Selective predation,parasitism, and trophic cascades in a bluegill–<Emphasis Type="Italic">Daphnia</Emphasis>–parasite system

As disease incidence increases worldwide, there is increased interest in determining the factors controlling parasitism in natural populations. Recently, several studies have suggested a possible role of predation in reducing parasitism, but this idea has received little experimental attention. Here, I present the results of an experiment in which I manipulated predation rate in large field enclosures to test the effects of predation on parasitism using a bluegill predator–Daphnia host–yeast parasite system. Based on previous work showing high bluegill sunfish selectivity for infected over uninfected Daphnia, I anticipated that predators would reduce infection levels. Contrary to expectations, predation did not reduce infection prevalence. Instead, there were large epidemics in all treatments, followed by reductions of host density to very low levels. As Daphnia density decreased, phytoplankton abundance increased and water clarity decreased, suggesting a parasite-driven trophic cascade. Overall, these results suggest that selective predation does not always reduce infection prevalence, and that parasites have the potential to drastically reduce host densities even in the presence of selective predators. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The diverse and pervasive chemistries of the <Emphasis Type="Italic">α</Emphasis>-keto acid dependent enzymes

The number of identified and confirmed α-keto acid dependent oxygenases is increasing rapidly. All of these enzymes have a relatively simple liganding arrangement for a single ferrous ion but collectively conduct a highly diverse set of chemistries. While hydroxylations and a variety of oxidation reactions have been most commonly observed, new reactions involving dealkylations, epimerizations and halogenations have recently been discovered. In this minireview we present what is known of the α-keto acid dependent enzymes and offer an argument that the chemistry that is unique to each enzyme occurs only after the production of a pivotal ferryl-oxo intermediate. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The genera <Emphasis Type="Italic">Bispira</Emphasis> Krøyer, 1856 and <Emphasis Type="Italic">Stylomma</Emphasis> Knight-Jones, 1997 (Polychaeta,Sabellidae): systematic revision,relationships with close related taxa and new species from Australia

A cladistic analysis undertaken to test monophyly of Bispira and Stylomma (including new species of both genera) and to ascertain relationships with related taxa reveals that Bispira is paraphyletic without the inclusion of Pseudobranchiomma and Branchiomma, and that Stylomma is monophyletic due to the presence of a structure on the dorsal basal flanges which has never been described before. New species of Bispira and Stylomma from Australia are described. Bispira serrata n. sp., differs from the other species of the genus in having serrated radiolar flanges whereas all other Bispira species have smooth flanges or lack them, and also by the shape of the thoracic and abdominal uncini, which are short-handled and have 2–3 rows of big teeth above the main fang, instead of having medium-sized handles and small, numerous rows of teeth over the main fang. Stylomma juani n. sp., is characterized by the presence of serrated radiolar flanges and unpaired compound eyes along the branchial radioles, whereas other species in the genus have smooth radiolar flanges and subterminal compound radiolar eyes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: K. Martens     

Combinational biosynthesis of a fluorescent cyanobacterial holo-α-allophycocyanin in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Allophycocyanin (APC) is a phycobiliprotein with various biological and pharmacological properties. An expression vector containing five essential genes in charge of biosynthesis of cyanobacterial APC holo-α subunit (holo-ApcA) was constructed, resulting in over-expression of a fluorescent holo-ApcA in E. coli. After being cultured for 16 h, the dry cell density reached 22.5 g l⁻¹, and the expression of holo-HT-ApcA was up to 1 g l⁻¹ broth. The recombinant protein showed similar spectral features to native APC. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Yu Yang and Baosheng Ge have contributed equally to this paper.     

