Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms

Single nucleotide polymorphisms (SNPs) are appealing genetic markers due to several beneficial attributes, but uncertainty remains about how many of these bi-allelic markers are necessary to have sufficient power to differentiate populations, a task now generally accomplished with highly polymorphic microsatellite markers. In this study, we tested the utility of 37 SNPs and 13 microsatellites for differentiating 29 broadly distributed populations of Chinook salmon ( n  = 2783). Information content of all loci was determined by In and     , and the top 12 markers ranked by In were microsatellites, but the 6 highest, and 7 of the top 10     ranked markers, were SNPs. The mean ratio of random SNPs to random microsatellites ranged from 3.9 to 4.1, but this ratio was consistently reduced when only the most informative loci were included. Individual assignment test accuracy was higher for microsatellites (73.1%) than SNPs (66.6%), and pooling all 50 markers provided the highest accuracy (83.2%). When marker types were combined, as few as 15 of the top ranked loci provided higher assignment accuracy than either microsatellites or SNPs alone. Neighbour-joining dendrograms revealed similar clustering patterns and pairwise tests of population differentiation had nearly identical results with each suite of markers. Statistical tests and simulations indicated that closely related populations were better differentiated by microsatellites than SNPs. Our results indicate that both types of markers are likely to be useful in population genetics studies and that, in some cases, a combination of SNPs and microsatellites may be the most effective suite of loci.     

Sublethal costs associated with the consumption of toxic prey by snakes

Costs of plant defences to herbivores have been extensively studied, but costs of chemical defences to carnivores are less well understood. We examine the costs to Australian keelback snakes (Tropidonophis mairii, Gray 1841) of consuming cane toads (Bufo[Rhinella]marinus Linnaeus 1758). Cane toads (an invasive species in Australia) are highly toxic. Although keelbacks can consume toads without dying (unlike most Australian snakes), we show that cane toads are poor quality prey for keelbacks. Toads are of low net nutritional value, take longer to consume than do native frogs and reduce the snake's locomotor performance for up to 6 h after ingestion of a meal. These latter effects may increase a snake's vulnerability to predation. Nutritional content of vertebrate prey is not the only factor driving the evolution of foraging behaviour; other more subtle costs, such as risk of predation, may be widespread.     

Immunoglobulin G galactosylation and sialylation are associated with pregnancy-induced improvement of rheumatoid arthritis and the postpartum flare: results from a large prospective cohort study

Introduction  

Improvement of rheumatoid arthritis (RA) during pregnancy has been causatively associated with increased galactosylation of immunoglobulin G (IgG) N-glycans. Since previous studies were small, did not include the postpartum flare and did not study sialylation, these issues were addressed in the present study.     

Multispectral fingerprinting for improved in vivo cell dynamics analysis

Background  

Tracing cell dynamics in the embryo becomes tremendously difficult when cell trajectories cross in space and time and tissue density obscure individual cell borders. Here, we used the chick neural crest (NC) as a model to test multicolor cell labeling and multispectral confocal imaging strategies to overcome these roadblocks.     

Chilling to zero degrees disrupts pollen formation but not meiotic microtubule arrays in Triticum aestivum L.

Throughout the wheat‐growing regions of Australia, chilling temperatures below 2 °C occur periodically on consecutive nights during the period of floral development in spring wheat (Triticum aestivum L.). In this study, wheat plants showed significant reductions in fertility when exposed to prolonged chilling temperatures in controlled environment experiments. Among the cultivars tested, the Australian cultivars Kite and Hartog had among the lowest levels of seed set due to chilling and their responses were investigated further. The developmental stage at exposure, the chilling temperature and length of exposure all influenced the level of sterility. The early period of booting, and specifically the +4 cm auricle distance class, was the most sensitive and corresponded to meiosis within the anthers. The response of microtubules to chilling during meiosis in Hartog was monitored, but there was little difference between chilled and control plants. Other abnormalities, such as plasmolysis and cytomixis increased in frequency, were associated with death of developing pollen cells, and could contribute to loss of fertility. The potential for an above‐zero chilling sensitivity in Australian spring wheat varieties could have implications for exploring the tolerance of wheat flower development to chilling and freezing conditions in the field.     

