Evolutionary relationships among bluetongue and related orbiviruses

Polymerase chain reaction (PCR) sequencing of specific viral gene segments was used to investigate the phylogenetic relationships among the orbiviruses. Sequence comparisons of the bluetongue virus (BTV) RNA3 from different regions of the world (North America, South Africa, India, Indonesian, Malaysia, Australia and the Caribbean region) showed that geographic separation had resulted in significant divergence, consistent with the evolution of distinct viral populations. There were at least 3 topotypes (Gould, 1987); the Australasian, African - American and another topotype represented by BTV 15 isolated in Australia in 1986. The topotypes of BTV had RNA3 nucleotide sequences that differed by approximately 20 per cent. Analysis of BTV-specific gene segments from animal and insect specimens showed that bluetongue viruses had entered northern Australia from South East Asia, possibly by wind-borne vectors. Nucleotide sequence comparisons were used to show the close genetic relationship between BTV 2 (Ona-A strain) from Florida and BTV 12 from Jamaica, and to investigate the reassortment of BTV genome segments in nature. The mutation rates of the BTV RNA2 and RNA3 segments were estimated to be of the order of 10(-4) nucleotide changes/site/year, similar in magnitude to that reported for other RNA viruses.

Upregulated MT1-MMP/TIMP-2 axis in the TSU-Pr1-B1/B2 model of metastatic progression in transitional cell carcinoma of the bladder

Muscle invasive transitional cell carcinoma (TCC) of the bladder is associated with a high frequency of metastasis, resulting in poor prognosis for patients presenting with this disease. Models that capture and demonstrate step-wise enhancement of elements of the human metastatic cascade on a similar genetic background are useful research tools. We have utilized the transitional cell carcinoma cell line TSU-Pr1 to develop an in vivo experimental model of bladder TCC metastasis. TSU-Pr1 cells were inoculated into the left cardiac ventricle of SCID mice and the development of bone metastases was monitored using high resolution X-ray. Tumor tissue from a single bone lesion was excised and cultured in vitro to generate the TSU-Pr1-B1 subline. This cycle was repeated with the TSU-Pr1-B1 cells to generate the successive subline TSU-Pr1-B2. DNA profiling and karyotype analysis confirmed the genetic relationship of these three cell lines. In vitro, the growth rate of these cell lines was not significantly different. However, following intracardiac inoculation TSU-Pr1, TSU-Pr1-B1 and TSU-Pr1-B2 exhibited increasing metastatic potential with a concomitant decrease in time to the onset of radiologically detectable metastatic bone lesions. Significant elevations in the levels of mRNA expression of the matrix metalloproteases (MMPs) membrane type 1-MMP (MT1-MMP), MT2-MMP and MMP-9, and their inhibitor, tissue inhibitor of metalloprotease-2 (TIMP-2), across the progressively metastatic cell lines, were detected by quantitative PCR. Given the role of MT1-MMP and TIMP-2 in MMP-2 activation, and the upregulation of MMP-9, these data suggest an important role for matrix remodeling, particularly basement membrane, in this progression. The TSU-Pr1-B1/B2 model holds promise for further identification of important molecules.

Analytical relationship between family history and genetic and environmental risks, with application to female breast cancer

It is well established in genetic epidemiology that family history is an important indicator of familial aggregation of disease in a family. A strong genetic risk factor or an environmental risk factor with high familial correlation can result in a strong family history. In this paper, family history refers to the number of first-degree relatives affected with the disease. Cui and Hopper (Journal of Epidemiology and Biostatistics 2001; 6: 331-342) proposed an analytical relationship between family history and relevant genetic parameters. In this paper we expand the relationship to both genetic and environmental risk factors. We established a closed-form formula for family history as a function of genetic and environmental parameters which include genetic and environmental relative risks, genotype frequency, prevalence and familial correlation of the environmental risk factor. The relationship is illustrated by an example of female breast cancer in Australia. For genetic and environmental relative risks less than 10, most of the female breast cancer cases occur between the age of 40 and 60 years. A higher genetic or environmental relative risk will move the peak of the distribution to a younger age. A more common disease allele or more prevalent environmental risk factor will move the peak to an older age. For a proband with breast cancer, it is most likely (with probability ge80%) that none of her first-degree relatives is affected with the disease. To enable the probability of having a positive family history to reach 50%, the environmental relative risks must be extremely as high as 100, the familial correlation as high as 0.8 and the prevalence as low as 0.1. For genetic risk alone, even the relative risk is as high as 100, the probability of having a positive family history can only reach about 30%. This suggests that the environmental risk factor seems to play a more important role in determining a strong family history than the genetic risk factor.

