bluuebunny/crossref_metadata_2025 huggingface dataset:
Responses of ant communities to experimental fire regimes on rangelands in the Victoria River District of the Northern Territory
Authors: Hoffmann Benjamin D.
Published: December 2004

Abstract  Fire is a significant feature of Australia's savannas. Its use is being encouraged for cattle rangeland management, but there is little knowledge of the ecological effects of prescribed fire regimes on native biodiversity. The responses of ant communities to five experimental fire regimes over 2 years are reported from the Victoria River District in the semi‐arid tropics of northern Australia. The experiment was stratified at two levels: soil type (red and black) and fire treatment (unburnt; burnt twice in successive years in early (May) or late (October) dry season and unburnt thereafter; and burnt twice, 3 years apart, in early or late dry season). Ants were sampled twice in April, corresponding with the end of the 1997 and 1998 wet seasons. Ant species richness was not responsive to fire treatment, but reduced with time since fire on black soil. Total ant abundance also reduced with time since fire on the black soil, with significant different abundances in burnt versus unburnt plots in the 1998 sample. Soil type and sampling time had the greatest influence on ant community composition in multivariate analysis than did fire regime, although there were moderate gradients of time since fire with the black soil plots. The abundance of 19 species were significantly different between fire regimes in anova, 13 on red soil and six on black soil. The abundance of eight species (four each on red and black soil) changed significantly with time since fire, with seven promoted by burning. Ant functional group profiles changed little with fire. Total ant abundance and richness had significant relationships with key pasture species and vegetative variables. The responses of ants largely recapitulated those of plants, birds and reptiles on the same plots. It is envisaged that ants will have an important role to play in the sustainable management of Australia's rangelands aiding the off‐reserve conservation of biodiversity.
Refuge sites used by the scincid lizard Tiliqua rugosa
Authors: Kerr Gregory D. , Bull C. Michael , Burzacott Dale
Published: December 2004

Abstract  We examined microhabitat use by the Australian scincid lizard Tiliqua rugosa (the sleepy lizard) in chenopod shrubland. Thirty radiotagged lizards were followed during their spring period of activity (September–November 2000). Characteristics of refuges used by the lizards were compared with the perennial woody plants in 10 10 m × 10 m randomly located quadrats at each of the three sites in the study area. We found that sleepy lizards used multiple refuge sites. Perennial woody bushes constituted an important habitat component for both active and inactive lizards. Use of refuge sites by the lizards was non‐random. They used large bushes with foliage in contact with the ground (‘dome shaped’), and they sheltered under thorny bushes more frequently than expected if choice was random. Bushes that were used repeatedly tended to be larger and were more likely to be dome‐shaped. Under these large and dome‐shaped bushes, daytime temperatures were lower than under smaller bushes. Refuge use was modified as the season progressed, with lizards using larger bushes and a greater proportion of dome‐shaped bushes later in the season. We suggest that sleepy lizards are modifying their refuge site use as ambient temperatures increase, based on microclimatic needs, implying an ability to discriminate among bushes.
Nutrient resorption from senescing leaves in twoStipaspecies native to central Argentina
Authors: Distel R. A. , Moretto A. S. , Didoné N. G.
Published: December 2004

Abstract Nutrient resorption from senescing leaves enables plants to conserve and reuse nutrients. As such, it could be expected that plant species adapted to infertile soils have a higher nutrient resorption efficiency (percentage reduction of nutrients between green and senesced leaves) and/or higher nutrient resorption proficiency (absolute reduction of nutrients in senesced leaves) than those adapted to fertile soils. Our objective was to compare nitrogen (N) and phosphorous (P) resorption of two congener grasses that successfully occupy uplands of relatively low fertility (Stipa gynerioides) or lowlands of relatively high fertility (Stipa brachychaeta) in natural grasslands of central Argentina. The twoStipaspecies did not differ in N and P resorption efficiency, butS. gynerioideshad a higher N and P resorption proficiency thanS. brachychaeta. As a consequence, leaf‐level N and P use efficiency were higher in the species adapted to low fertility conditions than in the species adapted to high fertility conditions. The higher nutrient resorption proficiency ofS. gynerioideswas also associated with relatively low leaf‐litter decomposition and nutrient release rates found in a previous study.
Indirect evidence of density‐dependent population regulation in Aponomma hydrosauri (Acari: Ixodidae), an ectoparasite of reptiles
Authors: Tyre Andrew J. , Bull C. Michael , Tenhumberg Brigitte , Chilton Neil
Published: December 2004

Abstract  The extent to which density‐dependent processes regulate natural populations is the subject of an ongoing debate. We contribute evidence to this debate showing that density‐dependent processes influence the population dynamics of the ectoparasite Aponomma hydrosauri (Acari: Ixodidae), a tick species that infests reptiles in Australia. The first piece of evidence comes from an unusually long‐term dataset on the distribution of ticks among individual hosts. If density‐dependent processes are influencing either host mortality or vital rates of the parasite population, and those distributions can be approximated with negative binomial distributions, then general host–parasite models predict that the aggregation coefficient of the parasite distribution will increase with the average intensity of infections. We fit negative binomial distributions to the frequency distributions of ticks on hosts, and find that the estimated aggregation coefficient k increases with increasing average tick density. This pattern indirectly implies that one or more vital rates of the tick population must be changing with increasing tick density, because mortality rates of the tick's main host, the sleepy lizard, Tiliqua rugosa, are unaffected by changes in tick burdens. Our second piece of evidence is a re‐analysis of experimental data on the attachment success of individual ticks to lizard hosts using generalized linear modelling. The probability of successful engorgement decreases with increasing numbers of ticks attached to a host. This is direct evidence of a density‐dependent process that could lead to an increase in the aggregation coefficient of tick distributions described earlier. The population‐scale increase in the aggregation coefficient is indirect evidence of a density‐dependent process or processes sufficiently strong to produce a population‐wide pattern, and thus also likely to influence population regulation. The direct observation of a density‐dependent process is evidence of at least part of the responsible mechanism.
Comparison of the nutrient ecology of coastal Banksia grandis elfinwood (windswept shrub‐like form) and low trees, Cape Leeuwin‐Naturaliste National Park, Western Australia
Authors: BARRICK KENNETH A.
Published: December 2004

