Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples

DNA studies of endangered or extinct species often rely on ancient or degraded remains.The majority of ancient DNA(aDNA)extraction protocols focus on skeletal elements,with skin and hair samples rarely explored.Similar to that found in bones and teeth,DNA extracted from historical or ancient skin and fur samples is also extremely fragmented with low endogenous content due to natural degradation processes.Thus,the development of effective DNA extraction methods is required for these materials.Here,we compared the performance of two DNA extraction protocols(commercial and custom laboratory aDNA methods)on hair and skin samples from decades-old museum specimens to Iron Age archaeological material.We found that apart from the impact sample-specific taphonomic and handling history has on the quantity and quality of DNA preservation,skin yielded more endogenous DNA than hair of the samples and protocols tested.While both methods recovered DNA from ancient soft tissue,the laboratory method performed better overall in terms of DNA yield and quality,which was primarily due to the poorer performance of the commercial binding buffer in recovering aDNA.

Expression of BSE-associated proteins in the CNS and lymphoreticular tissues of cattle and buffalo

Bovine spongiform encephalopathy(BSE),which has been documented in 190,000 cases of BSE-infected cattle,to our knowledge,has not been reported in buffalo.Prion protein(PrP) is critical to susceptibility and development of BSE.Moreover,a new PrP-like protein,Shadoo(Sho),has been shown to have overlapping expression patterns and shared functions with PrP.Therefore,we hypothesize that differences in expression at the transcriptional level and/or the post-transcriptional level of the two genes may be associated with these specific differences between cattle and buffalo.We compared the relative mRNA expression of the prion protein gene(PRNP) and the Shadoo gene(SPRN) in 3% RNA samples using real-time PCR.We also analyzed PrP/Sho protein from 96 samples by Western blot.Our results demonstrated significantly lower PrP expression in the cerebellum,obex,mesenteric lymph node,and bronchial lymph node tissues,but higher relative expression of Sho in the cerebrum and spleen in buffalos compared with catties.Although these results support our primary assumption,Sho and PrP expressions did not correlate with corresponding mRNA expression,suggesting that the biological modulations of both PrP and Sho proteins are at post-translational levels.Moreover,positive correlations between PRNP and SPRN were found in cattle and buffalo cerebrum as well as in buffalo obex.Conversely,negative correlations between PrP and Sho were detected in buffalo cerebellum and obex tissues.These findings suggest that additional post-transcriptional studies are warranted to elucidate mechanisms behind prion diseases.

Associations of autozygosity with economic important traits in a cross of Eurasian pigs

Inbreeding depression(ID)refers to the undesirable effects of inbreeding(mating of relatives)on fitness-associated phenotypes(Charlesworth and Willis,2009).ID on production,reproduction,and health traits is relevant to industrial profitability,making it important in animal management.Runs of homozygosity(ROH)is a good measure of inbreeding and autozygosity(the inheritance of two copies of an ancestral allele)(Alkuraya,2013).