Multilocus phylogeography of Australian teals (Anas spp.) : a case study of the relationship between vagility and genetic structure

Biogeographic barriers potentially restrict gene flow but variation in dispersal or vagility can influence the effectiveness of these barriers among different species and produce characteristic patterns of population genetic structure. The objective of this study was to investigate interspecific and intraspecific genetic structure in two closely related species that differ in several life-history characteristics. The grey teal Anas gracilis is geographically widespread throughout Australia with a distribution that crosses several recognized biogeographic barriers. This species has high vagility as its extensive movements track broad-scale patterns in rainfall. In contrast, the closely related chestnut teal A. castanea is endemic to the mesic southeastern and southwestern regions of Australia and is more sedentary. We hypothesized that these differences in life-history characteristics would result in more pronounced population structuring in the chestnut teal. We sequenced five nuclear loci (nuDNA) for 49 grey teal and 23 chestnut teal and compared results to published mitochondrial DNA (mtDNA) sequences. We used analysis of molecular variance to examine population structure, and applied coalescent based approaches to estimate demographic parameters. As predicted, chestnut teal were more strongly structured at both mtDNA and nuDNA (ΦST= 0.163 and 0.054, respectively) than were grey teal (ΦST < 0.0001 for both sets of loci). Surprisingly, a greater proportion of the total genetic variation was partitioned among populations within species (ΦSC= 0.014 and 0.047 for nuDNA and mtDNA, respectively) than between the two species (ΦCT < 0.0001 for both loci). The ‘Isolation with Migration’ coalescent model suggested a late Pleistocene divergence between the taxa, but remarkably, a deeper divergence between the southeastern and southwestern populations of chestnut teal. We conclude that dispersal potential played a prominent role in the structuring of populations within these species and that divergent selection associated with ecology and life history traits likely contributed to rapid and recent speciation in this pair.

Relationship of glutathione S-transferase genotypes with side-effects of pulsed cyclophsphamide therapy in patients with systemic lupus erythematosus

Aims
Cyclophosphamide (CTX) is an established treatment of severe systemic lupus erythematosus (SLE). Cytotoxic CTX metabolites are mainly detoxified by multiple glutathione S-transferases (GSTs). However, data are lacking on the relationship between the short-term side-effects of CTX therapy and GST genotypes. In the present study, the effects of common GSTM1, GSTT1, and GSTP1 genetic mutations on the severity of myelosuppression, gastrointestinal (GI) toxicity, and infection incidences induced by pulsed CTX therapy were evaluated in patients SLE.
Methods
DNA was extracted from peripheral leucocytes in patients with confirmed SLE diagnosis (n = 102). GSTM1 and GSTT1 null mutations were analyzed by a polymerase chain reaction (PCR)-multiplex procedure, whereas the GSTP1 codon 105 polymorphism (Ile→Val) was analyzed by a PCR-restriction fragment length polymorphism (RFLP) assay.
Results
Our study demonstrated that SLE patients carrying the genotypes with GSTP1 codon 105 mutation [GSTP1*-105I/V (heterozygote) and GSTP1*-105 V/V (homozygote)] had an increased risk of myelotoxicity when treated with pulsed high-dose CTX therapy (Odds ratio (OR) 5.00, 95% confidence interval (CI) 1.96, 12.76); especially in patients younger than 30 years (OR 7.50, 95% CI 2.14, 26.24), or in patients treated with a total CTX dose greater than 1.0 g (OR 12.88, 95% CI 3.16, 52.57). Similarly, patients with these genotypes (GSTP1*I/V and GSTP1*V/V) also had an increased risk of GI toxicity when treated with an initial pulsed high-dose CTX regimen (OR 3.33, 95% CI 1.03, 10.79). However, GSTM1 and GSTT1 null mutations did not significantly alter the risks of these short-term side-effects of pulsed high-dose CTX therapy in SLE patients.
Conclusions
The GSTP1 codon 105 polymorphism, but not GSTM1 or GSTT1 null mutations, significantly increased the risks of short-term side-effects of pulsed high-dose CTX therapy in SLE patients. Because of the lack of selective substrates for a GST enzyme phenotyping study, timely detection of this mutation on codon 105 may assist in optimizing pulsed high-dose CTX therapy in SLE patients.

