The ToxCast pipeline: updates to curve-fitting approaches and database structure.

Introduction: The US Environmental Protection Agency Toxicity Forecaster (ToxCast) program makes in vitro medium- and high-throughput screening assay data publicly available for prioritization and hazard characterization of thousands of chemicals. The assays employ a variety of technologies to evaluate the effects of chemical exposure on diverse biological targets, from distinct proteins to more complex cellular processes like mitochondrial toxicity, nuclear receptor signaling, immune responses, and developmental toxicity. The ToxCast data pipeline (tcpl) is an open-source R package that stores, manages, curve-fits, and visualizes ToxCast data and populates the linked MySQL Database, invitrodb. Methods: Herein we describe major updates to tcpl and invitrodb to accommodate a new curve-fitting approach. The original tcpl curve-fitting models (constant, Hill, and gain-loss models) have been expanded to include Polynomial 1 (Linear), Polynomial 2 (Quadratic), Power, Exponential 2, Exponential 3, Exponential 4, and Exponential 5 based on BMDExpress and encoded by the R package dependency, tcplfit2. Inclusion of these models impacted invitrodb (beta version v4.0) and tcpl v3 in several ways: (1) long-format storage of generic modeling parameters to permit additional curve-fitting models; (2) updated logic for winning model selection; (3) continuous hit calling logic; and (4) removal of redundant endpoints as a result of bidirectional fitting. Results and discussion: Overall, the hit call and potency estimates were largely consistent between invitrodb v3.5 and 4.0. Tcpl and invitrodb provide a standard for consistent and reproducible curve-fitting and data management for diverse, targeted in vitro assay data with readily available documentation, thus enabling sharing and use of these data in myriad toxicology applications. The software and database updates described herein promote comparability across multiple tiers of data within the US Environmental Protection Agency CompTox Blueprint.

A new method to analyze dGEMRIC measurements in femoroacetabular impingement: preliminary validation against arthroscopic findings.

OBJECTIVE: To validate a new method to analyze delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC) measurements in the hip for early assessment of cartilage defects in femoroacetabular impingement (FAI). METHODS: We performed a retrospective review of 10 hips in 10 FAI patients, who underwent hip arthroscopy. T1-weighted images and dGEMRIC T(1) maps were acquired at 1.5 T on coronal planes, including the anterior-superior, superior, posterior-superior hip cartilage. For all slices, a region of interest (ROI) was defined over the central portion of the femoral cartilage, assumed to be healthy, and T1 values (x) were transformed to standard scores (z) using z = (x -µ)/σ, where µ and σ are the average and standard deviation of T1 in the femoral ROI. Diagnostic performance of the resulting standardized dGEMRIC maps was evaluated against intraoperative findings and compared with that of a previously proposed dGEMRIC analysis as well as morphologic assessment. RESULTS: Assuming z = -2 or z = -3 as the threshold between normal and degenerated cartilage, sensitivity, specificity and accuracy were 88%, 51% and 62%, and 71%, 63% and 65%, respectively. By using T1 = 500 ms as single threshold for all dGEMRIC T1 maps, these values became 47%, 58% and 55%, whereas they were 47%, 79% and 70% for morphologic evaluation. CONCLUSIONS: Standardized dGEMRIC can increase the sensitivity in detecting abnormal cartilage in FAI and has the potential to improve the clinical interpretation of dGEMRIC measurements in FAI, by removing the effect of inter- and intra-patient T1 variability.

Photoaffinity labeling of the tight ADP binding site of the chloroplast coupling factor one (CF1): the effect on the CF1-ATPase activity.

Chloroplast thylakoid membranes contain tightly bound ADP which is intimately involved in the mechanism of photophosphorylation. The photoaffinity analog 2-azido-ADP binds tightly to spinach thylakoid membrane-bound coupling factor one (CF1) and, in a manner similar to ADP, inhibits the light-triggered ATPase activity (Czarnecki, J.J., Abbott, M.S. and Selman, B.R. (1983) Eur. J. Biochem. 136, 19-24). Ultraviolet irradiation of thylakoid membranes containing noncovalently, tightly bound 2-azido[beta-32P]ADP results in the inactivation of both the methanol-stimulated MgATPase activity of the membrane-bound CF1 and the octylglucoside-dependent MgATPase activity of the solubilized enzyme. There is a linear correlation between the loss of enzyme activity and the covalent incorporation of the photoaffinity analog. Full inactivation of catalytic activity is estimated to occur upon incorporation of 1.07 mol analog and 0.65 mol analog per mol enzyme for the methanol- and octylglucoside-stimulated activities, respectively. Since 2-azido-ADP modifies only the beta subunit of the CF1 and since there are probably three beta subunits per CF1, these results indicate strong cooperativity among beta subunits and between the site of tightly bound nucleotides and the catalytic sites.

