Phylogeny and evolution of the neotropical rodent genus Calomys: inferences from mitochondrial DNA sequence data

Field mice of the genus Calomys are small, mostly granivorous rodents common to several habitats in South America. To date, phylogenies for the genus have been proposed on the basis of morphological, chromosomal, and biochemical data, often with contradictory results due to incomplete species sampling or methodological shortcomings. In this paper, we propose relationships among 10 species of Calomys based on the complete cytochrome b gene sequence. Our analyses show that Calomys is constituted by two major clades, one mostly associated with mountain habitats with subsequent invasions to lowland habitats and another with species restricted to lowland habitats both north and south of the Amazon basin. The evolution of the genus was likely accompanied by a reduction of chromosome diploid numbers that occurred independently in each of the two evolutionary lineages. A "clock" calibrated on the split between Auliscomys and Loxodontomys suggests that the almost nonexistent fossil record for the genus greatly underestimates divergence times among its species.     

A genus-level supertree of the Dinosauria

One of the ultimate aims of systematics is the reconstruction of the tree of life. This is a huge undertaking that is inhibited by the existence of a computational limit to the inclusiveness of phylogenetic analyses. Supertree methods have been developed to overcome, or at least to go around this problem by combining smaller, partially overlapping cladograms. Here, we present a very inclusive generic-level supertree of Dinosauria (covering a total of 277 genera), which is remarkably well resolved and provides some clarity in many contentious areas of dinosaur systematics.     

Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA

Fission yeast Cid13 and budding yeast Trf4/5 are members of a newly identified nucleotidyltransferase family conserved from yeast to man. Trf4/5 are thought to be essential DNA polymerases. We report that Cid13 is a poly(A) polymerase. Unlike conventional poly(A) polymerases, which act in the nucleus and indiscriminately polyadenylate all mRNA, Cid13 is a cytoplasmic enzyme that specifically targets suc22 mRNA that encodes a subunit of ribonucleotide reductase (RNR). cid13 mutants have reduced dNTP pools and are sensitive to hydroxyurea, an RNR inhibitor. We propose that Cid13 defines a cytoplasmic form of poly(A) polymerase important for DNA replication and genome maintenance.     

The yield and composition of switchgrass and coastal panic grass grown as a biofuel in southern England

Switchgrass (Panicum virgatum L.) and coastal panic grass (Panicum amarum A.S. Hitchc. & Chase) are perennial grasses indigenous to North America. Switchgrass has been shown to have good potential as a biofuel crop in both the US and Canada. In the study reported here, seven varieties of switchgrass and one panic grass were evaluated for 5 years under the temperate maritime conditions in Southern England. Both species had 0 or 60 kg N ha(-1) applied annually in spring as treatment. Yield was measured after flowering and when stems were dead in the winter. Yield increased annually for 4-5 years except for the variety Dacotah, and in the fifth year dead stem yields ranged from 8.82 to 13.97 t dm ha(-1). There was no response to N except for one variety in one year. Mineral concentration in biomass was higher at flowering than at dead stem harvest and delaying harvesting further provided more time for P, K and Cl to be leached but yield also declined.     

DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics

The components of complex peptide mixtures can be separated by liquid chromatography, fragmented by tandem mass spectrometry, and identified by the SEQUEST algorithm. Inferring a mixture's source proteins requires that the identified peptides be reassociated. This process becomes more challenging as the number of peptides increases. DTASelect, a new software package, assembles SEQUEST identifications and highlights the most significant matches. The accompanying Contrast tool compares DTASelect results from multiple experiments. The two programs improve the speed and precision of proteomic data analysis.     

Proteomic characterization of wheat amyloplasts using identification of proteins by tandem mass spectrometry

We describe the initial characterization of the wheat amyloplast proteome, consisting of the identification and classification of 171 proteins. Whole amyloplasts and purified amyloplast membranes were prepared from wheat (Triticum aestivum). Protein extracts were examined by one-dimensional and two-dimensional electrophoresis, followed by high performance liquid chromatography-tandem mass spectrometry of separated proteins. Tandem mass spectrometry data of individual peptides was then searched by SEQUEST, using a database containing known protein sequences from both wheat and other homologous cereal crops. Using this approach we identified 108 proteins from whole amyloplasts and 63 proteins from purified amyloplast membranes. The majority of protein identifications were derived from protein sequences from cereal crops other than wheat, for which relatively little gene sequence data is available. The highest percentage of protein identifications obtained from any individual species was 46% of the total number of proteins identified, using sequence data found in our proprietary rice (Oryza sativa) genome database.     

Regulation of peptidergic vesicle mobility by secretagogues

Neuropeptides are released into the extracellular space from large secretory granules. In order to reach their release sites, these granules are translocated on microtubules and thought to interact with filamentous actin as they approach the cell membrane. We have used a green fluorescent protein-tagged neuropeptide prohormone (prepro-orphanin FQ) to visualize vesicle trafficking dynamics in NS20Y cells and cultures of primary hippocampal neurons. We found that the majority of secretory granules were mobile and accumulated at both the tips of neurites as well as other apparently specialized cellular sites. We also used live-cell imaging to test the notion that peptidergic vesicle mobility was regulated by secretagogues. We show that treatment with forskolin appeared to increase vesicle rates of speed, while depolarization with high K⁺ had no effect, even though both treatments stimulated neuropeptide secretion. In cultured hippocampal neurons the green fluorescent protein-tagged secretory vesicles were routed to both dendrites and axons, indicating that peptidergic vesicle transport was not polarized. Basal peptidergic vesicle mobility rates in hippocampal neurons were the same as those in NS20Y cells. Taken together, these studies suggest that secretory vesicle mobility is regulated by specific classes of secretagogues and that neuropeptide containing secretory vesicles may be released from dendritic structures.     

Proteomic characterization of the small subunit of Chlamydomonas reinhardtii chloroplast ribosome: identification of a novel S1 domain-containing protein and unusually large orthologs of bacterial S2, S3, and S5

To understand how chloroplast mRNAs are translated into functional proteins, a detailed understanding of all of the components of chloroplast translation is needed. To this end, we performed a proteomic analysis of the plastid ribosomal proteins in the small subunit of the chloroplast ribosome from the green alga Chlamydomonas reinhardtii. Twenty proteins were identified, including orthologs of Escherichia coli S1, S2, S3, S4, S5, S6, S7, S9, S10, S12, S13, S14, S15, S16, S17, S18, S19, S20, and S21 and a homolog of spinach plastid-specific ribosomal protein-3 (PSRP-3). In addition, a novel S1 domain-containing protein, PSRP-7, was identified. Among the identified proteins, S2 (57 kD), S3 (76 kD), and S5 (84 kD) are prominently larger than their E. coli or spinach counterparts, containing N-terminal extensions (S2 and S5) or insertion sequence (S3). Structural predictions based on the crystal structure of the bacterial 30S subunit suggest that the additional domains of S2, S3, and S5 are located adjacent to each other on the solvent side near the binding site of the S1 protein. These additional domains may interact with the S1 protein and PSRP-7 to function in aspects of mRNA recognition and translation initiation that are unique to the Chlamydomonas chloroplast.