Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus

The increased transcription of the Cyp6g1 gene of Drosophila melanogaster, and consequent resistance to insecticides such as DDT, is a widely cited example of adaptation mediated by cis-regulatory change. A fragment of an Accord transposable element inserted upstream of the Cyp6g1 gene is causally associated with resistance and has spread to high frequencies in populations around the world since the 1940s. Here we report the existence of a natural allelic series at this locus of D. melanogaster, involving copy number variation of Cyp6g1, and two additional transposable element insertions (a P and an HMS-Beagle). We provide evidence that this genetic variation underpins phenotypic variation, as the more derived the allele, the greater the level of DDT resistance. Tracking the spatial and temporal patterns of allele frequency changes indicates that the multiple steps of the allelic series are adaptive. Further, a DDT association study shows that the most resistant allele, Cyp6g1-[BP], is greatly enriched in the top 5% of the phenotypic distribution and accounts for ~16% of the underlying phenotypic variation in resistance to DDT. In contrast, copy number variation for another candidate resistance gene, Cyp12d1, is not associated with resistance. Thus the Cyp6g1 locus is a major contributor to DDT resistance in field populations, and evolution at this locus features multiple adaptive steps occurring in rapid succession.

New insights into the role of MHC diversity in devil facial tumour disease

Devil facial tumour disease (DFTD) is a fatal contagious cancer that has decimated Tasmanian devil populations. The tumour has spread without invoking immune responses, possibly due to low levels of Major Histocompatibility Complex (MHC) diversity in Tasmanian devils. Animals from a region in north-western Tasmania have lower infection rates than those in the east of the state. This area is a genetic transition zone between sub-populations, with individuals from north-western Tasmania displaying greater diversity than eastern devils at MHC genes, primarily through MHC class I gene copy number variation. Here we test the hypothesis that animals that remain healthy and tumour free show predictable differences at MHC loci compared to animals that develop the disease.

RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae

We describe methods for obtaining a quantitative description of RNA processing at high resolution in budding yeast. As a model gene expression system, we constructed tetON (for induction studies) and tetOFF (for repression, derepression, and RNA degradation studies) yeast strains with a series of reporter genes integrated in the genome under the control of a tetO7 promoter. Reverse transcription and quantitative real-time-PCR (RT-qPCR) methods were adapted to allow the determination of mRNA abundance as the average number of copies per cell in a population. Fluorescence in situ hybridization (FISH) measurements of transcript numbers in individual cells validated the RT-qPCR approach for the average copy-number determination despite the broad distribution of transcript levels within a population of cells. In addition, RT-qPCR was used to distinguish the products of the different steps in splicing of the reporter transcripts, and methods were developed to map and quantify 3′-end cleavage and polyadenylation. This system permits pre-mRNA production, splicing, 3′-end maturation and degradation to be quantitatively monitored with unprecedented kinetic detail, suitable for mathematical modeling. Using this approach, we demonstrate that reporter transcripts are spliced prior to their 3′-end cleavage and polyadenylation, that is, cotranscriptionally.

Maternal overnutrition programs changes in the expression of skeletal muscle genes that are associated with insulin resistance and defects of oxidative phosphorylation in adult male rat offspring.

