Canine population structure: assessment and impact of intra-breed stratification on SNP-based association studies

Background

In canine genetics, the impact of population structure on whole genome association studies is typically addressed by sampling approximately equal numbers of cases and controls from dogs of a single breed, usually from the same country or geographic area. However one way to increase the power of genetic studies is to sample individuals of the same breed but from different geographic areas, with the expectation that independent meiotic events will have shortened the presumed ancestral haplotype around the mutation differently. Little is known, however, about genetic variation among dogs of the same breed collected from different geographic regions.

Methodology/Principal Findings

In this report, we address the magnitude and impact of genetic diversity among common breeds sampled in the U.S. and Europe. The breeds selected, including the Rottweiler, Bernese mountain dog, flat-coated retriever, and golden retriever, share susceptibility to a class of soft tissue cancers typified by malignant histiocytosis in the Bernese mountain dog. We genotyped 722 SNPs at four unlinked loci (between 95 and 271 per locus) on canine chromosome 1 (CFA1). We showed that each population is characterized by distinct genetic diversity that can be correlated with breed history. When the breed studied has a reduced intra-breed diversity, the combination of dogs from international locations does not increase the rate of false positives and potentially increases the power of association studies. However, over-sampling cases from one geographic location is more likely to lead to false positive results in breeds with significant genetic diversity.

Conclusions

These data provide new guidelines for association studies using purebred dogs that take into account population structure.     

Lateral diffusion of CO2 in leaves is not sufficient to support photosynthesis

Lateral diffusion of CO(2) was investigated in photosynthesizing leaves with different anatomy by gas exchange and chlorophyll a fluorescence imaging using grease to block stomata. When one-half of the leaf surface of the heterobaric species Helianthus annuus was covered by 4-mm-diameter patches of grease, the response of net CO(2) assimilation rate (A) to intercellular CO(2) concentration (C(i)) indicated that higher ambient CO(2) concentrations (C(a)) caused only limited lateral diffusion into the greased areas. When single 4-mm patches were applied to leaves of heterobaric Phaseolus vulgaris and homobaric Commelina communis, chlorophyll a fluorescence images showed dramatic declines in the quantum efficiency of photosystem II electron transport (measured as F(q)'/F(m)') across the patch, demonstrating that lateral CO(2) diffusion could not support A. The F(q)'/F(m)' values were used to compute images of C(i) across patches, and their dependence on C(a) was assessed. At high C(a), the patch effect was less in C. communis than P. vulgaris. A finite-volume porous-medium model for assimilation rate and lateral CO(2) diffusion was developed to analyze the patch images. The model estimated that the effective lateral CO(2) diffusion coefficients inside C. communis and P. vulgaris leaves were 22% and 12% of that for free air, respectively. We conclude that, in the light, lateral CO(2) diffusion cannot support appreciable photosynthesis over distances of more than approximately 0.3 mm in normal leaves, irrespective of the presence or absence of bundle sheath extensions, because of the CO(2) assimilation by cells along the diffusion pathway.     

Bird terrestrial locomotion as revealed by 3D kinematics

Most birds use at least two modes of locomotion: flying and walking (terrestrial locomotion). Whereas the wings and tail are used for flying, the legs are mainly used for walking. The role of other body segments remains, however, poorly understood. In this study, we examine the kinematics of the head, the trunk, and the legs during terrestrial locomotion in the quail (Coturnix coturnix). Despite the trunk representing about 70% of the total body mass, its function in locomotion has received little scientific interest to date. This prompted us to focus on its role in terrestrial locomotion. We used high-speed video fluoroscopic recordings of quails walking at voluntary speeds on a trackway. Dorso-ventral and lateral views of the motion of the skeletal elements were recorded successively and reconstructed in three dimensions using a novel method based on the temporal synchronisation of both views. An analysis of the trajectories of the body parts and their coordination showed that the trunk plays an important role during walking. Moreover, two sub-systems participate in the gait kinematics: (i) the integrated 3D motion of the trunk and thighs allows for the adjustment of the path of the centre of mass; (ii) the motion of distal limbs transforms the alternating forward motion of the feet into a continuous forward motion at the knee and thus assures propulsion. Finally, head bobbing appears qualitatively synchronised to the movements of the trunk. An important role for the thigh muscles in generating the 3D motion of the trunk is suggested by an analysis of the pelvic anatomy.     

