Computational protein function prediction: Are we making progress?

The computational prediction of gene and protein function is rapidly gaining ground as a central undertaking in computational biology. Making sense of the flood of genomic data requires fast and reliable annotation. Many ingenious algorithms have been devised to infer a protein's function from its amino acid sequence, 3D structure and chromosomal location of the encoding genes. However, there are significant challenges in assessing how well these programs perform. In this article we explore those challenges and review our own attempt at assessing the performance of those programs. We conclude that the task is far from complete and that a critical assessment of the performance of function prediction programs is necessary to make true progress in computational function prediction.     

Cellular internalization of proinsulin C-peptide

Proinsulin C-peptide is known to bind specifically to cell membranes and to exert intracellular effects, but whether it is internalized in target cells is unknown. In this study, using confocal microscopy and immunostained or rhodamine-labeled peptide, we show that C-peptide is internalized and localized to the cytosol of Swiss 3T3 and HEK-293 cells. In addition, transport into nuclei was found using the labeled peptide. The internalization was followed at 37°C for up to 1 h, and was reduced at 4°C and after preincubation with pertussis toxin. Hence, it is concluded to occur via an energy-dependent, pertussis toxin-sensitive mechanism and without detectable degradation within the experimental time course. Surface plasmon resonance measurements demonstrated binding of HEK-293 cell extract components to C-peptide, and subsequent elution of bound material revealed the components to be intracellular proteins. The identification of C-peptide cellular internalization, intracellular binding proteins, absence of rapid subsequent C-peptide degradation and apparent nuclear internalization support a maintained activity similar to that of an intracrine peptide hormone. Hence, the data suggest the possibility of one further C-peptide site of action. Received 31 October 2006; received after revision 27 December 2006; accepted 30 December 2006     

Telomeres and meiosis in health and disease

Beyond their role in replication and chromosome end capping, telomeres are also thought to function in meiotic chromosome pairing, meiotic and mitotic chromosome segregation as well as in nuclear organization. Observations in both somatic and meiotic cells suggest that the positioning of telomeres within the nucleus is highly specific and believed to be dependent mainly on telomere interactions with the nuclear envelope either directly or through chromatin interacting proteins. Although little is known about the mechanism of telomere clustering, some studies show that it is an active process. Recent data have suggested a regulatory role for telomere chromatin structure in telomere movement. This review will summarize recent studies on telomere interactions with the nuclear matrix, telomere chromatin structure and factors that modify telomere chromatin structure as related to regulation of telomere movement.     

New findings of Hexalona-branch representatives in Brazil,with a description of Prenda gen. nov. (Crustacea: Anomopoda: Aloninae)

Altogether, Coronatella and Hexalona-branches are considered the main lineages of Aloninae – a subfamily of common bottom-dwelling microcrustaceans in freshwater environments. Although the taxonomic features of Brazilian members of the Hexalona-branch have been summarised for species from the costata-group and affinis-group, a revision of other widely distributed species in the world is still lacking in this country. The aim of this paper was to study the morphology of Brazilian populations from the guttata-group and intermedia-group, and to describe a new genus from the Hexalona-branch. The parthenogenetic females of Alona cf. guttata from Brazil have similar morphology when compared to data from the literature, but the armature of the terminal claw of its males seems to be different from those of Alona guttata sensu stricto, Alona barbulata and Alona werestschagini. The intermedia-group is formed by Alona elisae sp. nov., which seems to be endemic to the Cerrado of Brazil Central, and Alona isabellae sp. nov., which is widely distributed in Brazil; this species has a labral keel armed with 2–4 setulae, and postabdomen with setulae of lateral fascicles longer than the level of marginal denticles, morphological traits that differentiate it from Alona elisae sp. nov. Another endemic species from the Hexalona-branch is Prenda arvensis gen. nov. and sp. nov., which has two main head pores, a reduced seta on endite 1 of the first limb, sixth limb is a wide lobe. The potential of biodiversity from the Hexalona-branch from Brazil is still underestimated, and a global revision of the guttata-group and intermedia-group is very important for the progress of Aloninae taxonomy and systematics.

http://zoobank.org/urn:lsid:zoobank.org:pub:0A2E4A30-0C9C-43E8-8E72-1DEDA6AFF3C3     

Integrative taxonomy at the nexus of population divergence and speciation in insular speckled rattlesnakes

ABSTRACT

We describe two diminutive species of rattlesnakes (genus Crotalus) from small nearshore islands off the coast of Baja California in the western Gulf of California, Mexico. In order to test the hypothesis that some island populations represent cohesive species entities, we applied linear discriminant analysis and uniform validation procedures to multiple classes of intrinsic trait data. By using previously recognised species to establish a threshold for species recognition, we found that assignment of specimens to either new species was as probable as with other established rattlesnake species within the speckled rattlesnake (Crotalus mitchellii) complex. We also found that assignment of specimens from other island populations was not as probable as for the established species, and these populations are referable to C. pyrrhus. The species endemic to Piojo Island is most closely related to other island and mainland populations of C. pyrrhus whereas the species endemic to Cabeza de Caballo Island is apparently most closely related to C. angelensis, a nearby island endemic of large body size. However, patterns from both mitochondrial and nuclear phylogenies, and phenotypic variation, indicate that evolutionary trajectories of both of these species have been influenced by introgression from C. angelensis. We speculate that collective evidence based on contrasting patterns of nuclear and mitochondrial evolution supports a hybrid origin of the species from Cabeza de Caballo Island followed by exceptionally rapid mitochondrial evolution. Consistent with small body size, both species show a reduction in various scale counts relative to other species of the C. mitchellii species complex, suggesting that dwarfism is not simply a plastic response to insular conditions.

http://www.zoobank.org/urn.lsid:zoobank.org:pub:FBC8A11B-04A3-4231-85CA-3972DF5A42FF     

Coral reef tanaidacean assemblages along the SW and SE Gulf of Mexico: biodiversity,geographic distribution and community structure

The biodiversity, geographic distribution, and community parameters of the benthic tanaidaceans associated with three coral reefs along the SW and SE Gulf of Mexico were analysed. A total of 15,525 specimens were grouped in 36 species. The highest value of abundance was found in the PNSAV with 6382 tanaidaceans. The PNSAV presented 30 species, the ANPT-L 16 species, and the SABS 17 species. The species with the widest distribution were Pseudonototanais sp., Condrochelia dubia, Leptochelia forresti, Synapseudes sp., Haplopolemius propinquus, Alloleptochelia longimana, and Paradoxapseudes bermudeus. In the Veracruz System Reef, the highest abundance was recorded for Condrochelia dubia and Pseudonototanais sp. The highest value of diversity was obtained in the SABS (3.08 bits/ind in the reef Bajo Diez), and the lowest value was found in the PNSAV (0.07 bits/ind in the reef Isla de Enmedio). The highest value of abundance was found in coral rubble and macroalgae. A significant relationship between depth and specific richness was found in the three reef systems. Using cluster analysis, three groups were found in each system, mainly related to the proximity to the coast and to urban areas. This is one of the first studies to show the specific substrate and attributes of three communities of tanaidaceans along the SE–SW coast of the Gulf of Mexico.