Hypothetical 3D Research Articles

No species is an island: testing the effects of biotic interactions on models of avian niche occupation.

Traditionally, the niche of a species is described as a hypothetical 3D space, constituted by well-known biotic interactions (e.g. predation, competition, trophic relationships, resource–consumer interactions, etc.) and various abiotic environmental factors. Species distribution models (SDMs), also called “niche models” and often used to predict wildlife distribution at landscape scale, are typically constructed using abiotic factors with biotic interactions generally been ignored. Here, we compared the goodness of fit of SDMs for red-backed shrike Lanius collurio in farmlands of Western Poland, using both the classical approach (modeled only on environmental variables) and the approach which included also other potentially associated bird species. The potential associations among species were derived from the relevant ecological literature and by a correlation matrix of occurrences. Our findings highlight the importance of including heterospecific interactions in improving our understanding of niche occupation for bird species. We suggest that suite of measures currently used to quantify realized species niches could be improved by also considering the occurrence of certain associated species. Then, an hypothetical “species 1” can use the occurrence of a successfully established individual of “species 2” as indicator or “trace” of the location of available suitable habitat to breed. We hypothesize this kind of biotic interaction as the “heterospecific trace effect” (HTE): an interaction based on the availability and use of “public information” provided by individuals from different species. Finally, we discuss about the incomes of biotic interactions for enhancing the predictive capacities on species distribution models.

Selection of a human butyrylcholinesterase-like antibody single-chain variable fragment resistant to AChE inhibitors from a phage library expressed in E. coli

Organophosphates are potent poisoning agents that cause severe cholinergic toxicity. Current treatment has been reported to be unsatisfactory and novel antidotes are needed. In this study, we used a single-chain variable fragment (scFv) library to select a recombinant antibody fragment (WZ1–14.2.1) with butyrylcholinesterase-like catalytic activity by using an innovative method integrating genetic selection and the bait-and-switch strategy. Ellman assay demonstrated that WZ1–14.2.1 has Michaelis-Menten kinetics in the hydrolysis of all the three substrates used, acetylthiocholine, propionylthiocholine and butyrylthiocholine. Notably, the catalytic activity was resistant to the following acetylcholinesterase inhibitors: neostigmine, iso-OMPA, chlorpyrifos oxon, dichlorvos, and paraoxon ethyl. Otherwise, the enzymatic activity of WZ1–14.2.1 was inhibited by the selective butyrylcholinesterase inhibitor, ethopropazine, and by the Ser-blocking agent phenylmethanesuphonyl fluoride. A hypothetical 3D structure of the WZ1–14.2.1 catalytic site, compatible with functional results, is proposed on the basis of a molecular modeling analysis.

Molecular cloning, characterization and expression profile of a glutathione peroxidase-like thioredoxin peroxidase (TPxGl) of the rodent malaria parasite Plasmodium berghei

Glutathione peroxidases (GPx) comprise an important group of redox active proteins with diverse functions, including antioxidant defense and signaling. Although the genome of the malaria parasite Plasmodium does not contain a genuine GPx gene a glutathione peroxidase-like thioredoxin peroxidase (TPxGl) has recently been identified and biochemically characterized in the human malaria parasite P. falciparum. To gain more insight into the potential biological function of this enzyme we have cloned and expressed TPxGl of the rodent model system P. berghei (PbTPxGl). Biochemical characterization confirmed that the protein is redox active with the P. berghei thioredoxin system. We compared PbTPxGl to recently characterized thioredoxin-dependent GPx-type proteins of other organisms, and generated the first hypothetical 3D model of a Plasmodium TPxGl, which shows the conservation of the thioredoxin-fold as well as the spatial orientation of a classic GPx catalytic tetrad. In vivo studies indicate that PbTPxGl is continuously expressed in all P. berghei asexual blood stages, gametocytes and in early mosquito-stage parasites. Confocal microscopy suggest a cytoplasmic localization of PbTPxGl in all investigated parasite life stages, specifically in mature ookinetes. Our data provides new insights into the structure and ubiquitous expression of Plasmodium TPxGl and warrants further investigation into this potentially important redox enzyme.

