A combined bioinformatic approach oriented to the analysis and design of peptides with high affinity to MHC class I molecules

We report on a new method to compute the antigenic degree of peptides from available experimental data on peptide binding affinity to class I MHC molecules. The methodology is a combination of two strategies at different levels of information. The first, at the primary structure level, consists in expressing the peptides binding activity as a profile of amino acid contributions, amino acid similarity being accounted for by their characteristic physicochemical properties and their position within the sequence. The higher level of the strategy is based on a meticulous analysis of the contact interface of the peptides with the cleft constituting the receptor region of a particular class I MHC molecule. Interaction interfaces are inferred by docking the peptide onto the receptor groove of the MHC molecule; evaluation of the affinity of the peptide to the receptor is then performed by analysis of the electrostatic and hydrophobic energies on points of the interaction interface.The result is a robust system for analysis of peptide affinity to class I MHC molecules since while the first analysis dictates the composition of active sequences at the amino acid level, the second translates this information to the atomic level, where the molecular interaction can be analyzed in terms of the intrinsic interatomic forces and energies. Evaluation results for the methodology are encouraging since high affinity peptides are reflected by high scores at both levels of information, and are proportionally lower for peptides of medium and lower affinity for which interaction surfaces show relatively lower electrostatic complementarity and hydrophobic correlation than for the former.     

圈养猞猁多雄交配雄性的成功繁殖

研究了笼养猞猁多雄交配的结果以及雄性的成功繁殖。雄兽与发情雌兽随机配对,其繁殖成功(所产生的后代数量)不取决于与雌兽的交配顺序、交配次数与持续时间、遗传关系或雄兽的行为特征,但似乎取决于精子质量,特别是取决于形态正常精子的百分率。繁殖成功的雄兽比其竞争对手具有更多的形态正常的精子,似乎更能成功地诱发交配雌兽的排卵。证实了4窝(占总窝数的20%)幼兽的双重父亲身份。在所有情形下, 2雄1雌的交配间隔为24h 。     

Mating system, feeding type and ex situ conservation effort determine life expectancy in captive ruminants

Zoo animal husbandry aims at constantly improving husbandry, reproductive success and ultimately animal welfare. Nevertheless, analyses to determine factors influencing husbandry of different species are rare. The relative life expectancy (rLE; life expectancy (LE) as proportion of longevity) describes husbandry success of captive populations. Correlating rLE with biological characteristics of different species, reasons for variation in rLE can be detected. We analysed data of 166 901 animals representing 78 ruminant species kept in 850 facilities. The rLE of females correlated with the percentage of grass in a species' natural diet, suggesting that needs of species adapted to grass can be more easily accommodated than the needs of those adapted to browse. Males of monogamous species demonstrate higher rLE than polygamous males, which matches observed differences of sexual bias in LE in free-living populations and thus supports the ecological theory that the mating system influences LE. The third interesting finding was that rLE was higher in species managed by international studbooks when compared with species not managed in this way. Our method facilitates the identification of biological characteristics of species that are relevant for their husbandry success, and they also support ecological theory. Translating these findings into feeding recommendations, our approach can help to improve animal husbandry.     

Evolutionary history of the Paradoxurus palm civets – a new model for Asian biogeography