Relationship between genotype and enzyme activity of glutathione S-transferases M1 and P1 in Chinese

Glutathione S-transferases (GSTs) are the major detoxifying Phase II enzyme for eliminating electrophilic compounds. Mutations in GSTM1, GSTP1 and GSTT1 in Caucasian and GSTA1 in Chinese have been found to reduce enzyme activity. However, data on the impact of common genetic polymorphisms of GSTM1 and GSTP1 on enzyme activity in Chinese is lacking. This study aimed to investigate the effect of common GSTP1 and GSTM1 polymorphisms on erythrocyte GST activity in healthy Chinese (n = 196). GSTM1 null mutation (GSTM1*0) was analyzed by a PCR-Multiplex procedure, whereas GSTP1 313A → G polymorphism (resulting in Ile105Val at codon 105) was analyzed by PCR-restriction fragment length polymorphism (RFLP) analysis. Erythrocyte GST activity was measured using 1-chloro-2,4-dinitro-bezene (CDNB) as the model substrate. The frequency of GSTM1 null genotype was 54.3% and the frequency of GSTP1-Ile/Ile, -Ile/Val, and -Val/Val genotype was 60.7%, 35.2% and 4.1%, respectively, with a frequency of 21.7% for the 105 valine allele. Age, gender and smoking did not significantly affect the erythrocyte GST activities. The mean erythrocyte GST enzyme activity for GSTP1*-Ile/Val genotype group (3.53 ± 0.63 U/g Hb) was significantly lower than that for subjects with GSTP1-Ile/Ile genotype (4.25 ± 1.07 U/g Hb, P = 0.004), while subjects with the GSTP1-Val/Val genotype had the lowest enzyme activity (2.44 ± 0.67 U/g Hb). In addition, the GST activity in carriers of GSTM1*0/GSTP1-Ile/Ile was significantly higher than that of subjects inherited GSTM1*0/GSTP1-Ile/Val or GSTM1*0/GSTP1-Val/Val. However, there is no association between GSTM1 null mutation and reduced enzyme activity. GSTP1 codon 105 mutation led to reduced erythrocyte GST activity in Chinese. A combined GSTP1 and GSTM1 null mutations also resulted in significantly reduced GST activity. Further studies are needed to explore the clinical implications of GSTM1 and GSTP1 polymorphisms.

Does subjective well-being show a relationship between parents and their children?

The relationship between the subjective well-being of parents and their own 12–16-year-old children was explored in a Spanish sample of N = 266 families. A positive relationship was expected due to both a shared environment and the possibility of the genetic transmission of subjective well-being ‘set-points’. A positive significant relationship was found for the summated scale of satisfaction domains forming the Personal Well-being Index, and for the specific domains of health and security for the future. However, no relationship was found for the other five domains that make up this Index or for satisfaction with life as a whole. We conclude while these results provide some evidence for the expected influence of a shared environment, they have failed to provide evidence for high heritability of set-points for subjective well-being.

Optimizing the use of shed feathers for genetic analysis

Shed feathers obtained by noninvasive genetic sampling (NGS) are a valuable source of DNA for genetic studies of birds. They can be collected across a large geographical range and facilitate research on species that would otherwise be extremely difficult to study. A limitation of this approach is uncertainty concerning the quality of the extracted DNA. Here we investigate the relationship between feather type, feather condition and DNA quality (amplification success) in order to provide a simple, cost-effective method for screening samples prior to genetic analysis. We obtained 637 shed feathers of the powerful owl ( Ninox strenua) from across its range in southeastern Australia. The extracted DNA was amplified using polymerase chain reaction for a range of markers including mitochondrial DNA, ND3 and nuclear DNA, a simple sequence repeat (Nst02) and a portion of the CHD-1 gene (P2/P8). We found that feather condition significantly influenced the amplification success of all three loci, with feathers characterized as ‘good’ having greater success. Feather type was found to be of lower importance, with good quality feathers of all types consistently producing high success for all three loci. We also found that the successful amplification of multilocus genotypes was dependant on the condition of the starting material and was highly correlated with successful amplification of the sex-linked CHD-1 locus. Samples with low DNA quality have a higher probability of amplification failure and are more likely to produce incorrect genotypes; therefore, identifying samples with high DNA quality can save substantial time and cost associated with the genetic analysis of NGS. As a result, we propose a method for screening shed feathers in order to provide a subset of samples which will have a greater probability of containing high quality DNA suitable for the amplification of multilocus genotypes.

