Combined association,segregation and aggregation analysis on case-control family data

Recently genetic epidemiologists have begun using case-control family study designs to investigate the role of genetic and environmental risk factors in disease etiology. The objective of these studies is to assess the association of environmental factors with the disease trait; to characterize the disease genes using segregation analysis; and to quantify the residual familial aggregation after controlling for environmental and genetic factors. Typically these objectives are achieved by conducting separate studies and analysis. This paper describes an estimating equation based approach for a combined association, segregation and aggregation analysis on data from case-control family studies. Simulations indicate that the method performs well in a variety of settings. The method is illustrated using simulated family history data made available to participants in a recent Genetic Analysis Workshop.     

Coeliac disease patients carry conserved HLA-DR3-DQ2 haplotypes revealed by association of TNF alleles

Certain HLA-DQ alleles are known to contribute to predisposition to coeliac disease (CD). The existence of additional independent risk-modifying loci in the HLA complex is still being debated. The DR3-DQ2 haplotype has been studied most, but the evidence is conflicting. The discrepancies may stem from the absence of such an effect, insufficient statistical power to detect an effect (i.e. small studies) and/or incomplete control of linkage disequilibrium (LD) to the neighbouring DQ-loci, known to elicit a strong effect. In the present study, we aimed to undertake a statistically high-powered family-based analysis, fully controlling effects of LD between the major DQ-risk haplotypes and neighbouring candidate loci. We investigated five markers on DR3-DQ2, DR5-DQ7 and DR7-DQ2 haplotypes in 327 Norwegian and Swedish families. Our primary finding was that TNF-308A (TNF2) was significantly associated on the DR3-DQ2 haplotype [stratum specific odds ratio (OR)=2.40 (1.25–4.48), Pc=0.009, where P_c=Pn and n=number of tests performed]. Furthermore, we confirmed earlier indications that LD between TNF2 and DQA1*05-DQB1*02 on the DR3 haplotype is more strongly maintained in family-based cases than family-based controls. In conclusion, we confirmed in this study, the largest of its kind, that additional CD risk factors independent of DQ2 alleles do exist on the DR3 haplotype.     

American Association of Tissue Banks: A Historical Reflection Upon Entering the 21st Century

The American Association of Tissue Banks (AATB) is a scientific, not-for-profit, peer-group organization founded in 1976 to facilitate the provision of transplantable tissues of uniform high quality in quantities sufficient to meet national needs. The Association was created well before there was governmental oversight of tissue banking. The organization consists of individuals involved in tissue banking, medical users, and scientists in the field. Current structure consists of a 13-member Board of Governors with specific subgroups including Musculoskeletal, Reproductive, Skin, Tissue Bank Councils and Council of Accredited Tissue Banks. A historical review shows the evolution from development of guidelines to publication of standards, and from an inspection conducted by peers to one conducted by an independent, trained professional inspector. Association growth and historical accomplishments are highlighted.     

Inheritance of caffeine and heteroside contents in an interspecific cross between a cultivated coffee species Coffea liberica var dewevrei and a wild species caffeine-free C. pseudozanguebariae

 Coffee species originating from Africa, in particular the two major cultivated species C. arabica and C. canephora, usually contain caffeine in their beans, whereas almost all Malagasy coffee species are caffeine-free. However, one wild coffee species C. pseudozanguebariae, collected near the coast in south Kenya, is also caffeine-free. Beans of this species contain a specific heteroside diterpene (hereinafter referred to simply as heteroside) and give a bitter coffee beverage. We have investigated the inheritance of the caffeine and heteroside contents in the first and second generations of an interspecific cross between C. pseudozanguebariae and C. liberica var. dewevrei, for which the caffeine content is about 1% dmb (dry matter basis). The caffeine content of F₁ hybrids (0.2% dmb) was lower than the parental average (0.47% dmb). Caffeine and heteroside contents appeared to be under polygenic control with a strong genetic effect. Nevertheless, one major gene with two alleles seemed to be involved in the control of both compounds. Absence of caffeine was apparently controlled by one recessive gene. Heteroside content seemed to be controlled by one co-dominant gene, heterozygotes being intermediate between the two different groups of homozygotes. Received: 15 September 1997 / Accepted: 6 October 1997     

