Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock

Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.     

AID is essential for immunoglobulin V gene conversion in a cultured B cell line

Following productive V gene rearrangement, the functional immunoglobulin genes in the B lymphocytes of man and mouse are subjected to two further types of genetic modification. Class-switch recombination, a region-specific but largely nonhomologous recombination process, leads to a change in constant region of the expressed antibody. Somatic hypermutation introduces multiple single nucleotide substitutions in and around the rearranged V gene segments and underpins affinity maturation. However, in chicken and rabbits (but not man or mouse), an additional mechanism, gene conversion, is a major contributor to V gene diversification. It has been demonstrated recently that both switch recombination and hypermutation are ablated in mice and humans lacking AID, a B cell-specific protein of unknown molecular activity. Here we show that disruption of AID in the DT40 chicken B cell lymphoma leads to a failure to perform immunoglobulin V gene conversion. Thus, AID is required for all three immunoglobulin gene modification programs (gene conversion, hypermutation, and switch recombination) and acts in the initiation or execution of these processes rather than in bringing the B cell to an appropriate stage of differentiation.     

Age-related differences in corticospinal control during functional isometric contractions in left and right hands.

The purpose of the study was to examine age-related differences in electromyographic (EMG) responses to transcranial magnetic stimulation (TMS) during functional isometric contractions in left and right hands. EMG responses were recorded from the first dorsal interosseus muscle following TMS in 10 young (26.6 +/- 1.3 yr) and 10 old (67.6 +/- 2.3 yr) right-handed subjects. Muscle evoked potentials (MEPs) and silent-period durations were obtained in the left and right hands during index finger abduction, a precision grip, a power grip, and a scissor grip, while EMG was held constant at 5% of maximum. For all tasks, MEP area was 30% (P < 0.001) lower in the left hand of old compared with young subjects, whereas there was no age difference in the right hand. The duration of the EMG silent period was 14% (P < 0.001) shorter in old (150.3 +/- 2.9 ms) compared with young (173.9 +/- 3.0 ms) subjects, and the age differences were accentuated in the left hand (19% shorter, P < 0.001). For all subjects, the largest MEP area (10-12% larger) and longest EMG silent period (8-19 ms longer) were observed for the scissor grip compared with the other three tasks, and the largest task-dependent change in these variables was observed in the right hand of older adults. These differences in corticospinal control in the left and right hands of older adults may reflect neural adaptations that occur throughout a lifetime of preferential hand use for skilled (dominant) and unskilled (nondominant) motor tasks.     

Potential risk of biologic pollution associated to the introduction of <i>Pinus radiata</i> in grassland areas

Afforestation is a recommended practice to mitigate global warming. However, their implementation may generate undesirable impacts, mostly if exotic species are used. Plantations of Pinus radiata D Don in Ventania (Bs. As., Argentina) soils showed notorious increments of extractable P (Pe), which could affect the dynamic of this element as well as the degree of phosphorus saturation (GSP_Bray). The objectives of this study were: i) to quantify the GSP_Bray in Mollisols afforested with P. radiata comparing the results with those coming from adjacent, natural grassland areas (base line); ii) to evaluate the potential environmental risk induced by afforestation through the identification of a change point (PC) in the GSP_Bray indicative of a phosphate leaching increment. Treatments included mature stands of P. radiata (TB) and adjacent areas with natural grassland vegetation (TP). Samples were taken at 0-15; 15-30 and 30-45 cm soil depth, and texture, pH, total organic carbon (COT), Pe, soluble reactive phosphorus (PSR), phosphorus sorption index (ISP) and GSP_Bray were determined. The results showed a significant acidification in TB and an increase in the COT stock, indicating an additional atmospheric CO₂ sequestration by the trees. The Pe and PSR values were notoriously higher in TB, and they were reflected in a significant increment in the GSP_Bray with respect to TP. The detection of a significant PC in the GSP_Bray-PSR regression indicates higher chances of phosphate leaching in the forest stands, which could reach water courses, lakes and artificial reservoirs promoting their eutrophication. Because of the potential environmental pollution risk of biologic origin derived from the afforestation with P. radiata in Mollisols areas, their inclusion in clean development practices must be reconsidered.     

Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry

Recent work using chemical cross-linking to define interresidue distance constraints in proteins has shown that these constraints are useful for testing tertiary structural models. We applied this approach to the G-protein-coupled receptor bovine rhodopsin in its native membrane using lysine- and cysteine-targeted bifunctional cross-linking reagents. Cross-linked proteolytic peptides of rhodopsin were identified by combined liquid chromatography and FT-ICR mass spectrometry with automated data-reduction and assignment software. Tandem mass spectrometry was used to verify cross-link assignments and locate the exact sites of cross-link attachment. Cross-links were observed to form between 10 pairs of residues in dark-state rhodopsin. For each pair, cross-linkers with a range of linker lengths were tested to determine an experimental distance-of-closest-approach (DCA) between reactive side-chain atoms. In all, 28 cross-links were identified using seven different cross-linking reagents. Molecular mechanics procedures were applied to published crystal structure data to calculate energetically achievable theoretical DCAs between reactive atoms without altering the position of the protein backbone. Experimentally measured DCAs are generally in good agreement with the theoretical DCAs. However, a cross-link between C316 and K325 in the C-terminal region cannot be rationalized by DCA simulations and suggests that backbone reorientation relative to the crystal coordinates occurs on the timescale of cross-linking reactions. Biochemical and spectroscopic data from other studies have found that the C-terminal region is highly mobile in solution and not fully represented by X-ray crystallography data. Our results show that chemical cross-linking can provide reliable three-dimensional structural information and insight into local conformational dynamics in a membrane protein.     

Nitrate leaching stimulates subsurface root growth of wheat and increases rhizosphere alkalisation in a highly acidic soil

Subsurface acidity is a major factor limiting crop yield in some agricultural soils. The surface application of lime has limited effect on the subsurface acidity due to the slow downward movement, while deep incorporation of lime is costly. This paper tested the concept of biologically ameliorating subsurface acidity in a highly acidic soil through the net uptake of anions by plant roots. Nitrogen was supplied to the top soil (0–10 cm) as Ca(NO₃)₂ at rates equivalent to 30–240 kg N ha^?1. Four water levels were imposed (40, 60, 80 and 100% of field capacity). Aluminium-tolerant wheat was grown for 58 days. The high N and high water treatments stimulated root growth below 15 cm, which in turn increased N capture, resulting in a greater excess anion uptake over cations and thus alkalisation of subsurface soil layers. This study suggests that it is feasible to exploit the process of nitrate uptake by an aluminium-tolerant wheat genotype to increase pH in acidic subsoil.     

Intradomain distances in the regulatory domain of the myosin head in prepower and postpower stroke states: fluorescence energy transfer.

The relative movement of the catalytic and regulatory domains of the myosin head (S1) is likely to be the force generating conformational change in the energy transduction of muscle [Rayment, I., Holden, H. M., Whittaker, M., Yohn, C. B., Lorenz, M., Holmes, K. C., and Milligan, R. A. (1993) Science 261, 58-65]. To test this model we have measured, using frequency-modulated FRET, three distances between the catalytic domain and regulatory domains and within the regulatory domain of myosin. The donor/acceptor pairs included MHC cys707 and ELC cys177; ELC cys177 and RLC cys154; and ELC cys177 and gizzard RLC cys108. The IAEDANS (donor) or acceptor (DABMI or IAF) labeled light chains (ELC and RLC) were exchanged into monomeric myosin and the distances were measured in the putative prepower stroke states (in the presence of MgATP or ADP/AlF(4-)) and the postpower stroke states (ADP and the absence of nucleotides). For each of the three distances, the donor/acceptor pairs were reversed to minimize uncertainty in the distance measured, arising from probe orientational factors. The distances obtained from FRET were in close agreement with the distances in the crystal structure. Importantly, none of the measured distances varied by more than 2 A, putting a strong constraint on the extent of conformational changes within S1. The maximum axial movement of the distal part of myosin head was modeled using FRET distance changes within the myosin head reported here and previously. These models revealed an upper bound of 85 A for a swing of the regulatory domain with respect to the catalytic domain during the power stroke. Additionally, an upper bound of 22 A could be contributed to the power stroke by a reorientation of RLC with respect to the ELC during the power stroke.     

Elbow flexor evoked twitch contractile properties in untrained men and women and male bodybuilders

The influence of elbow joint angle on elbow flexor isometric evoked twitch contractile properties was assessed in 15 young women (F), 18 young men (M) and 11 male bodybuilders (BB). Measurements were made at elbow joint angles of 1.31, 1.57, 1.83, 2.09, 2.36, 2.62 and 2.88 rad (3.14 rad =180° =full extension). The largest peak twitch torque values [mean (SE) N · m] in F [3.77 (0.20)], M [10.38 (0.68)] and BB [11.38 (1.05)] occurred at 2.88 rad. Peak torque was progressively smaller at smaller joint angles, but the decline from 2.88 to 1.31 rad was greater in M (68%) and BB (76%) than F (59%). Thus, the magnitude of intergroup differences in peak twitch torque (PT) was joint angle dependent. Twitch time to peak torque (TPT) was influenced in a complex way by joint angle in the three groups; BB had the lowest values at small joint angles but the highest values at the largest angles. Half-relaxation time (HRT) generally increased from the smallest to largest joint angles in a pattern that did not differ significantly among the three groups. Maximum rates of twitch torque development and relaxation showed the same pattern of results as PT; indicating that these time-related measures were more sensitive to joint angle effects on PT than on TPT or HRT. The results of this study indicate that careful consideration should be given to the selection of joint angles in the measurement of evoked twitch contractile properties for the purpose of making group comparisons or investigating the effects of interventions such as training.