Whole body proteome response to a dietary lysine imbalance in zebrafish Danio rerio

Lysine (Lys) is an indispensable amino acid (AA) and is generally the first limiting AA in most vegetable proteins used in fish feeds. Lys availability may thus limit protein synthesis and accretion, and growth of fish. Metabolic effects of dietary Lys imbalance were examined by 2D-proteomics using zebrafish as model. The Control diet (Lys: 2.47 g kg(-1)) was based on zebrafish carcass AA profiles previously obtained. Two other experimental diets were deficient in Lys [Lys(-); 1.34 g kg(-1)] and Lys added in excess [Lys(+); 4.63 g kg(-1)]. Fish growth was monitored from 33 to 49 days post-fertilization and the whole body proteome screened by means of two-dimension gel electrophoresis and mass spectrometry. Growth rate was negatively affected in group Lys(-). Comparative proteomic analysis showed 45 spots differentially expressed among groups. Twenty-nine of these proteins were identified revealing proteins involved in muscle growth, energy and lipid metabolism, eye lens differentiation, chaperone activity and apoptosis. Lys deficiency is accompanied by a down-regulation of muscle proteins and up-regulation of proteins affected by fasting, energy deficit, growth arrest and apoptosis. Excess Lys was accompanied by an up-regulation of proteins related to glycolysis, steroidogenesis and sexual maturation.     

DNA barcoding of bark and ambrosia beetles reveals excessive NUMTs and consistent east‐west divergence across Palearctic forests

A comprehensive DNA barcoding library is very useful for rapid identification and detection of invasive pest species. We tested the performance of species identification in the economically most damaging group of wood‐boring insects – the bark and ambrosia beetles – with particular focus on broad geographical sampling across the boreal Palearctic forests. Neighbour‐joining and Bayesian analyses of cytochrome oxidase I (COI) sequences from 151 species in 40 genera revealed high congruence between morphology‐based identification and sequence clusters. Inconsistencies with morphological identifications included the discovery of a likely cryptic Nearctic species of Dryocoetes autographus, the possible hybrid origin of shared mitochondrial haplotypes in Pityophthorus micrographus and P. pityographus, and a possible paraphyletic Xyleborinus saxeseni. The first record of Orthotomicus suturalis in North America was confirmed by DNA barcoding. The mitochondrial data also revealed consistent divergence across the Palearctic or Holarctic, confirmed in part by data from the large ribosomal subunit (28S). Some populations had considerable variation in the mitochondrial barcoding marker, but were invariant in the nuclear ribosomal marker. These findings must be viewed in light of the high number of nuclear insertions of mitochondrial DNA (NUMTs) detected in eight bark beetle species, suggesting the possible presence of additional cryptic NUMTs. The occurrence of paralogous COI copies, hybridization or cryptic speciation demands a stronger focus on data quality assessment in the construction of DNA barcoding databases.     

Widespread Abundance of Functional Bacterial Amyloid in Mycolata and Other Gram-Positive Bacteria

