Germ-line DNA copy number variation frequencies in a large North American population

Genomic copy number variation (CNV) is a recently identified form of global genetic variation in the human genome. The Affymetrix GeneChip 100 and 500 K SNP genotyping platforms were used to perform a large-scale population-based study of CNV frequency. We constructed a genomic map of 578 CNV regions, covering approximately 220 Mb (7.3%) of the human genome, identifying 183 previously unknown intervals. Copy number changes were observed to occur infrequently (<1%) in the majority (>93%) of these genomic regions, but encompass hundreds of genes and disease loci. This North American population-based map will be a useful resource for future genetic studies. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Induction of matrix metalloproteinase-2 enhances systemic arterial contraction after hypoxia

This study was carried out to determine the role of increased vascular matrix metalloproteinase-2 (MMP-2) expression in the changes in systemic arterial contraction after prolonged hypoxia. Rats and mice were exposed to hypoxia (10% and 8% O(2), respectively) or normoxia (21% O(2)) for 16 h, 48 h, or 7 days. Aortae and mesenteric arteries were either mounted in organ bath myographs or frozen in liquid nitrogen. MMP-2 inhibition with cyclic CTTHWGFTLC (CTT) reduced contraction to phenylephrine (PE) in aortae and mesenteric arteries from rats exposed to hypoxia for 7 days but not in vessels from normoxic rats. Similarly, CTT reduced contraction to Big endothelin-1 (Big ET-1) in aortae from rats exposed to hypoxia for 7 days. Responses to PE were reduced in hypoxic MMP-2(-/-) mice compared with MMP-2(+/+) mice. Increased contraction to Big ET-1 after hypoxia was observed in MMP-2(+/+) mice but not in MMP-2(-/-) mice. Rat aortic MMP-2 and membrane type 1 (MT1)-MMP protein levels and MMP activity were increased after 7 days of hypoxia. Rat aortic MMP-2 and MT1-MMP mRNA levels were increased in the deep medial vascular smooth muscle. We conclude that hypoxic induction of MMP-2 expression potentiates contraction in systemic conduit and resistance arteries. This may preserve the capacity to regulate the systemic circulation in the transition between the alterations in vascular tone and structural remodeling that occurs during prolonged hypoxic epochs.     

Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: application to adaptor protein complexes in cell signaling

Multisite interactions and the formation of ternary or higher-order protein complexes are ubiquitous features of protein interactions. Cooperativity between different ligands is a hallmark for information transfer, and is frequently critical for the biological function. We describe a new computational platform for the global analysis of isothermal titration calorimetry (ITC) data for the study of binary and ternary multisite interactions, implemented as part of the public domain multimethod analysis software SEDPHAT. The global analysis of titrations performed in different orientations was explored, and the potential for unraveling cooperativity parameters in multisite interactions was assessed in theory and experiment. To demonstrate the practical potential and limitations of global analyses of ITC titrations for the study of cooperative multiprotein interactions, we have examined the interactions of three proteins that are critical for signal transduction after T-cell activation, LAT, Grb2, and Sos1. We have shown previously that multivalent interactions between these three molecules promote the assembly of large multiprotein complexes important for T-cell receptor activation. By global analysis of the heats of binding observed in sets of ITC injections in different orientations, which allowed us to follow the formation of binary and ternary complexes, we observed negative and positive cooperativity that may be important to control the pathway of assembly and disassembly of adaptor protein particles.     

Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain

The mitochondrial serine protease HtrA2/Omi helps to maintain mitochondrial function by handling misfolded proteins in the intermembrane space. In addition, HtrA2/Omi has been implicated as a proapoptotic factor upon release into the cytoplasm during the cell death cascade. The protein contains a C-terminal PDZ domain that packs against the protease active site and inhibits proteolytic activity. Engagement of the PDZ domain by peptide ligands has been shown to activate the protease and also has been proposed to mediate substrate recognition. We report a detailed structural and functional analysis of the human HtrA2/Omi PDZ domain using peptide libraries and affinity assays to define specificity, X-ray crystallography to view molecular details of PDZ-ligand interactions, and alanine-scanning mutagenesis to probe the peptide-binding groove. We show that the HtrA2/Omi PDZ domain recognizes both C-terminal and internal stretches of extended, hydrophobic polypeptides. High-affinity ligand recognition requires contacts with up to five hydrophobic side chains by distinct sites on the PDZ domain. However, no particular residue type is absolutely required at any position, and thus, the HtrA2/Omi PDZ domain appears to be a promiscuous module adapted to recognize unstructured, hydrophobic polypeptides. This type of specificity is consistent with the biological role of HtrA2/Omi in mitochondria, which requires the recognition of diverse, exposed stretches of hydrophobic sequences in misfolded proteins. The findings are less consistent with, but do not exclude, a role for the PDZ domain in targeting the protease to specific substrates during apoptosis.     

