Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida,Cycliophora, Plathelminthes,and Chaetognatha: a combined approach of 18S rDNA sequences and morphology

Triploblastic relationships were examined in the light of molecular and morphological evidence. Representatives for all triploblastic "phyla" (except Loricifera) were represented by both sources of phylogenetic data. The 18S ribosomal (rDNA) sequence data for 145 terminal taxa and 276 morphological characters coded for 36 supraspecific taxa were combined in a total evidence regime to determine the most consistent picture of triploblastic relationships for these data. Only triploblastic taxa are used to avoid rooting with distant outgroups, which seems to happen because of the extreme distance that separates diploblastic from triploblastic taxa according to the 18S rDNA data. Multiple phylogenetic analyses performed with variable analysis parameters yield largely inconsistent results for certain groups such as Chaetognatha, Acoela, and Nemertodermatida. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis having the least character incongruence yields the following scheme of relationships of four main clades: (1) Deuterostomia [((Echinodermata + Enteropneusta) (Cephalochordata (Urochordata + Vertebrata)))]; (2) Ecdysozoa [(((Priapulida + Kinorhyncha) (Nematoda + Nematomorpha)) ((Onychophora + Tardigrada) Arthropoda))]; (3) Trochozoa [((Phoronida + Brachiopoda) (Entoprocta (Nemertea (Sipuncula (Mollusca (Pogonophora (Echiura + Annelida)))))))]; and (4) Platyzoa [((Gnathostomulida (Cycliophora + Syndermata)) (Gastrotricha + Plathelminthes))]. Chaetognatha, Nemertodermatida, and Bryozoa cannot be assigned to any one of these four groups. For the first time, a data analysis recognizes a clade of acoelomates, the Platyzoa (sensu Cavalier-Smith, Biol. Rev. 73:203-266, 1998). Other relationships that corroborate some morphological analyses are the existence of a clade that groups Gnathostomulida + Syndermata (= Gnathifera), which is expanded to include the enigmatic phylum Cycliophora, as sister group to Syndermata.     

Gnathostomulid phylogeny inferred from a combined approach of four molecular loci and morphology

The phylogeny of the obscure metazoan phylum Gnathostomulida has previously only been addressed with cladistic analyses of morphological data. In the present study DNA sequence data from four molecular loci, including 18S rRNA, 28S rRNA, histone H3 and cytochrome c oxidase subunit I, are added to a revised morphological data matrix. The data set represents 23 gnathostomulid species that are analyzed under direct optimization using parsimony as the optimality criterion. The results obtained from analyzing the four molecular loci and combined morphological and molecular data under different parameter sets are generally very congruent, and differ only on minor points. The results clearly support gnathostomulid monophyly, as well as the basal division of Gnathostomulida into Filospermoidea and Bursovaginoidea. Filospermoidea were represented by species of Haplognathia and Cosmognathia, and generic monophyly is supported for both groups. Within Bursovaginoidea, Conophoralia (= Austrognathiidae) and Scleroperalia appear as sister groups. Monophyly of Mesognathariidae was confirmed as well, whereas the relationships between species of Gnathostomulidae and Onychognathiidae were contradicted by the molecular data when compared to morphological observations. ©The Willi Hennig Society 2006.     

Release of d-[3H]aspartic acid from the rat substantia nigra: effect of veratridine-evoked depolarization and cortical ablation

