Managing ecological traps: Logging and sapsucker nest predation by bears

We tested the equal preference ecological trap hypothesis for breeding yellow-bellied sapsuckers (Sphyrapicus varius) along a time-since-harvest gradient (1–5 yr, 16–20 yr, 21–25 yr, and >60 yr) in selection system-logged hardwood forests in Algonquin Provincial Park, Ontario. Yellow-bellied sapsuckers preferred 1–5 year and >60-year-old cuts equally and more than 16–20 year and 21–25-year-old cuts. More-abundant arthropod food and/or higher-quality sap resources may have attracted yellow-bellied sapsuckers to 1–5 year and >60-year-old cuts. Only 52% of pairs raised fledglings in 1- to 5-year-old cuts during years when nest predation by American black bears (Ursus americanus) was common, the incidence of which was negatively related to increased availability of American beech (Fagus grandifolia) nuts from the previous autumn. By contrast, 88% of pairs raised fledglings in all years in >60-year-old cuts. One- to 5-year-old cuts were demographic sinks that represent equal-preference ecological traps in years when nest predation by bears was common, whereas >60-year-old cuts were always demographic sources. High-quality habitat cues for nesting yellow-bellied sapsuckers appear to be retained for 1–5 years after selection system logging but fail to deliver safe nest sites. Cavities excavated in heart-rot-infected nest trees are least likely to be depredated because cavity walls are typically harder and deter entry by depredating bears. Retaining more potential nest trees per ha at harvest (especially American beech with heart-rot) may increase the proportion of sapsucker nests that are excavated in bear-resistant trees, thereby reducing nest predation and increasing fecundity. © 2012 The Wildlife Society.     

Population structure and behaviour of crop-raiding elephants in Kibale National Park, Uganda

We examined patterns of crop raiding by elephants across gender and age classes in relation to elephant life history and sociobiology and estimated the quantitative contribution of crops to elephant diet in Kibale National Park (KNP). Elephant dung‐boli sizes were used to estimate age and sex, while the presence of crop remains in the dung of crop‐raiding elephants was used as evidence of repeated raiding. To estimate the expected proportion of elephants raiding per age class, the age distribution of raiders was compared with the age distribution of all KNP elephants. Elephants raiding crops were predominantly males. They began raiding in expected proportions at 10–14 years while a higher than expected proportion raided crops at 20–24 years. These results suggest that crop raiding is initiated at an age when male elephants leave their families and a large proportion of elephants raid when they are approaching reproductive competition. Evidence from dung of crop raiders, suggests that repeated raiding increases with age. Crop raiders derived 38% of their daily forage from the short time spent raiding, consistent with expectations of foraging theory. Males may be more likely to learn crop raiding because they are socially more independent and experience intense mating competition than females.     

N-Terminal-oriented Proteogenomics of the Marine Bacterium Roseobacter Denitrificans Och114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) Labeling and Diagonal Chromatography