Abstract  Trees growing along windy coasts often have canopies that are greatly reduced in size by the sculpting effects of wind and salt spray. Trees with environmentally reduced stature are called elfinwood (windswept shrub‐form or krummholz) and are ecologically important because they represent outposts growing at the limit of tree success. The purpose of this study was to assess if Banksia grandis elfinwood growing at Cape Leeuwin had a different nutrient status than normal low‐form (LF) trees growing nearby, and if nutrient deficiencies, toxicities and/or imbalances were among the limiting factors imposed on elfinwood. The concentrations of N, P, K, Ca, Mg, Na, Cl–, Fe, Mn, Zn, Cu, Mo and B were analysed for mature green foliage, immature foliage, foliage litter, flowers and soil. When the elfinwood and LF trees were compared, the foliar nutrient status was generally similar, except that elfinwood foliage had significantly higher mean concentrations of N, Zn and Cu, while LF trees had higher Fe and Mn contents. Many nutrients were conserved before leaves were shed in both elfinwood and LF trees, including N, P, K, Na, Cl–, Mn and Cu (LF trees also conserved Ca and Mg). However, elfinwood and LF tree‐litter contained significantly higher Fe concentrations than green foliage (elfinwood litter also had higher levels of Mg and B). It is tempting to suggest that the translocation of Fe into leaves before they were shed is a regulation mechanism to prevent Fe toxicity, or imbalance in the Fe : Mn ratio. Proteoid roots strongly acidify the soil to mobilize P, which also chemically reduces Fe+3 to plant‐available Fe+2. The increased supply of Fe+2 in the rhizosphere, caused by the action of proteoid roots, might tend to defeat self‐regulation of Fe uptake. It is possible that excess Fe accumulation in the plant might be regulated, in part, by exporting Fe into the leaves before they are shed. The nutrient status of B. grandis elfinwood is compared with mountain elfinwood of North America. The extreme habitat of coastal elfinwood provides many theoretical pathways for nutrient limitation, but B. grandis elfinwood at Cape Leeuwin does not appear to be nutrient deficient.
Influence of canopy tree size on stand basal area may reflect uncoupling of crown expansion and trunk diameter growth
Authors: Lusk Christopher H. , Jara Carolina , Parada Teresa
Published: December 2004

Abstract  A recent article by Midgley and colleagues suggests that large trees give rise to inordinately high stand basal areas because they pack canopy space more efficiently than smaller trees. We argue that this phenomenon bears more relation to the fact that diameter increment is not necessarily accompanied by significant crown expansion during all stages of a tree's life. Using data from a canopy tree population in an old‐growth temperate forest, we found that crown area scaled as roughly the 3/5 power of trunk basal area. Rather than reflecting fixed scaling laws, we suggest that this pattern arises because of limited opportunities for crown expansion in dense stands. Old canopy trees in dense stands can thus accumulate large basal areas without occupying a commensurately large canopy area.
Effects of fire frequency on survival, growth and fecundity of Paspalum quadrifarium (Lam.) in a grassland of the Flooding Pampa (Argentina)
Authors: VIGNOLIO O. R. , LATERRA P. , FERNANDEZ O. N. , LINARES M. P. , MACEIRA N. O. , GIAQUINTA A.
Published: December 2004

Abstract  Fire and grazing are important factors in the regulation of the grassland structure of the Flooding Pampa (Buenos Aires Province, Argentina dominated by Paspalum quadrifarium plants (henceforth ‘pajonal’)). Winter burning of pajonal is a practice that increases P. quadrifarium growth and its nutritious value for cattle. The objective of this work was to determine the responses of different demographic variables of P. quadrifarium growing in a grassland managed with different fire frequencies. The work was carried out in a pajonal situated in San Ignacio (Ayacucho county, Buenos Aires Province, Argentina). The treatments were: high fire frequency (0.8 fires per year) and low fire frequency (0.4 fires per year). The population of P. quadrifarium was affected by fire frequency. Biomass, number of tillers, and the relative production of tillers per plant did not change with fire frequency. Plant height was negatively affected by fire frequency. Whereas no plant mortality was observed in high fire frequency, 30% of the mature plants died at the end of the experiment in low fire frequency. In both treatments, plant mortality was size‐dependent and juvenile plants were more affected than mature ones. Burning had an immediate negative effect on mature and juvenile plants in terms of fecundity, survival of tillers and basal cover. Tiller survival and fecundity were significantly lower in burned plants than in unburned ones. In the high fire frequency treatment the number of ramets and/or genets and basal cover were greater than in the low fire frequency treatment.
Effect of overwintering adults on juvenile survival ofCalomys venustus(Muridae: Sigmodontinae)
Authors: PRIOTTO JOSÉ , POLOP JAIME
Published: December 2004