The spontaneous and veratridine-evoked release of radioactive d-aspartic acid, previously taken up by rat substantia nigra slices, was studied by using a superfusion system. Veratridine (25 μM, 1 min) markedly produced a 14-fold increase in d-[³H]aspartic acid release from nigral slices. Omission of Ca²⁺ and increasing Mg²⁺ concentration to 12 mM in the superfusion medium did substantially block d-[³H]aspartate release induced by veratridine depolarization. Nevertheless, veratridine was able to evoke [³H]amino acid release which seemed to be, at least, 30% Ca²⁺-independent. Additional experiments showed that tetrodotoxin (0.01–0.1 μM), a blocker of voltage-dependent Na⁺ channels, totally abolished veratridine-evoked release of d-[³H]aspartate from nigral slices.Lesion studies were performed in order to learn about the nature of the neuronal compartment in the substantia nigra upon which veratridine-depolarization acted to induce d-[³H]aspartate release. Unilateral ablation of the fronto-parietal cortex was accompanied by a significant decrease in the accumulation of nigral d-[³H]aspartate and by a large loss from ipsilateral nigral slices in d-[³H]aspartate release evoked by veratridine. In contrast, both the accumulation and veratridine-evoked release of [³H]dopamine, remained unchanged in the ipsilateral substantia nigra slices to the lesion.The findings reported suggest that d-[³H]aspartic acid may be taken up and then released, in a Ca²⁺-dependent manner, by nerve terminals located in the substantia nigra. In addition, the results shown provide support to the view that l-glutamate and/or l-aspartate may act as neurotransmitters at the cortico-nigral neuronal pathway.     

Arundifungin, a novel antifungal compound produced by fungi: biological activity and taxonomy of the producing organisms

Echinocandins, the lipopeptide class of glucan synthase inhibitors, are an alternative to ergosterol-synthesis inhibitors to treat candidiasis and aspergillosis. Their oral absorption, however, is low and they can only be used parenterally. During a natural product screening program for novel types of glucan synthesis inhibitors with improved bioavailability, a fungal extract was found that inhibited the growth of both a wild-type Saccharomyces cerevisiae strain and the null mutant of the FKS1 gene (fks1::HIS). The mutant strain was more sensitive to growth inhibition, suggesting that the fungal extract could contain an inhibitor of glucan synthesis. A novel acidic steroid, named arundifungin, was purified from a fungal extract obtained from a liquid culture of Arthrinium arundinis collected in Costa Rica. Arundifungin caused the same pattern of hallmark morphological alterations in Aspergillus fumigatus hyphae as echinocandins, further supporting the idea that arundifungin belongs to a new class of glucan synthesis inhibitors. Moreover, its antifungal spectrum was comparable to those of echinocandins and papulacandins, preferentially inhibiting the growth of Candida and Aspergillus strains, with very poor activity against Cryptococcus. Arundifungin was also detected in nine other fungal isolates which were ecologically and taxonomically unrelated, as assessed by sequencing of the ITS1 region. Further, it was also found in two more Arthrinium spp from tropical and temperate regions, in five psychrotolerant conspecific isolates collected on Macquarie Island (South Pacific) and belonging to the Leotiales, and in two endophytes collected in central Spain (a sterile fungus belonging to the Leotiales and an undetermined coelomycete).     

A new model Gondwanan taxon: systematics and biogeography of the harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi), with a taxonomic revision of genera from Australia and New Zealand

The phylogeny of the temperate Gondwanan harvestman family Pettalidae is investigated by means of a new morphological matrix of 45 characters, and DNA sequence data from five markers, including two nuclear ribosomal genes (18S rRNA and 28S rRNA), one nuclear protein coding gene (histone H3), and two mitochondrial genes–one protein coding (cytochrome c oxidase subunit I) and one ribosomal (16S rRNA). Phylogenetic analyses using an array of homology schemes (dynamic and static), criteria (parsimony and maximum likelihood), and sampling strategies (optimal trees versus Bayesian phylogenetics) all agree on the monophyly of Pettalidae as well as several of its subclades, each of which is restricted to a modern landmass. While most genera as traditionally defined are monophyletic, Rakaia and Neopurcellia, distributed across Queensland (Australia) and New Zealand, are not. Instead, the species from Queensland, previously described under three genera, constitute a well‐supported clade, suggesting that in this case biogeography prevails over traditional taxonomy. A taxonomic emendation of the genera from Queensland and New Zealand is presented, and the new genus Aoraki is erected to include the species of the New Zealand denticulata group. A biogeographical hypothesis of the relationships of the former temperate Gondwana landmasses (with the exception of Madagascar) is presented, although ambiguity in the deep nodes of the pettalid tree renders such inference provisional. The data suggest that neither the South African fauna, the New Zealand fauna nor the Australian fauna is monophyletic but instead monophyly is found at smaller geographic scales (e.g., Western Australia, Queensland, NE South Africa). © The Willi Hennig Society 2007.     