Effects of nutrient and soil moisture on competition between shape Carex stricta,shape Phalaris arundinacea,and shape Typha latifolia

We investigated the importance of nutrients, soil moisture, arbuscular mycorrhizal fungi (AMF), and interspecific competition levels on the biomass allocation patterns of three wetland perennial plant species, Carex stricta Lam., Phalaris arundinacea L., and Typha latifolia L. A factorial experiment was conducted with high-low nutrient levels, high-low soil moisture levels, and with and without AMF inoculation. Under the experimental conditions, plant inoculation by AMF was too low to create a treatment and the AMF treatment was dropped from the total analysis. P. arundinacea and T. latifolia biomass were 73% and 77% higher, respectively, in the high nutrient treatment compared to the low nutrient treatment. Biomass allocation between shoots and roots remained relatively constant between environmental treatments, although shoot:root ratios of P. arundinacea declined in the low nutrient treatment. For C. stricta, the high nutrient and soil moisture treatments resulted in an increase in biomass of 50% and 15%, respectively. Shoot:root ratios were nearly constant among all environmental conditions. Biomass of T. latifolia and C. stricta was greatly decreased when grown with P. arundinacea. The rapid, initial height growth of P. arundinacea produced a spreading, horizontal canopy that overshadowed the vertical leaves of T. latifolia and C. stricta throughout the study. This pattern was repeated in both high and low nutrient and soil moisture treatments. When grown with P. arundinacea, C. stricta and T. latifolia significantly increased their mean shoot height, regardless of the nutrient or soil moisture level. The results of this experiment suggest that C. stricta and T. latifolia were light limited when growing with P. arundinacea and that canopy architecture is more important for biomass allocation than the other environmental conditions tested. The results also suggest that Phalaris arundinacea is an inherently better competitor (sensu Grime 1979) than C. stricta or T. latifolia.     

Guilt by Association: The Culture of Accusation and the American Anthropological Association's Investigation of Darkness in El Dorado

The American Anthropological Association's investigation of the charges in Darkness in El Dorado (Tierney 2000) found that the late James Neel and Napoleon Chagnon harmed the Yanomami in the course of their research in Venezuela and Brazil, and that Chagnon had violated the ethics code of the association. The association's inquiry contravened its own policy prohibiting ethics adjudications and was structured not by the standards of an objective investigation but by aspects of contemporary anthropology. Moralized approaches to information and postmodern rejection of objectivity mark the language and methods of the inquiry. The investigating task force did not observe reasonable standards of evidence, the targets of the investigation were not represented, and task force members were compromised by conflicts of interest. The investigation and its collateral activities reflect a culture of accusation and an anthropology uncertain of its ethical or scientific stature.     

Interference competition in entomopathogenic nematodes: male Steinernema kill members of their own and other species

There is evidence of competition within and between helminth species, but the mechanisms involved are not well described. In interference competition, organisms prevent each other from using the contested resource through direct negative interactions, either chemical or physical. Steinernema spp. are entomopathogenic nematodes; they enter a living insect host which they kill and consume with the aid of symbiotic bacteria. Several studies have demonstrated intra- and interspecific competition in Steinernema, mediated by a scramble for resources and by incompatibility of the bacterial symbiont. Here we describe a mechanism by which male Steinernema may compete directly for resources, both food (host) and females, by physically injuring or killing members of another species as well as males of their own species. A series of experiments was conducted in hanging drops of insect haemolymph. Males of each of four species (Steinernemalongicaudum, Steinernemacarpocapsae, Steinernemakraussei and Steinernemafeltiae), representing three of the five phylogenetic clades of the genus, killed each other. Within 48 h, up to 86% of pairs included at least one dead male, compared with negligible mortality in single male controls. There was evidence of intraspecific difference: one strain of S. feltiae (4CFMO) killed while another (UK76) did not. Males also killed both females and males of other Steinernema spp. There was evidence of a hierarchy of killing, with highest mortality due to S. longicaudum followed by S. carpocapsae, S. kraussei and S. feltiae. Wax moth larvae were co-infected with members of two Steinernema spp. to confirm that killing also takes place in the natural environment of an insect cadaver. When insects were co-infected with one infective juvenile of each species, S. longicaudum males killed both S. feltiae UK76 and Steinernema hermaphroditum. Wax moths co-infected with larger, equal numbers of S. longicaudum and S. feltiae UK76 produced mainly S. longicaudum progeny, as expected based on hanging drop experiments.     