Abstract The aim of this paper was to test the hypothesis that the presence of overwinteringCalomys venustusmales or females at the beginning of the breeding period reduced the survival of juveniles belonging to the first cohort of each year (C1). The study was carried out in four 0.25‐ha enclosures (two control and two experimental), each situated on natural pasture. This study was conducted between August 1997 and February 1999 and had two parts: removal of overwintering males (ROM) and removal of overwintering females (ROF). For the ROM treatment, overwintering males were removed immediately after C1 juveniles were born, in the ROF treatment overwintering females were removed after the C1 were weaned. Weekly censuses were taken for 3 successive days over 6 weeks. Juvenile survival was examined through a survivorship schedule. The survivorship values were compared by sex and treatment (removal of overwintering males or females) using repeated‐measuresanova. Removal of overwintering males and females did not improve the survival of C1 juveniles. This result could be related to the delay in maturation of C1 juvenile males.
Early development of metanephridia in the caudal budding zone of a clitellate annelid, Dero digitata (Naidida): an electron‐microscopical study
Authors: Bunke Dieter
Published: December 2004

Ultrastructural analysis has revealed that metanephridia in Dero digitata arise from three nephroblast cells in the frontal epithelium of a septum suggesting its mesodermal origin. Each cell has a fixed developmental destination, one nephroblast cell produces the entire canal part and two cells give rise to the nephrostome. The nephroblast cell nearest to the body wall enlarges and proliferates a first set of canal cells, then one of the two proximally adjacent nephroblast cells differentiates into the envelope of the nephrostome generating the marginal cilia of the opening (mantle cell) and the second one transforms into the anteriormost cell of the funnel, producing a flame of cilia that beats into the canal lumen (flame cell). Thereafter, new canal cells appear, mainly by mitosis of the first cell, enlarging the body of the nephridium whose further differentiation was not analysed. Comparison with other clitellate species suggests a mantle cell (or some marginal cells) and a flame cell (or a central cell) to be special characters of the metanephridium in the stem species of the Clitellata and that, compared to many polychaete species, its early development assumes a special course by a precocious determination and arrangement of nephroblast cells, which, in both groups, probably originate from an identical mesodermal stem cell. Results further indicate that the nonclitellate Aeolosomatidae, by virtue of corresponding nephrostomata, are possibly closer related to the Clitellata.
Follicular epithelium, theca and egg envelope formation in Serrasalmus spilopleura (Teleostei, Characiformes, Characidae)
Authors: Quagio‐Grassiotto I. , Guimarães A. C. D.
Published: December 2004

The follicular epithelium and theca of oocytes in Serrasalmus spilopleura differentiates during the initial primary growth phase. The follicular cells are squamous and the thecal cells are disposed in two layers. During the secondary growth phase, follicular cells become cuboidal, acquire characteristics typical of protein‐ or glycoprotein‐producing cells, and show dilated intercellular spaces. Formation of the egg envelope in S. spilopleura begins in the previtellogenic oocytes as a layer of amorphous electron‐dense material is laid down on the oolemma. During vitellogenesis, another layer of electron‐dense material appears beneath the first layer. Also during this phase, a layer of amorphous, less electron‐dense material is formed adjacent to the follicular epithelium. The secondary egg envelope appears at the postvitellogenic phase and is composed of a filamentous and undulant material. The morphology of the egg envelopes in S. spilopleura reflects not only its oviparous nature but also the fact that its eggs are adhesive.
Cauda epididymal spermatozoa of the rufous hare wallaby, Lagorchestes hirsutus (Metatheria, Mammalia) imaged by electron and confocal microscopy
Authors: Johnston S. D. , Daddow L. , Carrick F. N. , Jamieson B. , Smith L.
Published: December 2004

The ultrastructure of mature Lagorchestes hirsutus spermatozoa is described for the first time, revealing unusual aspects of sperm structure in macropodid species. The sperm head is ovoid rather than cuneiform, lacks a ventral nuclear groove and has an acrosomal distribution over approximately 85–90% of its dorsal surface. Immediately adjacent to the nuclear membrane the peripheral nucleoplasm in most spermatozoa form an irregular series of distinctive evaginations previously not described in the spermatozoa of any other marsupial. The midpiece is extremely thickened and short, containing no helical network or peripheral plasma membrane specializations. Axonemal structure is unspecialized with no connecting lamellae; dense outer fibres are closely adherent to axonemal doublets. The sperm morphology of this species is highly aberrant in comparison to other macropod taxa and supports the retention of Lagorchestes as a distinctive genus. In light of this new information, skeletal and serological data should be re‐evaluated to determine the true taxonomic and phylogenetic position of this species.
Effect of long‐term consumption of probiotic milk on infections in children attending day care centres: double blind, randomised trial.
Authors: Reading Richard
Published: December 2004

Objective To examine whether long‐term consumption of a probiotic milk could reduce gastrointestinal and respiratory infections in children in day care centres.

Design Randomised, double blind, placebo controlled study over 7 months.

Setting Eighteen day care centres in Helsinki, Finland.

Participants A total of 571 healthy children aged 1–6 years: 282 [mean (SD) age 4.6 (1.5) years] in the intervention group and 289 [mean (SD) age 4.4 (1.5) years] in the control group.

