Osteoporosis attacks 10% of the population worldwide. Humans or even the model animals of the disease cannot recover from porous bone. Regeneration in skeletal elements is the unique feature of our newly investigated osteoporosis model, the red deer (Cervus elaphus) stag. Cyclic physiological osteoporosis is a consequence of the annual antler cycle. This phenomenon raises the possibility to identify genes involved in the regulation of bone mineral density on the basis of comparative genomics between deer and human. We compare gene expression activity of osteoporotic and regenerating rib bone samples versus autumn dwell control in red deer by microarray hybridization. Identified genes were tested on human femoral bone tissue from non-osteoporotic controls and patients affected with age-related osteoporosis. Expression data were evaluated by Principal Components Analysis and Canonical Variates Analysis. Separation of patients into a normal and an affected group based on ten formerly known osteoporosis reference genes was significantly improved by expanding the data with newly identified genes. These genes include IGSF4, FABP3, FABP4, FKBP2, TIMP2, TMSB4X, TRIB, and members of the Wnt signaling. This study supports that extensive comparative genomic analyses, here deer and human, provide a novel approach to identify new targets for human diagnostics and therapy.

Aminoacyl tRNA synthetases (aaRS) are grouped into Class I and II based on primary and tertiary structure and enzyme properties suggesting two independent phylogenetic lineages. Analogously, tRNA molecules can also form two respective classes, based on the class membership of their corresponding aaRS. Although some aaRS–tRNA interactions are not extremely specific and require editing mechanisms to avoid misaminoacylation, most aaRS–tRNA interactions are rather stereospecific. Thus, class-specific aaRS features could be mirrored by class-specific tRNA features. However, previous investigations failed to detect conserved class-specific nucleotides. Here we introduce a discrete mathematical approach that evaluates not only class-specific ‘strictly present’, but also ‘strictly absent’ nucleotides. The disjoint subsets of these elements compose a unique partition, named extended consensus partition (ECP). By analyzing the ECP for both Class I and II tDNA sets from 50 (13 archaeal, 30 bacterial and 7 eukaryotic) species, we could demonstrate that class-specific tRNA sequence features do exist, although not in terms of strictly conserved nucleotides as it had previously been anticipated. This finding demonstrates that important information was hidden in tRNA sequences inaccessible for traditional statistical methods. The ECP analysis might contribute to the understanding of tRNA evolution and could enrich the sequence analysis tool repertoire.

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Previous morphological studies showed that the description of the Cyclotella genus was too general and according to new morphological criteria new genera were established based on both recent and fossil taxa (e.g. Discostella, Handmannia, Puncticulata, Tertiarius). Furthermore, previous molecular biological investigations proved that the Cyclotella genus was not monophyletic. Integrating the above mentioned knowledge the former Cyclotella genus has been split into 4 genera (Cyclotella s.s., Discostella, Tertiarius and Lindavia). Based on the position of rimoportula Lindavia genus was formed for involving the species of both the Cyclotella ocellata and C. bodanica lineages. Our morphological and molecular (genetic distance and phylogenetic analyses of rbcL and 18S rDNA sequences) investigations suggested that "Lindavia/Cyclotella ocellata group" could be raised from the Lindavia as a separate genus. Its distinctive morphological features are the followings: striae unequal in length, central area without areolae. We describe the new genus Pantocsekiella gen. nov. and we transferred several Lindavia taxa into it. We also provide an amended diagnosis for the genus Lindavia.

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