Assessment of Elk Highway Permeability by Using Global Positioning System Telemetry

Abstract: Highways have significant direct and indirect impact on natural ecosystems, including wildlife barrier and fragmentation effects, resulting in diminished habitat connectivity and highway permeability. We used Global Positioning System (GPS) telemetry to assess Rocky Mountain elk (Cervus elaphus nelsoni) permeability across a 30-km stretch of highway in central Arizona, USA, currently being reconstructed with 11 wildlife underpasses, 6 bridges, and associated ungulate-proof fencing. The highway was reconstructed in phases, allowing for comparison of highway crossing and passage rates during various stages of reconstruction. We instrumented 33 elk (25 F, 8 M) with GPS receiver collars May 2002 to April 2004. Our collars accrued 101,506 GPS fixes with 45% occurring within 1 km of the highway. Nearly 2 times the proportion of fixes occurred within 1 km of the highway compared with random. We think elk were attracted to the highway corridor by riparian—meadow foraging habitats that were 7 times more concentrated within the 1-km zone around the highway compared with the mean proportion within elk use areas encompassing all GPS fixes. Elk crossed the highway 3,057 times; crossing frequency and distribution along the highway were aggregated compared with random. Crossing frequency within 0.16-km highway segments was negatively associated with the distance to riparian—meadow habitats (r_s = -0.714, n = 190, P < 0.001). Mean observed crossing frequency (92.6 ± 23.5 [SE] crossings/elk) was lower than random (149.6 ± 27.6 crossings/elk). Females crossed 4.5 times as frequently as males. Highway permeability among reconstruction classes was assessed using passage rates (ratio of highway crossings to approaches); our overall mean passage rate was 0.67 ± 0.08 crossings per approach. The mean passage rate for elk crossing the highway section where reconstruction was completed (0.43 ± 0.15 crossings/approach) was half that of sections under reconstruction and control sections combined (0.86 ± 0.09 crossings/approach). Permeability was jointly influenced by the size of the widened highway and associated vehicular traffic on all lanes. Crossing frequency was used to delineate where ungulate-proof fencing yielded maximum benefit in intercepting and funneling crossing elk toward underpasses, promoting highway safety. Use of passage rates provides a quantitative measure to assess permeability, conduct future pre- and postconstruction comparisons, and to develop mitigation strategies to minimize highway impacts to wildlife.     

QSE: A new 3-D solvent exposure measure for the analysis of protein structure

Solvent exposure of amino acids measures how deep residues are buried in tertiary structure of proteins, and hence it provides important information for analyzing and predicting protein structure and functions. Existing methods of calculating solvent exposure such as accessible surface area, relative accessible surface area, residue depth, contact number, and half-sphere exposure still have some limitations. In this article, we propose a novel solvent exposure measure named quadrant-sphere exposure (QSE) based on eight quadrants derived from spherical neighborhood. The proposed measure forms a microenvironment around Cα atom as a sphere with a radius of 13??, and subdivides it into eight quadrants according to a rectangular coordinate system constructed based on geometric relationships of backbone atoms. The number of neighboring Cα atoms whose labels are the same is given as the QSE value of the center Cα atom at hand. As evidenced by histograms that show very different distributions for different structure configurations, the proposed measure captures local properties that are characteristic for a residue's eight-directional neighborhood within a sphere. Compared with other measures, QSE provides a different view of solvent exposure, and provides information that is specific for different tertiary structure. As the experimental results show, QSE measure can potentially be used in protein structure analysis and predictions.     

Self-absorption in spheres and cylinders of radioactive material

According to thereciprocity law, the total dose absorbed in a specimen irradiated by a point source can be inferred from the reciprocal situation, where the absorber is replaced by a source of the same shape and the radiation is measured at the position of the original point source. In this paper, for a spherical source of homogeneous radioactive material with absorption coefficient μ₁, we calculate the intensity of radiation (or flux) at a pointP, as well as the intensity which would be found at the same point if μ₁ were zero. The ratio between these two quantities is denoted byk. We assume throughout that absorption follows the simple exponential law. Self-absorption can also be characterized by the numberv, which is defined as the ratio between the total radiation current flowing through the surface of the source and the total current obtained if there were no absorption. For a homogeneous spherical source in a nonabsorbing medium it is shown that the quantityk becomes equal tov if the distance between the pointP and the center of the sphere is sufficiently large. This fact was used by W. K. Sinclair in estimating an absorption coefficient from his experimental results. We also derive an expression for the self-absorption ratio,v, of acylindrical source. In the limiting case of an infinitely long cylinder our result coincides with an equation previously found by S. Kushneriuk. This work was performed under the auspices of the U.S. Atomic Energy Commission.     