Exposure Analysis of C8- and C9-Alkylphenols,Alkylphenol Ethoxylates,and Their Metabolites in Surface Water Systems within the United States

This study was conducted to develop a statistical understanding of exposures to C8- and C9-alkylphenol ethoxylates (APEO) and their metabolites (APEM) in U.S. surface waters. Concentrations of APEO/APEM (all analytes) in freshwater have been reported by 19 investigations over the past 15 years. Only limited data are available for sediments and marine ecosystems. Based on the frequency of detection in surface waters, 67% of all analytes were below their detection limits. Although maximum reported concentrations varied with time, the average and 90th centile concentrations have remained relatively constant. Examination of frequency distributions for nonylphenol (NP) concentrations indicated that 99% of the levels in fresh surface waters are below the U.S. Environmental Protection Agency's Aquatic Life Ambient Chronic Water Quality Criteria for NP (6.6 μg/L). A conservative evaluation of aggregated NPEO/NPEM concentrations suggested that 97% of the samples contained aggregate NP equivalent concentrations that are also below 6.6 μg/L. These results suggest that on a nationwide basis, the likelihood of surface water concentrations exceeding the chronic USEPA Water Quality Criterion for NP is low.     

The unique-5 and -6 motifs of ZO-1 regulate tight junction strand localization and scaffolding properties

The proper cellular location and sealing of tight junctions is assumed to depend on scaffolding properties of ZO-1, a member of the MAGUK protein family. ZO-1 contains a conserved SH3-GUK module that is separated by a variable region (unique-5), which in other MAGUKs has proven regulatory functions. To identify motifs in ZO-1 critical for its putative scaffolding functions, we focused on the SH3-GUK module including unique-5 (U5) and unique-6 (U6), a motif immediately C-terminal of the GUK domain. In vitro binding studies reveal U5 is sufficient for occludin binding; U6 reduces the affinity of this binding. In cultured cells, U5 is required for targeting ZO-1 to tight junctions and removal of U6 results in ectopically displaced junction strands containing the modified ZO-1, occludin, and claudin on the lateral cell membrane. These results provide evidence that ZO-1 can control the location of tight junction transmembrane proteins and reveals complex protein binding and targeting signals within its SH3-U5-GUK-U6 region. We review these findings in the context of regulated scaffolding functions of other MAGUK proteins.     

Predictors of sprint start speed: the effects of resistive ground-based vs. inclined treadmill training

There is currently no consensus with regard to the most effective method to train for improved acceleration, or with regard to which kinematic variable provides the greatest opportunity for improvement in this important performance characteristic. The purpose of this study was to determine the effects of resistive ground-based speed training and incline treadmill speed training on speed-related kinematic measures and sprint start speed. The hypothesis tested was that incline treadmill training would improve sprint start time, while the ground-based resistive training would not. Corollary hypotheses were that treadmill training would increase stride frequency and ground-based training would not affect kinematics during the sprint start. Thirty-one high school female soccer players (15.7 +/- 0.5 years) were assigned to either treadmill (n = 17) or ground-based (n = 14) training groups and trained 2 times a week for 6 weeks. The treadmill group utilized incline speed training on a treadmill, while the ground-based group utilized partner band resistance ground-based techniques. Three-dimensional motion analysis was used (4.5 m mark) before and after training to quantify kinematics during the fastest of 3 recorded sprint starts (9.1 m). Both groups decreased average sprint start time from 1.75 +/- 0.12 to 1.68 +/- 0.08 seconds (p < 0.001). Training increased stride frequency (p = 0.030) but not stride length. After training, total vertical pelvic displacement and stride length predicted 62% of the variance in sprint start time for the resistive ground-based group, while stride length and stride frequency accounted for 67% prediction of the variance in sprint start time for the treadmill group. The results of this study indicate that both incline treadmill and resistive ground-based training are effective at improving sprint start speed, although they potentially do so through differing mechanisms.     