Unusual sevenfold coordination of Ru in complex hydride Na3RuH7: Prospect for formation of [FeH7]3– anion

We used density-functional calculations to clarify the origin of the unusual sevenfold coordination of Ru by H in Na3RuH7. We found that the D5h symmetry of the ligands enables the formation of strong covalent bonds of Ru and H through ligand-field effects, stabilizing the sevenfold coordination. We also examined the possible synthesis of the hypothetical 3d analog, Li3FeH7, which has a gravimetric hydrogen density of 8.4 mass%. The calculated enthalpy change of −16 kJ/mol H2 for the reaction, 3LiH+Fe+2H2→Li3FeH7, reveals a possible route to a stable complex hydride containing [FeH7]3–.

Quasi 3D modeling of water flow in vadose zone and groundwater

Summary The complexity of subsurface flow systems calls for a variety of concepts leading to the multiplicity of simplified flow models. One habitual simplification is based on the assumption that lateral flow and transport in unsaturated zone are not significant unless the capillary fringe is involved. In such cases the flow and transport in the unsaturated zone above groundwater level can be simulated as a 1D phenomenon, whereas the flow and transport through groundwater are viewed as 2D or 3D phenomena. A new approach for a numerical scheme for 3D variably saturated flow using quasi 3D Richards’ equation and finite difference scheme is presented. The corresponding numerical algorithm and the QUASI-3D computer code were developed. Results of the groundwater level simulations were compared with transient laboratory experimental data for 2D data constant–flux infiltration, quasi-3D HYDRUS-MODFLOW numerical model and a FULL-3D numerical model using Richards’ equation. Hypothetical 3D examples of infiltration, pumping and groundwater mound dissipation for different spatial–time scales are presented. Water flow simulation for the Alto Piura aquifer (Peru) demonstrates the QUASI-3D model application at the regional scale. Computationally the QUASI-3D code was found to be more efficient by an order of 10–300%, while being accurate with respect to the benchmark fully 3D variable saturation code, when the capillary fringe was considered.

The Campi Flegrei Blind Test: Evaluating the Imaging Capability of Local Earthquake Tomography in a Volcanic Area

During the 1982–1984 bradyseismic crises in the Campi Flegrei area (Italy), the University of Wisconsin deployed a network of seismological stations to record local earthquakes. In order to analyse the potential of the recorded data in terms of tomographic imaging, a blind test was recently set up and carried out in the framework of a research project. A model representing a hypothetical 3D structure of the area containing the Campi Flegrei caldera was also set up, and a synthetic dataset of time arrivals was in turn computed. The synthetic dataset consists of several thousand P- and S-time arrivals, computed at about fourteen stations. The tomographic inversion was performed by four independent teams using different methods. The teams had no knowledge of either the input velocity model or the earthquake hypocenters used to create the synthetic dataset. The results obtained by the different groups were compared and analysed in light of the true model. This work provides a thorough analysis of the earthquake tomography potential of the dataset recording the seismic activity at Campi Flegrei in the 1982–1984 period. It shows that all the tested earthquake tomography methods provide reliable low-resolution images of the background velocity field of the Campi Flegrei area, but with some differences. However, none of them succeeds in detecting the hypothetical structure details (i.e. with a size smaller than about 1.5–2 km), such as a magmatic chamber 4 km deep and especially the smaller, isolated bodies, which represent possible magmatic chimneys and intrusions.

Virtual 3D Microstructures with Specified Characteristics of State Variable Distributions

For a wide variety of model calculations a hypothetical 3D microstructure is required as input. Although experimental data are frequently used to this purpose, 3D microstructures are difficult to measure experimentally. In order to circumvent these difficulties, a virtual microstructure generator to simulate a specific 3D material microstructure is proposed. Such a virtual microstructure could serve as input for different types of models, would allow a faster model prototyping, would help to explore the boundary conditions of models and reduces the number of unnecessary experimental measurements. In the current paper, the method to generate and to control the grain size distribution as well as texture are discussed.

