Vertical and lateral variations in coccolithophore community structure across the subtropical frontal zone in the South Atlantic Ocean

In this study the coccolithophore compositions of 11 plankton depth stations along a N–S transect from the South Atlantic Subtropical Gyre to the Subantarctic Zone were examined qualitatively and quantitatively. The lateral and vertical distribution patterns of not only the most abundant taxa but also of the morphotypes of distinct species complexes, such as Calcidiscus leptoporus, Emiliania huxleyi, and Umbellosphaera tenuis were the focus. Geographic variation among morphotypes mirrors different ecological affinities of the members of a species complex. Multivariate statistics were used to infer the relationship between a set of known environmental data and species concentrations. The results of the detrended Canonical Correspondence Analysis (CCA) revealed the presence of distinct species assemblages. The Subtropical Gyre assemblage within the upper 50 m of the photic zone is mainly composed of Umbellosphaera irregularis, U. tenuis types III and IV, Discosphaera tubifera, Rhabdosphaera clavigera, S. pulchra and E. huxleyi var. corona, adapted to warm and oligotrophic conditions. In the deeper photic zone abundant Florisphaera profunda, Gephyrocapsa ericsonii and Oolithotus spp. are encountered, benefiting from higher nutrient concentrations in the vicinity of the nutricline. A well-defined Subtropical Frontal Zone (STFZ) association is clearly dominated by E. huxleyi types A and C throughout the upper 100 m of the water column. Secondary contributors in the upper photic zone are Syracosphaera spp. (mainly S. histrica, S. molischii), Michaelsarsia elegans, Ophiaster spp. and U. tenuis type II. This assemblage is associated with cooler, nutrient-rich waters. E. huxleyi type B is found deeper in the water column. Here it is accompanied by Algirosphaera robusta, G. muellerae, and S. anthos indicating a tolerance of lower light availability in environments with elevated productivity. C. leptoporus spp. leptoporus shows relatively high cell numbers in all sampled water levels throughout the STFZ. Interestingly, its coccoliths are often smaller 5 μm in lith diameter. The mean coccolithophore assemblages of a station were compared to the underlying surface sediment assemblages. For the most part, the distribution of the morphotypes is reflected in the sedimentary archive, thus proving their potential as paleoecological proxies.     

Constitutively activated barley ROPs modulate epidermal cell size, defense reactions and interactions with fungal leaf pathogens

RHO-like monomeric G-proteins of plants (ROPs, also called RACs), are involved in plant development and interaction with the environment. The barley (Hordeum vulgare) ROP protein HvRACB has been shown to be required for entry of the biotrophic powdery mildew fungus Blumeria graminis f.sp. hordei (Bgh) into living host cells. To get a deeper insight into evolutionarily conserved functions of ROPs in cell polarity and pathogen responses, we stably expressed constitutively activated (CA) mutant variants of different barley ROPs (HvRACB, HvRAC1, HvRAC3) in barley. CA HvROPs induced epidermal cell expansion and/or abolished polarity in tip growing root hairs. All three CA HvROPs enhanced susceptibility of barley to penetration by Bgh whereas only CA HvRAC1 supported whole cell H₂O₂ production in non-penetrated cells. Despite increasing penetration by Bgh, CA HvRAC1 promoted callose deposition at sites of fungal attack and resistance to penetration by Magnaporthe oryzae. The data show an involvement of ROPs in polar growth processes of the monocot barley and in responses to fungal pathogens with different life style.     

The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains

The signing authors together with the journal Systematic and Applied Microbiology (SAM) have started an ambitious project that has been conceived to provide a useful tool especially for the scientific microbial taxonomist community. The aim of what we have called "The All-Species Living Tree" is to reconstruct a single 16S rRNA tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria. This tree is to be regularly updated by adding the species with validly published names that appear monthly in the Validation and Notification lists of the International Journal of Systematic and Evolutionary Microbiology. For this purpose, the SAM executive editors, together with the responsible teams of the ARB, SILVA, and LPSN projects (www.arb-home.de, www.arb-silva.de, and www.bacterio.cict.fr, respectively), have prepared a 16S rRNA database containing over 6700 sequences, each of which represents a single type strain of a classified species up to 31 December 2007. The selection of sequences had to be undertaken manually due to a high error rate in the names and information fields provided for the publicly deposited entries. In addition, from among the often occurring multiple entries for a single type strain, the best-quality sequence was selected for the project. The living tree database that SAM now provides contains corrected entries and the best-quality sequences with a manually checked alignment. The tree reconstruction has been performed by using the maximum likelihood algorithm RAxML. The tree provided in the first release is a result of the calculation of a single dataset containing 9975 single entries, 6728 corresponding to type strain gene sequences, as well as 3247 additional high-fquality sequences to give robustness to the reconstruction. Trees are dynamic structures that change on the basis of the quality and availability of the data used for their calculation. Therefore, the addition of new type strain sequences in further subsequent releases may help to resolve certain branching orders that appear ambiguous in this first release. On the web sites: www.elsevier.de/syapm and www.arb-silva.de/living-tree, the All-Species Living Tree team will release a regularly updated database compatible with the ARB software environment containing the whole 16S rRNA dataset used to reconstruct "The All-Species Living Tree". As a result, the latest reconstructed phylogeny will be provided. In addition to the ARB file, a readable multi-FASTA universal sequence editor file with the complete alignment will be provided for those not using ARB. There is also a complete set of supplementary tables and figures illustrating the selection procedure and its outcome. It is expected that the All-Species Living Tree will help to improve future classification efforts by simplifying the selection of the correct type strain sequences. For queries, information updates, remarks on the dataset or tree reconstructions shown, a contact email address has been created (living-tree@arb-silva.de). This provides an entry point for anyone from the scientific community to provide additional input for the construction and improvement of the first tree compiling all sequenced type strains of all prokaryotic species for which names had been validly published.     