The allometric relationship between mean fibre diameter of mohair and the fleece-free liveweight of Angora goats over their lifetime

As mean fibre diameter (MFD) is the primary determinant of mohair price we aimed to quantify the lifetime changes in mohair MFDas Angora goats aged and grew. Measurements were made over 12 shearing periods on a population of Angora goats representing the current range and diversity of genetic origins including South African, Texan and interbred admixtures of these and Australian sources. Records of sire, dam, birthweight, birth parity, liveweight, fleece growth and fleece quality were taken for does and castrated males (wethers) (n = 267 animals). Fleece-free liveweights (FFL_wt) were determined for each goat at shearing time by subtracting the greasy fleece weight from the liveweight recorded immediately before shearing. A restricted maximum likelihood growth curve model was developed for relating MFD to FFL_wt, age and other measurements.Asimple way of describing the results is:MFD= k (FFL_wt)b E; where k is a parameter that can vary in a systematic way with shearing(age), breed, weaning weight, sire, dam and individual; b is a parameter that is the same for nearly the whole study; and E are independent errors from a log-normal distribution. The analysis shows that ^b = 0.34, with s.e. (^b) = 0.021. Thus, mohair MFD was allometrically related to the cube root of FFLwt over the lifetime of Angora goats. However, the allometric proportionality constant differed in a systematic way with age at shearing, genetic strain, weaning weight, sire, dam and individual. For Texan-breed goats, MFD decreased as weaning weight increased (P = 0.00016). The findings indicate that management factors that affect liveweight and weaning weight have lifetime effects on mohair fibre diameter and therefore the value of mohair and the profitability of the mohair enterprise.

Mitochondrial DNA analysis of field populations of Helicoverpa armigera (Lepidoptera : Noctuidae) and of its relationship to H. zea

Background
Helicoverpa armigera and H. zea are amongst the most significant polyphagous pest lepidopteran species in the Old and New Worlds respectively. Separation of H. armigera and H. zea is difficult and is usually only achieved through morphological differences in the genitalia. They are capable of interbreeding to produce fertile offspring. The single species status of H. armigera has been doubted, due to its wide distribution and plant host range across the Old World. This study explores the global genetic diversity of H. armigera and its evolutionary relationship to H zea.

Results
We obtained partial (511 bp) mitochondrial DNA (mtDNA) Cytochrome Oxidase-I (COI) sequences for 249 individuals of H. armigera sampled from Australia, Burkina Faso, Uganda, China, India and Pakistan which were associated with various host plants. Single nucleotide polymorphisms (SNPs) within the partial COI gene differentiated H. armigera populations into 33 mtDNA haplotypes. Shared haplotypes between continents, low F-statistic values and low nucleotide diversity between countries (0.0017 – 0.0038) suggests high mobility in this pest. Phylogenetic analysis of four major Helicoverpa pest species indicates that H. punctigera is basal to H. assulta, which is in turn basal to H. armigera and H. zea. Samples from North and South America suggest that H. zea is also a single species across its distribution. Our data reveal short genetic distances between H. armigera and H. zea which seem to have been established via a founder event from H. armigera stock at around 1.5 million years ago.

Conclusion
Our mitochondrial DNA sequence data supports the single species status of H. armigera across Africa, Asia and Australia. The evidence for inter-continental gene flow observed in this study is consistent with published evidence of the capacity of this species to migrate over long distances. The finding of high genetic similarity between Old World H. armigera and New World H. zea emphasises the need to consider work on both pests when building pest management strategies for either.