Highly fucosylated N-glycan ligands for mannan-binding protein expressed specifically on CD26 (DPPVI) isolated from a human colorectal carcinoma cell line, SW1116

The serum mannan-binding protein (MBP) is a host defense C-type lectin specific for mannose, N-acetylglucosamine, and fucose residues, and exhibits growth inhibitory activity toward human colorectal carcinoma cells. The MBP-ligand oligosaccharides (MLO) isolated from a human colorectal carcinoma cell line, SW1116, are large, multiantennary N-glycans with highly fucosylated polylactosamine-type structures having Le(b)-Le(a) or tandem repeats of the Le(a) structure at their nonreducing ends. In this study, we isolated the major MBP-ligand glycoproteins from SW1116 cell lysates with an MBP column and identified them as CD26/dipeptidyl peptidase IV (DPPIV) (110 kDa) and CD98 heavy chain (CD98hc)/4F2hc (82 kDa). Glycosidase digestion revealed that CD26 contained such complex-type N-glycans that appear to mediate the MBP binding. MALDI-MS of the N-glycans released from CD26 by PNGase F demonstrated conclusively that CD26 is the major MLO-carrying protein. More interestingly, a comparison of the N-glycans released from the MBP-binding and non-MBP-binding glycopeptides suggested that complex-type N-glycans carrying a minimum of 4 Le(a)/Le(b) epitopes arranged either as multimeric tandem repeats or terminal epitopes on multiantennary structures are critically important for the high affinity binding to MBP. Analysis of the N-glycan attachment sites demonstrated that the high affinity MLO was expressed preferentially at some N-glycosylation sites, but this site preference was not so stringent. Finally, hypothetical 3D models of tandem repeats of the Le(a) epitope and the MBP-Lewis oligosaccharide complex were presented.

SU-FF-J-04: A Method to Model 4D Organs for Monte Carlo Radiation Dosimetry

Purpose: The objective of this study is to construct a detailed 4D standard patient testbed for studying effects of organ motions on treatment planning. Method and Materials: Segmented Visible Human images, containing 80 organs and tissues defined in a 3D static model called VIP-Man, were combined with Non-Uniform Rational B-Splines (NURBS) and clinically obtained respiratory motion data to deform the surfaces of the lungs. Deformable image registration was performed to establish correct spatial definition of the organ boundaries. A lesion in the left lung was simulated. The 4D model containing 3D anatomical information for each of the eight simulated motion phases was then re-voxelized before being defined in the EGS Monte Carlo code. A hypothetical 3D static treatment plan for the lung lesion was considered in the Monte Carlo simulations. Results: Normalized doses to the lesion are plotted for each of the respiratory phases. It has been found that the lesion could be under-dosed by as much as 40% for different respiratory phases and for the irradiation conditions considered in this study. Although more analysis is underway, this study clearly demonstrates that the motion of the organs can be accurately modeled and implemented in the Monte Carlo code for 4D dose calculations. Conclusion: A partial-body 4D VIP-Man model has been developed using the NURBS and clinical respiratory data, and implemented into the EGS Monte Carlo code for dose calculations. The detailed anatomical information in this 4D model makes it a very convenient research tool to study radiation treatment planning and medical imaging involving moving organs and tissues. This study also identified issues to be further addressed for routine clinical research and applications. The procedures can be extended to patient specific models constructed, for example, from multi-slice CT data.

Computational investigation into the phase transitions from AlPO4-H3

Molecular dynamics simulation approach has been used to investigate the phase transitions from aluminophosphate AlPO 4 -H 3 . Derived from AlPO 4 -H 3 , several hypothetical models of its high-temperature phases are designed through removing the bridged water molecules and changing the up-down connected sequences of T-sites in the 4-membered rings. Full geometry optimizations are performed to obtain structural parameters for the models that are compared to the reported data, and their structure features and thermodynamic stabilities have been discussed. The simulation study suggests that AlPO 4 -H 3 is energetically favored to transform to AlPO 4 -C, and then to AlPO 4 -D as well as to other novel hypothetical 3D open-frameworks.