The Medium-Chain Dehydrogenase/reductase Engineering Database: a systematic analysis of a diverse protein family to understand sequence-structure-function relationship

The Medium-Chain Dehydrogenase/Reductase Engineering Database (MDRED, http://www.mdred.uni-stuttgart.de) has been established to serve as an analysis tool for a systematic investigation of sequence-structure-function relationships. It includes sequence and structure information of 2684 and 42 medium-chain dehydrogenases/reductases (MDRs), respectively. Although MDRs are very diverse in sequence, they have a conserved tertiary structure. MDRs are assigned to 199 homologous families and 29 superfamilies. For each family, annotated multiple sequence alignments are provided, and functionally relevant residues are annotated. Twenty-five superfamilies were classified as zinc-containing MDRs, four as non-zinc-containing MDRs. For the zinc-containing MDRs, three subclasses were identified by systematic analysis of a variable loop region, the quaternary structure determining loop (QSDL): the class of short, medium, and long QSDL, which include 11, 3, and 5 superfamilies, respectively. The length of the QSDL is predictive for tetramer (short QSDL) and dimer (long QSDL) formation. The class of medium QSDL includes both tetrameric and dimeric MDRs. The shape of the substrate-binding site is highly conserved in all zinc-containing MDRs with the exception of two variable regions, the substrate recognition sites (SRS): two residues located on the QSDL (SRS1) and, for the class of long QSDL, one residue located in the catalytic domain (SRS2). The MDRED is the first online-accessible resource of MDRs that integrates information on sequence, structure, and function. Annotation of functionally relevant residues assist the understanding of sequence-structure-function relationships. Thus, the MDRED serves as a valuable tool to identify potential hotspots for engineering properties such as substrate specificity.     

In vitro digestibility of fern and gymnosperm foliage: implications for sauropod feeding ecology and diet selection

Sauropod dinosaurs, the dominant herbivores throughout the Jurassic, challenge general rules of large vertebrate herbivory. With body weights surpassing those of any other megaherbivore, they relied almost exclusively on pre-angiosperm plants such as gymnosperms, ferns and fern allies as food sources, plant groups that are generally believed to be of very low nutritional quality. However, the nutritive value of these taxa is virtually unknown, despite their importance in the reconstruction of the ecology of Mesozoic herbivores. Using a feed evaluation test for extant herbivores, we show that the energy content of horsetails and of certain conifers and ferns is at a level comparable to extant browse. Based on our experimental results, plants such as Equisetum, Araucaria, Ginkgo and Angiopteris would have formed a major part of sauropod diets, while cycads, tree ferns and podocarp conifers would have been poor sources of energy. Energy-rich but slow-fermenting Araucaria, which was globally distributed in the Jurassic, was probably targeted by giant, high-browsing sauropods with their presumably very long ingesta retention times. Our data make possible a more realistic calculation of the daily food intake of an individual sauropod and improve our understanding of how large herbivorous dinosaurs could have flourished in pre-angiosperm ecosystems.     

