The impact of genotyping error on haplotype reconstruction and frequency estimation

The choice of genotyping families vs unrelated individuals is a critical factor in any large-scale linkage disequilibrium (LD) study. The use of unrelated individuals for such studies is promising, but in contrast to family designs, unrelated samples do not facilitate detection of genotyping errors, which have been shown to be of great importance for LD and linkage studies and may be even more important in genotyping collaborations across laboratories. Here we employ some of the most commonly-used analysis methods to examine the relative accuracy of haplotype estimation using families vs unrelateds in the presence of genotyping error. The results suggest that even slight amounts of genotyping error can significantly decrease haplotype frequency and reconstruction accuracy, that the ability to detect such errors in large families is essential when the number/complexity of haplotypes is high (low LD/common alleles). In contrast, in situations of low haplotype complexity (high LD and/or many rare alleles) unrelated individuals offer such a high degree of accuracy that there is little reason for less efficient family designs. Moreover, parent-child trios, which comprise the most popular family design and the most efficient in terms of the number of founder chromosomes per genotype but which contain little information for error detection, offer little or no gain over unrelated samples in nearly all cases, and thus do not seem a useful sampling compromise between unrelated individuals and large families. The implications of these results are discussed in the context of large-scale LD mapping projects such as the proposed genome-wide haplotype map.

Systemic administration of interleukin-1 beta activates select populations of central amygdala afferents

The central nucleus of the amygdala (CeA) is activated robustly by an immune challenge such as the systemic administration of the proinflammatory cytokine interleukin-1beta (IL-1beta). Because IL-1beta is not believed to cross the blood-brain barrier in any significant amount, it is likely that IL-1beta elicits CeA cell recruitment by means of activation of afferents to the CeA. However, although many studies have investigated the origins of afferent inputs to the CeA, we do not know which of these also respond to IL-1beta. Therefore, to identify candidate neurons responsible for the recruitment of CeA cells by an immune challenge, we iontophoretically deposited a retrograde tracer, cholera toxin b-subunit (CTb), into the CeA of rats 7 days before systemic delivery of IL-1beta (1 mug/kg, i.a.). By using combined immunohistochemistry, we then quantified the number of Fos-positive CTb cells in six major regions known to innervate the CeA. These included the medial prefrontal cortex, paraventricular thalamus (PVT), ventral tegmental area, parabrachial nucleus (PB), nucleus tractus solitarius, and ventrolateral medulla. Our results show that after deposit of CTb into the CeA, the majority of double-labeled cells were located in the PB and the PVT, suggesting that CeA cell activation by systemic IL-1beta is likely to arise predominantly from cell bodies located in these regions. These findings may have significant implications in determining the central pathways involved in generating acute central responses to a systemic immune challenge. J. Comp. Neurol. 452:288-296, 2002. (C) 2002 Wiley-Liss, Inc.

Low-density koala (Phascolarctos cinereus) populations in the mulgalands of south-west Queensland. III. Broad-scale patterns of habitat use

To date there have been few quantitative studies of the distribution of, and relative habitat utilisation by, koalas in the mulgalands of Queensland. To examine these parameters we applied habitat-accessibility and relative habitat-utilisation indices to estimates of faecal pellet density sampled at 149 sites across the region. Modelling the presence of pellets using logistic regression showed that the potential range of accessible habitats and relative habitat use varied greatly across the region, with rainfall being probably the most important determinant of distribution. Within that distribution, landform and rainfall were both important factors affecting habitat preference. Modelling revealed vastly different probabilities of finding a pellet under trees depending on the tree species, canopy size, and location within the region.

Low-density koala (Phascolarctos cinereus) populations in the mulgalands of south-west Queensland. II. Distribution and diet

This study used faecal pellets to investigate the broadscale distribution and diet of koalas in the mulgalands biogeographic region of south-west Queensland. Koala distribution was determined by conducting faecal pellet searches within a 30-cm radius of the base of eucalypts on 149 belt transects, located using a multi-scaled stratified sampling design. Cuticular analysis of pellets collected from 22 of these sites was conducted to identify the dietary composition of koalas within the region. Our data suggest that koala distribution is concentrated in the northern and more easterly regions of the study area, and appears to be strongly linked with annual rainfall. Over 50% of our koala records were obtained from non-riverine communities, indicating that koalas in the study area are not primarily restricted to riverine communities, as has frequently been suggested. Cuticular analysis indicates that more than 90% of koala diet within the region consists of five eucalypt species. Our data highlights the importance of residual Tertiary landforms to koala conservation in the region.