Crystal structure of the stromelysin catalytic domain at 2.0 A resolution: inhibitor-induced conformational changes.

Matrix metalloproteinases are believed to play an important role in pathological conditions such as osteoarthritis, rheumatoid arthritis and tumor invasion. Stromelysin is a zinc-dependent proteinase and a member of the matrix metalloproteinase family. We have solved the crystal structure of an active uninhibited form of truncated stromelysin and a complex with a hydroxamate-based inhibitor. The catalytic domain of the enzyme of residues 83-255 is an active fragment. Two crystallographically independent molecules, A and B, associate as a dimer in the crystals. There are three alpha-helices and one twisted, five-strand beta-sheet in each molecule, as well as one catalytic Zn, one structural Zn and three structural Ca ions. The active site of stromelysin is located in a large, hydrophobic cleft. In particular, the S1' specificity site is a deep and highly hydrophobic cavity. The structure of a hydroxamate-phosphinamide-type inhibitor-bound stromelysin complex, formed by diffusion soaking, has been solved as part of our structure-based design strategy. The most important feature we observed is an inhibitor-induced conformational change in the S1' cavity which is triggered by Tyr223. In the uninhibited enzyme structure, Tyr223 completely covers the S1' cavity, while in the complex, the P1' group of the inhibitor displaces the Tyr223 in order to fit into the S1' cavity. Furthermore, the displacement of Tyr223 induces a major conformational change of the entire loop from residue 222 to residue 231. This finding provides direct evidence that Tyr223 plays the role of gatekeeper of the S1' cavity. Another important intermolecular interaction occurs at the active sit of molecule A, in which the C-terminal tail (residues 251-255) from molecule B inserts. The C-terminal tail interacts extensively with the active site of molecule A, and the last residue (Thr255) coordinated to the catalytic zinc as the fourth ligand, much like a product inhibitor would. The inhibitor-induced conformational change and the intermolecular C-terminal-zinc coordination are significant in understanding the structure-activity relationships of the enzyme.

Design and synthesis of phosphinamide-based hydroxamic acids as inhibitors of matrix metalloproteinases.

A new series of hydroxamic acid-based matrix metalloproteinase (MMP) inhibitors containing a unique phosphinamide motif derived from D-amino acid was designed, synthesized, and tested for enzyme inhibition. Compounds with an R configuration at phosphorus were found to be potent MMP inhibitors while molecules with the S configuration were almost inactive. Structure-activity relationship studies of the series led to the discovery of the potent inhibitor 16 with IC50 = 20.5 nM and 24.4 nM against fibroblast collagenase (MMP-1) and stromelysin (MMP-3), respectively. The binding mode of this novel phosphinamide-based series of MMP inhibitors was established based on X-ray crystallography of the complex of stromelysin and 16.

New cyclooxygenase-2/5-lipoxygenase inhibitors. 2. 7-tert-butyl-2,3-dihydro-3,3-dimethylbenzofuran derivatives as gastrointestinal safe antiinflammatory and analgesic agents: variations of the dihydrobenzofuran ring.

A series of 5-keto-substituted 7-tert-buty1-2,3-dihydro-3,3- dimethylbenzofurans (DHDMBFs) were found to be nonsteroidal antiinflammatory and analgesic agents. These compounds are inhibitors of 5-lipoxygenase (5-LOX) and cyclooxygenase (COX) with selectivity for the COX-2 isoform. A series of analogues were prepared to investigate the scope of this lead. Five ketone side chains from active DHDMBFs were used to investigate the effects of changes in the DHDMBF "core": the size and identity of the heterocycle and the substituent requirements of the heterocycle and phenyl ring. Biological testing showed that a variety of structural changes can be accommodated, but no structure was clearly superior to the DHDMBF structure.