A 3D slope stability analysis method assuming parallel lines of intersection and differential straining of block contacts

A three-dimensional (3D) method of analysis of the stability of slopes was developed based on the sliding mechanism observed in the 1988 failure of the Kettleman Hills landfill slope (Kettleman City, California) and the associated model studies. By adopting a limit equilibrium concept, the method assumes the sliding mass as a block system in which the contacts between blocks are inclined. The lines of intersection of the block contacts are assumed to be parallel, which enables the sliding kinematics. In consideration of the differential straining between blocks, the shear stresses on the slip surface and the block contacts are evaluated based on the degree of shear strength mobilization on these contacts. The overall factor of safety is calculated based on the force equilibrium of the individual blocks and the entire block system as well. Based on comparisons with a series of hypothetical 3D and 2D problems with known solutions, the method was generally found to be accurate in predicting the stability of slopes involving a translational type of sliding failure. For rotational sliding failures in clays, however, the method appears to slightly overestimate the calculated factor of safety; up to as much as 10% in a typical problem examined in this study.Key words: slope stability, 3D method, limit equilibrium, block kinematics, strain incompatibility.

Efficient Folding of the Insect Neuropeptide Eclosion Hormone by Protein Disulfide Isomerase

Eclosion hormone is an insect neuropeptide that consists of 62 amino acid residues including three disulfide bonds. We have previously reported its hypothetical 3D structure consisting mainly of three alpha-helices. In this paper, we report the effects of chaperone proteins on the refolding of denatured eclosion hormone in a redox buffer containing reduced and oxidized glutathione. Urea-denatured eclosion hormone was spontaneously reactivated within 1 min with a yield of more than 90%, while beta-mercaptoethanol-denatured eclosion hormone was reactivated in a few minutes with a yield of 75%. Under the same experimental conditions, eclosion hormone treated with beta-mercaptoethanol and urea was reactivated slowly with a yield of 47% over a period of 2 h. Protein disulfide isomerase, a eucaryotic chaperone protein, markedly increased the reactivation yield and rate of the totally denatured hormone. GroE oligomers slightly improved the reactivation yield but peptidyl prolyl isomerase had no influence on yield or rate. We propose that the folding pathway of eclosion hormone involves at least two rate-limiting steps, and that protein disulfide isomerase is likely to be involved in the folding in insect neuronal cells.

Molecular Line Absorption in a Scattering Atmosphere. Part I: Theory

This paper revisits the classical problem of particle scattering‐gaseous absorption and considers the extent to which the growth of absorption lines of a known gas can be used to obtain information about the scattering particles. The focus of the study is directed toward interpretation of the reflection spectrum of the O 2 A band located in the spectral region between 0.759 and 0.771 mm and the results provide a theoretical foundation for the retrieval of particle information described in a related study. This study demonstrates that there are six main properties that affect the absorption and reflection spectra: the optical depth of the cloud or aerosol, the pressure level of the top of this layer, the (pressure) thickness of the layer, the scattering phase function, the particle single-scatter albedo, and the surface albedo. Measured quantities, such as the spectral radiance or the ratio of in-absorption to continuum radiances are shown to be sensitive to these parameters in a manner that varies according to the O 2 optical depth. This variation sensitivity offers a way of separating the dependence of the measurements on these parameters, thereby providing some basis for their retrieval with suitable spectral measurements that resolve a sufficient range of O2 optical depth. Specifically, it is shown that radiances reflected from thin layers are sensitive to optical depth and phase function whereas the radiance ratio is sensitive to layer height. For thick layers, the sensitivity to optical depth diminishes leaving primarily a sensitivity to bulk information about the scattering phase function. By measuring radiances as a function of changing O 2 absorption, it is possible to distinguish optically thin layers above brighter lower reflecting surfaces, providing an ability to distinguish high-level thin cloud over brighter lower-level clouds or reflecting surfaces. The effects of 3D geometry on the spectral radiances is also considered in the context of photon path. It is shown how the spectral radiances provide some insight on 3D effects and the probable importance of these 3D effects on the retrievals. The equivalence theorem is illustrated and is used to provide line-by-line simulations of the reflection spectrum from hypothetical 3D clouds. A method to identify the nature of the 3D bias on retrievals of optical depth is discussed.

