Linkage strategies for genetically complex traits. II. The power of affected relative pairs.

The power to detect disease-susceptibility loci through linkage analysis using pairs of affected relatives and affected-unaffected pairs is examined. Allelic identity by descent (ibd) for a completely polymorphic marker for sibling, uncle-nephew, grandparent-grandchild, half-sib, and first-cousin pairs is considered. Affected-unaffected pairs generally represent a poor strategy. For single-locus models, ibd depends on lambda R, the risk ratio for type R relatives compared with population prevalence, and the recombination fraction theta. The ibd for grandparent-grandchild pairs is least affected by recombination, followed by sibs, half-sib, uncle-nephew, and first-cousin pairs. For diseases with large lambda values and for small theta values, distant relatives offer greater power. For larger theta values, grandparent-grandchild pairs are best; for small lambda values, sibs are best. Additive and multiplicative multilocus models are considered. For the multiplicative model, the same formulas as in the single-locus model apply, except that lambda iR (for the ith contributing locus) is substituted for lambda R. For the additive model, the deviation from null expectation for ibd is divided among all contributing loci. Compared with the multiplicative model, for an additive model there is usually greater advantage in distant relationships. Multipoint analysis using linked marker loci for affected relative pairs is described. Simultaneous use of multiple markers diminishes the effect of recombination and allows for localization of the disease-susceptibility locus.     

Assessing the role of HLA-linked and unlinked determinants of disease.

The relationship between increased risk in relatives over population prevalence (lambda R = KR/K) and probability of sharing zero marker alleles identical by descent (ibd) at a linked locus (such as HLA) by an affected relative pair is examined. For a model assuming a single disease-susceptibility locus or group of loci tightly linked to a marker locus, the relationship is remarkably simple and general. Namely, if phi R is the prior probability for the relative pair to share zero marker alleles identical by descent, then P (sharing 0 markers/both relatives are affected) is just phi R/lambda R. Alternatively, lambda AR, the increased risk over population prevalence to a relative R due to a disease locus tightly linked to marker locus A, equals the prior probability that the relative pair share zero A alleles ibd divided by the posterior probability that they share zero alleles ibd, given that they are both affected. For example, for affected sib pairs, P (sharing 0 markers/both sibs are affected) = .25/lambda S. This formula holds true for any number of alleles at the disease locus and for their frequencies, penetrances, and population prevalence. Similar formulas are derived for sharing one and two markers. Application of these formulas to several well-studied HLA-associated diseases yields the following results: For multiple sclerosis, insulin-dependent diabetes mellitus, and coeliac disease, a single-locus model of disease susceptibility is rejected, implying the existence of additional unlinked familial determinants. For all three diseases, the effect of the HLA-linked locus on familiality is minor: for multiple sclerosis, it accounts for only a 2.5-fold increased risk to sibs over the population prevalence, compared to an observed value of 20; for coeliac disease, it accounts for approximately a 5.25-fold increased risk to sibs, while the observed value is on the order of 60; for insulin-dependent diabetes mellitus, it accounts for a 3.42-fold increased risk in sibs, while the observed value is 15. In all cases, the secondary determinants must be outside the HLA region. For tuberculoid leprosy, an unlinked familial determinant is also implicated (increased risk to sibs due to HLA = 1.49; observed value = 2.38). For hemochromatosis and Hodgkin's disease, there is little evidence for HLA-unlinked familial determinants. With this formula, it is also possible to examine the hypothesis of pleiotropy versus linkage dis-equilibrium by comparing lambda AS with the increased risk to sibs due to the associated allele(s).(ABSTRACT TRUNCATED AT 400 WORDS)     

Population stratification confounds genetic association studies among Latinos

In the United States, asthma prevalence and mortality are the highest among Puerto Ricans and the lowest among Mexicans. Case-control association studies are a powerful strategy for identifying genes of modest effect in complex diseases. However, studies of complex disorders in admixed populations such as Latinos may be confounded by population stratification. We used ancestry informative markers (AIMs) to identify and correct for population stratification among Mexican and Puerto Rican subjects participating in case-control studies of asthma. Three hundred and sixty-two subjects with asthma (Mexican: 181, Puerto Rican: 181) and 359 ethnically matched controls (Mexican: 181, Puerto Rican: 178) were genotyped for 44 AIMs. We observed a greater than expected degree of association between pairs of AIMs on different chromosomes in Mexicans (P < 0.00001) and Puerto Ricans (P < 0.00002) providing evidence for population substructure and/or recent admixture. To assess the effect of population stratification on association studies of asthma, we measured differences in genetic background of cases and controls by comparing allele frequencies of the 44 AIMs. Among Puerto Ricans but not in Mexicans, we observed a significant overall difference in allele frequencies between cases and controls (P = 0.0002); of 44 AIMs tested, 8 (18%) were significantly associated with asthma. However, after adjustment for individual ancestry, only two of these markers remained significantly associated with the disease. Our findings suggest that empirical assessment of the effects of stratification is critical to appropriately interpret the results of case-control studies in admixed populations.     