The Validity of theAspergillus nidulansLinkage Map

TheAspergillus nidulanslinkage map is reviewed as a background to physical mapping by cosmid cross-hybridization and genome sequencing. DNA-based methods depend on contiguity, so that the resulting maps are only as good as the weakest link, whereas each new marker added to a linkage map can provide independent confirmation of the positions of its neighbors. For all eight chromosomes ofA. nidulansa reliable framework has been provided by analysis of mitotic crossing over, in many cases substantiated by the study of translocation disomics. Building on this framework, there is a backbone of loci linked by reliable three-point meiotic mapping and a second set of less precisely mapped loci. The result is a map with a high degree of self-consistency although some areas of uncertainty or conflict are also noted.     

Behavioral responses of female oriental fruit flies to the odor of papayas at three ripeness stages in a laboratory flight tunnel (Diptera: Tephritidae)

Behavioral responses of adult female oriental fruit flies, Dacus dorsalisHendel, to the odor of papayas from three ripeness classes were studied using a threechoice flight tunnel bioassay. Laboratoryreared flies were allowed to respond freely to any of three papaya odors (mature green, colorbreak to one-fourth ripe, and one-half to full ripe) emanating from identical (spherical) fruit models. Five behaviors were measured in assessing the fly's relative attraction to the odors (number of landings), arrestment (total fly seconds on sphere), fly-fly interactions on the fruit model (maximum and modal fly density), and acceptance for oviposition (total eggs laid). Females showed no significant difference in total fly landings based on all age classes combined. Significant differences were noted among age classes. Females spent more total time on the sphere and showed a higher maximum density and modal fly density to ripe fruit than to green fruit odors. Ovipositional acceptance of fruit models based on the total number of eggs laid in a sphere was greater in response to the ripefruit odor than to the other two odor classes. Olfactorystimulated behavioral responses of females to the odor of ripe papayas were significantly different from the other ripeness classes for all behaviors at 8 days postemergence and then declined in 11-day-old flies. Behavioral responses were greater during the afternoon than in the morning. Observations of wild oriental fruit flies to papayas in the field indicated a preference for residing on riper fruit. The results of this study are discussed with regard to the role of olfactory inputs generated by the odor of ripening fruit on female attraction and oviposition behavior resulting in infestation of papayas by oriental fruit fly.     

A comparison of camera trap and permanent recording video camera efficiency in wildlife underpasses

In the current context of biodiversity loss through habitat fragmentation, the effectiveness of wildlife crossings, installed at great expense as compensatory measures, is of vital importance for ecological and socio‐economic actors. The evaluation of these structures is directly impacted by the efficiency of monitoring tools (camera traps…), which are used to assess the effectiveness of these crossings by observing the animals that use them. The aim of this study was to quantify the efficiency of camera traps in a wildlife crossing evaluation. Six permanent recording video systems sharing the same field of view as six Reconyx HC600 camera traps installed in three wildlife underpasses were used to assess the exact proportion of missed events (event being the presence of an animal within the field of view), and the error rate concerning underpass crossing behavior (defined as either Entry or Refusal). A sequence of photographs was triggered by either animals (true trigger) or artefacts (false trigger). We quantified the number of false triggers that had actually been caused by animals that were not visible on the images (“false” false triggers). Camera traps failed to record 43.6% of small mammal events (voles, mice, shrews, etc.) and 17% of medium‐sized mammal events. The type of crossing behavior (Entry or Refusal) was incorrectly assessed in 40.1% of events, with a higher error rate for entries than for refusals. Among the 3.8% of false triggers, 85% of them were “false” false triggers. This study indicates a global underestimation of the effectiveness of wildlife crossings for small mammals. Means to improve the efficiency are discussed.     

Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition

An efficient biologically enhanced sampling geometric docking method is presented based on the FTDock algorithm to predict the protein-protein binding modes. The active site data from different sources, such as biochemical and biophysical experiments or theoretical analyses of sequence data, can be incorporated in the rotation-translation scan. When discretizing a protein onto a 3-dimensional (3D) grid, a zero value is given to grid points outside a sphere centered on the geometric center of specified residues. In this way, docking solutions are biased toward modes where the interface region is inside the sphere. We also adopt a multiconformational superposition scheme to represent backbone flexibility in the proteins. When these procedures were applied to the targets of CAPRI, a larger number of hits and smaller ligand root-mean-square deviations (RMSDs) were obtained at the conformational search stage in all cases, and especially Target 19. With Target 18, only 1 near-native structure was retained by the biologically enhanced sampling geometric docking method, but this number increased to 53 and the least ligand RMSD decreased from 8.1 A to 2.9 A after performing multiconformational superposition. These results were obtained after the CAPRI prediction deadlines.     

A geometrical constraint approach for reproducing the native backbone conformation of a protein

It is known that the backbone conformation of a protein can be reproduced with precision once a correct contact map (two-dimensional representation showing residue pairs in contact) is given as geometrical constraints. There is, however, no way to infer the correct contact map for a protein of unknown structure. We started with one-dimensional constraints using the quantity N14 (the number of neighboring residues within the radius of 14 Å). Since the plot of N14 along a chain shows a good correlation with the corresponding amino acid sequence, the N14 profile obtained from the X-ray structure is predictable from the sequence. Construction of backbone conformations under a given N14 profile was carried out in the following two steps: (1) a contact map from the N14 profile was produced by taking the product of N14 values of every two residues; (2) backbone conformations were generated by applying the distance geometry technique to distance constraints given by the contact map. If present, disulfide bonds in a protein, as well as the secondary structure, were treated as additional constraints, and both cases with or without the additional information were examined. The method was tested for 11 proteins of known structure, and the results indicated that the reproduced conformation was fairly good, using an X-ray structure for comparison, for small proteins of less than 80 residues long. The basic assumption and effectiveness of the present method were compared with those of previous studies employing the geometrical constraint approach. It has become clear that the specific, one-dimensional information (e.g., N14 profile) is more effective than nonspecific, two-dimensional constraints, such as average interresidue distances between particular types of amino acids. © 1993 Wiley-Liss, Inc.     

Orientational potentials extracted from protein structures improve native fold recognition

We develop coarse-grained, distance- and orientation-dependent statistical potentials from the growing protein structural databases. For protein structural classes (alpha, beta, and alpha/beta), a substantial number of backbone-backbone and backbone-side-chain contacts stabilize the native folds. By taking into account the importance of backbone interactions with a virtual backbone interaction center as the 21st anisotropic site, we construct a 21 x 21 interaction scheme. The new potentials are studied using spherical harmonics analysis (SHA) and a smooth, continuous version is constructed using spherical harmonic synthesis (SHS). Our approach has the following advantages: (1) The smooth, continuous form of the resulting potentials is more realistic and presents significant advantages for computational simulations, and (2) with SHS, the potential values can be computed efficiently for arbitrary coordinates, requiring only the knowledge of a few spherical harmonic coefficients. The performance of the new orientation-dependent potentials was tested using a standard database of decoy structures. The results show that the ability of the new orientation-dependent potentials to recognize native protein folds from a set of decoy structures is strongly enhanced by the inclusion of anisotropic backbone interaction centers. The anisotropic potentials can be used to develop realistic coarse-grained simulations of proteins, with direct applications to protein design, folding, and aggregation.     

Patterns and conformations of commonly occurring supersecondary structures (basic motifs) in protein data bank

Short peptides connecting-helices and-strands have been analyzed in 240 proteins refined at resolutions of 0.25 nm or better. Connecting peptides of lengths between one and five residues have been classified as part of supersecondary motifs of four types:, , , and. Careful consideration has been given to the definition of secondary structures on the basis of hydrogen bonds and main-chain conformational angles. Using five classes of residue conformation—a, b, e, l, t—in the nonregular structure regions of, space, 34 classes of supersecondary motifs occurring at least five times have been identified. Among these 34 classes, 11 classes that occur more than 25 times are commonly occurring supersecondary structure motifs. The patterns and conformations of the 11 commonly occurring supersecondary structure motifs have been characterized, demonstrating that patterns and conformations adopted by supersecondary structure motifs are limited. The results have relevance to structure prediction, comparative modeling, and protein folding.     

