Localization of the binding site for a factor VIII activity neutralizing antibody to amino acid residues Asp1663-Ser1669

We have identified the Factor VIII amino acid sequence Asp-Tyr-Asp-Asp-Thr-Ile-Ser (1663-1669) as the binding site of a Factor VIII activity neutralizing antibody (28 Bethesda units/mg). The binding site of another neutralizing antibody (10 Bethesda units/mg) overlapped only at Asp1663 and Tyr1664, whereas an antibody with minimal neutralizing activity (0.2 Bethesda units/mg) bound only at Asp1665-Ser1669. Residues comprising antibody binding sites were determined by blocking Factor VIII neutralization and/or binding to insolubilized Factor VIII with overlapping peptides, or with variant peptides in which a single amino acid was deleted or replaced with glycine. Eight additional antibodies to flanking sequences, and with similar affinities for Factor VIII, had little or no neutralizing activity (0-3.0 Bethesda units/mg). These studies suggest that Asp1663 and Tyr1664 may be structural features important to Factor VIII function.     

First-trimester prenatal diagnosis of Tay-Sachs disease.

The prenatal diagnosis of Tay-Sachs disease was made in two at-risk fetuses by the analysis of chorionic villi obtained at 9 and 11 menstrual weeks, respectively. The diagnoses were based on the absence of beta-hexosaminidase A activity as determined by: (1) specific enzyme assays, (2) anion-exchange chromatography, and (3) cellulose acetate gel electrophoresis. The enzymatic diagnoses were confirmed on fetal tissue as well as by ultrastructural demonstration of the first-trimester fetal neuropathology. Optimal assay conditions for beta-hexosaminidase A in chorionic villi were established for the prenatal diagnosis of Tay-Sachs disease. Importantly, it was noted that a small amount of decidua or maternal blood could lead to misdiagnosis. Thus, extreme care must be taken in the preparation of chorionic villi for Tay-Sachs as well as other prenatal metabolic diagnoses.     

Technical note: Prediction of sex based on five skull traits using decision analysis (CHAID)

Osteologists commonly assess the sex of skeletal remains found in forensic and archaeological contexts based on ordinal scores of subjectively assessed sexually dimorphic traits. Using known‐sex samples, logistic regression (LR) discriminant functions have been recently developed, which allow sex probabilities to be determined. A limitation of LR is that it emphasizes main effects and not interactions. Chi‐square automatic interaction detection (CHAID) is an alternative classification strategy that emphasizes the information in variable interactions and uses decision trees to maximize the probability of correct sex determinations. We used CHAID to analyze the predictive value of the 31 possible combinations of five sexually dimorphic skull traits that Walker used previously to develop logistic regression sex determination equations. The samples consisted of 304 individuals of known sex of English, African American, and European American origin. Based on practical considerations, selection criteria for the best sex predictive trait combinations (SPTCs) were set at accuracies for both sexes of 75% or greater and sex biases lower than 5%. Although several of the trees meeting these criteria were produced for the English and European American samples, none met them for the African American sample. In the series of out‐of‐sample tests we performed, the trees from the English and combined sample of all groups predicted best. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Spatial ecology of female bighorn sheep in a prairie landscape in Nebraska

Understanding the spatial ecology of small populations at the periphery of their range is important for identifying factors limiting population growth and developing sound management strategies. Bighorn sheep were reintroduced to Nebraska in 1981 and persist in a small population at the easternmost extent of the distribution of the species, where 1 of the 2 subpopulations is declining. Bighorn sheep space use and movement has been studied extensively in mountain and desert populations, but information is sparse from prairie populations in the Northern Great Plains. We investigated the spatial ecology of female bighorn sheep in Nebraska, USA, with global positioning system (GPS) telemetry. We tested the hypothesis that space use and movements would vary across seasons, years, and individuals but predicted that migration would involve relatively short distances in this translocated population (relative to native populations) occupying a fragmented landscape. Overall, females used smaller seasonal home ranges (3.3–7.8 km²) than most of those reported previously for the species and exhibited a high degree of variability in space use and movements across seasons, subpopulations, and individuals. Most females (92–100%) exhibited fidelity to their home ranges across seasons and years. Six females migrated between spatially distinct core lambing and winter ranges, although the distances (range = 7.9–8.7 km) and mean elevations (range = 31–41 m) between these core seasonal ranges were less than those reported for most native, migratory bighorn sheep populations. After accounting for variation in season, subpopulation, and years, home range size was positively associated with road density in both subpopulations (P < 0.001), suggesting that females incur greater energetic costs associated with greater space use in areas of higher fragmentation. Our results establish the basic spatial ecology of female bighorn sheep in Nebraska where their behavior appears to reflect the isolated nature of suitable habitat in this fragmented prairie landscape.     