Intervention Milk with or without Lactobacillus GG. Average daily consumption of milk in both groups was 260 mL.

Main outcome measures Number of days with respiratory and gastrointestinal symptoms, absences from day care because of illness, respiratory tract infections diagnosed by a doctor, and course of antibiotics.

Results

Children in the Lactobacillus group had fewer days of absence from day care because of illness [4.9 (95% confidence interval 4.4–5.5) versus 5.8 (5.3–6.4) days, 16% difference, p = 0.03; age adjusted 5.1 (4.6–5.6) versus 5.7 (5.2–6.3) days, 11% difference, p = 0.09]. There was also a relative reduction of 17% in the number of children suffering from respiratory infections with complications and lower respiratory tract infections [unadjusted absolute percentage reduction 8.6 (17.2–0.1), p = 0.05; age adjusted odds ratio 0.75 (0.52–1.09), p = 0.13] and a 19% relative reduction in antibiotic treatments for respiratory infection [unadjusted absolute percentage reduction 9.6 (18.2–1.0), p = 0.03; adjusted odds ratio 0.72 (0.50–1.03), p = 0.08] in the Lactobacillus group.

Conclusions

Lactobacillus GG may reduce respiratory infections and their severity among children in day care. The effects of the probiotic Lactobacillus GG were modest but consistently in the same direction.
Combined Segregation and Linkage Analysis of Fibrinogen Variability in Israeli Families: Evidence for Two Quantitative‐trait Loci, One of Which is Linked to a Functional Variant (−58G > A) in the Promoter of the α‐fibrinogen Gene
Authors: Friedlander Y. , Kark J. D. , Sinnreich R. , Basso F. , Humphries S. E.
Published: December 2004

The association of α‐ and β‐fibrinogen polymorphisms with plasma fibrinogen levels was examined in a sample of 452 family members from 80 Israeli kindreds. The measured genotype analysis indicated that the β‐fibrinogen −455G > A polymorphism was not associated with fibrinogen levels, while the α‐fibrinogen −58G > A locus showed a significant association with fibrinogen levels (χ2= 17.7; df = 3; p < 0.001), with the −58A allele being associated with higher levels. Segregation analysis in this sample suggested a recessive quantitative‐trait locus (QTL) with a major effect that controlled the sex‐ and age‐adjusted fibrinogen levels. Results from a combined segregation/linkage analysis indicated that a single QTL influencing plasma fibrinogen is in gametic equilibrium with the β‐fibrinogen −455G > A and α‐fibrinogen −58G > A polymorphisms. An extended analysis with a two‐QTL model significantly improved the fit of the model (p ≤ 0.001), and gave support for linkage between the fibrinogen QTL and the α‐fibrinogen polymorphism. In vitro analysis with a DNA fragment containing this variant, linked to a reporter gene, showed 2‐fold higher expression of the A allele compared to the G allele in the liver cell line HepG2, both under basal conditions and after stimulation with interleukin 6. These results demonstrate that two QTLs are jointly involved in determining plasma fibrinogen levels in this sample of families, one of which is located close to a functional variant in the α‐fibrinogen locus.
The Human Complement Component C1R Gene: The Exon‐intron Structure and the Molecular Basis of Allelic Diversity
Authors: Nakagawa M. , Yuasa I. , Irizawa Y. , Umetsu K.
Published: December 2004

Human C1r is a component of the complement system, which is a major mediator of innate immunity. In this study we investigated the exon‐intron organization of the human C1R gene, which spans 11 kb from the initiation codon to the stop codon, and is very similar in exon‐intron structure to the C1S gene. Six common and rare alleles, C1R*1, C1R*2, C1R*5, C1R*8, C1R*9, and C1R*13, were characterized by five mutations at amino acid positions 114, 135, 146, 167 and 244, in exons 4, 5 and 7 where the CUB1, EGF and CUB2 domains are encoded, respectively. A comparison with the cDNA of the mouse C1r gene showed that C1R*2is likely to be an ancestral allele. In addition, nine nucleotide substitutions and one length polymorphism were found in introns 2, 3, 4, 8 and 10.
Saturation of the 5q31‐q33 Candidate Region for Coeliac Disease
Authors: Percopo S. , Babron M.‐C. , Whalen M. , De Virgiliis S. , Coto I. , Clerget‐Darpoux F. , Landolfo F. , Greco L.
Published: December 2004

The first genome wide screening performed on Italian affected sib‐pair families (Greco et al. 1998) gave evidence for linkage with coeliac disease in the 5q region. This finding was replicated in a second independent dataset (Greco et al. 2001). Overall, pooling both samples, the highest MLS value (2.92) was found for the most centromeric marker tested, D5S640. In the present study, the 5q31‐q33 region was saturated with 12 new markers around D5S640, in order to verify whether there would be a shift of the MLS position. This study allowed us to support our previous finding of linkage for the region 5q31‐q33, with the most significant MLS value at D5S2014, very close to the marker D5S640. No evidence for interaction between this risk factor and the one in the HLA region was found. Furthermore, many different groups have independently obtained analogous results for this region, confirming the presence of a susceptibility locus in the region 5q31‐q33. This region contains several interesting candidate genes for coeliac disease.
Smith‐Lemli‐Opitz Syndrome and the DHCR7 Gene
Authors: Jira P. E. , Waterham H. R. , Wanders R. J. A. , Smeitink J. A. M. , Sengers R. C. A. , Wevers R. A.
Published: December 2004