Survivors of suicide do grieve differently: empirical support for a common sense proposition.

Previous empirical investigations have produced mixed results on the question of whether mode of death differentially affects grief. To further investigate the influence of suicide on grief, 350 previously bereaved university students completed a questionnaire package consisting of several standardized measures. Participants were separated into four groups based on the mode of death experienced as either survivors of suicide (n = 34), accident (n = 57), unanticipated natural (n = 102), or anticipated natural (n = 157) deaths. Hierarchical multiple regression analyses indicated that suicide survivors, compared against the other groups, experienced more frequent feelings of rejection, responsibility, "unique" reactions, and more total grief reactions. Trends indicating increased levels of shame and perceived stigmatization were also evident. Aggregate factors of death "naturalness" and "expectedness" showed less influence than mode of death in influencing grief. Overall, results support previous clinical and research findings and intuitive logic in demonstrating that the grief experienced by suicide survivors includes elements that are less frequently seen in the case of nonsuicidal deaths.

Relationships between stress, coping resources, and satisfaction with family functioning in families of children with disabilities.

The purpose of the current descriptive correlational study was to examine relations between stress, coping resources, and satisfaction with family functioning in families caring for children with developmental disabilities at home. Fifty families who used the services of a respite care program were surveyed to examine relationships among child characteristics (behavioral problems and handicapping conditions); coping resources including mastery and health, esteem and communication, family hardiness, and social support; and the primary outcome variable of satisfaction with family functioning. Families of children with developmental disabilities experience significant stressors in terms of the severity of their child's handicapping conditions and behaviour problems. However, they reported satisfactory coping resources such as mastery and health, hardiness, and esteem and communication. Although they were lower than normative scores, social support scores for spouses and friends were related to satisfaction with family functioning. Implications for practitioners are discussed.

Using functional health patterns to predict outcome with seniors.

Two powerful forces in Canada's health care system today are the rapidly growing seniors population and the trend toward community care. Recently, five hospitals in southwestern Ontario initiated a program designed to avert the admission of seniors to hospital and provide them with supports at home to maintain their health. Simultaneous research was conducted to assess the impact and effectiveness of the program.

The influence of family groups on inferences made with the program Structure.

Unsupervised clustering algorithms, like the program Structure, are increasingly used to infer the presence of population structure from a sample of genotyped individuals. We evaluate the extent to which the presence of related individuals can lead such algorithms to the false inference that there is population structure. First, we demonstrate this problem using a real data set from a rainbow trout (Oncorhynchus mykiss) population. Then we perform an extensive series of simulations involving the program Structure. Our simulations encompass both a simple scenario with fixed numbers of full- and half-siblings in the sample, and a more complicated scenario in which we investigate 360 combinations of population divergence, fraction of population sampled, variance in family size, mating system and number of loci. We find that the inclusion of family members in a sample may produce very strong evidence of population structure, even when population structure is absent. This problem becomes more pronounced when more loci are genotyped, and it is particularly likely in studies of monogamous species, especially if variance in family size is high and a large fraction of a small population has been sampled. Researchers working in such situations should test observed clusters for the presence of family members to distinguish family-induced structure from real population structure. Additionally, this work shows that Structure's ability to estimate the number of subpopulations may be influenced by a number of factors, and therefore should be interpreted guardedly.

Interactions of inorganic phosphate with spinach coupling factor 1. Effects on ATPase and ADP binding activities.

Illumination of chloroplast thylakoid membranes results in both the release of adenine nucleotides from the tight nucleotide binding site(s) on chloroplast coupling factor 1 (CF1) and the activation of a light-triggered ATPase activity of CF1. Because inorganic phosphate stabilizes the light-triggered ATPase activity of CF1 in the dark, the effects of Pi on the rebinding of ADP to CF1 and on the light-triggered ATPase activity have been studied. Pi appears to be a partial noncompetitive inhibitor, with respect to ADP, of adenine nucleotide binding to the tight nucleotide binding site(s) on CF1 and induces negative cooperativity. The latter result suggests the existence of heterogeneous ADP binding sites in the presence of Pi. However, even under conditions where Pi causes a 50% reduction of tightly bound ADP, the ADP-induced dark decay of the ATPase activity is still complete. It was found that Pi inhibition of the light-induced dark binding of ADP can be reversed by the removal of the Pi. Removal of Pi also induces a small but significant ATPase activity. A model for the roles of the adenine nucleotide tight binding site(s) and Pi in the modulation of the spinach CF1 ATPase activity is proposed.