Aim Using molecular data and dental features, we investigated the genetic and morphological diversity among species of palm civets in the genus Paradoxurus, with a focus on the common palm civet, Paradoxurus hermaphroditus (Carnivora, Viverridae), in order to address biogeographic scenarios and provide recommendations for a taxonomic revision. Location Asia: Pakistan to the Lesser Sunda Islands. Methods We investigated the genetic diversity within Paradoxurus using two mitochondrial (cytochrome b, control region) and one nuclear (intron 7 of the β‐fibrinogen) markers. We used samples from 85 individuals of P. hermaphroditus (including 20 museum specimens) and one representative of each of the other species in the genus Paradoxurus: Paradoxurus jerdoni and Paradoxurus zeylonensis. DNA sequences were analysed using phylogenetic and haplotype network methods, and divergence dates were estimated for the clades retrieved. Furthermore, we examined dental characters from a large series of specimens and compared the morphological variation with the molecular data. Results Our phylogenetic analyses revealed that P. hermaphroditus is paraphyletic. We identified three major lineages distributed: (1) in the Indian subcontinent, south China, Hainan and in areas above 200 m in Indochina; (2) in Peninsular Malaysia, Java, Sumatra and in areas below 200 m in Indochina; and (3) in Borneo, the Philippines and the Mentawai archipelago. Our morphological observations were congruent with these three molecular lineages. Divergence date estimates inferred a Pliocene origin for Paradoxurus (2.8–5.7 Ma), with the three main clades diversifying from the mid–Early Pliocene to the end of the Pliocene. We suggest that the flooding of the Isthmus of Kra during the Pliocene was a major event shaping the diversification of Paradoxurus palm civets. We also hypothesize that the elevational segregation of the two lineages on the mainland could have resulted from the vegetational changes that were induced by Late Pliocene glacial episodes. Main conclusions The Isthmus of Kra is a major boundary between two major lineages of P. hermaphroditus. There is a need for a taxonomic revision for P. hermaphroditus, and we suggest that this species should be split into at least three species.     

Genetic structure of the Eurasian lynx population in north-eastern Poland and the Baltic states

We analyzed the genotypes of Eurasian lynx (Lynx lynx) from three populations in the westernmost part of the species main range. One population was situated at the distribution edge (NE Poland) and the two other (Latvia and Estonia) were located within the main, contiguous range of the species. The aim was to determine if the genetic composition varied among these populations and if there was evidence of isolation among them. Based on microsatellite allele frequencies, we found the allelic richness in Polish lynx to be lower than that in lynx from Latvia and Estonia. We also found significant differentiation among the lynx populations, with the NE Poland population forming a distinct genetic group relative to the two other populations (R _ST = 0.15 and 0.22, P < 0.0001). We suggest that genetic differentiation among lynx populations is the result of habitat insularisation that limits gene flow. This finding emphasizes the necessity to consider the lynx genetic differentiation in conservation planning of this species in Poland.     

Follicle-stimulating hormone receptor in felids: intra- and interspecies variation

Assisted reproductive technologies are increasingly applied to support breeding efforts for many endangered felids. To explain the highly variable responses among felids to exogenous gonadotropins (FSH, eCG), we analyzed a 567bp fragment spanning a hyper-variable region of the FSH receptor in the domestic cat (catFSHR) and nine wild felid species/subspecies (felFSHR). Phylogenetic analysis indicated that the newly sequenced felFSHRs, together with the bear FSHR, belong to the carnivore group closely related to the ungulate clade. Within Felidae, genetic distances were 0.0089 +/- 0.0018 for nucleotide and 0.0183 +/- 0.0044 for amino acid (aa) sequences. In pairwise comparisons among catFSHR and all new felFSHRs, similarity ranged from 98.6 to 99.5% for nucleotides and from 97.4 to 98.9% for aa. Besides interspecies variability, intraspecies variation was also detected on both the cDNA and the protein level. There were no indications for an expression of tissue-specific isoforms of FSHR in testis and ovary.     

Higher masseter muscle mass in grazing than in browsing ruminants

Using cranioskeletal measurements, several studies have generated evidence that grazing ruminants have a more pronounced mastication apparatus, in terms of muscle insertion areas and protuberances, than browsing ruminants, with the resulting hypothesis that grazers should have larger, heavier chewing muscles than browsers. However, the only investigation of this so far [Axmacher and Hofmann (J Zool 215:463-473, 1988)] did not find differences between ruminant feeding types in the masseter muscle mass of 22 species. Here, we expand the dataset to 48 ruminant species. Regardless of phylogenetic control in the statistical treatment, there was a significant positive correlation of body mass and masseter mass, and also a significant association between percent grass in the natural diet and masseter mass. The results support the concept that ruminant species that ingest more grass have relatively larger masseter muscles, possibly indicating an increased requirement to overcome the resistance of grass forage. The comparative chewing resistance of different forage classes may represent a rewarding field of ecophysiological research.