Smith‐Lemli‐Opitz syndrome, a severe developmental disorder associated with multiple congenital anomalies, is caused by a defect of cholesterol biosynthesis. Low cholesterol and high concentrations of its direct precursor, 7‐dehydrocholesterol, in plasma and tissues are the diagnostic biochemical hallmarks of the syndrome. The plasma sterol concentrations correlate with severity and disease outcome. Mutations in the DHCR7 gene lead to deficient activity of 7‐dehydrocholesterol reductase (DHCR7), the final enzyme of the cholesterol biosynthetic pathway. The human DHCR7 gene is localised on chromosome 11q13 and its structure has been characterized. Ninety‐one different mutations in the DHCR7 gene have been published to date. This paper is a review of the clinical, biochemical and molecular genetic aspects.
Qualitative Semi‐Parametric Test for Genetic Associations in Case‐Control Designs Under Structured Populations
Authors: Chen H.‐S. , Zhu X. , Zhao H. , Zhang S.
Published: December 2004

Recently, statistical methods have been proposed using genomic markers to control for population stratification in genetic association studies. However, these methods either have unacceptable low power when population stratification becomes strong or cannot control for population stratification well under admixture population models. In this paper, we propose a semiparametric association test to detect genetic association between a candidate marker and a qualitative trait of interest in case‐control designs. The performanceof the test is compared to other existing methods through simulations. The results show that our method gives correct type I error rate both under discrete population models and admixture population models, and our method is robust to the extent of the population stratification. In most of the cases we considered, our method has higher power and, in some cases, substantially higher power than that of existing methods.
Differentiation of Caucasians and Chinese at Bone Mass Candidate Genes: Implication for Ethnic Difference of Bone Mass
Authors: Dvornyk V. , Liu X.‐H. , Shen H. , Lei S.‐F. , Zhao L.‐J. , Huang Q.‐R. , Qin Y.‐J. , Jiang D.‐K. , Long J.‐R. , Zhang Y.‐Y. , Gong G. , Recker R. R. , Deng H.‐W.
Published: December 2004

Bone mineral density (BMD) is an important risk factor for osteoporosis and has strong genetic determination. While average BMD differs among major ethnic groups, several important candidate genes have been shown to underlie BMD variation within populations of the same ethnicity. To investigate whether important candidate genes may contribute to ethnic differences in BMD, we studied the degree of genetic differentiation among several important candidate genes between two major ethnic groups: Caucasians and Chinese. The genetic variability of these two populations (1131 randomly selected individuals) was studied at six restriction sites exhibiting polymorphisms of five important candidate genes for BMD: the BsaHI polymorphism of the calcium‐sensing receptor (CASR) gene, the SacI polymorphism of the α2HS‐glycoprotein (AHSG) gene, the PvuII and XbaI polymorphisms of the estrogen receptor α (ESR1) gene, the ApaI polymorphism of the vitamin D receptor (VDR) gene, and the BstBI polymorphism of the parathyroid hormone (PTH) gene. The two ethnic groups showed significant allelic and genotypic differentiation of all the polymorphisms studied. The mean FST was 0.103, which significantly differed from zero (P < 0.01). The Chinese population had lower mean heterozygosity (0.331) than the Caucasian one (0.444); the CASR‐BsaHI and PTH‐BstBI polymorphisms contributed most significantly to this difference. Analysis of the intra‐ and inter‐population variability suggests that various types of natural selection may affect the observed patterns of variation at some loci. If some of the candidate genes we studied indeed underlie variation in BMD, their population differentiation revealed here between ethnic groups may contribute to understanding ethnic difference in BMD.
CpG Islands in Human X‐Inactivation
Authors: Ke X. , Collins A.
Published: December 2004

Sequence comparison analyses have been carried out for 19 genes escaping X‐inactivation versus 73 genes subject to X‐inactivation, and 100 randomly chosen X chromosome genes versus 100 randomly chosen autosomal genes. The coding sequence of the genes and their upstream and downstream flanking sequences were investigated using a series of windows (1 kb, 2 kb, 5 kb, 10 kb and 100 kb). No significant difference in number of LINE‐L1 elements was observed in genes escaping X‐inactivation compared to genes subject to X‐inactivation. This result, therefore, does not support the suggestion that lack of LINE repeat elements is a key factor for genes escaping X‐inactivation. However, significantly reduced numbers of CpG islands and SINE MIR elements were found to be associated with genes escaping X‐inactivation. Compared to genes known to be inactivated, genes escaping X‐inactivation were observed to have fewer CpG islands, particularly within the 2 kb upstream flanking sequence close to the coding region. The results suggest that CpG islands may play a role in the process of X‐inactivation by providing sufficient DNA methylation targets for the maintenance of X‐inactivation. Lack of CpG islands may be a major reason for genes escaping X‐inactivation regulation.
Evaluating Innovations in Maternity Care: Methodological Approaches to a Baseline Postal Survey
Authors: Yelland Jane , Brown Stephanie , Krastev Ann
Published: December 2004

Abstract: Background: A network of four public maternity hospitals in Melbourne, Australia, has implemented a range of initiatives aimed at improving maternity care. Comprehensive evaluation aims to determine whether or not the maternity service enhancement strategies have led to improvements in women's views and experiences of care. This paper discusses the baseline survey study design and methodological issues associated with the recruitment and reminder processes.