Regulation of spinach chloroplast coupling factor 1 ATPase activity.

Illumination of chloroplast thylakoid membranes results in the activation of the light-triggered ATPase (coupling factor 1) and in exchange of tightly bound adenine nucleotides. The dark decay of the light-triggered ATPase activity is accelerated significantly by the addition of ADP. Both the decay of the ATPase activity and the rebinding of ADP appear to be rate limited by the same unimolecular step which is estimated to have a rate constant of 0.058 +/- 0.005 s-1. ADP is a noncompetitive inhibitor of the ATPase, if sufficient time for binding is allowed. The Kis for ADP inhibition of the ATPase is equivalent to the K0.5 for ADP binding to the nucleotide tight binding site (K0.5 = 2 +/- 1 microM). A kinetic model is proposed which suggests that the binding of one ADP to chloroplast coupling factor 1 inhibits three ATPase active sites.

Factor structure of the Grief Experience Questionnaire (GEQ).

The Grief Experience Questionnaire (GEQ; T.W. Barrett & T.B. Scott, 1989) is a self-report measure of grief responses, including some that have been associated with grief after a suicide (e.g., feelings of rejection, responsibility, shame, stigmatization, etc.). In this study, a sample of 350 university students who had experienced the death of a significant other completed the GEQ. A principal components analysis with varimax rotation yielded an 8-factor solution with satisfactory psychometric properties. Results clearly document that the GEQ is a multidimensional measure of grief phenomenology. It is concluded that although the GEQ has broad applicability, the scale as revised herein may have a special relevance to suicide bereavement, and may be of use in both research and clinically based applications.

Early embryonic death of glutamate carboxypeptidase II (NAALADase) homozygous mutants.

Glutamate carboxypeptidase II (EC 3.4.17.21) catalyzes the hydrolysis (Km = 0.2 microM) of the neuropeptide N-acetylaspartylglutamate to yield N-acetylaspartate and glutamate and also serves as a high-affinity folate hydrolase in the gut, cleaving the polyglutamate chain to permit the absorption of folate. N-acetylaspartylglutamate is an agonist at the mGluR3 metabotropic receptor and a source of extracellular glutamate through hydrolysis by glutamate carboxypeptidase II. Given the important role of glutamate in brain development and function, we were interested in the effects of a null mutation of glutamate carboxypeptidase II that would potentiate the effects of N-acetylaspartylglutamate. The PGK-Neomycin cassette was inserted to delete exons 9 and 10, which we previously demonstrated encode for the zinc ligand domain essential for enzyme activity. Successful germline transmission was obtained from chimeras derived from embryonic stem cells with the targeted mutation of glutamate carboxypeptidase II. Homozygous null mutants did not survive beyond embryonic day 8. Folate supplementation of the heterozygous mothers did not rescue the homozygous embryos. Mice heterozygous for the null mutation appeared grossly normal and expressed both mutated and wild-type mRNA but the activity of glutamate carboxypeptidase II is comparable to the wild-type mice. The results indicate that the expression of glutamate carboxypeptidase II is upregulated when one allele is inactivated and that its activity is essential for early embryogenesis.

Heterocycle-based MMP inhibitors with P2' substituents.

Potent and selective inhibition of matrix metalloproteinases was demonstrated for a series of sulfonamide-based hydroxamic acids. The design of the heterocyclic sulfonamides incorporates a six- or seven-member central ring with a P2' substituent that can be modified. Binding interactions of this substituent at the S2' site are believed to contribute to high inhibitory potency against stromelysin, collagenase-3 and gelatinases A and B, and to provide selectivity against collagenase-1 and matrilysin. An X-ray structure of a stromelysin inhibitor complex was obtained to provide insights into the SAR and selectivity trends observed for the series.