Congenital, low penetrance lymphedema of lower limbs maps to chromosome 6q16.2–q22.1 in an inbred Pakistani family

Hereditary lymphedema is a rare, lymphatic disorder resulting in the chronic swelling of the extremities. It shows wide inter- and intra-familial clinical heterogeneity as well as variability in the age of onset. There are more than four genetically distinct lymphedema conditions known and mutations in three genes have been discovered in families with lymphedema. However, many other familial lymphedemas do not show linkage with the known loci, suggesting genetic heterogeneity. Here, we describe a large inbred Pakistani family with congenital, progressive lymphedema confined to the lower limbs, which fades away at 40–45 years of age. This condition segregates in an autosomal dominant fashion with reduced penetrance. The features are close to primary lymphedema I, Nonne–Milory type (MIM 153100). We exclude this condition for linkage to the known loci for lymphedema by employing highly polymorphic microsatellite markers from these intervals. Then, through a genome-wide linkage study we show that the malformation in our family maps to chromosome 6q16.2–q22.1. The highest pair-wise LOD score (Z _max = 3.19) was obtained with microsatellite marker D6S1671, and a multipoint score of 3.75 was obtained at 108 cM. Haplotype analysis indicated that the critical interval in this family flanks between markers D6S1716 and D6S303. Mutation analysis in FOXO3, a likely candidate within this interval, did not show any pathogenic change in the affected family subjects. Our study provides an evidence of a second locus for lymphedema type I. The discovery of the underlying gene could be helpful for the understanding of this heterogeneous hereditary condition.     

Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor

A total community DNA sample from an agricultural biogas reactor continuously fed with maize silage, green rye, and small proportions of chicken manure has recently been sequenced using massively parallel pyrosequencing. In this study, the sample was computationally characterized without a prior assembly step, providing quantitative insights into the taxonomic composition and gene content of the underlying microbial community. Clostridiales from the phylum Firmicutes is the most prevalent phylogenetic order, Methanomicrobiales are dominant among methanogenic archaea. An analysis of Operational Taxonomic Units (OTUs) revealed that the entire microbial community is only partially covered by the sequenced sample, despite that estimates suggest only a moderate overall diversity of the community. Furthermore, the results strongly indicate that archaea related to the genus Methanoculleus, using CO(2) as electron acceptor and H(2) as electron donor, are the main producers of methane in the analyzed biogas reactor sample. A phylogenetic analysis of glycosyl hydrolase protein families suggests that Clostridia play an important role in the digestion of polysaccharides and oligosaccharides. Finally, the results unveiled that most of the organisms constituting the sample are still unexplored.     

Improved sandwich-hybridization assay for an electrical DNA-chip-based monitoring of bioprocess-relevant marker genes

Recently, it was shown that electrical DNA-chips in connection with a magnetic bead-based sandwich-hybridization assay can be a suitable alternative for the analysis of gene expression by monitoring the respective mRNA levels. In this study, we established an improved assay which allowed for a significantly shortened but sensitive detection of specific mRNAs. These improvements include the change to a solution-based sandwich-hybridization and the rearrangement of the used oligonucleotide probes. The introduction of a second labeled detection probe further increased the hybridization signals and, in turn, leads to a substantial time reduction of the detection protocol. The presented solution-based sandwich-hybridization protocol for the electrochemical detection of specific mRNAs requires about 60 min and the whole procedure, including sampling, cell disruption, and RNA isolation, approx. 80 min. The assay of this study was verified by nutrient-limited growth experiments and the analysis of selected starvation marker genes of the industrial host Bacillus licheniformis. The expression profiles determined with the electrical chip and the optimized protocol were, in most cases, comparable with the profiles determined by real-time RT-PCR measurements.     

Characterization of a family 54 α-<Emphasis Type="SmallCaps">l</Emphasis>-arabinofuranosidase from <Emphasis Type="Italic">Aureobasidium pullulans</Emphasis>

A glycosyl hydrolase family 54 (GH54) α-l-arabinofuranosidase gene (abfA) of Aureobasidium pullulans was amplified by polymerase chain reaction from genomic DNA and a 498-amino-acid open reading frame deduced from the DNA sequence. Modeling of the highly conserved A. pullulans AbfA protein sequence on the crystal structure of Aspergillus kawachii AkabfB showed that the catalytic amino acid arrangement and overall structure were highly similar including the N-terminal catalytic and C-terminal arabinose binding domains. The abfA gene was expressed in Saccharomyces cerevisiae, and the heterologous enzyme was purified. The protein was monomeric, migrating at 49 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and eluting at 36 kDa upon gel filtration. AbfA showed maximal activity at 55°C and between pH 3.5 and pH 4. The enzyme had a K _m value for p-nitrophenyl-α-l-arabinofuranoside of 3.7 mM and a V _max of 34.8 μmol min⁻¹ mg protein⁻¹. Arabinose acted as a noncompetitive inhibitor with a K _i of 38.4 mM. The enzyme released arabinose from maize fiber, oat spelt arabinoxylan, and wheat arabinoxylan, but not from larch wood arabinogalactan or α-1,5-debranched arabinan. AbfA displayed low activity against α-1,5-l-arabino-oligosaccharides. The enzyme acted synergistically with endo-β-1,4-xylanase in the breakdown of wheat arabinoxylan. Binding of AbfA to xylan from several sources confirmed the presence of a functional carbohydrate-binding module. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.