Method: All women who gave birth over a 14‐week period in 1999 at one of the four maternity units, except those who had a stillbirth or neonatal death, were invited to participate in the baseline postal survey. Questionnaires were sent to women at 3 months postpartum. A system of written and telephone reminders was instituted.

Results: The overall response fraction to the baseline survey was 65.2 percent (1256/1922). The sample was representative in terms of maternal age, method of birth, and infant birthweight. Women born overseas of non‐English speaking background, single women, and women having their second or subsequent baby were underrepresented.

Conclusions: The pleasing response fraction in part may be attributed to the method of recruitment and the reminder processes. Rigorous and careful approaches to methodology enhance study integrity and provide context to the interpretation of study findings. (BIRTH 30:3 September 2003)
Methods for testing familial aggregation of diseases in population‐based samples: application to hodgkin lymphoma in swedish registry data
Authors: Pfeiffer R. M. , Goldin L. R. , Chatterjee N. , Daugherty S. , Hemminki K. , Pee D. , X L. I. , Gail M. H.
Published: December 2004

We use data on lymphoma in families of Hodgkin lymphoma (HL) cases from the Swedish Family Cancer Database (Hemminki et al. 2001) to illustrate survival methods for detecting familial aggregation in first degree relatives of case probands compared to first degree relatives of control probands, from registries that permit sampling of all cases. Because more than one case may occur in a given family, the first degree relatives of case probands are not necessarily independent, and we present procedures that allow for such dependence. A bootstrap procedure also accommodates matching of case and control probands by resampling the matching clusters, defined as the combined set of all first degree relatives of the matched case and control probands. Regarding families as independent sampling units leads to inferences based on “sandwich variance estimators” and accounts for dependencies from having more than one proband in a family, but not for matching. We compare these methods in analysis of familial aggregation of HL and also present simulations to compare survival analyses with analyses of binary outcome data.
Evidence for Non‐additive Influence of Single Nucleotide Polymorphisms within the Apolipoprotein E Gene
Authors: Hamon S. C. , Stengard J. H. , Clark A. G. , Salomaa V. , Boerwinkle E. , Sing C. F.
Published: December 2004

We analyzed 13 single nucleotide polymorphisms (SNPs) within the apolipoprotein E (APOE) gene, to identify pairs of SNPs that interact in a non‐additive manner to influence genotypic mean levels of the ApoE protein in blood. An overparameterized general linear model of two‐SNP genotype means was applied to data from 456 female and 398 male unrelated European Americans from Rochester, MN, USA. We found statistically significant evidence for non‐additivity between SNPs within the male sample, but not within the female sample. We observed nine pairs of SNPs with evidence of non‐additivity at the α= 0.05 level of statistical significance within the male sample, when approximately three were expected by chance. Five of the nine pairs involved three SNPs (560, 624 and 1163) that did not have a statistically significant influence when considered separately in a single‐site analysis. Three of the nine pairs involving four SNPs (832, 1998, 3937 and 4951) showed significant evidence for non‐additivity in at least one of two other male samples from Jackson, MS, USA and North Karelia, Finland. Although all four of these SNPs had a statistically significant influence in Rochester when considered separately, only SNP 3937 gave a significant result in the other male samples. The four SNPs are located in the promoter, intronic and exonic regions, and 3' to the polyadenylation signal in the APOE gene. Our study suggests that analyses that only consider SNPs located in exons and ignore contexts such as those indexed by gender and population, and disregard non‐additivity of SNP effects, may inappropriately model the contribution of a gene to the genetic architecture of a trait that has a complex multifactorial etiology.
Novel HMBS founder mutation and significant intronic polymorphism in Spanish patients with acute intermittent porphyria
Authors: Guillén‐Navarro E. , Carbonell P. , Glover G. , Sánchez‐Solís M. , Fernández‐Barreiro A.
Published: December 2004

Acute intermittent porphyria (AIP) is an autosomal dominant disorder of heme biosynthesis, caused by a partial deficiency of hydroxymethylbilane synthase (HMBS). Knowledge of the nature of the HMBS mutations causing AIP in Spanish families is very limited. Here we report a novel 669_698del of the HMBS gene in twenty‐two individuals from five independent Spanish AIP families, settled in Murcia (southeastern region of Spain). All mutation carriers shared a common disease associated haplotype indicating an ancestral founder effect. Identification of the 669_698del founder mutation allowed rapid and simple molecular diagnosis of AIP in families from this region in Spain. In addition, 771 + 58C>T in intron 12 on the non‐669_698del allele was identified in six AIP patients, which promoted homozygous AIP misdiagnosis.
Compound haplotypes at Xp11.23 and human population growth in Eurasia
Authors: Alonso S. , Armour J. A. L.
Published: December 2004

