Estimating and testing haplotype-trait associations in non-diploid populations

Malaria is an infectious disease that is caused by a group of parasites of the genus Plasmodium. Characterizing the association between polymorphisms in the parasite genome and measured traits in an infected human host may provide insight into disease aetiology and ultimately inform new strategies for improved treatment and prevention. This, however, presents an analytic challenge since individuals are often multiply infected with a variable and unknown number of genetically diverse parasitic strains. In addition, data on the alignment of nucleotides on a single chromosome, which is commonly referred to as haplotypic phase, is not generally observed. An expectation–maximization algorithm for estimating and testing associations between haplotypes and quantitative traits has been described for diploid (human) populations. We extend this method to account for both the uncertainty in haplotypic phase and the variable and unknown number of infections in the malaria setting. Further extensions are described for the human immunodeficiency virus quasi-species setting. A simulation study is presented to characterize performance of the method. Application of this approach to data arising from a cross-sectional study of n=126 multiply infected children in Uganda reveals some interesting associations requiring further investigation.

Mitochondrial DNA variation in Mauritania and Mali and their genetic relationship to other Western Africa populations

Mitochondrial DNA (mtDNA) variation was analyzed in Mauritania and Mali, and compared to other West African samples covering the considerable geographic, ethnic and linguistic diversity of this region. The Mauritanian mtDNA profile shows that 55% of their lineages have a west Eurasian provenance, with the U6 cluster (17%) being the best represented. Only 6% of the sub-Saharan sequences belong to the L3A haplogroup a frequency similar to other Berber speaking groups but significantly different to the Arabic speaking North Africans. The historic Arab slave trade may be the main cause of this difference. Only one HV west Eurasian lineage has been detected in Mali but 40% of the sub-Saharan sequences belong to cluster L3A. The presence of L0a representatives demonstrates gene flow from eastern regions. Although both groups speak related dialects of the Mande branch, significant genetic differences exist between the Bambara and Malinke groups. The West African genetic variation is well structured by geography and language, but more detailed ethnolinguistic clustering suggest that geography is the main factor responsible for this differentiation.

A complement receptor-1 polymorphism with high frequency in malaria endemic regions of Asia but not Africa

Complement receptor-1 (CR1) is a ligand for rosette formation, a phenomenon associated with cerebral malaria (CM). Binding is dependent on erythrocyte CR1 copy number. In Caucasians, low CR1 expressors have two linked mutations. We determined the Q981H and HindIII RFLP distribution in differing population groups to ascertain a possible role in adaptive evolution. We examined 194 Caucasians, 180 Choctaw Indians, 93 Chinese-Taiwanese, 304 Cambodians, 89 Papua New Guineans (PNG) and 366 Africans. PCR/RFLP used HindIII for CR1 expression and BstNI for the Q981H mutation. DNA sequencing and pyrosequencing were performed to resolve inconclusive results. Gene frequencies for the L allele were 0.15 in Africans, 0.16 in Choctaws, 0.18 in Caucasians, 0.29 in Chinese-Taiwanese, 0.47 in Cambodians and 0.58 in PNG. Allelic frequency for 981H were 0.07 in Africans, 0.15 in Caucasians, 0.18 in Choctaws, 0.29 in Chinese-Taiwanese, 0.47 in Cambodians and 0.54 in PNG. The Q981H polymorphism correlates with the HindIII RFLP in most groups except West Africans and appears to be part of a low CR1 expression haplotype. The gene frequency for the haplotype is highest in the malaria-endemic areas of Asia, suggesting that this haplotype may have evolved because it protects from rosetting and CM.

Zoonotic infections in Nigeria: overview from a medical perspective

Infections of domestic and wild animals that are transmitted directly or by an arthropod vector to humans are a major cause of morbidity and mortality worldwide and particularly in Nigeria. With a population of over 100 million and the need for improved health care delivery, Nigerians are at considerable risk considering the seriousness of these infections. Zoonotic infections that are endemic in Nigeria include tuberculosis, trypanosomiasis, toxoplasmosis, taeniasis, rabies, lassa fever and yellow fever. Zoonotic food-borne infections (caused by Campylobacter, Salmonella and Escherichia coli O157:H7) and cryptosporidiosis are emerging. Sporadic cases such as strongyloidiasis, ascariasis, leptospirosis, scabies, pentastomiasis and African histoplasmosis have been reported. There is a need to determine the prevalence of tick-borne zoonoses. Prevention and control of zoonoses in humans is by vaccination, treatment and health education. As a first measure to improve control, the link between veterinary and medical officers, which is presently very weak, needs to be strengthened. Furthermore, regional multidisciplinary approaches to the control of zoonotic infections should be adopted in West Africa, which take into consideration the huge inter-border traffic.

Lipid Tubule Self-Assembly: Length Dependence on Cooling Rate Through a First-Order Phase Transition

The formation kinetics and self-assembly of multilamellar tubules of the diacetylenic phospholipid 1,2-bis(tricosa-10,12-diynoyl)-sn-glycerol-3-phosphocholine formed under controlled cooling rates were studied by x-ray diffraction and optical, atomic force, and scanning electron microscopy. Tubule formation was driven by a reversible first-order phase transition from an intralamellar, chain-melted L(alpha) phase to a chain-frozen L(beta), phase. These observations are the basis of a highly efficient method of tubule production in which tubule lengths can be controlled, between 1 and 100 micrometers, by varying the cooling rate. These tubules can be made in suspensions with 10 percent lipid by mass, far exceeding the lipid solubility limit.

Ethanol-induced disordering of membranes from different age groups of C57BL/6NNIA mice

In previous studies, we have shown that many of the pharmacological effects of ethanol administered in vivo are greater in older mice compared to younger mice. This study determined if there are age-related differences in membrane order when ethanol is administered in vitro. Synaptic plasma membranes, brain microsomal membranes and erythrocyte membranes were isolated from young (3-5 month), middle (11-13 months), and old (22-24 months) C57BL/6NNIA mice. The order parameter of each age group was measured using a 5-nitroxide stearic acid spin label in the presence of 0, 250 and 500 mM ethanol added in vitro. No age-related differences in order parameter were seen in the absence of ethanol. However, membranes from young animals were disordered to the greatest degree by ethanol. The synaptic plasma and erythrocyte membranes from young mice were disordered by both 250 and 500 mM ethanol. Membranes from old mice were disordered significantly by 500 mM ethanol only and the disordering was not as great as was seen in the membranes from the young mice. In the microsomal membrane preparation, 500 mM ethanol significantly disordered the membranes from the young animals, but it had no effect on membranes from old animals. Age differences were also observed generally for cholesterol and total phospholipid which both increased with increasing age for synaptic plasma and brain microsomes. Membrane disorder induced by ethanol differs with age and is associated with cholesterol and phospholipid content of membranes.