Reggie/flotillin proteins are organized into stable tetramers in membrane microdomains

Reggie-1 and -2 proteins (flotillin-2 and -1 respectively) form their own type of non-caveolar membrane microdomains, which are involved in important cellular processes such as T-cell activation, phagocytosis and signalling mediated by the cellular prion protein and insulin; this is consistent with the notion that reggie microdomains promote protein assemblies and signalling. While it is generally known that membrane microdomains contain large multiprotein assemblies, the exact organization of reggie microdomains remains elusive. Using chemical cross-linking approaches, we have demonstrated that reggie complexes are composed of homo- and hetero-tetramers of reggie-1 and -2. Moreover, native reggie oligomers are indeed quite stable, since non-cross-linked tetramers are resistant to 8 M urea treatment. We also show that oligomerization requires the C-terminal but not the N-terminal halves of reggie-1 and -2. Using deletion constructs, we analysed the functional relevance of the three predicted coiled-coil stretches present in the C-terminus of reggie-1. We confirmed experimentally that reggie-1 tetramerization is dependent on the presence of coiled-coil 2 and, partially, of coiled-coil 1. Furthermore, since depletion of reggie-1 by siRNA (small interfering RNA) silencing induces proteasomal degradation of reggie-2, we conclude that the protein stability of reggie-2 depends on the presence of reggie-1. Our data indicate that the basic structural units of reggie microdomains are reggie homo- and hetero-tetramers, which are dependent on the presence of reggie-1.     

Characterization of the NADP malic enzyme gene family in the facultative,single-cell C<Subscript>4</Subscript> monocot <Emphasis Type="Italic">Hydrilla verticillata</Emphasis>

Hydrilla verticillata has a facultative single-cell system that changes from C₃ to C₄ photosynthesis. A NADP⁺-dependent malic enzyme (NADP-ME) provides a high [CO₂] for Rubisco fixation in the C₄ leaf chloroplasts. Of three NADP-ME genes identified, only hvme1 was up-regulated in the C₄ leaf, during the light period, and it possessed a putative transit peptide. Unlike obligate C₄ species, H. verticillata exhibited only one plastidic isoform that may perform housekeeping functions, but is up-regulated as the photosynthetic decarboxylase. Of the two cytosolic forms, hvme2 and hvme3, the latter exhibited the greatest expression, but was not light-regulated. The mature isoform of hvme1 had a pI of 6.0 and a molecular mass of 64 kD, as did the recombinant rHVME1m, and it formed a tetramer in the chloroplast. The recombinant photosynthetic isoform showed intermediate characteristics between isoforms in terrestrial C₃ and C₄ species. The catalytic efficiency of rHVME1m was four-fold higher than the cytosolic rHVME3 and two-fold higher than recombinant cytosolic isoforms of rice, but lower than plastidic forms of maize. The K _m (malate) of 0.6 mM for rHVME1 was higher than maize plastid isoforms, but four-fold lower than found with rice. A comprehensive phylogenetic analysis of 25 taxa suggested that chloroplastic NADP-ME isoforms arose from four duplication events, and hvme1 was derived from cytosolic hvme3. The chloroplastic eudicot sequences were a monophyletic group derived from a cytosolic clade after the eudicot and monocot lineages separated, while the monocots formed a polyphyletic group. The findings support the hypothesis that a NADP-ME isoform with specific and unusual regulatory properties facilitates the functioning of the single-cell C₄ system in H. verticillata. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

High-throughput culturing of fungi from plant litter by a dilution-to-extinction technique

