Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.     

Lack of correlation between the levels of soluble cytotoxic T-lymphocyte associated antigen-4 (CTLA-4) and the CT-60 genotypes

Background

Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) plays a critical role in downregulation of antigen-activated immune response and polymorphisms at the CTLA-4 gene have been shown to be associated with several autoimmune diseases including type-1 diabetes (T1D). The etiological mutation was mapped to the CT60-A/G single nucleotide polymorphism (SNP) that is believed to control the processing and production of soluble CTLA-4 (sCTLA-4).

Methods

We therefore determined sCTLA-4 protein levels in the sera from 82 T1D patients and 19 autoantibody positive (AbP) subjects and 117 autoantibody negative (AbN) controls using ELISA. The CT-60 SNP was genotyped for these samples by using PCR and restriction enzyme digestion of a 268 bp DNA segment containing the SNP. Genotyping of CT-60 SNP was confirmed by dye terminating sequencing reaction.

Results

Higher levels of sCTLA-4 were observed in T1D (2.24 ng/ml) and AbP (mean = 2.17 ng/ml) subjects compared to AbN controls (mean = 1.69 ng/ml) with the differences between these subjects becoming significant with age (p = 0.02). However, we found no correlation between sCTLA-4 levels and the CTLA-4 CT-60 SNP genotypes.

Conclusion

Consistent with the higher serum sCTLA-4 levels observed in other autoimmune diseases, our results suggest that sCTLA-4 may be a risk factor for T1D. However, our results do not support the conclusion that the CT-60 SNP controls the expression of sCTLA-4.

     

Investigation of co‐infections with pathogens associated with gill disease in Atlantic salmon during an amoebic gill disease outbreak

Gill diseases are a complex and multifactorial challenge for marine farmed Atlantic salmon. Co‐infections with putative pathogens are common on farms; however, there is a lack of knowledge in relation to the potential effect co‐infections may have on pathology. The objective of this study was to determine the prevalence and potential effects of Neoparamoeba perurans, Desmozoon lepeophtherii, Candidatus Branchiomonas cysticola, Tenacibaculum maritimum and salmon gill poxvirus (SGPV) during a longitudinal study on a marine Atlantic salmon farm. Real‐time PCR was used to determine the presence and sequential infection patterns of these pathogens on gill samples collected from stocking until harvest. A number of multilevel models were used to determine the effect of these putative pathogens on gill health (measured as gill histopathology score), while adjusting for the effect of water temperature and time since the last freshwater treatment. Results indicate that between 12 and 16 weeks post‐seawater transfer (wpst), colonization of the gills by all pathogens had commenced and by week 16 of marine production each of the pathogens had been detected. D. lepeophtherii and Candidatus B. cysticola were by far the most prevalent of the potential pathogens detected during this study. Detections of T. maritimum were found to be significantly correlated with temperature showing distinct seasonality. Salmon gill poxvirus was found to be highly sporadic and detected in the first sampling point, suggesting a carryover from the freshwater stage of production. Finally, the model results indicated no clear effect between any of the pathogens. Additionally, the models showed that the only variable which had a consistent effect on the histology score was N. perurans.     

Association of KASP markers with Hessian fly resistance in wheat of diverse origin

Hessian fly (Mayetiola destructor (Say)) is a major pest in wheat producing areas of United States, Canada, Europe, and North Africa but has not been found in Australia. Host plant resistance is thought to involve a similar strategy used against plant pathogen, and in this study, we sought to investigate whether disease-resistance gene markers can also be useful in selecting against Hessian fly attack. The genome-wide association study involved 251 wheat genotypes of diverse origin and 72 SNPs, selected on the basis of significant similarity of their associated contig sequences to putative disease resistance genes. A novel statistical approach for genome-wide scan was applied, which utilised genotype data scored as Null alleles in the mixed model, instead of deleting or treating them as missing alleles. The analyses identified four markers with significant associations at the 5% level, after applying the false discovery rate. These were located on chromosomes 4A, 4B, 5A and 7D, with the 5A locus mapping to the cluster of major genes that confer resistance to multiple Hessian fly biotypes. Amongst the diverse wheat accessions analysed, most of the susceptible phenotypes carried the A–G–C–C haplotype at the BS00064369, BS00007416, BS00077047 and HfrDrd_nt_143 loci, respectively. When heterozygotes were excluded, all the Australian wheat accessions carried this allelic combination. The combination of alleles conferring resistance depended on the origin of the wheat accessions, with ICARDA accessions carrying a preponderance of the C–C–CG–T. Of the 11 USA accessions used for this study, only Lola carried a favourable combination of alleles for resistance at these loci.     

Changes in Ghanaian farming systems: stagnation or a quiet transformation?

This research was designed to understand better the patterns of agricultural intensification and transformation occurring in Africa south of the Sahara using the Ghanaian case. The paper examines changes in farming systems and the role of various endogenous and exogenous factors in driving the conversion of arable lands to agricultural uses in four villages within two agro-ecologically distinct zones of Ghana: the Guinea Savannah and Transition zones. Using historical narratives and land-cover maps supplemented with quantitative data at regional levels, the research shows that farming has intensified in the villages, as farmers increased their farm size in response to factors such as population growth, market access, and changing rural lifestyle. The overall trend suggests a gradual move toward intensification through increasing use of labor-saving technologies rather than land-saving inputs—a pattern that contrasts with Asia’s path to its Green Revolution. The findings in this paper provide evidence of the dynamism occurring in African farming systems; hence, they point toward a departure from stagnation narratives that have come to prevail in the debate on agricultural transformation and intensification in Africa south of the Sahara. We conclude that it is essential for future research to expand the scope of this work, while policies should focus on lessons learned from these historical processes of genuine change and adaptation.