Characteristics and Genetic Determinants of Bacteriocin Activities Produced by Carnobacterium piscicola CP5 Isolated from Cheese

Carnobacterium piscicola CP5, isolated from a French mold-ripened soft cheese, produced a bacteriocin activity named carnocin CP5, which inhibited Carnobacterium, Enterococcus and Listeria spp. strains, and among the Lactobacillus spp. only Lactobacillus delbrueckii spp. [24]. The activity was purified by ammonium sulfate precipitation, anion exchange, and hydrophobic interaction chromatography followed by reverse-phase high-performance liquid chromatography (RP-HPLC). This latter step separated two peaks with anti-listerial activity (CP51 and CP52). Carnocin CP51 was partially sequenced, and the N-terminal part revealed the presence of the “pediocin-like consensus” sequence-Tyr-Gly-Asn-Gly-Val-. Then, a degenerated 24-mer oligonucleotide probe was constructed from the N-terminal sequence and used to detect the structural gene. It was localized on a plasmid of about 40 kb. Cloning of restriction fragments of this one, followed by DNA sequencing, revealed the presence of the second anti-Listeria bacteriocin gene (CP52). By comparing sequences in data banks and confirming results with PCR reactions, carnocin CP51 shared homologies with carnobacteriocin BM1, and carnocin CP52 was similar to carnobacteriocin B2, both produced by C. piscicola LV17 [2]. However, carnobacteriocin A from C. piscicola LV17 gene was lacking in C. piscicola CP5, and the two microorganisms have been isolated from different ecological environments: C. piscicola CP5 and C. piscicola LV17 were isolated from soft cheese and vacuum-packed meat respectively. This fact could allow different application perspectives for C. piscicola CP5. Received: 16 April 1997 / Accepted: 9 May 1997     

Contribution to the analysis of gaits: practical elements to complement the Hildebrand method

This paper suggests three additions to the Hildebrand method for gait-pattern specification. The first allows an extension of this method by the use of the forelimb as reference. Thus, dataset could be gathered indifferently from fore or hindlimbs cycles to identify a symmetrical gait or compare gaits of diverse species. On the basis of Hildebrand's definitions, the second suggestion permits to check the proportion of symmetrical and asymmetrical gaits adopted by different individuals of one or different species. The third addition makes a graphical clear-cut between four basic modes of gallops: rotary, transverse, half-bound and bound. These additions will facilitate extensive data comparison either to evaluate the range of variation within a single species or to specify the preferred gaits in diverse species.     

A new target capture phylogeny elucidates the systematics and evolution of wing coupling in sack-bearer moths

The frenulum is a wing coupling structure that is found on the wings of most families of Lepidoptera. It is a single bristle or set of bristles that originate from the base of the hindwing that often interlocks with the forewing during flight. This wing coupling mechanism is thought to have been a major evolutionary innovation that allowed for enhanced flight in Lepidoptera. The sack-bearer moths (Mimallonidae) are unusual among Lepidoptera in that not all species within the family have a frenulum. We test the hypothesis that the frenulum is not necessary and is therefore lost in mimallonids that have longer male forewings, because such wings are perhaps better suited to be coupled by other means. To understand the evolution of the frenulum, we inferred the most taxonomically and genetically sampled anchored hybrid enrichment-based phylogeny of Mimallonidae, including 604 loci from all 41 genera and from 120 species, covering about 40% of the described species in the family. The maximum likelihood tree robustly supports major relationships within the family, and ancestral state reconstruction clearly recovers the frenulum as the plesiomorphic condition in Mimallonidae. Our results show that the frenulum is more often observed in species that have shorter, rather than longer, male forewings. The frenulum has historically been used as an important character for intrafamilial classification in Mimallonidae, but our results conclusively show that this character system is more variable than previously thought. Based on our results, we erect two new subfamilies, Roelofinae St Laurent & Kawahara, subfam.n. and Meneviinae St Laurent, Herbin, & Kawahara, subfam.n. , for four genera previously considered incertae sedis. In the predominantly frenulum-lacking clade Cicinninae, we describe a new genus, Cerradocinnus St Laurent, Mielke, & Kawahara, gen.n. , and the genus Gonogramma stat. rev. is revalidated to include many species previously placed in Cicinnus sensu lato. With these changes, Cicinnus can now be considered monophyletic. Thirty-three species are transferred to Gonogramma from Cicinnus sensu lato. This published work has been registered on Zoobank, http://zoobank.org/urn:lsid:zoobank.org:pub:E33100E1-DA6A-4814-A312-36CBAA168B8B .     

A comparative study between a brain Na+,K(+)-ATPase inhibitor (endobain E) and ascorbic acid

In the search of Na⁺,K⁺-ATPase modulators, we have reported the isolation by gel filtration and HPLC of a brain fraction, termed endobain E, which highly inhibits Na⁺,K⁺-ATPase activity. In the present study we compared some properties of endobain E with those of ascorbic acid. Kinetic experiments assaying synaptosomal membrane K⁺-p-nitrophenylphosphatase (K⁺-p-NPPase) activity in the presence of endobain E or ascorbic acid showed that in neither case did enzyme inhibition prove competitive in nature versus K⁺ or p-NPP concentration. At pH 5.0, endobain E and ascorbic acid maximal UV absorbance was 266 and 258 nm, respectively; alkalinization to pH 14.0 led to absorption drop and shift for endobain E but to absorbance disappearance for ascorbic acid. After cysteine treatment, endobain E absorbance decreased, whereas that of ascorbic acid remained unaltered; iodine treatment led to absorbance drop and shift for endobain E but to absorbance disappearance for ascorbic acid. HPLC analysis of endobain E disclosed the presence of two components: one eluting with retention time and UV spectrum indistinguishable from those of ascorbic acid and a second, as yet unidentified, both exerting Na⁺,K⁺-ATPase inhibition.