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 .     

Molecular Aspects of Fibrin Clot Solubilization

THE human plasma protein, fibrinogen, is a disulphide bonded¹ dimer², each unit containing an Aα, Bβ and 8 chain^*, interconnected by disulphide bridges³. Thrombin (E.C.3.4.4.-13) releases fibrinopeptides A and B from the Aα and Bβ chains respectively⁴ to form fibrin monomer (α₂β₂γ₂) ? which polymerizes to form fibrin polymer or clotted fibrin. This polymer, following factor XIII (plasma transglutaminase, fibrin stabilizing factor) mediated crosslinking among the α chains and among the γ chains⁵, is one of the major and initiating constituents of a thrombus. Fibrinolytic activators, for example, streptokinase (SK) and urokinase (UK), are of thrombolytic value as they convert the thrombus plasminogen to plasmin (E.C.3.4.4.14) which by fibrinolytic action dissolves the thrombus. Whereas the interaction of fibrinogen and plasmin has been well studied^6–9, little is known concerning the mechanism of plasmin mediated fibrin clot lysis. I report here on the mechanism of non-cross-linked fibrin clot solubilization in near physiological conditions.     

Linked Genes for Calmodulin and E2 Ubiquitin-Conjugating Enzyme in Trichomonas vaginalis

ABSTRACT In searching the genomes of early-diverging protists to study whether the possession of calmodulin is ancestral to all eukaryotes, the gene for calmodulin was identified in Trichomonas vaginalis. This flagellate is a member of the Parabasalia, one of the earliest lineages of recognized eukaryotes to have diverged. This sequence was used to isolate a homologous 1.250-kb fragment from the T. vaginalis genome by inverse polymerase chain reaction. This fragment was also completely sequenced and shown to contain the 3' end of the single-copy calmodulin gene and the 3' end of a gene encoding a protein with high similarity to E2 ubiquitin-conjugating enzymes, a family which has previously only been identified in animals, plants, and fungi. Phylogenetic analysis of 50 members of the E2 family distinguishes at least nine separate subfamilies one of which includes the T. vaginalis E2-homologue and an uncharacterized gene from yeast chromosome XII.     

Caterpillars escape predation in habitat and thermal refuges

1. Climate and, therefore, abiotic conditions, are changing rapidly, and many ecological interactions depend on them. In this study, how abiotic conditions mediate a predator–prey interaction were examined. 2. Caterpillars of Platyprepia virginalis (Boisduval) (Arctiidae) were found previously to be more abundant in wet habitats and thick litter cover compared with drier habitats and little or no litter. We hypothesised that wet litter provided caterpillars with refuges from an important ant predator, Formica lasioides. It was further hypothesised that caterpillars would be able to move at lower temperatures than ants, thus providing them with a thermal refuge. 3. In the lab, caterpillars were more likely to escape ant predation and survive on wet litter and at lower temperatures. At all temperatures, ant recruitment was lower in wet litter than dry litter although ants were more active on litter than bare soil. Thus, wet litter may serve as a habitat refuge for caterpillars from ants. 4. Caterpillars were able to maintain activity at temperatures 8–14 °C lower than F. lasioides. Thus colder temperatures may serve as a thermal refuge for caterpillars from ants. 5. It was hypothesised that caterpillars can escape ant predation when precipitation causes wet litter and at temperatures that they experience commonly in the field. This mismatch between caterpillars and their predators in ability to tolerate wet litter and low temperatures may affect their field distribution and abundance. Expected future warmer and drier conditions may not provide these refuges.     

Metal cation binding by the hyperthermophilic microorganism,Archaea Methanocaldococcus Jannaschii,and its effects on silicification

Abstract: A series of experiments was conducted to determine the capacity of an archaeal strain, Methanocaldococcus jannaschii, to bind metals and to study the effects of metal binding on the subsequent silicification of the microorganisms. The results showed that M. jannaschii can rapidly bind several metal cations (Fe³⁺, Ca²⁺, Pb²⁺, Zn²⁺, Cu²⁺). Considering the lack of silicification of this strain without metal binding, these experiments demonstrate that Fe(III) ion binding to the cell wall components was of fundamental importance for successful silicification and, especially, for the excellent preservation of the cell wall. This study brings new elements to the understanding of fossilization processes, showing that the positive effect of Fe(III) on silicification, already known for Bacteria, can also apply to Archaea and that this preliminary binding can be decisive for the subsequent fossilization of these organisms. Knowledge of these mechanisms can be helpful for the search and the identification of microfossils in both terrestrial and extraterrestrials rocks, and in particular on Mars.     

Cellular Structures, Plasma Membrane Surface Areas and Plasmodesmatal Frequencies of the Stem of Phaseolus vulgaris L. in Relation to Radial Photosynthate Transfer

At an early stage of secondary development, the metaphloem sieveelements appeared to be the only functional axial transportconduit in fully elongated stems of P. vulgaris plants. Thereis no apparent barrier to the radial transfer of solutes inthe stem apoplast. However, radial transfer through the stemsymplast could be limited by discontinuities resulting fromprotoplast degeneration of the protophloem fibres and developingsecondary xylem fibres. Estimates of possible sucrose fluxesthrough the apoplastic and symplastic routes indicated thatradial photosynthate transfer from the sieve element-companioncell (se-cc) complexes of the stem metaphloem could follow eithercellular route. In the case of apoplastic transfer, the plasmamembrane surface area of the se-cc complexes is only sufficientto support some form of facilitated movement of sucrose. Incontrast, the plasma membrane surface area of the phloem parenchymais sufficient to permit passive diffusion of sucrose to theapoplast. Plasmodesmatal frequencies suggest that any symplastictransfer to the phloem parenchyma from the sieve elements wouldbe via the companion cells. Phaseolus vulgaris, french bean, stem, photosynthate, radial transfer (photosynthates), cellular pathway     

NEUROPEPTIDE Y RECEPTORS FROM CALF BRAIN: EFFECT OF CRUDE CONUS VENOM PREPARATIONS ON [H]NPY BINDING

NPY receptors are identified in calf frontal cortex and hippocampus membrane preparations by binding of N-[propionyl-³H] neuropeptide Y. Saturation and competition binding data with PYY, NPY-(18–36) and NPY itself fit with a single class of sites: for the radioligand K_D = 1.4 ± 0.5 nM, B_max = 434 ± 180 fmol/mg protein in frontal cortex, K_D = 0.7 ± 0.2 nM, B_max = 267 ± 50 fmol/mg protein in hippocampus. Competition curves of the Y₁-subtype selective agonist [Leu³¹, Pro³⁴]NPY are biphasic in both membrane preparations: high affinity sites (i.e. Y₁-subtype) amount to 80% in frontal cortex and 23% in hippocampus. The remaining sites are of the Y₂-subtype. Out of 23 Conus venom preparations, 17 inhibit the binding of [³H]NPY in both membrane preparations, but only two of them (from Conus aulicus and C. pennaceus) do so with high potency (ic₅₀ < 5 μg protein/ml). Only one venom preparation (from C. mercator) had weak discriminatory properties (ic₅₀Y₂/ic₅₀Y₁ = 6). Venom from C. anemone increased the [³H]NPY binding 5-fold and with an ic₅₀ of 15–18 μg protein/ml. This binding occurred to the venom itself and was unrelated to the NPY receptors since it was equally potent when displaced by [Leu³¹, Pro³⁴]NPY, NPY-(18–36), PYY and NPY. Copyright © 1996 Elsevier Science Ltd