Coupling backbone flexibility and amino acid sequence selection in protein design.

Using a protein design algorithm that considers side-chain packing quantitatively, the effect of explicit backbone motion on the selection of amino acids in protein design was assessed in the core of the streptococcal protein G beta 1 domain (G beta 1). Concerted backbone motion was introduced by varying G beta 1's supersecondary structure parameter values. The stability and structural flexibility of seven of the redesigned proteins were determined experimentally and showed that core variants containing as many as 6 of 10 possible mutations retain native-like properties. This result demonstrates that backbone flexibility can be combined explicitly with amino acid side-chain selection and that the selection algorithm is sufficiently robust to tolerate perturbations as large as 15% of G beta 1's native supersecondary structure parameter values.     

LINUS: A hierarchic procedure to predict the fold of a protein

We describe LINUS, a hierarchic procedure to predict the fold of a protein from its amino acid sequence alone. The algorithm, which has been implemented in a computer program, was applied to large, overlapping fragments from a diverse test set of 7 X-ray-elucidated proteins, with encouraging results. For all proteins but one, the overall fragment topology is well predicted, including both secondary and supersecondary structure. The algorithm was also applied to a molecule of unknown conformation, groES, inwhich X-ray structure determination is presently ongoing. LINUS is an acronym for Local Independently Nucleated Units of Structure. The procedure ascends the folding hierarchy in discrete stages, with concomitant accretion of structure at each step. The chain is represented by simplified geometry and folds under the influence of a primitive energy function. The only accurately described energetic quantity in this work is hard sphere repulsion–the principal forceinvolved in organizing protein conformation [Richards, F. M. Ann. Rev. Biophys. Bioeng. 6:151–176, 1977]. Among other applications, the method is a natural tool for use in the human genome initiative. © 1995 Wiley-Liss, Inc.     

Further data on the polarity of the paba1 locus of Aspergillus nidulans

Newly mapped paba1 alleles are better distributed on the fine-structure map than those mapped earlier. They provide a proximal, a middle and a distal cluster, of four, one and four sites respectively (Fig. 1). The recombination fractions indicate map expansion (Fig. 2). The large samples of paba ⁺ recombinants classified show that classes I and I III are positively correlated with increased recombination fraction, and classes I II and I II III are negatively correlated (Fig. 3). No polarity reversal was found. The results are explained in terms of a hybrid DNA model for crossing over.     

Accuracy of the functional method of hip joint center location: effects of limited motion and varied implementation.

Accurate location of the hip joint center is essential for computation of hip kinematics and kinetics as well as for determination of the moment arms of muscles crossing the hip. The functional method of hip joint center location involves fitting a pelvis-fixed sphere to the path traced by a thigh-fixed point while a subject performs hip motions; the center of this sphere is the hip joint center. The aim of the present study was to evaluate the potential accuracy of the functional method and the dependence of its accuracy on variations in its implementation and the amount of available hip motion. The motions of a mechanical linkage were studied to isolate the factors of interest, removing errors due to skin movement and the palpation of bony landmarks that are always present in human studies. It was found that reducing the range of hip motion from 30 degrees to 15 degrees did significantly increase hip joint center location errors, but that restricting motion to a single plane did not. The magnitudes of these errors, however, even in the least accurate cases, were smaller than those previously reported for either the functional method or other methods based on pelvis measurements of living subjects and cadaver specimens. Neither increasing the number of motion data observations nor analyzing the motion of a single thigh marker (rather than the centroid of multiple markers) was found to significantly increase error. The results of this study (1) imply that the limited range of motion that is often evident in subjects with hip pathology does not preclude accurate determination of the hip joint center when the functional method is used; and (2) provide guidelines for the use of the functional method in human subjects.     

