The Integrating Network Objects with Hierarchies (INOH) database is a highly structured, manually curated database of signal transduction pathways including Mammalia, Xenopus laevis, Drosophila melanogaster, Caenorhabditis elegans and canonical. Since most pathway knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable...

Little is known about the origin and long-term evolutionary mode of retroviruses. Retroviruses can integrate into their hosts' genomes, providing a molecular fossil record for studying their deep history. Here we report the discovery of an endogenous foamy virus-like element, which we designate 'coelacanth endogenous foamy-like virus' (CoeEFV), within the genome of the coelacanth (Latimeria cha...

End sequencing of random BAC clones from a Hydractinia symbiolongicarpus (Cnidaria: Hydrozoa) genomic library revealed a gene across a approximately 37.5kb region of the H. symbiolongicarpus genome sharing highest sequence identity and domain architecture to mammalian polydom that we in turn named cnidarian polydom (CnPolydom). Sharing all eight domain types characteristic of polydom and organi...

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker...

An inquiry into the biological meaning of the human amniotic fluid demands, first of all, a sufficient knowledge of its physical properties and chemical composition, information which many investigators have attempted to gain. Prochownick (1) studied the sodium chloride, solid substances, and urea in the amniotic fluid; Schroeder (2) determined the quantities of solid substances, ash, and album...

TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains (DBDs), available online at http://tfclass.bioinf.med.uni-goettingen.de. The classification scheme of TFClass was originally derived for human TFs and is expanded here to the whole taxonomic class of mammalia. Combining information from different resources, checking manually the r...

We examine the relationship between mesowear variables and carbon and nitrogen isotopes in 16 species of African antelope (Mammalia: Bovidae). We show significant differences in carbon and nitrogen isotope values between individuals exhibiting sharp versus round cusps, and high versus low occlusal relief. We show significant correlations between mesowear variables and both carbon and nitrogen i...

Positive selection is usually considered in the context of a higher rate of substitutions in non-synonymous as compared to synonymous sites in complete coding sequences of genes or individual positions. We show that genes conserved in eukaryota, coelomata, and bilateria, that is, proteins that arose earlier in evolution as compared to mammalia specific genes evolve slowly and are subjected to n...

DNA barcoding provides an operational framework for mammalian taxonomic identification and cryptic species discovery. Focused effort to build a reference library of genetic data has resulted in the assembly of over 35 K mammalian cytochrome c oxidase subunit I sequences and outlined the scope of mammal-related barcoding projects. Based on the above experience, this chapter recounts three typica...

This paper analyzed representatives of the class Mammalia on International Union for Conservation Nature’s (IUCN) Red List threatened species and evaluated whether Protected Areas have fulfilled their function protecting habitats. In literature review, were found to be part programs protection recovery species. However, these areas continue insufficient due increasing destruction caused by huma...