Molecular genetic markers for abalone aquaculture

Describes the development and mapping of molecular markers in the blacklip and greenlip abalones. By means of a genome scan using a novel selective DNA pooling strategy, markers associated with growth were discovered that could potentially be applied to increase genetic gain in abalone aquaculture, whilst minimising inbreeding.

Molecular genetic variation in Galaxias maculatus (Osteichthys: Galaxiidae)

The "common jollytail", Galaxias maculatus, is a freshwater minnow-like fish that is distributed across the Southern Hemisphere and occurs abundantly in inland waterways of south-eastern Australia. Molecular genetic data were collected from samples of this species throughout western Victoria to evaluate hypotheses concerning the taxonomy and evolution of this ecologically important fish.

Systematic investigation of oxygen and growth factors in clinically valid ex vivo expansion of cord blood CD34+ hematopoietic progenitor cells

Background aims. Cord blood is considered to be a superior source of hematopoietic stem and progenitor cells for transplantation, but clinical use is limited primarily because of the low numbers of cells harvested. Ex vivo expansion has the potential to provide a safe, effective means of increasing cell numbers. However, an absence of consensus regarding optimum expansion conditions prevents standard implementation. Many studies lack clinical applicability, or have failed to investigate the combinational effects of different parameters.

Methods. This is the first study to characterize systematically the effect of growth factor combinations across multiple oxygen levels on the ex vivo expansion of cord blood CD34 hematopoietic cells utilizing clinically approvable reagents and methodologies throughout.

Results. Optimal fold expansion, as assessed both phenotypically and functionally, was greatest with thrombopoietin, stem cell factor, Flt-3 ligand and interleukin-6 at an oxygen level of 10%. With these conditions, serial expansion showed continual target population expansion and consistently higher expression levels of self-renewal associated genes.

Conclusions. This study has identified optimized fold expansion conditions, with the potential for direct clinical translation to increase transplantable cell dose and as a baseline methodology against which future factors can be tested.

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.

A modified micro genetic algorithm for undertaking multi-objective optimization problems

In this paper, a Modified micro Genetic Algorithm (MmGA) is proposed for undertaking Multi-objective Optimization Problems (MOPs). An NSGA-II inspired elitism strategy and a population initialization strategy are embedded into the traditional micro Genetic Algorithm (mGA) to form the proposed MmGA. The main aim of the MmGA is to improve its convergence rate towards the pareto optimal solutions. To evaluate the effectiveness of the MmGA, two experiments using the Kursawe test function in MOPs are conducted, and the results are compared with those from other approaches using a multi-objective evolutionary algorithm indicator, i.e. the Generational Distance (GD). The outcomes positively demonstrate that the MmGA is able to provide useful solutions with improved GD measures for tackling MOPs.

Estrogen-related receptor γ is an in vivo receptor of bisphenol A

Bisphenol A (BPA) is an endocrine disruptor that displays estrogenic activity. Several reports suggest that BPA may have estrogen receptor-independent effects. In zebrafish, 50 μM BPA exposure induces otic vesicle abnormalities, including otolith aggregation. The purpose of this study was to test if BPA action was mediated in vivo during zebrafish development by the orphan nuclear estrogen related receptor (ERR) γ. Combining pharmacological and functional approaches, we demonstrate that the zebrafish ERRγ mediates BPA-induced malformations in otoliths. Using different bisphenol derivatives, we show that different compounds can induce a similar otolith phenotype than BPA and that the binding affinity of these derivatives to the zebrafish ERRγ correlates with their ability to induce otolith malformations. Morpholino knockdown of ERRγ function suppresses the BPA effect on otoliths whereas overexpression of ERRγ led to a BPA-like otolith phenotype. Moreover, a subphenotypical dose of BPA (1 μM) combined with ERRγ overexpression led to a full-dose (50 μM) BPA otolith phenotype. We therefore conclude that ERRγ mediates the otic vesicle phenotype generated by BPA. Our results suggest that the range of pathways perturbed by this compound and its potential harmful effect are larger than expected.—Tohmé, M., Prud’homme, S. M., Boulahtouf, A., Samarut, E., Brunet, F., Bernard, L., Bourguet, W., Gibert, Y., Balaguer, P., Laudet, V. Estrogen-related receptor γ is an in vivo receptor of bisphenol A.