The allometric relationship between clean mohair growth and the fleece-free liveweight of Angora goats is affected by liveweight change

Clean fleece weight (CFWt) is affected by liveweight and change in liveweight in Merino sheep, Angora and cashmere goats. However, how these relationships progress as animals age has not been elucidated. Measurements were made over 12 shearing periods on a population of Angora goats representing the current range and diversity of genetic origins including South African, Texan and interbred admixtures of these and Australian sources. Records of breed, sire, dam, date of birth, dam age, birthweight, birth parity, weaning weight, liveweight, fleece growth and fleece quality were taken for does and castrated males (wethers) (n = 267 animals). Fleece-free liveweights (FFLwt) were determined for each goat at shearing time by subtracting the greasy fleece weight from the liveweight recorded immediately before shearing. The average of the FFLwt at the start of the period and the FFLWt at the end of the period was calculated (AvFFLwt). Liveweight change (LwtCh) was the change in FFLwt over the period between shearings. A restricted maximum likelihood model was developed for CFWt, after log10 transformation, which allowed the observations of the same animal at different ages to be correlated in an unstructured manner. A simple way of describing the results is: CFWt = κ (AvFFLwt)β, where κ is a parameter that can vary in a systematic way with shearing age, shearing treatment and LwtCh; and β is an allometric coefficient that only varies with LwtCh. CFWt was proportional to FFLwt0.67 but only when liveweight was lost at the rate of 5–10 kg during a shearing interval of 6 months. The allometric coefficient declined to 0.3 as LwtCh increased from 10 kg loss to 20 kg gain during a shearing interval. A consequence is that, within an age group of Angora goats, the largest animals will be the least efficient in converting improved nutrition to mohair.

Ocean currents influence the genetic structure of an intertidal mollusc in southeastern Australia – implications for predicting the movement of passive dispersers across a marine biogeographic barrier

Major disjunctions among marine communities in southeastern Australia have been well documented, although explanations for biogeographic structuring remain uncertain. Converging ocean currents, environmental gradients, and habitat discontinuities have been hypothesized as likely drivers of structuring in many species, although the extent to which species are affected appears largely dependent on specific life histories and ecologies. Understanding these relationships is critical to the management of native and invasive species, and the preservation of evolutionary processes that shape biodiversity in this region. In this study we test the direct influence of ocean currents on the genetic structure of a passive disperser across a major biogeographic barrier. Donax deltoides (Veneroida: Donacidae) is an intertidal, soft-sediment mollusc and an ideal surrogate for testing this relationship, given its lack of habitat constraints in this region, and its immense dispersal potential driven by year-long spawning and long-lived planktonic larvae. We assessed allele frequencies at 10 polymorphic microsatellite loci across 11 sample locations spanning the barrier region and identified genetic structure consistent with the major ocean currents of southeastern Australia. Analysis of mitochondrial DNA sequence data indicated no evidence of genetic structuring, but signatures of a species range expansion corresponding with historical inundations of the Bassian Isthmus. Our results indicate that ocean currents are likely to be the most influential factor affecting the genetic structure of D. deltoides and a likely physical barrier for passive dispersing marine fauna generally in southeastern Australia.

Conservation of genetic diversity in British populations of the diploid endemic Coincya monensis ssp monensis (Isle of Man Cabbage): the risk of hybridisation with the tetraploid alien, Coincya monensis ssp cheiranthos

Coincya monensis is represented in the British flora by two, cytologically distinct subspecies. Coincya monensis ssp monensis is an endemic diploid with a coastal sand dune distribution that includes a number of isolated populations. Coincya monensis ssp cheiranthos is a tetraploid alien, well established in South Wales in early successional habitats. Both subspecies share similar life form traits, flowering times and pollinators. Cluster analysis and phylogenetic reconstruction based on sequences of the mitochondrial nad4 gene confirmed the distinction between alien and endemic taxa. Tetraploid populations carry more polymorphic RAPDs loci and their genetic diversity is partitioned more within than among populations. In contrast, C. monensis ssp monensis has a distinct population genetic structure. Analysis of the multilocus genetic data confirmed a structure of genetically isolated, endemic population clusters in Scotland, Arran, the Isle of Man and South Wales. Experimental hybridisation showed the two subspecies are interfertile. Multivariate analysis of RAPDs data resolved hybrids between alien and endemic clusters and hybrids contained a proportion of alien-specific polymorphic loci. Hybrids of alien maternal parentage contained the mitochondrial nad4 sequence characteristic of the alien subspecies. Since the alien subspecies can invade mobile sand dune communities from urban sites and compete for pollinators, there is a risk that alien and endemic populations will mix and introgress. Conservation of endemic genetic diversity in Britain will require protection for all C. monensis ssp monensis populations. Currently, the most disjunct endemic population in South Wales is most at risk from introgression.

