Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Next‐generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan ‘BIN’ ontology, which is tailored for functional annotation of plant ‘omics’ data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan‐to‐GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator .     

Lost in translation – a history of systematic confusion and comments on the type species of Squalodon and Patriocetus (Cetacea,Odontoceti)

Abstract: The two odontocete taxa Squalodon grateloupii and Patriocetus ehrlichii, both the type species of their respective genera, have been at the centre of a great deal of taxonomic confusion. Originally regarded to be conspecific, these two taxa have been the subject of a bewildering taxonomic debate lasting for more than a century, which recently led to the suggestion to abandon these widely used names and replace S. grateloupii with the similar, yet independently and later proposed name S. gratelupi as the type species of Squalodon. Here, we attempt to summarise the events leading to the current confused situation in the hope of resolving this issue once and for all and argue that the name Squalodon grateloupii, as originally proposed, should be reinstated.     

The maritime species of Abronia (Nyctaginaceae)

An analysis of the variation patterns in the three Pacific Coast maritime species ofAbronia (Nyctaginaceae) based on 95 population studies, is presented in the form of scatter diagrams. The relationship of this group of species to other members of the genus, such asA. gracilis Benth., is considered. Despite widespread evidence of hybridization and introgression, the three maritime species (A. latifolia Eschsch.,A. maritima Nutt. ex S. Wats., andA. umbellata Lam.) maintain their distinctness. Most of the taxonomic segregants in this group have been based on what appear to be hybrid or introgressed individuals, many of which closely resemble members of a series of artificial hybrids made in the greenhouse. The chromosome number of all three species is estimated as 2n = ca. 46. The species are shown to differ markedly in ecological preference:A. latifolia competing successfully on stable areas of dunes from Vancouver Island, British Columbia, to Santa Barbara Co., California;A. maritima being the major foredune former along the strand from San Luis Obispo Co., California, south to Nayarit, Mexico; andA. umbellata occurring on more stable dunes from San Luis Obispo to San Diego Co., California, and sporadically north and south of this area. The latter species is pollinated chiefly by nocturnal insects and is fragrant in the evening, whereas the other two have diurnal flowers. One widespread and two rarer, more northern subspecies ofA. umbellata are recognized in the taxonomic revision, while the other two species are not subdivided taxonomically.     

Mutation of Phe102 to Ser in the carboxyl terminal helix of Escherichia coli thioredoxin affects the stability and processivity of T7 DNA polymerase

Processivity of T7 DNA polymerase relies on the coupling of its cofactor Escherichia coli thioredoxin (Trx) to gene 5 protein (gp5) at 1:1 stoichiometry. We designed a coexpression system for gp5 and Trx that allows in vivo reconstitution of subunits into a functional enzyme. The properties of this enzyme were compared with the activity of commercial T7 DNA polymerase. Examination of purified enzymes by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the thioredoxin subunit of the two enzymes did not comigrate. To our surprise, we identified a mutation (Phe102 to Ser) in the Trx component from the commercial T7 DNA polymerase (gp5/TrxS102) that was not in the enzyme from the coexpression system (wild type gp5/Trx). A comparison of polymerase activity of the T7 DNA polymerases shows that both enzymes possessed similar specific activity but they were different in their residual activity at 37 degrees C. The half-life of gp5/TrxS102 was 7 min at 37 degrees C and 12 min for gp5/Trx. gp5/TrxS102 polymerase activity was reduced by fourfold with 3'-5' exonuclease activity as the prominent activity detected after 10 min of heat inactivation at 37 degrees C. Supplementation of reaction mixtures containing gp5/TrxS102 with exogenous nonmutant thioredoxin restored the enzyme activity levels. Pulse proteolysis was used to demonstrate that TrxS102 unfolded at lower urea concentrations than wild type thioredoxin. Thus, Ser substitution at position 102 affected the structural stability of thioredoxin resulting in a reduced binding affinity for gp5 and loss of processivity.     

Protein-ligand interactions measured by 15N-filtered diffusion experiments

NMR diffusion coefficient measurements have been shown to be sensitive to the conformational and oligomeric states of proteins. Recently, heteronuclear-filtered diffusion experiments have been proposed [Dingley et al. (1997) J. Biomol. NMR, 10, 1–8]. Several new heteronuclear-filtered diffusion pulse sequences are proposed which are shown to have superior sensitivity to those previously proposed. One of these new heteronuclear-filtered diffusion experiments has been used to study the binding of an SH3 domain to a peptide. Using this system, we show that it is possible to measure binding constants from diffusion coefficient measurements.     

Inferring pathogen inactivation from the surface temperatures of compost heaps

A sufficiently high composting temperature should inactivate many common pathogens likely to be present in solid animal waste. Monitoring core temperatures inside compost heaps is not straightforward, which means that heaps are not generally monitored. An alternative is to monitor surface temperatures and use those data to infer core temperatures, and thus whether pathogen inactivation has occurred. This paper describes two methods (thermal imaging and thermocouples) for the measurement of surface temperature, and a modelling approach using time series analysis to predict the temperatures obtained in the core of aerated heaps of composting pig farmyard manure (FYM) from surface temperature data. The model was able to predict core temperatures in the heap quite closely for a period of time for well insulated parts of the heap, although predictions were further from observed values close to the surface of the heap and the aeration pipe.