Comparing genomic prediction accuracy from purebred,crossbred and combined purebred and crossbred reference populations in sheep

Background

The accuracy of genomic prediction depends largely on the number of animals with phenotypes and genotypes. In some industries, such as sheep and beef cattle, data are often available from a mixture of breeds, multiple strains within a breed or from crossbred animals. The objective of this study was to compare the accuracy of genomic prediction for several economically important traits in sheep when using data from purebreds, crossbreds or a combination of those in a reference population.

Methods

The reference populations were purebred Merinos, crossbreds of Border Leicester (BL), Poll Dorset (PD) or White Suffolk (WS) with Merinos and combinations of purebred and crossbred animals. Genomic breeding values (GBV) were calculated based on genomic best linear unbiased prediction (GBLUP), using a genomic relationship matrix calculated based on 48 599 Ovine SNP (single nucleotide polymorphisms) genotypes. The accuracy of GBV was assessed in a group of purebred industry sires based on the correlation coefficient between GBV and accurate estimated breeding values based on progeny records.

Results

The accuracy of GBV for Merino sires increased with a larger purebred Merino reference population, but decreased when a large purebred Merino reference population was augmented with records from crossbred animals. The GBV accuracy for BL, PD and WS breeds based on crossbred data was the same or tended to decrease when more purebred Merinos were added to the crossbred reference population. The prediction accuracy for a particular breed was close to zero when the reference population did not contain any haplotypes of the target breed, except for some low accuracies that were obtained when predicting PD from WS and vice versa.

Conclusions

This study demonstrates that crossbred animals can be used for genomic prediction of purebred animals using 50 k SNP marker density and GBLUP, but crossbred data provided lower accuracy than purebred data. Including data from distant breeds in a reference population had a neutral to slightly negative effect on the accuracy of genomic prediction. Accounting for differences in marker allele frequencies between breeds had only a small effect on the accuracy of genomic prediction from crossbred or combined crossbred and purebred reference populations.     

Cell Hybridization Study of Resistance to Alkylating Agents

5-Aziridinyl-2,4-Dinitrobenzamide (CB 1954) has been reported to be a highly selective inhibitor of the Walker tumour, with a therapeutic index of 60 (refs. 1 and 2). This compound, however, differs from other tumour inhibitory alkylating agents in that it is monofunctional and fails to inhibit the growth of several animal tumours which respond to difunctional alkylating agents. Compounds closely related in structure to CB 1954 are either much less active or inactive against the Walker tumour³. The structural specificity and biological properties of CB 1954 indicate that its mechanism of action is different from that of the tumour inhibitory difunctional alkylating agents. Whereas the latter are thought to be cytotoxic primarily as a result of their reaction with DNA, CB 1954 may interfere with a specific stage of purine biosynthesis². We have shown by cell hybridization that, unlike resistance to a difunctional alkylating agent, cellular resistance to CB 1954 is lost on fusion with a sensitive cell.     

Aspiration cytodiagnosis of pancreatic endocrine tumours

We have reviewed fine needle aspirates from 11 patients with pancreatic endocrine tumours and evaluated the diagnostic criteria as well as those proposed in the literature in an attempt to formulate reliable criteria for the cytological diagnosis of these tumours. As expected, no single criterion was reliable for diagnosis: however, cells with rounded or polygonal rather than a columnar shape, cytoplasmic granularity, and eccentricity of round or oval nuclei with a finely stippled, evenly distributed chromatin pattern were features which taken together, usually enabled one to make a reliable diagnosis. A striking feature of the smears was the cellular monotony and absence of pleomorphism of the tumour cells. Immunocytochemistry and electron microscopy identified tumour products and confirmed the diagnosis.     

The effect of partially resistant potato clones and aldicarb on the multiplication of the potato cyst nematode Globodera pallida in field trials

Potato cultivars with different degrees of resistance to Globodera pallida (PCN) were trialled at three infested sites in 1983, 1984 and 1985. These trials were primarily intended to assess the effects of PCN damage on the yield of tubers and consequently the sites chosen had high initial population densities of G. pallida. The population density of G. pallida was determined from samples taken both pre-planting and post-harvest and results showed that there were significant differences between the clones in the nematode multiplication rates. Although actual rates of multiplication varied between sites the relative differences between clones were maintained across sites. Under the susceptible control cultivars the populations generally increased even in the presence of nematicide. The partially resistant clones gave best control, as measured by nematode multiplication, at the sites with the highest initial population densities but gave good control at all sites when treated with nematicide irrespective of initial population density. The role of partial resistance in integrated control systems and the effectiveness of nematicides against G. pallida is discussed.