Identification of a <Emphasis Type="Italic">Lotus</Emphasis> viral pathogen

A virus collection was used to identify a pathogen suitable for laboratory use with the model legume Lotus japonicus. Several Lotus species or L. japonicus accessions were tested and various degrees of susceptibility to the Arabis mosaic virus derived from barley (ArMV-ba) were found. Virus multiplication and persistence in Lotus tissue were examined, as well as plant responses to it. Sensitivity to the virus among the accessions and species is discussed in light of their geographical origin. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Mitogen-activated protein kinase OsMPK6 negatively regulates rice disease resistance to bacterial pathogens

Mitogen-activated protein kinase (MAPK) cascades play important roles in diverse developmental and physiological processes of plants, including pathogen-induced defense responses. Although at least 17 rice MAPKs have been identified and more than half of these MAPK genes have been shown to be pathogen or elicitor responsive, the exact role of most of the MAPKs in host-pathogen interaction is unknown. Here we report that OsMPK6 is an important regulator in rice disease resistance. Suppressing OsMPK6 or knocking out of OsMPK6 enhanced rice resistance to different races of Xanthomonas oryzae pv. oryzae, causing bacterial blight, one of the most devastating diseases of rice worldwide. The resistant plants showed increased expression of a subset of defense-responsive genes functioning in the NH1 (an Arabidopsis NPR1 orthologue)-involved defense signal transduction pathway. These results suggest that OsMPK6 functions as a repressor to regulate rice defense responses upon bacterial invasion. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Cloning of milk-derived bioactive peptides in <Emphasis Type="Italic">Streptococcus thermophilus</Emphasis>

The enzymatic breakdown of milk proteins releases bioactive peptides. Two such peptides are the 11-residue antimicrobial peptide from bovine lactoferrin (BL-11) and the 12-residue hypotensive peptide from α_s1-casein (C-12). These two peptides have now been cloned in Streptococcus thermophilus to develop strains that enhance the functionality and nutritional value of dairy food products. Nucleic acid sequences encoding the peptides were generated by overlapping PCR and were subsequently cloned into a new expression vector under control of the ST₂₂₀₁ promoter. S. thermophilus transformants were successfully identified using GFP as a selectable marker. The presence of the synthetic gene constructs in S. thermophilus was confirmed by PCR. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Do teashirt family genes specify trunk identity? Insights from the single tiptop/teashirt homolog of Tribolium castaneum

The Drosophila teashirt gene acts in concert with the homeotic selector (Hox) genes to specify trunk (thorax and abdomen) identity. There has been speculation that this trunk-specifying function might be very ancient, dating back to the common ancestor of insects and vertebrates. However, other evidence suggests that the role of teashirt in trunk identity is not well conserved even within the Insecta. To address this issue, we have analyzed the function of Tc-tiotsh, the lone teashirt family member in the red flour beetle, Tribolium castaneum. Although Tc-tiotsh is important for aspects of both embryonic and imaginal development including some trunk features, we find no evidence that it acts as a trunk identity gene. We discuss this finding in the context of recent insights into the evolution and function of the Drosophila teashirt family genes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Multiple subfamilies of mariner transposable elements are present in stalk-eyed flies (Diptera: Diopsidae)

The Diopsid stalk-eyed flies are an increasingly well-studied group. Presented here is evidence of the first known transposable elements discovered in these flies. The vertumnana mariner subfamily was identified in the Diopsini tribe, but could not be amplified in species of the Sphyracephalini tribe. PCR screening with degenerate primers revealed that multiple mariner subfamilies are present within the Diopsidae. Most of the sequenced elements appear to be pseudogenes; however two subfamilies are shown to be evolving under purifying selection, raising the possibility that mariner is active in some Diopsid species. Evidence is presented of a possible horizontal transfer event involving an unknown Teleopsis species and the Tephritid fly Bactrocera neohumeralis. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Tuareg, a novel miniature-inverted repeat family of pearl millet (Pennisetum glaucum) related to the PIF superfamily of maize

Miniature-inverted repeat transposable elements (MITEs) are abundantly repeated in plant genomes and are especially found in genic regions where they could contribute regulatory elements for gene expression. We describe with molecular and cytological tools the first MITE family reported in pearl millet: Tuareg. It was initially detected in the pearl millet ortholog of Teosinte-branched1, an important developmental gene involved in the domestication of maize. The Tuareg family was amplified recently in the pearl millet genome and elements were found more abundant in wild than in domesticated plants. We found that they shared similarity in their terminal repeats with the previously described mPIF MITEs and that they are also present in other Pennisetum species, in maize and more distantly related grasses. The Tuareg family may be part of MITEs activated by PIF-like transposases and it could have been mobile since pearl millet domestication. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users. O. Robin contributed the FISH and fiber-FISH hybridizations.     