To investigate patterns of diversity and the evolutionary history of Eurasians, we have sequenced a 2.8 kb region at Xp11.23 in a sample of African and Eurasian chromosomes. This region is in a long intron of CLCN5 and is immediately flanked by a highly variable minisatellite, DXS255, and a human‐specific Ta0 LINE. Compared to Africans, Eurasians showed a marked reduction in sequence diversity. The main Euro‐Asiatic haplotype seems to be the ancestral haplotype for the whole sample. Coalescent simulations, including recombination and exponential growth, indicate a median length of strong linkage disequilibrium, up to ∼9kb for this area. The Ka/Ks ratio between the coding sequence of human CLCN5 and its mouse orthologue is much less than 1. This implies that the region sequenced is unlikely to be under the strong influence of positive selective processes on CLCN5, mutations in which have been associated with disorders such as Dent's disease. In contrast, a scenario based on a population bottleneck and exponential growth seems a more likely explanation for the reduced diversity observed in Eurasians. Coalescent analysis and linked minisatellite diversity (which reaches a gene diversity value greater than 98% in Eurasians) suggest an estimated age of origin of the Euro‐Asiatic diversity compatible with a recent out‐of‐Africa model for colonization of Eurasia by modern Homo sapiens.
Contribution of Chromosome 1q21‐q23 to Familial Combined Hyperlipidemia in Mexican Families
Authors: Huertas‐Vázquez A. , del Rincón J. P. , Canizales‐Quinteros S. , Riba L. , Vega‐Hernández G. , Ramírez‐Jiménez S. , Aurón‐Gómez M. , Gómez–Pérez F. J. , Aguilar‐Salinas C. A. , Tusié‐Luna M. T.
Published: December 2004

Familial combined hyperlipidemia (FCHL) is the most common familial dyslipidemia, with a prevalence of 1‐2% in the general population. A major locus for FCHL has been mapped to chromosome 1q21‐q23 in Finnish, Chinese, German and US families. We studied seven extended Mexican families with 153 members, including 64 affected subjects. A total of 11 markers were genotyped, including D1S104 which has been linked to FCHL in other studies. Two point linkage analysis for the FCHL phenotype, and for the elevated triglyceride (TG) trait, allowing for heterogeneity, gave a maximum HLOD of 1.67 (α= 0.49) and 1.93 (α= 0.43) at D1S2768 (2.69 cM proximal to D1S104) respectively. Heterogeneity and non‐parametric (NPL) multipoint analyses for the FCHL phenotype and the TG trait showed maximum HLODs of 1.27 (α= 0.46) and 1.64 (α= 0.38), and NPLs of 4.00 (P = 0.0001) and 3.68 (P = 0.0003) near D1S2768, respectively. In addition, analysis of four candidate genes putatively involved in the expression of FCHL showed no evidence of linkage for the LCAT gene or the APOA1/C3/A4/A5 gene cluster. However, we cannot exclude the participation of these genes, or the LIPC and LPL genes, as minor susceptibility loci in the expression of FCHL, or the TG or elevated total cholesterol (TC) traits in our families. In conclusion, our data confirm the involvement of a major susceptibility locus on chromosome 1q21‐q23 in FCHL Mexican families, consistent with findings in other populations.
Genetic Dissection of Human Stature in a Large Sample of Multiplex Pedigrees
Authors: Liu Yao‐Zhong , Xu Fu‐Hua , Shen Hui , Liu Yong‐Jun , Zhao Lan‐Juan , Long Ji‐Rong , Zhang Yuan‐Yuan , Xiao Peng , Xiong Dong‐Hai , Dvornyk Volodymyr , Li Jin‐Long , Conway Theresa , Davies K. Michael , Recker Robert R. , Deng Hong‐Wen
Published: December 2004

Recently, we reported a whole genome scan on a sample of 630 Caucasian subjects from 53 human pedigrees. Several genomic regions were suggested to be linked to height. In an attempt to confirm the identified genomic regions, as well as to identify new genomic regions linked to height, we conducted a whole genome linkage study on an extended sample of 1,816 subjects from 79 pedigrees, which includes the 53 pedigrees containing the original 630 subjects from our previous whole genome study and an additional 128 new subjects, and 26 further pedigrees containing 1,058 subjects. Several regions achieved suggestive linkage signals, such as 9q22.32 [MLS (multipoint LOD score) = 2.74], 9q34.3 [MLS = 2.66], Xq24 [two‐point LOD score = 2.64 at the marker DXS8067], and 7p14.2 [MLS = 2.05]. The importance of the above regions is supported either by other whole genome studies or by candidate genes within these regions relevant to linear growth or pathogenesis of short stature. In addition, this study has tentatively confirmed the Xq24 region's linkage to height, as this region was also detected in the previous whole genome study. To date, our study has achieved the largest sample size in the field of genetic linkage studies of human height. Together with the findings of other studies, the current study has further delineated the genetic basis of human stature.
Y Chromosome and Mitochondrial DNA Variation in Lithuanians
Authors: Kasperavičiūtė D. , Kučinskas V. , Stoneking M.
Published: December 2004

The genetic composition of the Lithuanian population was investigated by analysing mitochondrial DNA hypervariable region 1, RFLP polymorphisms and Y chromosomal biallelic and STR markers in six ethnolinguistic groups of Lithuanians, to address questions about the origin and genetic structure of the present day population. There were no significant genetic differences among ethnolinguistic groups, and an analysis of molecular variance confirmed the homogeneity of the Lithuanian population. MtDNA diversity revealed that Lithuanians are close to both Slavic (Indo‐European) and Finno‐Ugric speaking populations of Northern and Eastern Europe. Y‐chromosome SNP haplogroup analysis showed Lithuanians to be closest to Latvians and Estonians. Significant differences between Lithuanian and Estonian Y chromosome STR haplotypes suggested that these populations have had different demographic histories. We suggest that the observed pattern of Y chromosome diversity in Lithuanians may be explained by a population bottleneck associated with Indo‐European contact. Different Y chromosome STR distributions in Lithuanians and Estonians might be explained by different origins or, alternatively, be the result of some period of isolation and genetic drift after the population split.
Gene Expression Profile Analysis in Human T Lymphocytes from Patients with Down Syndrome
Authors: Giannone S. , Strippoli P. , Vitale L. , Casadei R. , Canaider S. , Lenzi L. , D'Addabbo P. , Frabetti F. , Facchin F. , Farina A. , Carinci P. , Zannotti M.
Published: December 2004