The relationship between the incidence of medullated fibres in mohair and live weight over the lifetime of Angora goats

The presence of even a small amount of medullated fibre, in otherwise high quality mohair, may have a pronounced adverse effect on its value and end-use potential. However, there is considerable confusion about the effects, if any, of environmental variables and management upon the incidence of medullated fibres in mohair. This study examined how the incidence of medullated fibres (Med, % by number) is related to the fleece-free live weight (FFLwt) of Angora goats of different genetic origins over their lifetime, and how the relationship varies with other lifetime factors. Measurements were made over 11 shearing periods of 6 months, on a population of Angora goats representing the current range and diversity of genetic origins in Australia, including South African, Texan and interbred admixtures of these and Australian sources. Records of breed, sire, dam, date of birth, dam age, birth weight, birth parity, weaning weight, live weight, fleece growth and fleece quality were taken for castrated males (wethers) (n = 94 animals). A restricted maximum likelihood (REML) model was developed for log10(Med + 1), which allowed the observations of the same animal at different ages to be correlated in an unstructured manner. Med varied between 0.1% and 4.3%. The median average FFLwt during a shearing interval increased from 15 kg at 1 year old to 59 kg at 6 years old. Generally, within each shearing interval, Med increased with increasing average FFLwt. However, the size and shape of the relationship differed greatly between shearing ages. For example, at 3.5 years of age Med increased from about 1.1% at an average FFLwt of 26 kg to 2.6% at 50 kg, whilst at 5.0 years of age Med only changed from 1.4% at 32 kg to 1.6% at 56 kg. Goats with mixed genetic parentage showed an increase in Med at some shearings, particularly at younger ages. Variation in animal nutrition, as measured by live weight change during shearing periods, did not affect Med. The results supplement our earlier findings that mohair mean fibre diameter and clean mohair fleece weight, but not staple length, are greater in larger Angora goats. Live weight needs to be taken into account in genetic evaluation of the incidence of medullated fibres. We conclude that any advantage in handling fewer but larger Angora goats rather than more but smaller goats will come at the detriment of producing lower quality mohair, both in terms of increased Med and mean fibre diameter.

At the crossroads : the relationship between heritage and intellectual property in traditional knowledge protection in Southeast Asia

Matters related to traditional knowledge (TK) and traditional cultural expressions (TCEs) are 'at the crossroads' in various respects. From a legal perspective, TK is discussed in several international forums and is at the intersection of several already established or still emerging fields of law. Of particular interest here is the relationship between heritage and intellectual property. It is discussed in international diplomatic negotiations on intellectual property (IP) protection for TK/TCEs in the context of the Intergovernmental Committee on Intellectual Property and Genetic Resources, Traditional Knowledge and Folklore of the World Intellectual Property Organization (WIPO) and in the context of the UNESCO Convention for the Safeguarding of Intangible Cultural Heritage. Geographically, TK is also located 'at the crossroads'. It is linked to cultural spaces associated with certain peoples and certain territories and these are often not identical with the borders of nation states. Such borders are a colonial artefact that often fails to reflect the ethno-geographical reality of a region. The divergent national and ethnic boundaries create overlapping claims in situations that may be further complicated by both ancient and modern transmigrations and/or shared heritage. The Southeast Asian region, which is the geographical focus of this article, has been at the crossroads of trade and religious and cultural influences for centuries and it provides, therefore, excellent examples for such overlapping cultural spaces and resulting conflicting or competing claims. The article examines the legal and geographical intersections that have contributed to the current situation and the relationship between cultural and intellectual property in regional claims as well as examples of disputes that have arisen and the reasons for them.