Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation

One of the benefits of Digital PCR (dPCR) is the potential for unparalleled precision enabling smaller fold change measurements. An example of an assessment that could benefit from such improved precision is the measurement of tumour-associated copy number variation (CNV) in the cell free DNA (cfDNA) fraction of patient blood plasma. To investigate the potential precision of dPCR and compare it with the established technique of quantitative PCR (qPCR), we used breast cancer cell lines to investigate HER2 gene amplification and modelled a range of different CNVs. We showed that, with equal experimental replication, dPCR could measure a smaller CNV than qPCR. As dPCR precision is directly dependent upon both the number of replicate measurements and the template concentration, we also developed a method to assist the design of dPCR experiments for measuring CNV. Using an existing model (based on Poisson and binomial distributions) to derive an expression for the variance inherent in dPCR, we produced a power calculation to define the experimental size required to reliably detect a given fold change at a given template concentration. This work will facilitate any future translation of dPCR to key diagnostic applications, such as cancer diagnostics and analysis of cfDNA.     

Examining the complexity of human RNA polymerase complexes using HaloTag technology coupled to label free quantitative proteomics

Efficient determination of protein interactions and cellular localization remains a challenge in higher order eukaryotes and creates a need for robust technologies for functional proteomics studies. To address this, the HaloTag technology was developed for highly efficient and rapid isolation of intracellular complexes and correlative in vivo cellular imaging. Here we demonstrate the strength of this technology by simultaneous capture of human eukaryotic RNA polymerases (RNAP) I, II, and III using a shared subunit, POLR2H, fused to the HaloTag. Affinity purifications showed successful isolation, as determined using quantitative proteomics, of all RNAP core subunits, even at expression levels near endogenous. Transient known RNAP II interacting partners were identified as well as three previously uncharacterized interactors. These interactions were validated and further functionally characterized using cellular imaging. The multiple capabilities of the HaloTag technology demonstrate the ability to efficiently isolate highly challenging multiprotein complexes, discover new interactions, and characterize cellular localization.     

Estimating the Active Space of Male Koala Bellows: Propagation of Cues to Size and Identity in a Eucalyptus Forest

Examining how increasing distance affects the information content of vocal signals is fundamental for determining the active space of a given species’ vocal communication system. In the current study we played back male koala bellows in a Eucalyptus forest to determine the extent that individual classification of male koala bellows becomes less accurate over distance, and also to quantify how individually distinctive acoustic features of bellows and size-related information degrade over distance. Our results show that the formant frequencies of bellows derived from Linear Predictive Coding can be used to classify calls to male koalas over distances of 1–50 m. Further analysis revealed that the upper formant frequencies and formant frequency spacing were the most stable acoustic features of male bellows as they propagated through the Eucalyptus canopy. Taken together these findings suggest that koalas could recognise known individuals at distances of up to 50 m and indicate that they should attend to variation in the upper formant frequencies and formant frequency spacing when assessing the identity of callers. Furthermore, since the formant frequency spacing is also a cue to male body size in this species and its variation over distance remained very low compared to documented inter-individual variation, we suggest that male koalas would still be reliably classified as small, medium or large by receivers at distances of up to 150 m.     

What Insights Can Baboon Feeding Ecology Provide for Early Hominin Niche Differentiation?

Several authors have proposed that papionin baboons provide appropriate analogs for early hominin niche differentiation. Savanna-dwelling baboons and australopiths both radiated around the same time after Neogene expansion of C₄ grasslands, likely experiencing similar environmental changes and faced with solving similar ecological problems. We explore the insights baboons may provide into dietary ecology of savanna-occupying hominins. We compare dietary information from stable isotope data for feces, hair, and tooth dentine collagen of modern chacma baboons (Papio ursinus) with dietary data for Plio-Pleistocene papionins and hominins from South African savannas. Results confirm that, like the australopiths, baboons consume substantial amounts of C₄ food sources. However, the magnitude of inter- and intraindividual variation in baboon diets across different seasons and habitats is less than that from specimens of Australopithecus africanus and Paranthropus robustus analyzed to date. Hominins also consumed greater amounts of C₄ resources. Thus, though the data demonstrate that the radiation of both primate groups was closely linked with the spread of C₄ grasslands, hominins were even more extreme ecological generalists than baboons were. The absence of a fixed-diet in papionins implies that it was unlikely that the more ecologically flexible hominins evolved specializations for any one food type, an interpretation consistent with recent carbon isotope, dental microwear, and ecomorphological studies. We propose that researchers place less emphasis on resolving the foods that were most important for hominin differentiation; instead, future research should focus on questions related to ecological generalism.     

Effective number of breeders and maintenance of genetic diversity in the captive bearded vulture population

We combined pedigree data with data derived from 14 microsatellite loci to investigate genetic diversity and its maintenance in the captive source population for the reintroduction of the bearded vulture into the Alps. We found the captive population to be genetically more variable than the largest natural population in Europe, both in terms of mean number of alleles per locus and mean observed and expected heterozygosity. Allelic diversity of the captive population was higher than, and mean heterozygosity measurements were comparable with the ones found in two large, extinct populations from Sardinia and the Alps represented by museum specimens. The amount of genetic variability recruited with the founders was still present in the captive population of the year 2000, mainly because the carriers of rare alleles were still alive. However, the decline in expected heterozygosity and the loss of alleles over generations in captivity was significant. Point estimates of effective population size, N(e), based on pedigree data and estimates of effective number of breeders, N(b), based on allele frequency changes, ranged from 20 to 30 and were significantly smaller than the census size. The results demonstrate that the amount of genetic variability in the captive bearded vulture population is comparable or even larger than the amount present in natural populations. However, the population is in danger to lose genetic variability over time because of genetic drift. Management strategies should therefore aim at preserving genetic variability by minimising kinship, and at increasing N(e) by recruiting additional founders and enhancing gene flow between the released, the captive and natural populations.     

