec^–1 and limiting anisotropyr =0.11. Based on equilibrium fluorescence titrations, the membrane monomer-dimer (M-D) dissociation constant,K _d=[M]²/[D][BBMV], is 0.0013, where BBMV is expressed as membrane phospholipid concentration. Three distinct kinetic processes are identified by stopped-flow experiments in which BBMV are mixed with diS–C₃-(5). There is rapid binding of diS–C₃-(5) to the membrane to form bound monomer with a 6-msec exponential time constant. The membrane monomer at the membrane outer surface then aggregates to form bound dimer at the outer surface with a concentration independent time constant of 30 msec. The overall dimerization reaction probably consists of a rate-limiting reorientation process (30 msec) followed by a rapid dimerization which occurs on a nanosecond time scale. Finally, there is a 0.8 to 1 sec translocation of membrane dimer between symmetric sites at the inner and outer membrane surfaces. The translocation reaction is the step which is probably sensitive to changes in transmembrane electrical potential.     

Thermodynamics of hCG–monoclonal antibody interaction: an analysis of real time kinetics data obtained using radiolabeled hCG probe

A thermodynamic analysis of the interaction of ¹²⁵I-labeled human chorionic gonadotropin (IhCG) with two of its monoclonal antibodies (MAbs) was carried out. The dissociation profile of IhCG–MAb complex conforms to a two-step model. vant Hoff enthalpies were calculated with the K_A (equilibrium constant) values obtained from dissociation at different temperatures. Free energy and entropy changes were calculated using the standard equations. ΔH values for one of the MAbs, viz. VM7 were favorable at temperatures beyond 30 °C. Interestingly, the ΔS values were also favorable at all temperatures. In the case of MAb VM4a, however, the interaction throughout the temperature range was driven by large favorable entropic contributions, indicating the importance of hydrophobic interaction in the binding of this MAb to hCG. The energetics of the interaction of these two monoclonals with hCG is discussed.