Traffic Volume Alters Elk Distribution and Highway Crossings in Arizona

ABSTRACT We used 38,709 fixes collected from December 2003 through June 2006 from 44 elk (Cervus elaphus) fitted with Global Positioning System collars and hourly traffic data recorded along 27 km of highway in central Arizona, USA, to determine how traffic volume affected elk distribution and highway crossings. The probability of elk occurring near the highway decreased with increasing traffic volume, indicating that elk used habitat near the highway primarily when traffic volumes were low (<100 vehicles/hr). We used multiple logistic regression followed by model selection using Akaike's Information Criterion to identify factors influencing probability of elk crossings. We found that increasing traffic rates reduced the overall probability of highway crossing, but this effect depended on both season and the proximity of riparian meadow habitat. Elk crossed highways at higher traffic volumes when accessing high quality foraging areas. Our results indicate that 1) managers assessing habitat quality for elk in areas with high traffic-volume highways should consider that habitat near highways may be utilized at low traffic volumes, 2) in areas where highways potentially act as barriers to elk movement, increasing traffic volume decreases the probability of highway crossings, but the magnitude of this effect depends on both season and proximity of important resources, and 3) because some highway crossings still occurred at the high traffic volumes we recorded, increasing traffic alone will not prevent elk-vehicle collisions. Managers concerned with elk-vehicle collisions could increase the effectiveness of wildlife crossing structures by placing them near important resources, such as riparian meadow habitat.     

Crossing experiments within theCampanula dichotoma group (Campanulaceae)

Four supposedly closely related taxa were crossed artificially to test for hybridization barriers. Intra- as well as inter-specific crossings were made. The intra-specific crossings resulted in a high portion of viable hybrids, whereas hybridization barriers were found in all inter-specific combinations except one. The hybrids were non-viable at different levels, viz., (1) no seeds germinated, (2) seeds formed lethal chlorotic seedings, or (3) seeds formed chlorophyllous seedlings which survived the cotyledonary stage, but developed into intermediate forms with low pollen production and/or a strongly reduced pollen viability. Crossings betweenCampanula afra and any of the other three taxa resulted in a non-viable progeny. The crossing capacity amongC. occidentalis, C. kremeri, andC. dichotoma varied. Combinations with large-flowered maternal taxa and small-flowered paternal ones usually failed, whereas a high number of the reciprocal crossings produced hybrids which survived the cotyledonary stage. The hybrid plants varied in pollen viability and pollen production, however. It is concluded that theCampanula dichotoma group should be treated as comprising four distinct species.     

An Automatic Search for Similar Spatial Arrangements of α-Helices and β-Strands in Globular Proteins

Abstract

A fast search algorithm to reveal similar polypeptide backbone structural motifs in proteins is proposed. It is based on the vector representation of a polypeptide chain fold in which the elements of regular secondary structures are approximated by linear segments (Abagyan and Maiorov, J. Biomol. Struct. Dyn. 5, 1267–1279 (1988)). The algorithm permits insertions and deletions in the polypeptide chain fragments to be compared. The fast search algorithm implemented in FASEAR program is used for collecting βαβ supersecondary structure units in a number of α/β proteins of Brookhaven Data Bank. Variation of geometrical parameters specifying backbone chain fold is estimated. It appears that the conformation of the majority of the fragments, although almost all of them are right-handed, is quite different from that of standard βαβ units. Apart from searching for specific type of secondary structure motif, the algorithm allows automatically to identify new recurrent folding patterns in proteins. It may be of particular interest for the development of tertiary template approach for prediction of protein three-dimensional structure as well for constructing artificial polypeptides with goal-oriented conformation.     

Spatial orientation in the bushcricket <Emphasis Type="Italic">Leptophyes punctatissima</Emphasis> (Phaneropterinae; Orthoptera): I. Phonotaxis to elevated and depressed sound sources

Many species of acoustically interacting insects live in a complex, arboreal or semi-arboreal habitat. Thus mate finding by phonotaxis requires sound localization in the horizontal and vertical plane. Here we investigated the ability of the duetting bushcricket Leptophyes punctatissima to orient to one of three speakers, positioned at different levels in an artificial grid system, where each point in space could be reached by the male with almost equal probability. The system was designed analogous to a spherical calotte model of bismuth, where, once the male arrived at any nodal point had to decide between only three directions: either up or down and/or left and right. This design does not favour any phonotactic path of the males. All 12 males tested reached the three speaker positions (one in the horzontal plane, one elevated by 45°, one depressed by 45° relative to the starting position) with only little deviation from the shortest possible path. There was no significant difference with respect to the whole phonotactic time needed, the number of segments passed, or the number of stimuli received for the different speaker positions. This remarkable spatial orientation is achieved although the insects have no specialized external ear structures such as mammals, or some owls.