Can interaction coefficients be determined from cencus data?

Summary The method of estimating interactions proposed independently by Pimm and Schoener is studied using field data from the community of rodents which lives in the arid, rocky habitats of Israel. One important problem the method addresses is how to remove the effects of habitat heterogeneity on the estimate. We tried six different variations of the analysis scheme outlined by Crowell and Pimm, and found their results qualitatively inconsistent. This was especially true when we compared the results produced from separate habitat variables with those produced from the principal components of the habitat variation.Another problem, this one not previously addressed, is great variation in the average abundance of the different species. We discovered that the ratio of the average abundances of two species is the best predictor of the value of their coefficients of interaction. Common species appear to have weak influence on rare ones; rare ones appear to have strong influence on common ones. The statistical mechanism which produces this relationship is clear, indicating that the relationship is an artifact.     

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.     

Specific changes of circular dichroism spectra upon interaction of 5′-GMP with poly-L-lysine

The CD spectra of poly-L-lysine in the presence of several 5′-nucleoside monophosphates have been measured at pH 7 and at low nucleotide concentrations. The spectra of the mixtures differ substantially from the sum of the spectra of the respective components only in the case of 5′-GMP. The binding of 5′-GMP induces a strong negative band at about 260 nm and large changes at shorter wavelengths. The spectral changes, which are due to a rather slow kinetic process, indicate that guanosine nucleotides are able to form regular structures upon binding by poly-L-lysine. The formation of these structures is presumably accompanied by a change of the conformation of the polyamino acid.     

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.     

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.     

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.     

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.     

Distribution of Na+, K+ and Cl− between nucleus and cytoplasm inChironomus salivary gland cells

Summary Previous studies of the electrochemical activity coefficients of intracellular Na⁺ and K⁺ have suggested that the free form of these ions may be unevenly distributed within the intracellular fluids. One possible site of such subcellular compartmentalization is the cell nucleus. In order to examine this possibility, the cells ofChironomus salivary glands were studied with conventional liquid ion-exchange microelectrodes sensitive to K⁺ and Cl^–, with a new liquid ion-exchange microelectrode sensitive to Na⁺, and with open-tipped micropipets. Both the electrochemical activities for Na⁺, K⁺ and Cl^–, and the electrical potential were the same on both sides of the nuclear membrane. The possibility was considered that a difference in the junction potentials within the nucleoplasm and cytoplasm might have masked a real difference in electrical potential between these two phases. To study that possibility, changes were induced in the junction potentials by altering the composition of the fluid filling the exploring micropipets. The results have suggested that the magnitudes of the junction potentials are the same on both sides of the nuclear envelope. The simplest interpretation of the data is that the chemical activities of Na⁺, K⁺ and Cl^– are the same within the nucleus and cytoplasm. This suggests that other subcellular structures, possibly the endoplasmic reticulum and mitochondria, are responsible for subcellular compartmentalization.     

M?ssbauer spectra of photosystem-I-reaction centres from the blue-green alga Chlorogloea fritschii.

Substantial amounts of iron have been shown by Mössbauer spectroscopy to be present in Photosystem-I preparations from the blue-green alga Chlorogloeta fritschii. Changes in the spectra on chemical reduction provide evidence that some of this iron is very similar to that found in the 4Fe-4S centres of ferredoxins. Such reduced samples also show e.p.r. signals consistent with maximum reduction of iron-sulphur centres A and B of Photosystem I. An unchanged component in the spectra indicates, assuming all centres A and B are reduced, the presence of another iron-containing species.     

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).