Robust score statistics for QTL linkage analysis

The traditional variance components approach for quantitative trait locus (QTL) linkage analysis is sensitive to violations of normality and fails for selected sampling schemes. Recently, a number of new methods have been developed for QTL mapping in humans. Most of the new methods are based on score statistics or regression-based statistics and are expected to be relatively robust to non-normality of the trait distribution and also to selected sampling, at least in terms of type I error. Whereas the theoretical development of these statistics is more or less complete, some practical issues concerning their implementation still need to be addressed. Here we study some of these issues such as the choice of denominator variance estimates, weighting of pedigrees, effect of parameter misspecification, effect of non-normality of the trait distribution, and effect of incorporating dominance. We present a comprehensive discussion of the theoretical properties of various denominator variance estimates and of the weighting issue and then perform simulation studies for nuclear families to compare the methods in terms of power and robustness. Based on our analytical and simulation results, we provide general guidelines regarding the choice of appropriate QTL mapping statistics in practical situations.     

Efficacy model for antibody-mediated pre-erythrocytic malaria vaccines

Antibodies to the pre-erythrocytic antigens, circumsporozoite protein (CSP), thrombospondin-related adhesive protein (TRAP) and liver-stage antigen 1, have been measured in field studies of semi-immune adults and shown to correlate with protection from Plasmodium falciparum infection. A mathematical model is formulated to estimate the probability of sporozoite infection as a function of antibody titres to multiple pre-erythrocytic antigens. The variation in antibody titres from field data was used to estimate the relationship between the probability of P. falciparum infection per infectious mosquito bite and antibody titre. Using this relationship, we predict the effect of vaccinations that boost baseline CSP or TRAP antibody titres. Assuming the estimated relationship applies to vaccine-induced antibody titres, then single-component CSP or TRAP antibody-mediated pre-erythrocytic vaccines are likely to provide partial protection from infection, with vaccine efficacy of approximately 50 per cent depending on the magnitude of the vaccine-induced boost to antibody titres. It is possible that the addition of a TRAP component to a CSP-based vaccine such as RTS,S would provide an increase in infection-blocking efficacy of approximately 25 per cent should the problem of immunological interference between antigens be overcome.     

Rethinking the dispersal of Homo sapiens out of Africa

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.     

MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms

SUMMARY: MeSHer uses a simple statistical approach to identify biological concepts in the form of Medical Subject Headings (MeSH terms) obtained from the PubMed database that are significantly overrepresented within the identified gene set relative to those associated with the overall collection of genes on the underlying DNA microarray platform. As a demonstration, we apply this approach to gene lists acquired from a published study of the effects of angiotensin II (Ang II) treatment on cardiac gene expression and demonstrate that this approach can aid in the interpretation of the resulting 'significant' gene set. AVAILABILITY: The software is available at http://www.tm4.org. SUPPLEMENTARY INFORMATION: Results from the analysis of significant genes from the published Ang II study.     

Skeletal muscle fatigue, strength, and quality in the elderly: the Health ABC Study.

We examined the muscle fatigue characteristics in older men and women and determined whether these were related to the size, strength, or quality of muscle. A total of 1,512 men and women aged 70-79 yr from the Health, Aging, and Body Composition Study participated in this study. Muscle cross-sectional area and attenuation were determined with computed tomography. Skeletal muscle fatigue and strength (peak torque) of the knee extensors and flexors were measured using isokinetic dynamometry. Men were more fatigue resistant than women for both knee extension (fatigue index: 70.4 +/- 15.3 vs. 66.9 +/- 14.3%; P < 0.05) and knee flexion (67.9 +/- 16.4 vs. 64.9 +/- 17.6%; P < 0.05). Peak torque and muscle quality (specific torque) were higher in men than women for knee extension (99.6 +/- 28.2 vs. 63.0 +/- 16.8 N x m and 1.62 +/- 0.43 vs. 1.51 +/- 0.39 N x m/cm2; both P < 0.05) and for knee flexion (74.0 +/- 26.4 vs. 49.6 +/- 15.9 N x m and 2.47 +/- 1.29 vs. 2.22 +/- 0.78 N x m/cm2; both P < 0.05). Total work and power output was greater in men compared with women for both the quadriceps (1,353 +/- 451 vs. 832 +/- 264 J and 87.7 +/- 33.5 vs. 53.3 +/- 19.2 W; both P < 0.05) and the hamstrings (741 +/- 244 vs. 510 +/- 141 J and 35.4 +/- 16.0 vs. 23.7 +/- 10.2 W; both P < 0.05). In both genders, the quadriceps was able to perform more work with greater power compared with the hamstrings. Those who were stronger actually had greater fatigue after adjusting for age, race, physical activity, and total body fat. In conclusion, older men were more fatigue resistant than women, although in both men and women greater fatigue was not related to muscle weakness.     