Children of obese mothers have increased risk of metabolic syndrome as adults. Here we report the effects of a high-fat diet in the absence of maternal obesity at conception on skeletal muscle metabolic and transcriptional profiles of adult male offspring. Female Sprague Dawley rats were fed a diet rich in saturated fat and sucrose [high-fat diet (HFD): 23.5% total fat, 9.83% saturated fat, 20% sucrose wt:wt] or a normal control diet [(CD) 7% total fat, 0.5% saturated fat, 10% sucrose wt:wt] for the 3 wk prior to mating and throughout pregnancy and lactation. Maternal weights were not different at conception; however, HFD-fed dams were 22% heavier than controls during pregnancy. On a normal diet, the male offspring of HFD-fed dams were not heavier than controls but demonstrated features of insulin resistance, including elevated plasma insulin concentration [40.1 ± 2.5 (CD) vs 56.2 ± 6.1 (HFD) mU/L; P = 0.023]. Next-generation mRNA sequencing was used to identify differentially expressed genes in the offspring soleus muscle, and gene set enrichment analysis (GSEA) was used to detect coordinated changes that are characteristic of a biological function. GSEA identified 15 upregulated pathways, including cytokine signaling (P < 0.005), starch and sucrose metabolism (P < 0.017), inflammatory response (P < 0.024), and cytokine-cytokine receptor interaction (P < 0.037). A further 8 pathways were downregulated, including oxidative phosphorylation (P < 0.004), mitochondrial matrix (P < 0.006), and electron transport/uncoupling (P < 0.022). Phosphorylation of the insulin signaling protein kinase B was reduced [2.86 ± 0.63 (CD) vs 1.02 ± 0.27 (HFD); P = 0.027] and mitochondrial complexes I, II, and V protein were downregulated by 50-68% (P < 0.005). On a normal diet, the male offspring of HFD-fed dams did not become obese adults but developed insulin resistance, with transcriptional evidence of muscle cytokine activation, inflammation, and mitochondrial dysfunction. These data indicate that maternal overnutrition, even in the absence of prepregnancy obesity, can promote metabolic dysregulation and predispose offspring to type 2 diabetes.

Selection on mitochondrial variants occurs between and within individuals in an expanding invasion

Mitochondria are critical for life, yet their underlying evolutionary biology is poorly understood. In particular, little is known about interaction between two levels of evolution: between individuals and within individuals (competition between cells, mitochondria or mitochondrial DNA molecules). Rapid evolution is suspected to occur frequently in mitochondrial DNA, whose maternal inheritance predisposes advantageous mutations to sweep rapidly though populations. Rapid evolution is also predicted in response to changed selection regimes after species invasion or removal of pathogens or competitors. Here, using empirical and simulated data from a model invasive bird species, we provide the first demonstration of rapid selection on the mitochondrial genome within individuals in the wild. Further, we show differences in mitochondrial DNA copy number associated with competing genetic variants, which may provide a mechanism for selection. We provide evidence for three rarely documented phenomena: selection associated with mitochondrial DNA abundance, selection on the mitochondrial control region, and contemporary selection during invasion.

Genetic variation and obesity in Australian women: A prospective study.

Objective: A number of candidate genes have been implicated in the pathogenesis of obesity in humans. This study examines associations between longitudinal changes in body mass and composition and the presence of polymorphisms in the ß-3 adrenergic receptor, tumor necrosis factor-α, leptin, and leptin receptor (Lepr) in a cohort of Australian women.

Research Methods and Procedures: Healthy white Australian women (n = 335) were randomly selected from the Barwon region of Victoria and underwent baseline anthropometry and double-energy X-ray absorptiometry for assessment of body mass and adiposity. These measurements were repeated again at 2-year follow-up. Genomic DNA was extracted and used for polymerase chain reaction-based genotyping of all polymorphisms.

Results: The Pro1019Pro Lepr polymorphism was associated with longitudinal increases in body weight (p = 0.02), fat mass (p = 0.05), and body mass index (p = 0.01) in this study, and individuals homozygous for the A allele at this locus had a greater propensity to gain body fat over time. The largest effects on body composition seemed to be in individuals already obese at baseline. Changes in body weight, fat mass, percent body fat, and body mass index over a 2-year period were not associated with genetic variation in the ß-3 adrenergic receptor (Trp64Arg), tumor necrosis factor-α promoter, or leptin genes in non-obese or obese women.

Discussion: These results suggest that a Lepr polymorphism is involved in the regulation of body mass and adiposity in obese Australian white women, which may have implications for the treatment of obesity in this population.