Is There a Genetic Basis for Fluctuating Asymmetry and Does it Predict Fitness in the Plant Lotus corniculatus Grown in Different Environmental Conditions?

Fluctuating asymmetry (FA) is considered to be a good measure of developmental stability. We measured the asymmetry of leaves and flowers of 16 different genotypes of Lotus corniculatus grown in four different experimental environments to estimate the plasticity or developmental stability of asymmetry itself. We found that an index of FA (absolute difference between size of left and right sides, corrected for trait size) differed significantly across environments, with the treatment CO2+/N+ inducing the greatest FA for both flowers and leaves. Genotypes did not differ in FAs. Individual plants showed significantly different FAs only for flowers. At the individual level, we found no significant relationship between flower FA and fitness. Previous work indicates that change in asymmetry in a poor or perturbing environment versus a good environment could reflect the intrinsic quality of a particular genotype. However, in our experiment, genotype effect was significant only for change in asymmetry of leaves, and this last trait was not significantly correlated with our fitness estimate for each genotype in either the most or the least perturbing environment.     

Significance of diet type and diet quality for ecological diversity of African ungulates

1. We test two nutritional hypotheses for the ecological diversity of ungulates, the browser/grazer (diet type) and diet quality models, among free-ranging herbivores in a South African savanna, the Kruger National Park. Tests are based on assessment of relationships between diet type and diet quality with body mass and hypsodonty, two morphological features that have been associated with both elements. 2. We use stable carbon isotope ratios of faeces to reconstruct diet in terms of proportions of C(3) plants (browse) and C(4) plants (grass) consumed by different species in different seasons. These data are combined with proxies for diet quality (per cent nitrogen, neutral detergent fibre, acid detergent fibre, and acid detergent lignin) from faeces to track changes in diet quality. 3. Two statistical approaches are used in model selection, i.e. tests of significant correlations based on linear regression analyses, and an information-theory approach (Akaike's Information Criterion) providing insight into strength of evidence for models. 4. Results of both methods show that, contrary to many predictions, body mass and diet type are not related, but these data confirm predictions that diet quality decreases with increasing body size, especially during the dry season. Hypsodonty, as expected, varies with diet type, increasing with increased grass intake. 5. These findings support both a diet type and diet quality model, implying some degree of exclusivity. We propose that congruence between models may be achieved through addition of diet quality proxies not included here, because hypsodonty is more likely a reflection of the abrasive properties of consumed foods, i.e. related to food quality, rather than food type. This implies that adaptation to diets of varying quality, through changes in body size and dental features, has been the primary mechanism for diversification in ungulates. 6. Our interpretation contrasts with several recent studies advocating diet type as the primary factor, exemplifying that further reconciliation between the two models is needed. We discuss the implications of this study for future approaches to achieve a more cohesive understanding of the evolutionary outcomes of herbivore nutrition.     

Stable isotope characterization of mammalian predator–prey relationships in a South African savanna

This paper characterizes predator–prey interactions amongst African mammals from C₄ savanna environments using stable carbon and nitrogen isotope proxies for diet. Stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope data from hair and faeces of large African mammal carnivores, and herbivores as potential prey, are presented for a diverse range of taxa. Carbon-isotope data imply that most carnivores from the “lowveld” savanna of South Africa form part of C₄ grass-based food webs. Nitrogen isotope data show clear differences between trophic levels, although it appears that the magnitude of these differences varies between predators feeding on invertebrates and vertebrates, respectively. Whilst the number of carnivore samples for which data are available is relatively few, and data for prey are restricted mainly to large ungulate herbivores, results clearly demonstrate the potential for future applications of this technique to predator–prey food webs in African savannas. In tandem with traditional approaches, stable isotopes can help elucidate patterns of predator impacts on prey populations, domestic livestock, and resolving similar food webs in palaeoenvironmental contexts.     

PAR1 specifies ciliated cells in vertebrate ectoderm downstream of aPKC

Partitioning-defective 1 (PAR1) and atypical protein kinase C (aPKC) are conserved serine/threonine protein kinases implicated in the establishment of cell polarity in many species from yeast to humans. Here we investigate the roles of these protein kinases in cell fate determination in Xenopus epidermis. Early asymmetric cell divisions at blastula and gastrula stages give rise to the superficial (apical) and the deep (basal) cell layers of epidermal ectoderm. These two layers consist of cells with different intrinsic developmental potential, including superficial epidermal cells and deep ciliated cells. Our gain- and loss-of-function studies demonstrate that aPKC inhibits ciliated cell differentiation in Xenopus ectoderm and promotes superficial cell fates. We find that the crucial molecular substrate for aPKC is PAR1, which is localized in a complementary domain in superficial ectoderm cells. We show that PAR1 acts downstream of aPKC and is sufficient to stimulate ciliated cell differentiation and inhibit superficial epidermal cell fates. Our results suggest that aPKC and PAR1 function sequentially in a conserved molecular pathway that links apical-basal cell polarity to Notch signaling and cell fate determination. The observed patterning mechanism may operate in a wide range of epithelial tissues in many species.