Sebaceous Lipid Profiling of Bat Integumentary Tissues: Quantitative Analysis of Free Fatty Acids,Monoacylglycerides, Squalene,and Sterols

White‐nose syndrome (WNS) is a fungal disease caused by Pseudogymnoascus destructans and is devastating North American bat populations. Sebaceous lipids secreted from host integumentary tissues are implicated in the initial attachment and recognition of host tissues by pathogenic fungi. We are interested in determining if ratios of lipid classes in sebum can be used as biomarkers to diagnose severity of fungal infection in bats. To first establish lipid compositions in bats, we isolated secreted and integral lipid fractions from the hair and wing tissues of three species: big brown bats (Eptesicus fuscus), Eastern red bats (Lasiurus borealis), and evening bats (Nycticeius humeralis). Sterols, FFAs, MAGs, and squalene were derivatized as trimethylsilyl esters, separated by gas chromatography, and identified by mass spectrometry. Ratios of sterol to squalene in different tissues were determined, and cholesterol as a disease biomarker was assessed. Free sterol was the dominant lipid class of bat integument. Squalene/sterol ratio is highest in wing sebum. Secreted wing lipid contained higher proportions of saturated FFAs and MAGs than integral wing or secreted hair lipid. These compounds are targets for investigating responses of P. destructans to specific host lipid compounds and as biomarkers to diagnose WNS.     

The Role of Wood Ants (Formica rufa group) in Carbon and Nutrient Dynamics of a Boreal Norway Spruce Forest Ecosystem

Wood ants (Formica rufa group) are regarded as keystone species in boreal and mountain forests of Europe and Asia by their effect on ecosystem carbon (C) and nutrient pools and fluxes. To quantify the impact of their activity on boreal forest ecosystems, C, nitrogen (N), phosphorus (P), potassium (K) and calcium (Ca) pools and fluxes in wood ant nests (WAN), and soil were assessed along a 5-, 30-, 60-, and 100-year-old Norway spruce (Picea abies L. Karsten) dominated successional gradient in eastern Finland. Amounts of C and nutrients in WAN increased with stand age, but contained less than 1% of total C and nutrient pools in these stands. The CO₂-efflux from nests was also insignificant, as compared to CO₂-efflux from the forest floor. Annually, the amount of C brought by wood ants into their nests as honeydew, prey and nest-building materials ranged from 2.7 to 49.3 kg ha^?1 C, but this is only 0.1–0.7% of the combined net primary production of trees and understorey in boreal forests. The difference between wood ant nest C inputs and outputs was very small in the younger-aged stands, and increased in the older stands. Carbon accumulation rates in nests over a 100 year period are estimated to be less than 10 kg ha^?1 a^?1. In contrast to C, annual inputs of N, P, and K are larger compared to wood ant nest nutrient pool size, ranging from 3 to 6% of the annual tree stand and understorey uptake. This indicates a more rapid turnover and transport of N, P, and K out of WAN, and suggests that wood ants increase the cycling rate of these nutrients in boreal forests.     

Growth and polyhydroxybutyrate production by Ralstonia eutropha in emulsified plant oil medium

Polyhydroxyalkanoates (PHAs) are natural polyesters synthesized by bacteria for carbon and energy storage that also have commercial potential as bioplastics. One promising class of carbon feedstocks for industrial PHA production is plant oils, due to the high carbon content of these compounds. The bacterium Ralstonia eutropha accumulates high levels of PHA and can effectively utilize plant oil. Growth experiments that include plant oil, however, are difficult to conduct in a quantitative and reproducible manner due to the heterogeneity of the two-phase medium. In order to overcome this obstacle, a new culture method was developed in which palm oil was emulsified in growth medium using the glycoprotein gum arabic as the emulsifying agent. Gum arabic did not influence R. eutropha growth and could not be used as a nutrient source by the bacteria. R. eutropha was grown in the emulsified oil medium and PHA production was measured over time. Additionally, an extraction method was developed to monitor oil consumption. The new method described in this study allows quantitative, reproducible R. eutropha experiments to be performed with plant oils. The method may also prove useful for studying growth of different bacteria on plant oils and other hydrophobic carbon sources.     

Stand type is more important than red wood ant abundance for the structure of ground‐dwelling arthropod assemblages in managed boreal forests

• 1 The relationships between red wood ants (Formica rufa group) and other ground‐dwelling arthropods were studied in young managed forests stands in Eastern Finland. The main objectives were: (i) to test the influence of stand type (dominant tree species; age: sapling versus pole stage) and numbers of red wood ants on the occurrence of other ground‐dwelling arthropods and (ii) to study the occurrence of red wood ants versus other arthropods on a distance gradient from ant mounds. We used pitfall traps set in 5–14‐year‐old sapling stands and 30–45‐year‐old pole‐stage stands of Scots pine (Pinus sylvestris L.) and birch (Betula spp.) forests.
• 2 Pitfall trap catches of red wood ants did not vary significantly between the forest stand types, although some groups of other arthropods showed clear responses to stand type (e.g. catches of other Formicinae and Gnaphosidae were higher in sapling stands than in pole‐stage stands). The number of red wood ants clearly explained less of the variation in assemblages of other ground‐dwelling arthropods than the forest stand type.
• 3 Red wood ant numbers decreased significantly with distance from the mounds, but the other ground‐dwelling arthropods were insensitive to this gradient or even showed a preference for proximity to ant mounds and high ant activity.
• 4 The results obtained in the present study suggest that wood ants do not have strong effects on several other ground‐dwelling arthropod groups in young managed forests other than in the immediate vicinity of their mounds.