Multiplex specific PCR for identification of the genera Actinopolyspora and Streptomonospora, two groups of strictly halophilic filamentous actinomycetes

The genera Actinopolyspora and Streptomonospora are two groups of extremely halophilic filamentous actinomycetes. Members of these two genera are isolated frequently, probably due to the high occurrence of these actinomycetes in the hypersaline soil environment. Although members of these genera can be identified by micromorphological criteria, the extensive chemotaxonomic characterization of each new isolates is a time-consuming task which cannot always be undertaken when handling large numbers of isolates as is the case in natural products screening programmes. In this work, the design of one set of genus-specific PCR primers which allows rapid detection of members of the genus Actinopolyspora by means of PCR amplification is presented. And we developed a multiplex PCR protocol for identification of the species of the genera Actinopolyspora and Streptomonospora, simultaneously. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Fast co-evolution of sevenless and bride of sevenless in endopterygote insects

Activation of Ras signaling by the receptor tyrosine kinase Sevenless plays important roles during retinal patterning and male germline development in Drosophila. Sevenless is orthologous to the vertebrate receptor tyrosine kinase c-ros. Remarkably, vertebrate ligands of c-Ros as well as non-Drosophila orthologs of the Sevenless ligand Bride of sevenless have remained elusive. Using newly available insect genome sequence information, we investigated the evolutionary conservation of the seven transmembrane domain protein gene bride of sevenless. Single orthologs were identified in the genomes of mosquito, flour beetle, and honeybee due to strong sequence conservation in the seven transmembrane domain. The extracellular region, however, is only detectably conserved within but not outside Diptera. Analysis of domain-specific substitution rates demonstrates correlated fast rates of evolutionary change in the extracellular domains of both bride of sevenless and sevenless. The rapid pace of sequence change explains why Sevenless ligands are difficult to detect by sequence similarity in distantly related phyla. Second, the conservation of bride of sevenless in flour beetle and honeybee raises the possibility of conserved Sevenless signaling controlled patterning processes in endopterygote insects. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Study of tauopathies by comparing <Emphasis Type="Italic">Drosophila</Emphasis> and human <Emphasis Type="Italic">tau</Emphasis> in <Emphasis Type="Italic">Drosophila</Emphasis>

The microtubule-binding protein tau has been investigated for its contribution to various neurodegenerative disorders. However, the findings from transgenic studies, using the same tau transgene, vary widely among different laboratories. Here, we have investigated the potential mechanisms underlying tauopathies by comparing Drosophila (d-tau) and human (h-tau) tau in a Drosophila model. Overexpression of a single copy of either tau isoform in the retina results in a similar rough eye phenotype. However, co-expression of Par-1 with d-tau leads to lethality, whereas co-expression of Par-1 with h-tau has little effect on the rough eye phenotype. We have found analogous results by comparing larval proteomes. Through genetic screening and proteomic analysis, we have identified some important potential modifiers and tau-associated proteins. These results suggest that the two tau genes differ significantly. This comparison between species-specific isoforms may help to clarify whether the homologous tau genes are conserved. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. This study was supported by the National Science Foundation of China (30270341; 30630028), the Multidisciplinary Program (Brain and Mind) of the Chinese Academy of Sciences, the Major State Basic Research Program (“973 program”; G2000077800; G2006CB806600; 2006CB911003), the Precedent Project of Important Intersectional Disciplines in the Knowledge Innovation Engineering of the Chinese Academy of Sciences (KJCX1-09-03).     