Phytoferritin and its implications for human health and nutrition

Background

Plant and animal ferritins stem from a common ancestor, but plant ferritins exhibit various features that are different from those of animal ferritins. Phytoferritin is observed in plastids (e.g., chloroplasts in leaves, amyloplasts in tubers and seeds), whereas animal ferritin is largely found in the cytoplasm. The main difference in structure between plant and animal ferritins is the two specific domains (TP and EP) at the N-terminal sequence of phytoferritin, which endow phytoferritin with specific iron chemistry. As a member of the nonheme iron group of dietary iron sources, phytoferritin consists of 24 subunits that assemble into a spherical shell storing up to ∼ 2000 Fe^3 + in the form of an iron oxyhydroxide-phosphate mineral. This feature is distinct from small molecule nonheme iron existing in cereals, which has poor bioavailability.

Scope of review

This review focuses on the relationship between structure and function of phytoferritin and the recent progress in the use of phytoferritin as iron supplement.

Major conclusions

Phytoferritin, especially from legume seeds, represents a novel alternative dietary iron source.

General significance

An understanding of the chemistry and biology of phytoferritin, its interaction with iron, and its stability against gastric digestion is beneficial to design diets that will be used for treatment of global iron deficiency.     

Spatial dynamics and morphological plasticity of common reed (Phragmites australis) and cattails (Typha sp.) in freshwater marshes and roadside ditches

Over the last decades, the abundance of common reed has significantly increased in freshwater wetlands of eastern North America, and stands of this species are now commonly alternating with stands of cattails. Since these species share many characteristics, the contact zone between common reed and cattail stands may witness strong interspecific interactions. We surveyed stand dynamics in roadside ditches and freshwater marshes at these contact zones over three years, and we examined the morphological plasticity in response to neighbors. Results indicate that common reed is clearly gaining ground over time, while cattails stands are retreating. We also found annual variability in the spatial dynamics, suggesting that other factors, such as the effect of weather conditions on water level, may affect population processes. Interspecific interactions had a detrimental effect on both common reed and cattail biomass. However, common reed showed morphological plasticity in shoot height, number of nodes, and internodes length, while cattails did not. Our observations suggest that common reed has a net competitive advantage over cattails in roadside ditches and freshwater marshes.     

Interspecific hybridization of <Emphasis Type="Italic">Prunus persica</Emphasis> with <Emphasis Type="Italic">P. armeniaca</Emphasis> and <Emphasis Type="Italic">P. salicina</Emphasis> using embryo rescue

Embryo rescue technique was used successfully to produce interspecific hybrids by crossing peach (P. persica) as a female parent with apricot (P. armeniaca) and plum (P. salicica). In those crosses that had ‘Yuhualu’ or ‘Zhonghuashoutao’ as female parents, hybrid embryos aborted from the 7th or 8th week after pollination mainly due to post-pollination incompatibility. An embryo rescue protocol was established to rescue such embryos and recover hybrid plants. Modified half-strength MS medium containing 4 mg l⁻¹ 6-BA and 0.5 mg l⁻¹ IBA produced up to 90% germination in the embryos. Modified MS medium with 1.0 mg l⁻¹ 6-BA and 1.0 mg l⁻¹ IBA gave the highest bud induction and multiplication whereas modified MS medium containing 0.5 mg l⁻¹ IAA and 0.2 mg l⁻¹ NAA gave the best rooting percentage. All the hybrids obtained using this embryo rescue technique were verified using simple sequence repeat (SSR) markers. A series of pollen treatments were carried out to partially overcome pre-pollination incompatibility, and it was found accidentally that pollen treatment with electrostatic field not only improved pollen germination but also increased the multiplication coefficient of embryo-induced shoots.