Obesity is associated with worse peritoneal dialysis outcomes in the Australia and New Zealand patient populations

Although obesity is associated with increased risks of morbidity and death in the general population, a number of studies of patients undergoing hemodialysis have demonstrated that increasing body mass index (BMI) is correlated with decreased mortality risk. Whether this association holds true among patients treated with peritoneal dialysis (PD) has been less well studied. The aim of this investigation was to examine the association between BMI and outcomes among new PD patients in a large cohort, with long-term follow-up monitoring. Using data from the Australia and New Zealand Dialysis and Transplant Registry, an analysis of all new adult patients (n = 9679) who underwent an episode of PD treatment in Australia or New Zealand between April 1, 1991, and March 31, 2002, was performed. Patients were classified as obese (BMI of greater than or equal to30 kg/m(2)), overweight (BMI of 25.0 to 29.9 kg/m(2)), normal weight (BMI of 20 to 24.9 kg/m(2)), or underweight (BMI of

Gene flow in great bustard populations across the Strait of Gibraltar as elucidated from excremental PCR and mtDNA sequencing

Recent advances in molecular biology have made it possible to use the trace amounts of DNA in faeces to non-invasively sample endangered species for genetic studies. Here we use faeces as a source of DNA and mtDNA sequence data to elucidate the relationship among Spanish and Moroccan populations of great bustards. 834 bp of combined control region and cytochrome-b mtDNA fragments revealed four variable sites that defined seven closely related haplotypes in 54 individuals. Morocco was fixed for a single mtDNA haplotype that occurs at moderate frequency (28%) in Spain. We could not differentiate among the sampled Spanish populations of Caceres and Andalucia but these combined populations were differentiated from the Moroccan population. Estimates of gene flow (Nm = 0.82) are consistent with extensive observations on the southern Iberian peninsular indicating that few individuals fly across the Strait of Gibraltar. We demonstrate that both this sea barrier and mountain barriers in Spain limit dispersal among adjacent great bustard populations to a similar extent. The Moroccan population is of high ornithological significance as it holds the only population of great bustards in Africa. This population is critically small and genetic and observational data indicate that it is unlikely to be recolonised via immigration from Spain should it be extirpated. In light of the evidence presented here it deserves the maximum level of protection.

Genetic structure of Mycosphaerella fijiensis populations from Australia, Papua New Guinea and the Pacific Islands

Single-copy restriction fragment length polymorphism (RFLP) markers were used to determine the genetic structure of Mycosphaerella fijiensis, the cause of black leaf streak (black Sigatoka) disease of banana and plantain, in the Torres Strait, Papua New Guinea (PNG), and the Pacific Islands. A moderate level of genetic variation was observed in all populations with genotypic diversity values of 60-78% of the theoretical maximum, and gene diversity (H) values between 0.269 and 0.336. All populations were at gametic equilibrium, and with the high level of genotypic diversity observed this indicated that sexual reproduction has a major role in the genetic structure of the M. fijiensis populations examined. Population differentiation was tested on several hierarchical scales. No evidence of population differentiation was observed between sites on Mer Island. A moderate level of population differentiation was observed within the Torres Strait, between Badu and Mer Islands (F-ST = 0.097). On a regional scale, the greatest differentiation was found between the populations of the Torres Strait and the Pacific. Populations from these regions were more closely related to the PNG population than to each other, suggesting they were founded in separate events from the same population.

Morphological and phytochemical characterization of Piper hispidinervum DC. and Piper aduncum L. populations in the state of Acre

Because of the increasing demand of the industry for the production of essential oils, studies highlight the genetic variability of Piper hispidinervum and P. aduncum species according to their patterns of spatial distribution, showing the Amazon region as the source of superior genetic material in the production of safrole and dillapiole. Thus, the objective this study was to characterize the morphology and the phytochemistry of Piper hispidinervum and P. aduncum populations in the Active Germplasm Bank of Embrapa Acre to generate subsidies for the genetic improvement of these species. The results showed that the average values for leaf width and length were 141.67 and 48.04 mm, and petioles length and diameter measurements were 2.83 and 1.78 mm for P. hispidinervum and 189.22; 67.74; 6.03 and 2.22 mm for P. aduncum respectively. The average height and canopy volume measurements were 2.39 m and 6.30 m3 and 2.70 m and 7.78 m3 respectively for each species. For P. hispidinervum, the population with higher performance indried yield and content of safrole was population 02, with 3.9%, and the population 04 showed 94.3% safrole content, both with genetic material from the region of Acrelândia and Plácido de Castro. To P. aduncum, the populations with better performance were 207, 208 and 209, forming a homogeneous group with dried yield average of 3.8% and dillapiol content of 84-85%. Such populations are indicated for selection in breeding program of these species due to better performance.