Biochemical characterization of the minichromosome maintenance protein from the archaeon Thermoplasma acidophilum

Minichromosome maintenance (MCM) proteins are thought to function as the replicative helicases in archaea. Studies have shown that the MCM complex from the thermoacidophilic euryarchaeon Thermoplasma acidophilum (TaMCM) has some properties not reported in other archaeal MCM helicases. Here, the biochemical properties of the TaMCM are studied. The protein binds single-stranded DNA, has DNA-dependent ATPase activity and ATP-dependent 3′ → 5′ helicase activity. The optimal helicase conditions with regard to temperature, pH and salinity are similar to the intracellular conditions in T. acidophilum. It is also found that about 1,000 molecules of TaMCM are present per actively growing cell. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The distributions of howling monkeys (<Emphasis Type="Italic">Alouatta pigra</Emphasis> and <Emphasis Type="Italic">A. palliata</Emphasis>) in southeastern Mexico and Central America

We compared the distributions of Alouatta palliata and A. pigra in southeastern Mexico and Central America with geographic and ecological features to infer current barriers and ecological preferences. Distribution data were obtained from museum specimen localities, study sites, historic records and field surveys and integrated into digital elevation and ecosystem maps using GIS. A. pigra evidently occurs at a number of sites above 2,000 m, where temperatures can even drop below zero on some days of the year, thus indicating a broader ecological tolerance than previously reported. Both species occupy a number of vegetation types and can be found in seasonal and nonseasonal forests. We identified the highland massif of northern Central America and its associated coniferous and subalpine vegetation as a geographic barrier that separates the species. In the past, distribution maps for these species have indicated adjacent contiguous ranges, but we propose that they are largely separated by these mountains. There are two contact zones: a broad area of sympatry north of the highland massif in Mexico and a narrow zone in eastern Guatemala where parapatry is maintained by a river barrier and where only A. pigra occurs in the high elevations and cooler habitats inland. We explore an alternative biogeographic scenario for the split of the two species that accounts for the current distribution and differences in elevation and cold tolerances. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Nodal regulates neural tube formation in the <Emphasis Type="Italic">Ciona intestinalis</Emphasis> embryo

Overexpression of a lefty orthologue, Ci-lefty, caused a failure of neural tube closure in the protochordate ascidian Ciona intestinalis. The body bent dorsally, and anterior–posterior elongation was inhibited. A similar phenotype was observed in embryos treated with SB431542, an inhibitor of Nodal receptors, suggesting that Ci-Lefty antagonized Nodal signaling as reported in other deuterostome species. Overexpression of Ci-nodal also resulted in a similar phenotype, suggesting that a correct quantity and/or a spatial restriction of Nodal signaling are important for the neural tube to form. In addition to known Ci-Nodal target genes, orthologues of Zic (Ci-ZicL) and cdx (Ci-cdx) were activated by Ci-Nodal. Expression of a dominant negative Ci-cdx caused defects in neural tube formation similar to those obtained on treatment with SB431542 or overexpression of Ci-lefty. A regulatory cascade composed of Ci-Nodal, Ci-ZicL, and Ci-Cdx may play an important role in neural tube formation in the Ciona embryo. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Enhancement of stress tolerance in transgenic tobacco plants constitutively expressing AtIpk2β, an inositol polyphosphate 6-/3-kinase from <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Inositol phosphates (IPs) and their turnover products have been implicated to play important roles in stress signaling in eukaryotic cells. In higher plants genes encoding inositol polyphosphate kinases have been identified previously, but their physiological functions have not been fully resolved. Here we expressed Arabidopsis inositol polyphosphate 6-/3-kinase (AtIpk2β) in two heterologous systems, i.e. the yeast Saccharomyces cerevisiae and in tobacco (Nicotiana tabacum), and tested the effect on abiotic stress tolerance. Expression of AtIpk2β rescued the salt-, osmotic- and temperature-sensitive growth defects of a yeast mutant strain (arg82Δ) that lacks inositol polyphosphate multikinase activity encoded by the ARG82/IPK2 gene. Transgenic tobacco plants constitutively expressing AtIpk2β under the control of the Cauliflower Mosaic Virus 35S promoter were generated and found to exhibit improved tolerance to diverse abiotic stresses when compared to wild type plants. Expression patterns of various stress responsive genes were enhanced, and the activities of anti-oxidative enzymes were elevated in transgenic plants, suggesting a possible involvement of AtIpk2β in plant stress responses. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genome-wide analysis of intronless genes in rice and <Emphasis Type="Italic">Arabidopsis</Emphasis>