High-throughput bacterial cultivation has improved the recovery of slow-growing and previously uncultured bacteria. The most robust high-throughput methods are based on techniques of 'dilution to extinction' or 'extinction culturing'. The low-density partitioning of CFUs in tubes or microwells exploits the fact that the number of culturable species typically increases as inoculum density decreases. Bacterial high-throughput culturing methods were adapted to fungi to generate large numbers of fungal extinction cultures. The efficiency of extinction culturing was assessed by comparing it with particle filtration and automated plate-streaking. Equal volumes of particle suspension from five litter collections of the New Zealand forest tree Elaeocarpus dentatus were compared. Dilute particle suspensions of litter were pipetted into 48-well tissue culture plates containing 1 mL of agar medium per well. Particle volumes from the same samples were applied to continuous agar surfaces in Omnitray plates by automated streaking, and fungal diversity and richness were measured. The spectrum of isolates was assessed by microscopy and sequencing of the ITS or 28S region of the rRNA gene. Estimates of species diversity between the two methods were comparable, but extinction culturing increased species richness. Compared with plating methods using continuous surfaces, extinction culturing distributes fungal propagules over partitioned surfaces. Intercolony interactions are reduced, permitting longer incubation times, and colony initiation and recovery improved. Effort to evaluate and recover colonies from fungal isolation plates was substantially reduced.     

Increased stability and DNA site discrimination of "single chain" variants of the dimeric beta-barrel DNA binding domain of the human papillomavirus E2 transcriptional regulator

Human papillomavirus infects millions of people worldwide and is a causal agent of cervical cancer in women. The HPV E2 protein controls the expression of all viral genes through binding of its dimeric C-terminal domain (E2C) to its target DNA site. We engineered monomeric versions of the HPV16 E2C, in order to probe the link of the dimeric beta-barrel fold to stability, dimerization, and DNA binding. Two single-chain variants, with 6 and 12 residue linkers (scE2C-6 and scE2C-12), were purified and characterized. Spectroscopy and crystallography show that the native structure is unperturbed in scE2C-12. The single chain variants are stabilized with respect to E2C, with effective concentrations of 0.6 to 6 mM. The early folding events of the E2C dimer and scE2C-12 are very similar and include formation of a compact species in the submillisecond time scale and a non-native monomeric intermediate with a half-life of 25 ms. However, monomerization changes the unfolding mechanism of the linked species from two-state to three-state, with a high-energy intermediate. Binding to the specific target site is up to 5-fold tighter in the single chain variants. Nonspecific DNA binding is up to 7-fold weaker in the single chain variants, leading to an overall 10-fold increased site discrimination capacity, the largest described so far for linked DNA binding domains. Titration calorimetric binding analysis, however, shows almost identical behavior for dimer and single-chain species, suggesting very subtle changes behind the increased specificity. Global analysis of the mechanisms probed suggests that the dynamics of the E2C domain, rather than the structure, are responsible for the differential properties. Thus, the plastic and dimeric nature of the domain did not evolve for a maximum affinity, specificity, and stability of the quaternary structure, likely because of regulatory reasons and for roles other than DNA binding played by partly folded dimeric or monomeric conformers.     

High-risk HPV E6 oncoproteins assemble into large oligomers that allow localization of endogenous species in prototypic HPV-transformed cell lines

The E6 oncoproteins of high-risk HPV types 16 and 18 are involved in the development of cervical cancer. Besides its determinant role in carcinogenic progression, HPV E6 oncoprotein has also been instrumental in elucidating fundamental aspects of p53 function and its ubiquitin-proteasome degradation, with counterpart activities in various DNA tumor viruses. Establishing the conformational state and cellular distribution unequivocally for the endogenous protein in HPV-transformed cell lines derived from carcinomas is essential for understanding the underlying mechanism. Recombinant E6 from high-risk strains 16 and 18 folds into soluble oligomers of approximately 1.2 MDa, which are thermostable and display cooperative loss of tertiary and secondary structure upon chemical denaturation. Antibodies raised against these assemblies locate E6 evenly distributed in the cells. By depleting the polyclonal serum by immunoblocking with monomeric E6, the nuclei of Hela and CaSki cells become completely devoid of label, indicating that monomeric species are mainly localized in the nucleus and that both monomers and oligomers share epitopes. The monomeric species promote degradation of p53 by the proteasome, which correlates with the nuclear localization we describe. In contrast, the oligomeric E6 does not promote p53 degradation, in agreement with its cytoplasmic localization inferred from the immunoneutralization experiments. Our results indicate that the cytoplasmic species contain conformational epitopes that may arise from yet undefined homo or hetero-oligomers, but its localization otherwise agrees with that of the other group of major E6 targets, those involving PDZ binding domains, which requires further investigation.