PCA-correlated SNPs for structure identification in worldwide human populations

Existing methods to ascertain small sets of markers for the identification of human population structure require prior knowledge of individual ancestry. Based on Principal Components Analysis (PCA), and recent results in theoretical computer science, we present a novel algorithm that, applied on genomewide data, selects small subsets of SNPs (PCA-correlated SNPs) to reproduce the structure found by PCA on the complete dataset, without use of ancestry information. Evaluating our method on a previously described dataset (10,805 SNPs, 11 populations), we demonstrate that a very small set of PCA-correlated SNPs can be effectively employed to assign individuals to particular continents or populations, using a simple clustering algorithm. We validate our methods on the HapMap populations and achieve perfect intercontinental differentiation with 14 PCA-correlated SNPs. The Chinese and Japanese populations can be easily differentiated using less than 100 PCA-correlated SNPs ascertained after evaluating 1.7 million SNPs from HapMap. We show that, in general, structure informative SNPs are not portable across geographic regions. However, we manage to identify a general set of 50 PCA-correlated SNPs that effectively assigns individuals to one of nine different populations. Compared to analysis with the measure of informativeness, our methods, although unsupervised, achieved similar results. We proceed to demonstrate that our algorithm can be effectively used for the analysis of admixed populations without having to trace the origin of individuals. Analyzing a Puerto Rican dataset (192 individuals, 7,257 SNPs), we show that PCA-correlated SNPs can be used to successfully predict structure and ancestry proportions. We subsequently validate these SNPs for structure identification in an independent Puerto Rican dataset. The algorithm that we introduce runs in seconds and can be easily applied on large genome-wide datasets, facilitating the identification of population substructure, stratification assessment in multi-stage whole-genome association studies, and the study of demographic history in human populations.     

Dental microwear from Natufian hunter-gatherers and early Neolithic farmers: comparisons within and between samples

Microwear patterns from Natufian hunter-gatherers (12,500-10,250 bp) and early Neolithic (10,250-7,500 bp) farmers from northern Israel are correlated with location on facet nine and related to an archaeologically suggested change in food preparation. Casts of permanent second mandibular molars are examined with a scanning electron microscope at a magnification of 500x. Digitized micrographs are taken from the upper and lower part of facet nine. Microwear patterns are recorded with an image-analysis computer program and compared within and between samples, using univariate and multivariate analyses. Comparisons within samples reveal a greater frequency of pits on the lower part of the facet among the farmers, compared to the upper part. Microwear does not vary over the facet among the hunter-gatherers. Comparisons between samples reveal larger dental pits (length and width) and wider scratches among the farmers at the bottom of the facet, compared to the hunter-gatherers. Microwear does not vary between samples at the top of the facet. The microwear patterns suggest that the Natufian to early Neolithic development led to a harder diet, and this is related to an archaeologically suggested change in food processing. The harder diet of the early farmers may have required higher bite forces that were exerted at the bottom of facet nine, in the basin of the tooth.     

Impact of lactic acid on cell proliferation and free radical‐induced cell death in monolayer cultures of neural precursor cells

Biomaterials prepared from polyesters of lactic acid and glycolic acid, or a mixture of the two, degrade in the presence of water into the naturally occurring metabolites, lactic acid and glycolic acid. While the lactic acid degradation product that is released from biomaterials is well tolerated by the body, lactic acid can influence the metabolic function of cells; it can serve as an energy substrate for cells, and has been shown to have antioxidant properties. Neural precursor cells, a cell population of considerable interest as a source of cells for neural tissue regeneration strategies, generate a high amount of reactive oxygen species, and when associated with a degradable biomaterial, may be impacted by released lactic acid. In this work, the effect of lactic acid on a neural cell population containing proliferative neural precursor cells was examined in monolayer culture. Lactic acid was found to scavenge exogenously added free radicals produced in the presence of either hydrogen peroxide or a photoinitiator (I2959) commonly utilized in the preparation of photopolymerizable biomaterials. In addition to its effect on exogenously added free radicals, lactic acid reduced intracellular redox state, increased the proliferation of the cell population, and modified the cell composition. The findings of this study provide insight into the role that lactic acid plays naturally on developing neural cells and are also of interest to biomaterials scientists that are focused on the development of degradable lactic‐acid‐based polymers for cell culture devices. The effect of lactic acid on other cell populations may differ and should be characterized to best understand how cells function in degradable cell culture devices. Biotechnol. Bioeng. 2009;103: 1214–1223. © 2009 Wiley Periodicals, Inc.     

Augmenting the activity of antifungal agents against aspergilli using structural analogues of benzoic acid as chemosensitizing agents

A number of benzoic acid analogues showed antifungal activity against strains of Aspergillus flavus, Aspergillus fumigatus and Aspergillus terreus, causative agents of human aspergillosis, in in vitro bioassays. Structure-activity analysis revealed that antifungal activities of benzoic and gallic acids were increased by addition of a methyl, methoxyl or chloro group at position 4 of the aromatic ring, or by esterification of the carboxylic acid with an alkyl group, respectively. Thymol, a natural phenolic compound, was a potent chemosensitizing agent when co-applied with the antifungal azole drugs fluconazole and ketoconazole. The thymol-azole drug combination demonstrated complete inhibition of fungal growth at dosages far lower than the drugs alone. Co-application of thymol with amphotericin B had an additive effect on all strains of aspergilli tested with the exception of two of three strains of A. terreus, where there was an antagonistic effect. Use of two mitogen-activated protein kinase (MAPK) mutants of A. fumigatus, sakAΔ and mpkCΔ, having gene deletions in the oxidative stress response pathway, indicated antifungal and/or chemosensitization activity of the benzo analogues was by disruption of the oxidative stress response system. Results showed that both these genes play overlapping roles in the MAPK system in this fungus. The potential of safe, natural compounds or analogues to serve as chemosensitizing agents to enhance efficacy of commercial antifungal agents is discussed.