Non-referenced genome assembly from epigenomic short-read data

Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.

Variation at the DRD4 locus is associated with wariness and local site selection in urban black swans

 BACKGROUND: Interactions between wildlife and humans are increasing. Urban animals are often less wary of humans than their non-urban counterparts, which could be explained by habituation, adaptation or local site selection. Under local site selection, individuals that are less tolerant of humans are less likely to settle in urban areas. However, there is little evidence for such temperament-based site selection, and even less is known about its underlying genetic basis. We tested whether site selection in urban and non-urban habitats by black swans (Cygnus atratus) was associated with polymorphisms in two genes linked to fear in animals, the dopamine receptor D4 (DRD4) and serotonin transporter (SERT) genes.

RESULTS: Wariness in swans was highly repeatable between disturbance events (repeatability = 0.61) and non-urban swans initiated escape from humans earlier than urban swans. We found no inter-individual variation in the SERT gene, but identified five DRD4 genotypes and an association between DRD4 genotype and wariness. Individuals possessing the most common DRD4 genotype were less wary than individuals possessing rarer genotypes. As predicted by the local site selection hypothesis, genotypes associated with wary behaviour were over three times more frequent at the non-urban site. This resulted in moderate population differentiation at DRD4 (FST = 0.080), despite the sites being separated by only 30 km, a short distance for this highly-mobile species. Low population differentiation at neutrally-selected microsatellite loci and the likely occasional migration of swans between the populations reduces the likelihood of local site adaptations.

CONCLUSION: Our results suggest that wariness in swans is partly genetically-determined and that wary swans settle in less-disturbed areas. More generally, our findings suggest that site-specific management strategies may be necessary that consider the temperament of local animals.

The relative importance of spatial proximity, kin selection and potential ‘greenbeard’ signals on provisioning behaviour among helpers in a cooperative bird

© 2015 Springer-Verlag Berlin Heidelberg Many hypotheses have been proposed to account for cooperative behaviour, with those favouring kin selection receiving the greatest support to date. However, the importance of relatedness becomes less clear in complex societies where interactions can involve both kin and non-kin. To help clarify this, we examined the relative effect of indirect versus key direct benefit hypotheses in shaping cooperative decisions. We assessed the relative importance of likely reciprocal aid (as measured by spatial proximity between participants), kin selection (using molecular-based relatedness indices) and putative signals of relatedness (vocal similarity) on helper/helper cooperative provisioning dynamics in bell miners (Manorina melanophrys), a species living in large, complex societies. Using network analysis, we quantified the extent of shared provisioning (helping at the same nests) among individual helpers (excluding breeding pairs) over three seasons and 4290 provisioning visits, and compared these with the location of individuals within a colony and networks built using either genetic molecular relatedness or call similarity indices. Significant levels of clustering were observed in networks; individuals within a cluster were more closely related to each other than other colony members, and cluster membership was stable across years. The probability of a miner helping at another’s nest was not simply a product of spatial proximity and thus the potential for reciprocal aid. Networks constructed using helping data were significantly correlated to those built using molecular data in 5 of 10 comparisons, compared to 8 of 10 comparisons for networks constructed using call similarity. This suggests an important role of kinship in shaping helping dynamics in a complex cooperative society, apparently determined via an acoustic ‘greenbeard’ signal in this system.

Egg production curve fitting using nonlinear models for selected and nonselected lines of White Leghorn hens

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Test-day milk yield as a selection criterion for dairy buffaloes (Bubalus bubalis Artiodactyla, Bovidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effect of lactation length adjustment procedures on genetic parameter estimates for buffalo milk yield

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evaluation of TFAM and FABP4 gene polymorphisms in three lines of Nellore cattle selected for growth

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Pollen Dispersal Between Isolated Trees in the Brazilian Savannah: A Case Study of the Neotropical Tree Hymenaea stigonocarpa

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Rabies virus in a pregnant naturally infected southern yellow bat (Lasiurus ega)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)