Site-specific racemization in aging alpha A-crystallin

Of all aspartyl residues in bovine alpha A-crystallin, only Asp-151 exhibits pronounced racemization. Asp-151 is also one of the sites where peptide bond cleavage occurs in in vivo aging alpha A-crystallin. This aspartyl residue is followed by an alanyl residue and resides in a flexible carboxyl terminal extension of alpha-crystallin. Both in vivo and in vitro racemization studies indicate that the pronounced and site-specific racemization of Asp-151 proceeds via formation of a succinimide intermediate. The in vivo racemization of aspartyl residues in alpha A-crystallin is discussed with regard to the proposed tertiary structure of alpha-crystallin.     

A high‐density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour

High‐density SNP microarrays (“SNP chips”) are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this article, we describe the development and application of a high‐density Affymetrix Axiom chip with around 500,000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per‐SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation. The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genomewide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays; (ii) detecting SNPs by more than one pipeline, and in independent data sets, ensures a high proportion of working assays; (iii) allele frequency ascertainment bias is minimized by performing SNP discovery in individuals from multiple populations; and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.     

A consensus linkage map for swine chromosome 7

The First International Workshop on Swine Chromosome 7 (SSC7) was held in Minnesuing, Wisconsin, USA on 21–24 September 1995. The objective was to develop a comprehensive linkage map for porcine chromosome 7 by combining genotypic data from four swine reference populations. Contributions of genotypic data were made from the US Meat Animal Research Center, the University of Minnesota, the PiGMaP consortium and the Scandinavian consortium. Primers for selected sequence tagged site markers, to be genotyped across the reference populations, were exchanged to integrate individual maps of SSC7. Eighty-six loci were genotyped; these loci represented microsatellite, minisatellite, single-strand conformation polymorphism, restriction fragment length polymorphism, erythrocyte antigen and protein polymorphisms. Eighteen genes were mapped, including 12 markers within class I, class II and class III regions (four markers in each class) of the swine major histocompatibility complex. Forty-two markers were either genotyped on more than one population or were included in a haplotype system and used to develop skeletal linkage maps that spanned 147·6, 212·7 and 179·5 cM for the male, female and sex-average maps, respectively. A comprehensive linkage map was developed incorporating those markers with more than 30 informative meioses. The comprehensive map was slightly longer than the skeletal map, at 153·3, 215·3 and 183·8 cM, respectively, with only three intervals greater than 10 cM. These results significantly improve the genetic resolution of the porcine chromosome 7 map and represent an accurate approach for the merging of genetic maps produced in different reference populations.     

GO‐FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO‐FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass‐roots organization formed to advance the annotation of newly assembled genomes of domesticated and non‐model organisms ( www.faang.org ). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org . In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO‐FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta‐data analysis standards were established.     

Genomic diversity and differentiation of a managed island wild boar population

The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (F_ST=0.126–0.138), and from DP (F_ST=0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, F_ST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status.     

Lucky rugose corals on crinoid stems: unusual examples of subepidermal epizoans from the Devonian of Morocco

Berkowski, B & Klug, C. 2011: Lucky rugose corals on crinoid stems: unusual examples of subepidermal epizoans from the Devonian of Morocco. Lethaia, Vol. 45, pp. 24–33. In the fossil record, evidence for true epizoans, i.e. living animals inhabiting other living host‐animals, is rather rare. A host reaction is usually needed to proof the syn vivo‐settling of the epizoan. Herein, we provide a first report of such an epizoan biocoenosis from various strata of the Early Devonian of Hamar Laghdad, the world‐renowned Moroccan mud‐mound locality. In this case, solitary rugose corals settled as larvae on crinoid stems, perhaps at a spot where the epidermis was missing for some reason (injury, disease). Both the crinoid and the coral began to grow around each other. By doing so, the affected crinoid columnals formed a swelling, where ultimately only an opening slightly larger than the coral orifice remained. We discuss both macroecological and small‐scale synecological aspects of this biocoenosis. The coral profited from its elevated home because it reached into more rapid currents providing the polyp with more food than at the densely populated seafloor, which was probably covered by a coral‐meadow around the mounds and hydrothermal vents. □Corals, crinoids, Early Devonian, epizoans, Morocco, Rugosa.     

Meta-analysis of the literature on diagnostic accuracy of SPECT in parkinsonian syndromes

Background  

Parkinson's disease (PD) is the second most common neurodegenerative disorder. One of the most widely used techniques to diagnose PD is a Single Photon Emission Computer Tomography (SPECT) scan to visualise the integrity of the dopaminergic pathways in the brain. Despite this there remains some discussion on the value of SPECT in the differential diagnosis of PD. We did a meta-analysis of all the existing literature on the diagnostic accuracy of both pre- and post-synaptic SPECT imaging in the differential diagnosis of PD.