Sequence variation in the guillemot (Alcidae: Cepphus) mitochondrial control region and its nuclear homolog

We describe sequence variation in the mitochondrial control region and its nuclear homolog in three species and seven subspecies of guillemots (Cepphus spp.). Nuclear homologs of the 5' end of the control region were found in all individuals. Nuclear sequences were approximately 50% divergent from their mitochondrial counterparts and formed a distinct phylogenetic clade; the mitochondrial-nuclear introgression event must have predated the radiation of Cepphus. As in other vertebrates, the guillemot control region has a relatively conserved central block flanked by hypervariable 5' and 3' ends. Mean pairwise interspecific divergence values among control regions were lower than those in other birds. All individuals were heteroplasmic for the number of simple tandem nucleotide repeats (A(n)C) at the 3' end of the control region. Phylogenetic analyses suggest that black guillemots are basal to pigeon and spectacled guillemots, but evolutionary relationships among subspecies remain unresolved, possibly due to incomplete lineage sorting. Describing molecular variation in nuclear homologs of mitochondrial genes is of general interest in phylogenetics because, if undetected, the homologs may confound interpretations of mitochondrial phylogenies.      

Implications from predictions of HLA-DRB1 binding peptides in the membrane proteins of Corynebacterium diphtheriae

The aerobic gram positive bacterium Corynebacterium diphtheriae causes diphtheria, a respiratory tract illness characterized by symptoms such as sore throat, low fever, and an adherent membrane on the tonsils, pharynx, and/or nasal cavity. Therefore, it is important to develop preventive vaccines for diphtheria. The availability of the 2,488,635 bp long complete sequence for the C. diphtheriae genome provides an opportunity to understand cell mediated immune response using Computational Biology tools from the bacterial proteome sequence data. We selected 355 membrane proteins from the C. diphtheriae proteome using annotation data to identify potential HLA-DRB1 binding short peptide using modeling, simulations and predictions. This exercise identified 30 short peptides in membrane proteins showing binding capability to HLA-DRB1 alleles. These peptides serve as outline for the understanding of cell mediated immune response to C. diphtheriae. It should be noted that the predicted data to be verified using binding assays for further consideration.     

A quantitative assessment of bone area increase due to ornamentation in the Crocodylia

Bone ornamentation, in the form of highly repetitive motives created by pits and ridges, is a frequent feature on vertebrate skull roofs and osteoderms. The functional significance of this character remains a matter of controversy and speculation. The many diverging hypotheses proposed to explain it all share a common logical prerequisite: bone ornamentation should increase significantly the surface area of the bones that bear it. In order to test this assumption in the Crocodylia, we developed a method for quantifying the gain in area due to ornamentation using a three‐dimensional‐surface scanner. On crocodylian osteoderms, the gain in area can be up to 40%, and on the cranial table, it ranges between 10 and 32% in adult specimens (in both cases, it shows substantial differences between the adults of the various species included in the sample). Area gain on the snout is lesser (0–20% in adults), and more variable between species. In general, bone ornamentation is less pronounced, and results in fewer area gains in juvenile specimens. The main morphometric results yielded by this study are discussed in reference to the few comparative data available hitherto, and to the functional interpretations proposed by previous authors. J. Morphol. 276:1183–1192, 2015. © 2015 Wiley Periodicals, Inc.