Ecotypic variation in the response of Arabidopsis thaliana to Phytophthora cinnamomi

A variety of reactions to inoculation with Phytophthora cinnamomi ranging from high susceptibility to moderate resistance were found in 20 ecotypes of Arabidopsis thaliana. P. cinnamomi zoospores successfully colonised both root and leaf tissue of Arabidopsis and sporulation in the form of chlamydospores and sporangia occurred in leaves and roots of each ecotype but the number varied considerably between ecotypes. In the more susceptible ecotypes, colonisation was characterised by rapid intercellular growth and sporulation of the pathogen from 48 h post inoculation. In less susceptible ecotypes, P. cinnamomi was limited to a defined region within tissues. In response to P. cinnamomi infection, several ecotypes expressed active defence responses in both root and leaf tissue. Callose formation was closely associated with lesion restriction as was the production of the reactive oxygen species, hydrogen peroxide. The oxidative burst was not limited to the site of pathogen ingress but also occurred in distant, uninfected tissues. We have characterised an Arabidopsis–P. cinnamomi system that will be useful for further studies of active resistance mechanisms.

Genetic variation in BEACON influences quantitative variation in metabolic syndrome-related phenotypes

The BEACON gene (also known as UBL5) was identified as differentially expressed between lean and obese Psammomys obesus, a polygenic animal model of obesity, type 2 diabetes, and dyslipidemia. The human homologue of BEACON is located on chromosome 19p, a region likely to contain genes affecting metabolic syndrome–related quantitative traits as established by linkage studies. To assess whether the human BEACON gene may be involved in influencing these traits, we exhaustively analyzed the complete gene for genetic variation in 40 unrelated individuals and identified four variants (three novel). The two more common variants were tested for association with a number of quantitative metabolic syndrome–related traits in two large cohorts of unrelated individuals. Significant associations were found between these variants and fat mass (P = 0.026), percentage of fat (P = 0.001), and waist-to-hip ratio (P = 0.031). The same variants were also associated with total cholesterol (P = 0.024), LDL cholesterol (P = 0.019), triglycerides (P = 0.006), and postglucose load insulin levels (P = 0.018). Multivariate analysis of these correlated phenotypes also yielded a highly significant association (P = 0.0004), suggesting that BEACON may influence phenotypic variation in metabolic syndrome–related traits.

Host intra-clutch variation, cuckoo egg matching and egg rejection by great reed warblers

Prevailing theory predicts that lower levels of intra-clutch variation in host eggs facilitate the detection of brood parasitism. We assessed egg matching using both human vision and UV-VIS spectrophotometry and then followed the nest fate of great reed warblers naturally parasitised by European cuckoos. Rejection was predicted by the following three variables: matching between cuckoo and host eggs on the main chromatic variable defined by principal components analysis of the egg spectra (which has a strong loading in the UV); the number of host eggs in the nest; and human estimates of intra-clutch variation. The first variable is not correlated to human estimates of matching, which do not predict rejection. In line with another recent study, rejection rates were predicted by higher levels of intra-clutch variation in the host eggs, suggesting that higher rather than lower levels of intra-clutch variation can facilitate the discrimination of cuckoo eggs by hosts. We suggest that the importance of intra-clutch variation is context dependent, with intra-clutch variation being important when there is good matching between the host and the cuckoo eggs. Our results also suggest that both spectrometric and human visual assessments of egg matching and intra-clutch variation are prudent: the former provide the best method of estimating reflectance variation, whereas the latter include some assessment of patterns of maculation.

Within-population variation in ejaculate characteristics in a prolonged breeder, Peron's tree frog, Litoria peronii

Sperm number is often a good predictor of success in sperm competition; however, it has become increasingly clear that, for some species, variation in probability of paternity cannot be explained by sperm number alone. Intraspecific variation in ejaculate characteristics, such as the number of viable sperm and sperm longevity, may play an equally important role in determining fertilization success. Here, we assess variation among ejaculates in three factors that may contribute to fertilization success (number of sperm per ejaculate, viability, and longevity), in a population of Peron’s tree frog (Litoria peronii). We detected large variation among males in the number of sperm per ejaculate and the proportion of viable sperm within ejaculates, which could not be explained by variation in either male size or body condition. However, the proportion of viable sperm released by males increased over the season. Finally, we assessed sperm longevity (proportion viable sperm determined using a dual-fluorochrome vital dye) at two different temperatures. At 23°C, on average, 75% of sperm remained viable after 2 h, but there were significant differences amongst males with the percentage of viable sperm ranging from 43% to 95%. For sperm incubated at 4°C, ejaculates varied fivefold in sperm longevity with some males having 50% viable sperm after 5 days. Our data suggest that ejaculate characteristics (sperm number, viability, and longevity) vary widely in Peron’s tree frog and may therefore play an important role in determining siring success both in the presence and absence of sperm competition. We discuss the results in relation to selection on ejaculate traits via natural and sexual selection in this and other amphibians.