Hierarchical patterns of paternity within crowns of Albizia julibrissin (Fabaceae)

The floral architecture and phenology of the tree species Albizia julibrissin (Fabaceae) offer the potential for flowers within inflorescences to share common pollen donors. Patterns of paternity within individual tree crowns may differ among isolated individuals and those in populations due to differences in pollinator foraging behavior. To determine how genetic diversity is partitioned within individual seed pools and whether these patterns differ among isolated and population trees, we obtained all fruits from three inflorescences from four clusters from three isolated trees and from three population trees in Athens, Georgia. We assayed 14 polymorphic allozymes to genotype all progeny within singly sired fruits to determine the multilocus genotype of each fruit's pollen donor. Inflorescences had multiple pollen donors, but simulation analyses revealed that redundancy of pollen donors tended to be more likely within inflorescences than randomly across the crown. Analysis of genetic and genotypic diversity indicated that individual maternal trees received pollen from many donors in uneven frequencies. Results suggest that isolated trees receive pollen from slightly fewer pollen donors and experience more within-plant pollinator movement than trees in populations. However, isolated trees receive qualitatively similar pollen from many sources, suggesting that these trees are not effectively isolated and that pollen moves long distances in this species.     

The Role of <Emphasis Type="Italic">Habitus</Emphasis> in the Maintenance of Traditional Noongar Plant Knowledge in Southwest Western Australia

We examine the role that habitus, an individual’s or group’s dispositions, has played in the retention of traditional ecological knowledge among the Noongar people of south-western Australia. We sought to determine if current plant knowledge reflects Noongar habitus or, alternatively, the use of fall-back species that were important due to the intermittency of agricultural employment and the social exclusion of Aboriginal people up until at least the 1960s in Western Australia. We compared the seasonal availability of Noongar food plant resources currently known by Noongar Elders to those described at the time of European settlement. We used non-metric Multidimensional Scaling (nMDS) and multivariate statistics to compare the seasonal availability of plant resources with the seasonal availability of work prior to the introduction of civil rights for Aboriginal Australians in the 1960s. We show that the seasonal pattern of plant knowledge has changed little since settlement and that there was no significant relationship between the seasonal availability of work and plant knowledge. This result suggests that prior to 1960 Noongars maintained a reasonably traditional round of seasonal activities involving traditional plant use. We suggest that Noongar habitus guided their response to the colonising culture and helped preserve traditional ecological knowledge.     

Vaccinia virus activation of CCR5 invokes tyrosine phosphorylation signaling events that support virus replication

Vaccinia virus, a poxvirus, produces structurally distinct forms of virions for which the immediate events following cell entry are ill-defined. We provide evidence that intracellular mature virus (IMV) enters both permissive and nonpermissive T-cell lines and that introduction of CCR5 into nonpermissive mouse fibroblasts or human primary T cells renders the cells permissive for vaccinia replication. Notably, T cells expressing CCR5 in which tyrosine 339 in the intracellular region is replaced by phenylalanine no longer support virus replication or virus-inducible activation of specific host cell signaling effectors IRS-2, Grb2, and Erk1/2. We show that following IMV entry into the cell, the intact but not the tyrosine-deficient CCR5 is rapidly internalized and colocalizes with virus. This colocalization precedes virus-inducible signaling and replication.