Prevalence of antibodies to the BK and JC papovaviruses in isolated populations

A total of 173 sera from isolated Brazilian Indian populations, 39 from the Diauarun area, and 68 from the Alto Xingú area, respectively in the North and the South of the Xingú National Park and 66 Kren-Akorore Indians, were examined for hemagglutination - inhibiting (HI) antibodies against BK and JC viruses. The global percentages of positive sera (> 1:40) were 5.2% for BK virus and 1.7% for JC virus. The distribution of positive sera according to the population groups showed one individual to be positive for BK virus in the Diauarun Indians and none of the sera contained HI antibody to JC virus; in the Alto Xingú Indians, 4 were positive for BK virus and 3 others were positive for JC virus; as regards Kren-Akorore Indians none of the sera contained antibody to JC virus, and only 4 were BK positive. Due to the limited number of observations it was neither possible to determine the time of occurrence of seroconversion nor correlate the positivity rates for both viruses in the different tribes with the respective "contact" with the white population.

Populations of larvae of Anopheles spp. in natural breeding sites in Western Venezuela, an area of refractory malaria

Studies have been un dertaken into on the diversity and relative abundance of larvae of Anopheles (Nyssorhynchus) spp. in 22 permanent or temporary pools in an area of 70 km² in the eastern piedmont of the Venezuela Andes, between the mountains and the plains, an area in which malaria is refractory and A. nuñeztovari is present. Twelve species were identified, the most frequent, abundant and sympatric being A. triannulatus, A. albitarsis, A. nuñeztovari, A. oswaldoi and A. strodei. The samples from the permanent pools showed greater diversity of species and greater numbers of larvae than the samples from the temporary pools. The existence of the same larval associations in pools of other localities in the eastern piedmont of the Venezuelan Andes suggests the possibility of the making an ecological map of the breeding sites of A. nuñeztovari and for these anophelines in a region extending for 430 km.

Physiological age in Lutzomyia youngi (Diptera: Psychodidae) populations from an endemic area for cutaneous leishmaniasis, Venezuela

Batches of sylvatic females of Lutzomyia youngi (Phlebotominae) captured in a Shannon trap on twelve occasions over one year in a locality where subcutaneous leishmaniasis is endemic, near the city of Trujillo, Venezuela, were used to study: 1) the percentages of parous females according to previously established criteria and 2) the average number of eggs laid spontaneously by isolated females during 7 days after feeding on hamsters. The data on the batches of females captured on nights previous to the rainy period (prepluvial) were compared with those on females captured after the rains (postpluvial) . Significant differences were detected by variation analysis for two variables and different number of N, as also were consistent groupings by Duncan's Test for pre-and postpluvial lots of females. The females captured on nights prior to the rainy periods (January-March and August-September) presented higher rates of nulliparity (86-72%) and contained or laid a greater number of eggs (71-67) than those captured after the rains (March-June and November-December) which presented lower rates of nulliparity (60-24%) and a smaller number of eggs (50-30). The rainfall peaks occurred in April and September-October, respectively. It is considered that these differences can be used by epidemiological studies as a means of estimating the physiological age of female populations of L. youngy.

Cyanobacteria toxicity: potential public health impact in South Portugal populations

Cyanobacteria are prokaryotic, plantlike organisms present in lakes, recreational waters, and reservoirs, and often dominate phytoplankton communities in warm, nutrient-enriched hard waters. A stable water column rich in certain nutrients, especially nitrogen and phosphorus, is associated with favorable environmental conditions that support development of cyanobacterial population maxima or "blooms." Under specific conditions, cyanobacteria produce toxins that are responsible for acute poisoning and death of animals and humans. The main aim of this study was to correlate the presence of cyanobacteria blooms with potential toxicity to humans as a public health issue. In Portugal, seven reservoirs located in the southern region were selected and studied between 2000 and 2008. Reservoirs were characterized by physical and chemical aspects, and identification of phytoplankton communities. In the case of cyanobacterial blooms, toxins that affected the liver, nervous system, and skin were detected, namely, Microcystis aeruginosa, Aphanizomenon spp., and Oscillatoria. These findings suggest the presence of a potential risk for public health, and indicate the need to implement mitigation measures in all studied reservoirs. These measures may involve (1) water eutrophication control to avoid blooms, (2) appropriate treatment of water for human consumption, and (3) public warnings or information to those individuals that use these reservoirs for several recreational activities.

Conservation of limpet populations: a heavily exploited resource in Azores, NE-Atlantic

10th International Temperate Reefs Symposium, The University of Western Australia, 12-17 de janeiro.