Possible 3D Carbon Structures as Progressive Intermediates in Graphite to Diamond Phase Transition

Modeling successive contractions of conventional graphite structure in different directions, together with some chemical reactions (consisting of Csp2 to Csp3 hybridization changes, followed by new bonding between closing carbons), simulates a graphite to diamond phase transition. The stable intermediate structures were optimized by a molecular mechanic approach, giving rise to new hypothetical 3D crystal structures which progress along the transition in the order of increasing density from 2.22 to 3.30 gcm−3. There are graphite bilayers with planar and pyramidal Csp2, graphite bilayers with Csp2 and Csp3, diamonds with Csp2 and Csp3, and diamonds with only Csp3. We present eight different models: seven orthorhombic and one cubic Ia-3, the latter close to one structure proposed for supercubane C8. Additionally, some other noncrystalline models, made by optimizing unconstrained clusters from the above crystal models, are proposed. Although these structures are speculative, some of them present synthetic polycrystal X-ray diffraction with their highest peaks among those observed in reported experimental phases between graphite and diamond, which gives more reality to the proposed models.

The functional residues and their representation by a hypothetical 3D model of silkworm eclosion hormone.

We have previously reported that an insect neuropeptide, eclosion hormone contained an alpha-helix in the N-terminal region and the helix was likely to play an important role in constructing an active globular structure. Furthermore, Met24 and Phe25 were found to be indispensable for the biological activity. On the other hand, no strict structure at the C-terminal side was found. In this paper, we predicted the secondary structure in the C-terminal side and analyzed the functional residues by a Gly-substitution technique. As a result, we speculated that the eclosion hormone contains three alpha-helices throughout the molecule which are essential for an active peptide structure. Moreover, we found four residues important for the biological activity of silkworm eclosion hormone: Phe29, Ile55, Phe58 and Leu59. In order to understand these results stereochemically, we have constructed a 3D structure using computer aided molecular modelling. The hypothetical 3D model showed that Phe25 and Phe58 interact together in a hydrophobic manner to keep a globular form. Met24, Phe29, and Ile55 are exposed to solvent to have a hydrophobic interaction with an eclosion hormone receptor. Leu59 can also play an important role by forming a functional conformation with Phe29 and Ile55.

Secondary structure of ShK toxin, a potassium-channel-blocking peptide

Sea anemones possess small K-channel-blocking peptides about the same size as the scorpion K-channel toxins. We have estimated the secondary structure content (33% helix, 26% β-sheet) of one of these toxins, ShK toxin, using CD, Raman, and FTIR spectroscopy. A hypothetical 3D structure of the peptide core has been constructed using secondary structure and disulfide-linkage constraints; a single helical segment running from Ala14 through Leu25 is predicted.

Neuropeptide Y: identification of the binding site

Based on the hypothetical 3D structure of neuropeptide Y (NPY), NPY 1-4-Aca-25-36, a 17 amino acid analogue, has been synthesized replacing the sequence NPY 5-24 by epsilon-aminocaproic acid (Aca). This low-molecular weight deletion analogue showed nearly comparable receptor affinity to NPY. In order to elucidate the structural requirements for receptor recognition each amino acid of 1-4-Aca-25-36 was exchanged by its D-enantiomer, glycine and L-alanine. In addition distinct amino acids were replaced by closely related residues. Multiple peptide synthesis was applied using Fmoc-strategy and BOP activation. Binding assay was performed on rabbit kidney membrane preparations. The results of structure affinity studies suggest that the C-terminal tetrapeptide NPY 33-36 is essential for receptor recognition.

The systematic enumeration of (4;2)-connected 3D nets related to the tridymite group

Forty-two hypothetical 3D nets are derived by applying four types of transformations (or combinations thereof) to the previously described tridymite group of structures. Two novel transformations are proposed, one preserving the (hexagonal or orthorhombic) symmetry and another converting the hexagonal symmetry into orthorhombic. Correspondingly, groups of hypothetical 3D framework structures are derived. The properties of frameworks belonging to these groups are compared and discussed.