Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model

Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK₂) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.     

Genetic variation at pig plasma protein locus PLP1 and its assignment to chromosome 5

A new genetic polymorphism of an unidentified plasma protein (PLP1) in pigs was described by using a method of two-dimensional gel electrophoresis and protein staining. Two codominant alleles, with frequencies of 0.83 and 0.17, were found in the Swedish Yorkshire breed. The PLP1 marker was typed in a three-generation pedigree and tested for linkage against a set of 128 markers. The PLP1 locus showed significant LOD score values with three different microsatellite markers (S0092, DAGK and S005), previously assigned to chromosome 5.     

Spatial distributional patterns of macroinvertebrates along rivers within and among biomes

This study was designed to test the biome dependency hypothesis, which predicts that similar assemblages of macroinvertebrates occur along rivers both within and among drainage basins if the basins occupy the same biome. Benthic macroinvertebrates were collected from three drainage basins within each of three biomes in Canada, the eastern deciduous forests (EDF) of southwestern Ontario, the grasslands of south-central Alberta, and the montane coniferous forests (MCF) of southeastern British Columbia. A total of 225 benthic samples (3 biomes × 3 rivers/biome × 5 sites/river × 5 samples/site) was collected in spring using a cylinder sampler.The significant interaction effect between biome and a site's location along a river indicated that spatial patterns of variation in total density and taxonomic composition were not spatially consistent among sites along rivers or among biomes. Total macroinvertebrate densities were equivalent between the EDF and grassland sites. However, total density was substantially lower at the MCF sites than at sites in the other two biomes. The greatest differences in taxonomic composition occurred among biomes, although significant differences also occurred for all other sources of variation examined. Macroinvertebrate composition was more strongly associated with local, site-specific factors (riparian vegetation and land use) than with longitudinal gradients. Distinct site-specific taxonomic assemblages were evident in EDF, but not in the other two biomes where land use was more homogeneous.     

A biomechanical study of the relationship between running velocity and three-dimensional lumbosacral kinetics

Faster running is not performed with proportional increase in all joint torque/work exertions. Although previous studies have investigated lumbopelvic kinetics for a single velocity, it is unclear whether each lumbopelvic torque should increase for faster running. We examined the relationship between running velocity and lumbopelvic kinetics. We calculated the three-dimensional lumbosacral kinetics of 10 male sprinters during steady-state running on a temporary indoor running track at five target velocities: 3.0 (3.20 ± 0.16), 4.5 (4.38 ± 0.18), 6.0 (5.69 ± 0.47), 7.5 (7.30 ± 0.41), and maximal sprinting (9.27 ± 0.36 m/s). The lumbosacral axial rotation torque increased more markedly (from 0.37 ± 0.06 to 1.99 ± 0.46 Nm/kg) than the extension and lateral flexion torques. The increase in the axial rotation torque was larger above 7.30 m/s. Conversely, the extension and lateral flexion torques plateaued when running velocity increased above 7.30 m/s. Similar results were observed for mechanical work. The results indicate that faster running required larger lumbosacral axial rotation torque. Conversely, the extension and lateral flexion torques were relatively invariant to running velocity above 7 m/s, implying that faster running below 7 m/s might increase the biomechanical loads causing excessive pelvic posterior tilt and excessive pelvic drop which has the potential to cause pain/injury related to lumbopelvic extensors and lateral flexors, whereas these biomechanical loads might not relate with running velocity above 7 m/s.     

Evaluating regional water security through a freshwater ecosystem service flow model: A case study in Beijing-Tianjian-Hebei region,China

Freshwater ecosystem service is essential to human’s survival and development. Many studies have documented the spatial differences in the supply and demand of ecosystem services and proposed the concept of ecosystem services flows. However, few studies characterize freshwater ecosystem service flow quantitatively. Therefore, our paper aims to quantify the effects of freshwater ecosystem service flow on downstream areas. We developed a freshwater ecosystem service flow model and applied it in the Beijing–Tianjin–Hebei (BTH) region, China, for the year of 2000, 2005, and 2010. We assessed the regional water security with an improved freshwater security index by integrating freshwater service provision, consumption and flow; and found that most areas of the BTH region (69.2%) were affected by upstream freshwater flows. The areas achieving water security in the region also expanded to 66.9%, 66.1%, and 71.3%, which were 6.4%, 6.8% and 5.7% increments compared to no-flow situation, in 2000, 2005 and 2010, respectively. Setting quota for human water consumption is suggested to further improve water security. These results highlight the need to fully understand the connections between distant freshwater ecosystem service provision and local freshwater ecosystem service consumption. This approach may also help managers to choose more sustainable strategies for critical freshwater resource management across different regions.     