Down Syndrome (DS) is caused by the presence of three copies of the whole human chromosome 21 (HC21) or of a HC21 restricted region; the phenotype is likely to have originated from the altered expression of genes in the HC21. We apply the cDNA microarray method to the study of gene expression in human T lymphocytes with trisomy 21 in comparison to normal cells.

Two patients with DS were investigated, along with two normal subjects as a control, all being tested in independent, duplicated cell culture experiments. The most consistent finding was the overexpression of the superoxide dismutase gene (SOD1), located on 21q, and of MHC DR beta 3 (HLA‐DRB3), GABA receptor A gamma 2 (GABRG2), acetyltransferase Coenzyme, A 2 (ACAT2) and ras suppressor protein 1 (RSU1) genes. When the data were clustered according to chromosome localization, the HC21 gene set showed, on average, the highest expression in DS cells in all the experiments. Moreover, separate clustering of patients and controls was obtained when analysis was restricted to HC21 gene expression values.

These findings reinforce the specific gene dosage theory for the pathogenesis of the DS phenotype, and show a consistent overexpression of the SOD1 gene on 21q.
Linkage Disequilibrium and Haplotype Architecture for two ABC Transporter Genes (ABCC1 and ABCG2) in Chinese Population: Implications for Pharmacogenomic Association Studies
Authors: Wang Haijian , Hao Bingtao , Zhou Kaixin , Chen Xiaoping , Wu Songfeng , Zhou Gangqiao , Zhu Yunping , He Fuchu
Published: December 2004

Information about linkage disequilibrium (LD) patterns and haplotype structures for candidate genes is instructive for the design and analysis of genetic association studies for complex diseases and drug response. ABCC1 and ABCG2 are genes coding for two multidrug resistance (MDR) associated transporters; they are also related to some pathophysiological traits. To pinpoint the LD profiles of these MDR genes in Chinese, we systemically screened 27 unrelated individuals for single nucleotide polymorphisms (SNPs) in the coding and regulatory regions of these genes, and thereby characterized their haplotype structures. Despite marked variations in haplotype diversity, LD pattern and intragenic recombination intensity between the two genes, both loci could be partitioned into several LD blocks, in which a modest number of haplotypes accounted for a high fraction of the sampled chromosomes. We concluded that each locus has its own genomic LD profile, but that they still share a common segmental LD architecture with low haplotype diversity. Our data will benefit genetic association studies of complex traits and drug response possibly related to these genes.
A Tale of Aborigines, Conquerors and Slaves: Alu Insertion Polymorphisms and the Peopling of Canary Islands
Authors: Maca‐Meyer N. , Villar J. , Pérez‐Méndez L. , De León A. Cabrera , Flores C.
Published: December 2004

Classical, mitochondrial DNA (mtDNA) and Y chromosome markers have been used to examine the genetic admixture in present day inhabitants of the Canary Islands. In this study, we report the analysis of ten autosomal Alu insertion polymorphisms in 364 samples from the seven main islands of the Archipelago, and their comparison to continental samples. The detection of population‐specific alleles from the Iberian Peninsula and Northwest Africa, as well as their affinities on the basis of genetic distances and principal component analysis, support a clear link between these populations. Coincident with previous results, the Canarian gene pool can be distinguished as being halfway between those of its putative parents, although with a major Iberian contribution (62‐78%). Both the substantial Northwest African contribution (23‐38%), and the minor sub‐Saharan African input (3%), suggest that the genetic legacy from the aborigines and slaves still persists in the Canary Islanders.
DNA Sequence Variation and Haplotype Structure of the ICAM1 and TNF Genes in 12 Ethnic Groups of India Reveal Patterns of Importance in Designing Association Studies
Authors: Sengupta Sanghamitra , Farheen Shabana , Mukherjee Neelanjana , Dey Badal , Mukhopadhyay Barun , Sil Samir K. , Prabhakaran N. , Ramesh A. , Edwin Deepa , Rani M.V. Usha , Mitra Mitashree , Mahadik Chitra Thakur , Singh Sunita , Sehgal Subhash C. , Majumder Partha P.
Published: December 2004

We have examined the patterns of DNA sequence variation in and around the genes coding for ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India. We aimed to (a) quantify the nature and extent of the variation, and (b) analyse the observed patterns of variation in relation to population history and ethnic background. At the ICAM1 and TNF loci, respectively, the total numbers of SNPs that were detected were 28 and 12. Many of these SNPs are not shared across ethnic groups and are unreported in the dbSNP or TSC databases, including two fairly common non‐synonymous SNPs at positions 13487 and 13542 in the ICAM1 gene. Conversely, the TNF‐376A SNP that is reported to be associated with susceptibility to malaria was not found in our study populations, even though some of the populations inhabit malaria endemic areas. Wide between‐population variation in the frequencies of shared SNPs and coefficients of linkage disequilibrium have been observed. These findings have profound implications in case‐control association studies.