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 .     

Engagement of NKG2D on Bystander Memory CD8 T Cells Promotes Increased Immunopathology following Leishmania major Infection

One of the hallmarks of adaptive immunity is the development of a long-term pathogen specific memory response. While persistent memory T cells certainly impact the immune response during a secondary challenge, their role in unrelated infections is less clear. To address this issue, we utilized lymphocytic choriomeningitis virus (LCMV) and Listeria monocytogenes immune mice to investigate whether bystander memory T cells influence Leishmania major infection. Despite similar parasite burdens, LCMV and Listeria immune mice exhibited a significant increase in leishmanial lesion size compared to mice infected with L. major alone. This increased lesion size was due to a severe inflammatory response, consisting not only of monocytes and neutrophils, but also significantly more CD8 T cells. Many of the CD8 T cells were LCMV specific and expressed gzmB and NKG2D, but unexpectedly expressed very little IFN-γ. Moreover, if CD8 T cells were depleted in LCMV immune mice prior to challenge with L. major, the increase in lesion size was lost. Strikingly, treating with NKG2D blocking antibodies abrogated the increased immunopathology observed in LCMV immune mice, showing that NKG2D engagement on LCMV specific memory CD8 T cells was required for the observed phenotype. These results indicate that bystander memory CD8 T cells can participate in an unrelated immune response and induce immunopathology through an NKG2D dependent mechanism without providing increased protection.     

The dipteran sperm tail: ultrastructural characteristics and phylogenetic considerations

The sperm tail from representatives of several families of Diptera has been examined by high resolution electron microscopy and a computer analysis that improved the visualization of recorded patterns. A considerable variability in sperm tail structure is found within Diptera, and is actually greater than that of any other insect order. The 'generalized insect sperm axoneme'. which is characterized as a 9+9+2 axoneme and by the accessory microtubules having 16 protofilaments, was found only in some dipterans; these are members of Mycetophilidae. From this fact we conclude that Mycetophilidae is likely to be the most primitive extant dipteran group. Another mycetophilid, Boletina , was seen to have accessory tubules with 15 protofilaments as have members of families Dixidae, Chironomidae, Culicidae, and Bibionidae. The last two families have spermatozoa of a type designated as 9+9+'1' there is a central rod rather than two microtubules. We regard this 9+9+'1'pattern with 15 protofilaments to represent a synapomorphic feature. Representatives of the neatoceran families Tipulidae and Trichoceridae have accessory tubules with 13 protofilaments as do examined members of several brachyceran families. Brachycera is hence likely to be derived from the vicinity of the tipulid family. The intertubular material is small in Mycetophilidae and most nematoceran groups, whereas in Tipulidae and Brachycera it is enlarged; here it bridges the space between the accessory tubules and contains various inclusions.     

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.     

Morphology and Infraciliature of Trochiliopsis australis N. Sp., Pelagohalteria viridis (Fromentel, 1876) N. G., N. Comb., and Strobilidium lacustris N. Sp. (Protozoa,Ciliophora)1

Three ciliate species from Australia and Norway were examined by silver impregnation, biometry, and scanning electron microscopy. Trochiliopsis australis n. sp. (order Nassulida, family Microthoracidae) differs from the single other known species of the genus, T. opaca, by its prominent ridges on the left side, the distinctly longer anterior segment of somatic kinety 2, and by the doubled total number of kinetosomes. Pelagohalteria n. g. (order Oligotrichida, family Halteriidae) differs from Halteria by the structure of the bristle complexes, which are composed of a vertically and a horizontally oriented row of kinetosomes. Two Halteria species belong to the new genus: P. viridis (Fromentel, 1876) n. comb., which is redescribed here, and P. cirrifera (Kahl, 1935) n. comb. Strobilidium lacustris n. sp. (order Oligotrichida, family Strobilidiidae) differs from its nearest relative, S. velox, by the smooth pellicle, the absence of symbiotic green algae, and by its larger size.     

APPLIED ISSUES Replacement of the native crayfish Astacus astacus by the introduced species Pacifastacus leniusculus in a Swedish lake: possible causes and mechanisms

1. The introduced North American crayfish Pacifastacits leniusculus is currently replacing the native crayfish Astacus astacus in a Swedish lake. Using field data from co-occurring populations on life-history traits and population size structure of the two species, this study evaluated possible mechanisms behind the replacement. 2. Pacifastacus showed a higher capacity for population increase; the species had a higher individual growth rate, reached sexual maturity at a smaller size and lower age, and had a higher per capita egg production than Astacus. 3. A higher frequency of non-lethal injuries in Astacus suggested the predominance of Pacifastacus in interference interactions. These results support a competitive exclusion hypothesis. 4. A dramatic change in relative abundance of the two species in recent years was the result of an almost complete cessation in recruitment of young-of-the-year (YOY) in Astacus. Poor recruitment in Astacus was probably caused by the combined effects of interspecific competition and predation, resulting in increased mortality among YOY Astacus, and by reproductive interference, suppressing the less common species. 5. The results support the hypothesis that the observed replacement of Astacus by Pacifastacus is governed by a combination of several interacting mechanisms, of which     

Simple Methods for the Calibration of Light Measuring Equipment

Simple methods are described for

• a) absolute calibration of thermal radiation detectors (thermopiles, bolometers);
• b) absolute calibration at various wavelengths of photoelectric devices;
• c) obtaining the relative spectral sensitivity of the detector systems of spectrofluorimeters.

The procedures require no special standard lamp or other exotic equipment. The methods depend on the computation of the radiation characteristics of an ordinary tungsten lamp at various measured voltages and currents.     

The ciliated epidermis of Xenoturbella bocki (Platyhelminthes, Xenoturbellida) with some phylogenetic considerations

The epidermis of Xenoturbella bocki Westblad was studied by scanning and transmission electron microscopy. Two cell types predominate in the epidermis: multiciliated epidermal cells and non-ciliated or monociliated gland cells. A conspicuous feature is the dense ciliary coverage and the numerous gland cell openings. Xenoturbella has a characteristic pattern of axonemal filament termination in the distal tips of their cilia. Each epidermal cilium has the typical 9 + 2 patten through the major part of its shaft. Near the tip there is a shelf at which doublets 4–7 terminate. Doublets 1, 2, 3, 8 and 9 continue into the thinner distal part of the cilium. A similar shelf in cilia is known only from the turbellarian orders Nemertodermatida and Acoela, and hence may be an apomorphic feature which indicates a close relationship between Xenoturbellida, Nemertoder-matida and Acoela. The basal body is provided with a so-called basal foot which has a cross-striated appearance and an expanded distal plate that seems to act as a microtubule organizing center. Approximately 15–25 microtubuli radiate from the endplate of the basal foot to the basal bodies caudally. The arrangement of basal foot and ciliary rootlets in Xenoturbella differs from that of Acoela and related orders in that there are two striated rootlets only (an anterior and a posterior one), rather than one main rootlet and two lateral rootlets.     

Molecular evolution of rodent insulins

Several trees of amino acid sequences of rodent insulins were derived with the maximum-parsimony procedure. Possible orthologous and paralogous relationships were investigated. Except for a recent gene duplication in the ancestor of rat and mouse, there are no strong arguments for other paralogous relationships. Therefore, a tree in agreement with other biological data is the most reasonable one. According to this tree, the capacity to form zinc-binding hexamers was lost once in the ancestor of the hystricomorph rodents, followed by moderately increased evolutionary rates in the lineages to African porcupine and chinchilla but highly increased rates in at least three independent lines to other taxa of this suborder: guinea pig, cuis, and Octodontoidea (coypu and casiragua).