Intronless genes, a characteristic feature of prokaryotes, constitute a significant portion of the eukaryotic genomes. Our analysis revealed the presence of 11,109 (19.9%) and 5,846 (21.7%) intronless genes in rice and Arabidopsis genomes, respectively, belonging to different cellular role and gene ontology categories. The distribution and conservation of rice and Arabidopsis intronless genes among different taxonomic groups have been analyzed. A total of 301 and 296 intronless genes from rice and Arabidopsis, respectively, are conserved among organisms representing the three major domains of life, i.e., archaea, bacteria, and eukaryotes. These evolutionarily conserved proteins are predicted to be involved in housekeeping cellular functions. Interestingly, among the 68% of rice and 77% of Arabidopsis intronless genes present only in eukaryotic genomes, approximately 51% and 57% genes have orthologs only in plants, and thus may represent the plant-specific genes. Furthermore, 831 and 144 intronless genes of rice and Arabidopsis, respectively, referred to as ORFans, do not exhibit homology to any of the genes in the database and may perform species-specific functions. These data can serve as a resource for further comparative, evolutionary, and functional analysis of intronless genes in plants and other organisms. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

New taxa of Neosartorya and Aspergillus in Aspergillus section Fumigati

Three new species of Neosartorya and one new Aspergillus of section Fumigati are proposed using a polyphasic approach based on morphology, extrolite production and partial β-tubulin, calmodulin, and actin gene sequences. The phylogenetic analyses using the three genes clearly show that the taxa grouped separately from the known species and confirmed the phenotypic differences. Neosartorya denticulata is characterized by its unique denticulate ascospores with a prominent equatorial furrow; N. assulata by well developed flaps on the convex surface of the ascospores which in addition have two distinct equatorial crests and N. galapagensis by a funiculose colony morphology, short and narrow conidiophores and ascospores with two wide equatorial crests with a microtuberculate convex surface. Aspergillus turcosus can be distinguished by velvety, gray turquoise colonies and short, loosely columnar conidial heads. The four new taxa also have unique extrolite profiles, which contain the mycotoxins gliotoxin and viriditoxin in N. denticulate; apolar compounds provisionally named NEPS in N. assulata and gregatins in N. galapagensis. A. turcosus produced kotanins. N. denticulata sp. nov., N. assulata sp. nov., N. galapagensis sp. nov., and A. turcosus sp. nov. are described and illustrated. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Spatiotemporal metabolic regulation of anthocyanin and related compounds during the development of marginal picotee petals in <Emphasis Type="Italic">Petunia hybrida</Emphasis> (Solanaceae)

Structures and levels of anthocyanin-related compounds were analyzed during the development of marginal picotee petals in white-center and white-marginal cultivars of Petunia hybrida. In the white site of a white-center cultivar, higher concentrations of quercetin derivatives possessing 7-O-glucoside and/or 3′-O-glucoside occurred than in the colored site, suggesting that these two quercetin glycosylation steps are site-specifically regulated. The boundary areas of petal coloration were composed of cells showing various color densities, whose uniformity among adjacent cells varied between these cultivars. These results indicate diversity in spatiotemporal regulation of anthocyanin biosynthesis and flavonol glycosylations between Petunia cultivars during marginal picotee formation. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.