Morphological and morphometrical analysis of Heterodera spp. populations in Jordan

Phenotypic diversity of five Jordanian populations of cyst nematodes, Heterodera spp. collected from five regions from Jordan (Ar-Ramtha, Madaba, Dana, Al-Karak, and Jerash) was investigated. Soil samples were collected from one representative field in each region. Morphological and morphometrical characteristics revealed that Heterodera latipons is dominated in cereal fields at Ar-Ramtha, Madaba, Dana and Al-Karak regions and Heterodera schachtii in Jerash. Cysts populations from all cereal fields had bifenestrate vulval cone and a strong underbridge. Wherever, cysts of the cabbage population had ambifenestrate vulval cone with long vulval slit. The bullae were absent in Ar-Ramtha, Madaba and Dana populations, but present in Al-Karak and Jerash. Based on 12 morphometrical characters, the first three functions in canonical discriminant analysis accounted 99.3% of the total variation. Distance from dorsal gland duct opening to stylet base, underbridge length, a = L/W (body length/midbody width) and length of hyaline tail tip had strong and significant contributions in the first function. While the second function was strongly influenced by length of hyaline tail, fenestral length, fenestral width and tail length. However, the third canonical discriminate function was found to be influenced by stylet length, fenestral length, a = L/W (body length/midbody width) and underbridge width. The graphical representation of the distribution of the samples showed that the first canonical discriminant function clearly separated H. schachtii from Jerash from other populations. Whereas, H. latipons collected from Madaba and Dana were clearly separated in the second function. The results indicated that differences at morphological and morphometrical levels revealed diverse populations of Heterodera spp. in Jordan.     

Effects of nitrogen limitation on water relations of jack pine (Pinus banksiana Lamb.) seedlings

The water relations of shoots of young jack pine (Pinus banksiana Lamb.) seedlings were examined 6 and 15 weeks after the initiation of four different dynamic nitrogen (N) treatments using a pressure-volume analysis. The N treatments produced a wide range of needle N concentrations from 12 to 32 mg g^?1 dry mass and a 10-fold difference in total dry mass at 15 weeks. Osmotic potential at full turgor did not change over the range of needle N concentrations observed. Osmotic potential at turgor-loss point, however, declined as N concentrations decreased, indicating an increased ability of N-deficient jack pine plants to maintain turgor. The increase could be attributed largely to an increase in cell wall elasticity, suggesting that elasticity changes may be a common, significant adaptation of plants to environmental stresses. Dry mass per unit saturated water almost doubled as needle N level dropped from 32 to 12 mg g^?1 and was inversely correlated to the bulk modulus of elasticity. This suggests that cell wall elasticity is determined more by the nature of its cross-linking matrix than by the total amount of cell wall material present. Developmental change was evident in the response of some water relation variables to N limitation.     

Correcting for finite spatial scales of self-similarity when calculating fractal dimensions of real-world structures

Fractal geometry is a potentially valuable tool for quantitatively characterizing complex structures. The fractal dimension (D) can be used as a simple, single index for summarizing properties of real and abstract structures in space and time. Applications in the fields of biology and ecology range from neurobiology to plant architecture, landscape structure, taxonomy and species diversity. However, methods to estimate the D have often been applied in an uncritical manner, violating assumptions about the nature of fractal structures. The most common error involves ignoring the fact that ideal, i.e. infinitely nested, fractal structures exhibit self-similarity over any range of scales. Unlike ideal fractals, real-world structures exhibit self-similarity only over a finite range of scales.Here we present a new technique for quantitatively determining the scales over which real-world structures show statistical self-similarity. The new technique uses a combination of curve-fitting and tests of curvilinearity of residuals to identify the largest range of contiguous scales that exhibit statistical self-similarity. Consequently, we estimate D only over the statistically identified region of self-similarity and introduce the finite scale- corrected dimension (FSCD). We demonstrate the use of this method in two steps. First, using mathematical fractal curves with known but variable spatial scales of self-similarity (achieved by varying the iteration level used for creating the curves), we demonstrate that our method can reliably quantify the spatial scales of self-similarity. This technique therefore allows accurate empirical quantification of theoretical Ds. Secondly, we apply the technique to digital images of the rhizome systems of goldenrod (Solidago altissima). The technique significantly reduced variations in estimated fractal dimensions arising from variations in the method of preparing digital images. Overall, the revised method has the potential to significantly improve repeatability and reliability for deriving fractal dimensions of real-world branching structures.