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.     

Conservation genetics: beyond the maintenance of marker diversity

One of the major problems faced by conservation biologists is the allocation of scarce resources to an overwhelmingly large number of species in need of preservation efforts. Both demographic and genetic information have been brought to bear on this problem; however, the role of information obtained from genetic markers has largely been limited to the characterization of gene frequencies and patterns of diversity. While the genetic consequences of rarity may be a contributing factor to endangerment, it is widely recognized that demographic factors often may be more important. Because patterns of genetic marker variation are influenced by the same demographic factors of interest to the conservation biologist, it is possible to extract useful demographic information from genetic marker data. Such an approach may be productive for determining plant mating systems, inbreeding depression, effective population size, and metapopulation structure. In many cases, however, data consisting only of marker frequencies are inadequate for these purposes. Development of genealogical based analytical methods coupled with studies of DNA sequence variation within and among populations is likely to yield the most information on demographic processes from genetic marker data. Indeed, in some cases it may be the only means of obtaining information on the long-term demographic properties that may be most useful for determining the future prospects of a species of interest.     

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.     

The detection of two antigenic groups among Renibacterium salmoninarum isolates

The analysis of the membrane proteins and their antigenic properties in a group of 14 geographically diverse strains of Renibacterium salmoninarum revealed the existence of antigenic diversity within this species. Eleven isolates, including the type strain ATCC 33209, shared a similar protein profile with a major component of 57 kDa whereas three strains showed a common pattern with a major protein of 30 kDa. The quantitative agglutination tests and Western blotting assays seem to indicate the existence of serological heterogeneity, with two distinct groups being detected.     

Some new variants of serum protease inhibitors in Meishan pigs

Serum samples of Meishan (13 animals) and Meishan x Wild Boar crosses (361 animals) were analysed by means of two-dimensional electrophoresis. Some new variants in protease inhibitor systems PO1A, PO1B and PI2 are reported.     

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.     

Thermal tolerance and recovery behaviour of Thorectes lusitanicus (Coleoptera,Geotrupidae)

1. Population differences in physiological responses are examined in Thorectes lusitanicus, an endemic Iberian dung beetle species, by submitting individuals of different populations to the same experimental and acclimation conditions. 2. An infrared thermography protocol was used, consisting of three assays: start of activity, cold response, and heat response. Individuals of 12 populations were studied and the comparative explanatory capacities of several environmental factors in relation to the observed inter‐population differences were examined. 3. The heating rate from chill coma to the beginning of activity was the variable with the highest discrimination power among the studied populations, accounting for 94% of the observed variance. Regarding the heat response, only six of the 16 thermal variables reached significance (inter‐population differences accounted for 52–74% in these six thermal parameters). 4. From the three considered environmental factors (Mediterranean climate, land cover, and trophic characteristics) only land cover characteristics remain statistically significant, affecting the cold response of individuals. 5. Thorectes lusitanicus is a species characterised by a high diversity of thermotolerance and recovery traits across populations with a low degree of association with broad environmental factors. Finally, it is suggested that the apterous character of this species could be a determinant factor explaining the high diversity of ecophysiological traits related to thermal stress tolerance and the recovery time.     

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.