Sources of variation in fibre diameter attributes of Australian alpacas and implications for fleece evaluation and animal selection

Sources of variation in fibre diameter attributes of Australian alpacas and implications for fleece evaluation and animal selection were investigated using data collected in the years 1994–97, from 6 properties in southern Australia. Data were analysed using REML (multiple regression analysis) to determine the effect on mean fibre diameter (MFD) and coefficient of variation of MFD (CV(FD)) of age, origin (property), sex (entire male, female), breed (Huacaya, Suri), liveweight, fibre colour, individual, and interactions of these effects. The mean (n = 100) age (range) was 4.2 years (0.1–11.9), liveweight 72.0 kg (12.0–134 kg), MFD 29.1 μm (17.7–46.6 μm), CV(FD) 24.33% (15.0–36.7%).

A number of variables affected MFD and CV(FD). MFD increased to 7.5 years of age, and correlations between MFD at 1.5 and 2 years of age with the MFD at older ages were much higher than correlations at younger ages. Fibre diameter 'blowout' (increase with age) was positively correlated with the actual MFD at ages 2 years and older. There were important effects of farm, and these effects differed with year and shearing age. Suris were coarser than Huacayas with the effect reducing with increased liveweight; there was no effect of sex. Fleeces of light shade were 1 μm finer than dark fleeces. CV(FD) declined rapidly between birth and 2 years of age, reaching a minimum at about 4 years of age and then increasing; however, CV(FD) measurements on young animals were very poor predictors of CV(FD) at older ages, and the response of CV(FD) to age differed with farm and year. Suris had a higher CV(FD) than Huacayas on most properties, and MFD, liveweight, and sex did not affect CV(FD). Fleeces of dark shade had higher CV(FD) than fleeces of light shade in 2 of the years. It is concluded that there are large opportunities to improve the MFD and CV(FD) of alpaca fibre through selection and breeding. The potential benefit is greatest from reducing the MFD and CV(FD) of fibre from older alpacas, through reducing the between-animal variation in MFD and CV(FD). Sampling alpacas at ages <2 years is likely to substantially decrease selection efficiency for lifetime fibre diameter attributes.

The trophic effect of dietary fibre is not associated with a change in total crypt number in the distal colon of rats

Soluble fibres, such as guar gum, promote and wheat bran or methylcellulose protect from chemically induced colon carcinogenesis, relative to the effect of a fibre-free diet in rats. Mechanisms are poorly understood. Whereas all fibres are trophic to the colonic epithelium, the heterogeneity of effects on carcinogenesis may reflect different effects on the total number of crypts and, therefore, the size of the stem cell population. This study aimed to assess this hypothesis. Sprague–Dawley rats were fed one of fibre-free diets with or without 10% wheat bran, methylcellulose or guar gum for 4 weeks. The distal colons were stained with methylene blue and quantified for the number and density of crypts using an image analysis system. Epithelial proliferative kinetics was measured stathmokinetically. Methodology for quantifying crypts was valid and reproducible. Rats fed a fibre-free diet had atrophic distal colon, as shown by a decrease in crypt column height and a lower mitotic index. Fibre supplementation prevented the atrophy and was associated with crypt mouth areas that were 30–60% larger than those in the fibre-free group (P < 0.001, ANOVA), with the methylcellulose group being the largest (1.16 µm2). The crypt density of the fibre-free group was 16–19% greater than those in fibre fed groups (P + 0.006), due to the smaller size of the crypts. However, there was no difference in the total number of crypts across the four dietary groups (P > 0.1). Distal colons in all of the dietary groups contained ~105 crypts. In conclusion, although variation in the amount or type of dietary fibre exerts heterogeneous effects on the growth of the colonic epithelium and on colon carcinogenesis, the total number of crypts in the distal colon remains constant. It is, therefore, unlikely that fibres influence carcinogenic events by altering the size of the stem cell population.