Until recently, extracellular functional bacterial amyloid (FuBA) has been detected and characterized in only a few bacterial species, including Escherichia coli, Salmonella, and the gram-positive organism Streptomyces coelicolor. Here we probed gram-positive bacteria with conformationally specific antibodies and revealed the existence of FuBA in 12 of 14 examined mycolata species, as well as six other distantly related species examined belonging to the phyla Actinobacteria and Firmicutes. Most of the bacteria produced extracellular fimbriae, sometimes copious amounts of them, and in two cases large extracellular fibrils were also produced. In three cases, FuBA was revealed only after extensive removal of extracellular material by saponification, indicating that there is integrated attachment within the cellular envelope. Spores of species in the genera Streptomyces, Bacillus, and Nocardia were all coated with amyloids. FuBA was purified from Gordonia amarae (from the cell envelope) and Geodermatophilus obscurus, and they had the morphology, tinctorial properties, and β-rich structure typical of amyloid. The presence of approximately 9-nm-wide amyloids in the cell envelope of G. amarae was visualized by transmission electron microscopy analysis. We conclude that amyloid is widespread among gram-positive bacteria and may in many species constitute a hitherto overlooked integral part of the spore and the cellular envelope.The gram-positive bacterial group mycolata (mycolic acid-containing actinomycetes) comprises a number of genera with disease-causing species, including the severely pathogenic organisms Corynebacterium diphtheriae and Mycobacterium tuberculosis. The latter species is the leading cause of death due to a single infectious agent globally (17). Furthermore, mycolata have great environmental and economical impact, since several species (e.g., Gordonia spp.) may lead to unwanted foaming in wastewater treatment plants (10, 27, 43). M. tuberculosis was recently shown to use long entangled pili (MTP) to adhere to endothelium, eventually invading and infecting human and animal tissue (1). MTP''s morphology and tinctorial properties are very similar to those of the amyloid-like curli fibrils found in Escherichia coli and Salmonella species (7), although it has not been determined whether they contain the characteristic cross-β structure with β-strands perpendicular to the long fibril axis (44). In higher organisms, amyloid occurs mainly as an aberrant product of protein misfolding in, e.g., neurodegeneration and systemic amyloidosis, but bacteria are adept at turning amyloid to good use. In addition to the two bacteria mentioned above, functional bacterial amyloid (FuBA) has also been reported for streptomycetes (8) and xanthomonads (35). These examples are only the tip of the iceberg. Our recent in situ studies using WO2 antibodies specific for the amyloid conformation (36) in conjunction with 16S rRNA-targeted oligonucleotide probes for identification of the microbes revealed that amyloid-like adhesins are widespread in many phyla in environmental biofilms (29). In view of the occurrence of potential amyloid-like fibrils in one species belonging to the mycolata and the observed link between infection by a mycolata genus (Nocardia) and neurodegenerative Parkinson''s disease (13, 25, 26, 47), we have investigated this group of bacteria more closely for the presence of amyloid. Here we show that 12 of 14 different species of mycolata, as well as 6 of 6 other gram-positive bacteria, harbor amyloid. Furthermore, in some cases the amyloid can be visualized only after harsh saponification procedures which remove surrounding lipid molecules, indicating that the amyloid is deeply embedded in the cell envelope. Thus, amyloid may play a hitherto unappreciated central role in the composition of the bacterial envelope in many gram-positive bacteria.     

Revision of the genus Phloeoditica Schedl - with description of two new genera and two new species in Phloeosinini (Coleoptera, Curculionidae, Scolytinae)

The genus Phloeoditica Schedl currently includes four species from Southeast Asia. These species vary substantially in important morphological characters and indicate the existence of multiple genera for these species. A revision based on morphological and in part molecular data resulted in the transfer of Phloeoditica setosa to Pseudoxylechinus the erection of a new genus Asiophilus for Phloeoditica phloeosinoides and a new species Asiophilus macropunctatus from Vietnam. Another new genus with affinities to Phloeoditica is described based on the new species Microditica uniseriata from Thailand. The new genera are included in a revised key to the tribe Phloeosinini.     

<Emphasis Type="Italic">Staphylococcus aureus</Emphasis> sigma B-dependent emergence of small-colony variants and biofilm production following exposure to <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> 4-hydroxy-2-heptylquinoline-<Emphasis Type="Italic">N-</Emphasis> oxide

Background  

Staphylococcus aureus and Pseudomonas aeruginosa are often found together in the airways of cystic fibrosis (CF) patients. It was previously shown that the P. aeruginosa exoproduct 4-hydroxy-2-heptylquinoline-N-oxide (HQNO) suppresses the growth of S. aureus and provokes the emergence of small-colony variants (SCVs). The presence of S. aureus SCVs as well as biofilms have both been associated with chronic infections in CF.     

Phylogeny of a Macaronesian radiation: host-plant use and possible cryptic speciation in Liparthrum bark beetles

The Macaronesian islands are well known for their unique endemic floras of woody plants. Many of these unusual plant groups provide important novel resources for bark and wood boring beetles which breed in dead or moribund parts of their host plants. The bark beetle genus Liparthrum exploits a wide range of unusual host plants and has its highest proportion of species living on the Macaronesian Islands. We used DNA sequences of the mitochondrial Cytochrome Oxidase I gene and the nuclear Elongation Factor 1 alpha gene, and morphological characters, to estimate the phylogenetic relationships among species endemic to these archipelagos, and to trace the evolution of host-plant use. All parsimony and Bayesian analyses of the combined data, and maximum likelihood analyses of the molecular data, showed that species associated with Euphorbia are monophyletic. We also found genetic and subtle morphological evidence for three cases of cryptic speciation in one polyphyletic species associated with different Euphorbia plants, showing that high levels of host specialisation can occur also in insects breeding in older and very dry, dead plant tissues.     

Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon

Background  

Salmonid fishes are among the most widely studied model fish species but reports on systematic evaluation of reference genes in qRT-PCR studies is lacking.     

Extraordinary haplotype diversity in haplodiploid inbreeders: phylogenetics and evolution of the bark beetle genus Coccotrypes

Regular inbreeding by sib-mating is one of the most successful ecological strategies in the bark beetle family Scolytinae. Within this family, the many species (119) in Coccotrypes are found breeding in an exceptional variety of untraditional woody tissues different from bark and phloem. Species delineation by morphological criteria is extremely difficult, however, as in most other inbreeding groups of beetles, perhaps due to the unusual evolutionary dynamics characterizing sib-mating organisms. Hence, we here performed a phylogenetic analysis using molecular data in conjunction with morphological data to better understand morphological and ecological evolution in this sib-mating group. We used partial DNA sequences from the nuclear gene EF-alpha and the mitochondrial genes 12S and CO1 to elucidate patterns of morphological evolution, haplotype variation, and evolutionary pathways in resource use. Sequence variation was high among species and far above that expected at the species level (e.g., 19% for CO1 within Coccotrypes advena). The tendency for exhaustive sequence variation at deeper nodes resulted in ambiguous reconstructions of the deepest splits. However, all results suggested that species with the broadest diets were clustered in a single derived position-another piece of evidence against specialization as a derived evolutionary feature.     

Can large unmanaged trees replace ancient pollarded trees as habitats for lichenized fungi,non-lichenized fungi and bryophytes?

Management of ancient trees constitutes a major dilemma in the conservation of associated biodiversity. While traditional methods are often advocated, such practices may incur considerable costs and their effects have rarely been scientifically evaluated. We compared the communities of lichenized fungi, non-lichenized fungi, and bryophytes among equal number of coarse previously pollarded and unmanaged trees (n = 340). On 400 Ulmus glabra and 280 Fraxinus excelsior trees at 62 sites in Norway, we found 209 lichenized fungi, 128 non-lichenized fungi, and 115 bryophytes. Pollarded trees were richer in microhabitats than unmanaged trees and had significantly higher richness of bryophytes (ash) and non-lichenized fungi (ash and elm), the latter increasing with the availability of dead wood, cavities and coarse bark structure in pollarded trees. Further, the average total number of red-listed species, and red-listed lichenized fungi separately, were significantly higher on pollarded versus unmanaged trees, with diversity related to trunk circumference, depth of bark fissures and number of cavities. Our results underline the importance of microhabitats associated with old trees, but we cannot establish with certainty the importance of pollarding per se. Since we did not find any negative effect of canopy cover for community diversity, we assume that old trees with rich epiphytic communities can develop without management intervention. The high share (37 out of 49) of red-listed species occurring on unmanaged trees, and the fact that 11 red-listed species were found exclusively on unmanaged trees, may further indicate that unmanaged trees can with time replace the ancient pollarded trees as habitats for rich cryptogamic communities.     

Secondary structure alignment and direct optimization of 28S rDNA sequences provide limited phylogenetic resolution in bark and ambrosia beetles (Curculionidae: Scolytinae)

Phylogenetic relationships in Scolytinae were reconstructed from 107 DNA sequences that spanned the D2 and D3 expansion segments, and related core regions of the nuclear large ribosomal subunit (28S). Sequences were analysed by parsimony and Bayesian analyses of aligned sequences aided by a new secondary structure model for the D2–D3 domains. Direct optimization was performed on ambiguous alignment regions in combination with fixed states optimization of unambiguous regions, but performed poorly compared to the Bayesian and parsimony analyses. Generally, the phylogenetic signal mainly resolved relationships within tribes, while deeper divergences were either not resolved or received marginal support. In addition to confirming several previously established clades, we found that Micracini formed the sister group to Cactopinus , a group of mainly cactus feeding scolytine beetles. Furthermore, Ipini was monophyletic with Pseudips and Acanthotomicus subtending to the most basal node of that clade. The monophyly of Corthylini, which consists of the bark and cone feeding Pityophtorina and the ambrosia fungus-feeding Corthylina, was supported in some of the analyses. A close relationship was found between Phloeotribus and the two Phloeosinini genera Chramesus and Pseudochramesus , suggesting an evolutionary trajectory for the origin of a lamellate antennal club in Phloeotribus .