Analysis of acute explosive training modalities to improve lower-body power in baseball players

Complex training is the simultaneous combination of heavy resistance training and plyometrics. The objective of this study was to test the effects of complex training vs. heavy resistance or plyometric interventions alone on various power-specific performance measures. Forty-five male division II junior college baseball players participated in 3 separate 4-week resistance training interventions. Subjects were randomly assigned to one of three groups. In a counterbalanced rotation design, each group participated in complex, heavy resistance, and plyometric training interventions. Each individual was tested in 20-yd (SP20), 40-yd (SP40), 60-yd (SP60), vertical jump, standing broad jump, and T-agility measures pre- and post-4-week training interventions. There was no statistical significant difference (p = 0.11) between groups across all performance measures. Review of each distinct training intervention revealed greater percent improvements in SP20 (0.55; -0.49; -0.12), SP40 (0.26; -0.72; -1.33), SP60 (0.27; 0.15; -0.27), standing broad jump (1.80; 0.67; 1.1), and T-agility (2.33; 1.23; -0.04) with complex training interventions than with the heavy resistance or plyometric training interventions, respectively. Plyometric-only training showed greater percent changes in vertical jump (1.90) than with complex (0.97) or heavy resistance training (0.36). The present results indicate that complex training can provide strength and conditioning professionals equal, if not slightly greater, improvements in muscular power than traditional heavy resistance- and plyometric-only interventions in moderately trained athletes. Complex training can be another valuable method for short-term power and speed improvements in athletes in isolation or in conjunction with other power development methods.     

The body size of the New Zealand orb-weaving spider Waitkera waitakerensis (Uloboridae) is directly related to temperature and affects fecundity

Abstract. Waitkera waitakerensis occupies lowland forests of New Zealand's North Island, where temperatures decrease in a southwestward direction. The mean annual temperatures of 18 collecting sites, as extracted from GIS data, are directly related to the first femur length of adult females. Neither site elevation nor phylogeny affected spider size or other variables examined. The direct relationship between spider body size and environmental temperature followed a pattern observed in other terrestrial arthropods with a univoltine life cycle and can probably be explained by the longer growing season of warmer regions. Egg diameter was uniform across the species. Site temperature and female first femur length were each directly related to the number of eggs deposited in egg sacs. The date of egg sac collection was inversely related to egg number, suggesting that clutch size declines during the reproductive season. Females deposit eggs beneath a triangular platform and then cover them with a lower silk sheet. The area of this upper platform and the volume of the egg sac were each directly related to egg number, but not to female first femur length. The depth of the lower covering was not related to egg number or to spider first femur length. This suggests that spiders use information about the volume of eggs in their abdomens to construct an egg sac whose volume will accommodate the volume of eggs to be laid and that females do so principally by adjusting the size of the sac's upper triangular platform.     

Dealing with uncertain absences in habitat modelling: a case study of a rare ground-dwelling parrot

In the development of a species distribution model based on regression techniques such as generalized linear or additive modelling (GLM/GAM), a basic assumption is that records of species presence and absence are real. However, a common concern in many studies examining species distributions is that absences cannot be inferred with certainty. This is particularly the case where the species is rare, difficult to detect and/or does not occupy all available habitat considered suitable. The western ground parrot ( Pezoporus wallicus flaviventris ) of southern Western Australia, Australia, is a case in point, as not only is it rare and difficult to detect, but it is also unlikely to occupy all available suitable habitat. A recent survey of ground parrots provided the opportunity to develop a predictive distribution model. As the data were susceptible to false absences, these were replaced with randomly selected 'pseudo' absences and modelled using GLM. As a comparison, presence-only information was modelled using a relatively new approach, MAXENT, a machine-learning technique that has been shown to perform comparatively well. The predictive performance of both models, as assessed by the receiver operating characteristic plot (ROC) was high (AUC > 0.8), with MAXENT performing only marginally better than the GLM. These approaches both indicated that the ground parrot prefers areas relatively high in altitude, distant from rivers, gently sloping to level habitat, with an intermediate cover of vegetation and where there is a mosaic of vegetation ages. In this case, the use of presence-only information resulted in the identification of important environmental attributes defining the occurrence of the ground parrot, but additional factors that account for the inability of the bird to occupy all suitable habitat should be a component of model refinement.