Effects of variation in modulator temperature during cryogenic modulation in comprehensive two-dimensional gas chromatography

Many modulation systems in comprehensive 2D GC (GC×GC) are based on cryogenic methods. High trapping temperatures in these systems can result in ineffective trapping of the more volatile compounds, whilst temperatures that are too low can prevent efficient remobilisation of some compounds. To better understand the trapping and release of compounds over a wide range of volatilities, we have investigated a number of different constant temperature modulator settings, and have also examined a constant temperature differential between the cryo-trap and the chromatographic oven. These investigations have led us to modify the temperature regulation capabilities of the longitudinally modulated cryogenic system (LMCS). In contrast to the current system, where the user sets a constant temperature for the cooling chamber, the user now sets the temperature difference between the cryo-trap and the chromatographic oven. In this configuration, the cooling chamber temperature increases during the chromatographic run, tracking the oven temperature ramp. This produces more efficient, volatility-dependent modulation, and increases the range of volatile compounds that can be analysed under optimal trap-and-release conditions within a single analytical run. This system also reduces cryogenic fluid consumption.

Dematerialised data and human desire : the Internet and copy culture

Since Licklider in the 1960s [27] influential proponents of networked computing have envisioned electronic information in terms of a relatively small (even singular) number of 'sources', distributed through technologies such as the Internet. Most recently, Levy writes, in Becoming Virtual, that "in cyberspace, since any point is directly accessible from any other point, there is an increasing tendency to replace copies of documents with hypertext links. Ultimately, there will only need to be a single physical exemplar of the text" [13 p.61]. Hypertext implies, in theory, the end of 'the copy', and the multiplication of access points to the original. But, in practice, the Internet abounds with copying, both large and small scale, both as conscious human practice, and also as autonomous computer function. Effective and cheap data storage that encourages computer users to keep anything of use they have downloaded, lest the links they have found, 'break'; while browsers don't 'browse' the Internet - they download copies of everything to client machines. Not surprisingly, there is significant regulation against 'copying' - regulation that constrains our understanding of 'copying' to maintain a legal fiction of the 'original' for the purposes of intellectual property protection. In this paper, I will firstly demonstrate, by a series of examples, how 'copying' is more than just copyright infringement of music and software, but is a defining, multi-faceted feature of Internet behaviour. I will then argue that the Internet produces an interaction between dematerialised, digital data and human subjectivity and desire that fundamentally challenges notions of originality and copy. Walter Benjamin noted about photography: "one can make any number of prints [from a negative]; to ask for the 'authentic' print makes no sense" [4 p.224]. In cyberspace, I conclude, it makes no sense to ask which one is the copy.

Phenological response of sea turtles to environmental variation across a species' northern range

Variations in environmental parameters (e. g. temperature) that form part of global climate change have been associated with shifts in the timing of seasonal events for a broad range of organisms. Most studies evaluating such phenological shifts of individual taxa have focused on a limited number of locations, making it difficult to assess how such shifts vary regionally across a species range. Here, by using 1445 records of the date of first nesting for loggerhead sea turtles (Caretta caretta) at different breeding sites, on different continents and in different years across a broad latitudinal range (25-39 degrees ' N), we demonstrate that the gradient of the relationship between temperature and the date of first breeding is steeper at higher latitudes, i.e. the phenological responses to temperature appear strongest at the poleward range limit. These findings support the hypothesis that biological changes in response to climate change will be most acute at the poleward range limits and are in accordance with the predictions of MacArthur's hypothesis that poleward range limit for species range is environmentally limited. Our findings imply that the poleward populations of loggerheads are more sensitive to climate variations and thus they might display the impacts of climate change sooner and more prominently.