Given the ease of whole genome sequencing with next-generation sequencers, structural and functional gene annotation is now purely based on automated prediction. However, errors in gene structure are frequent, the correct determination of start codons being one of the main concerns. Here, we combine protein N termini derivatization using (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP Ac-OSu) as a labeling reagent with the COmbined FRActional DIagonal Chromatography (COFRADIC) sorting method to enrich labeled N-terminal peptides for mass spectrometry detection. Protein digestion was performed in parallel with three proteases to obtain a reliable automatic validation of protein N termini. The analysis of these N-terminal enriched fractions by high-resolution tandem mass spectrometry allowed the annotation refinement of 534 proteins of the model marine bacterium Roseobacter denitrificans OCh114. This study is especially efficient regarding mass spectrometry analytical time. From the 534 validated N termini, 480 confirmed existing gene annotations, 41 highlighted erroneous start codon annotations, five revealed totally new mis-annotated genes; the mass spectrometry data also suggested the existence of multiple start sites for eight different genes, a result that challenges the current view of protein translation initiation. Finally, we identified several proteins for which classical genome homology-driven annotation was inconsistent, questioning the validity of automatic annotation pipelines and emphasizing the need for complementary proteomic data. All data have been deposited to the ProteomeXchange with identifier PXD000337.Recent developments in mass spectrometry and bioinformatics have established proteomics as a common and powerful technique for identifying and quantifying proteins at a very broad scale, but also for characterizing their post-translational modifications and interaction networks (1, 2). In addition to the avalanche of proteomic data currently being reported, many genome sequences are established using next-generation sequencing, fostering proteomic investigations of new cellular models. Proteogenomics is a relatively recent field in which high-throughput proteomic data is used to verify coding regions within model genomes to refine the annotation of their sequences (2–8). Because genome annotation is now fully automated, the need for accurate annotation for model organisms with experimental data is crucial. Many projects related to genome re-annotation of microorganisms with the help of proteomics have been recently reported, such as for Mycoplasma pneumoniae (9), Rhodopseudomonas palustris (10), Shewanella oneidensis (11), Thermococcus gammatolerans (12), Deinococcus deserti (13), Salmonella thyphimurium (14), Mycobacterium tuberculosis (15, 16), Shigella flexneri (17), Ruegeria pomeroyi (18), and Candida glabrata (19), as well as for higher organisms such as Anopheles gambiae (20) and Arabidopsis thaliana (4, 5).The most frequently reported problem in automatic annotation systems is the correct identification of the translational start codon (21–23). The error rate depends on the primary annotation system, but also on the organism, as reported for Halobacterium salinarum and Natromonas pharaonis (24), Deinococcus deserti (21), and Ruegeria pomeroyi (18), where the error rate is estimated above 10%. Identification of a correct translational start site is essential for the genetic and biochemical analysis of a protein because errors can seriously impact subsequent biological studies. If the N terminus is not correctly identified, the protein will be considered in either a truncated or extended form, leading to errors in bioinformatic analyses (e.g. during the prediction of its molecular weight, isoelectric point, cellular localization) and major difficulties during its experimental characterization. For example, a truncated protein may be heterologously produced as an unfolded polypeptide recalcitrant to structure determination (25). Moreover, N-terminal modifications, which are poorly documented in annotation databases, may occur (26, 27).Unfortunately, the poor polypeptide sequence coverage obtained for the numerous low abundance proteins in current shotgun MS/MS proteomic studies implies that the overall detection of N-terminal peptides obtained in proteogenomic studies is relatively low. Different methods for establishing the most extensive list of protein N termini, grouped under the so-called “N-terminomics” theme, have been proposed to selectively enrich or improve the detection of these peptides (2, 28, 29). Large N-terminome studies have recently been reported based on resin-assisted enrichment of N-terminal peptides (30) or terminal amine isotopic labeling of substrates (TAILS) coupled to depletion of internal peptides with a water-soluble aldehyde-functionalized polymer (31–35). Among the numerous N-terminal-oriented methods (2), specific labeling of the N terminus of intact proteins with N-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinamide (TMPP-Ac-OSu)¹ has proven reliable (21, 36–39). TMPP-derivatized N-terminal peptides have interesting properties for further LC-MS/MS mass spectrometry: (1) an increase in hydrophobicity because of the trimethoxyphenyl moiety added to the peptides, increasing their retention times in reverse phase chromatography, (2) improvement of their ionization because of the introduction of a positively charged group, and (3) a much simpler fragmentation pattern in tandem mass spectrometry. Other reported approaches rely on acetylation, followed by trypsin digestion, and then biotinylation of free amino groups (40); guanidination of lysine lateral chains followed by N-biotinylation of the N termini and trypsin digestion (41); or reductive amination of all free amino groups with formaldehyde preceeding trypsin digestion (42). Recently, we applied the TMPP method to the proteome of the Deinococcus deserti bacterium isolated from upper sand layers of the Sahara desert (13). This method enabled the detection of N-terminal peptides allowing the confirmation of 278 translation initiation codons, the correction of 73 translation starts, and the identification of non-canonical translation initiation codons (21). However, most TMPP-labeled N-terminal peptides are hidden among the more abundant internal peptides generated after proteolysis of a complex proteome, precluding their detection. This results in disproportionately fewer N-terminal validations, that is, 5 and 8% of total polypeptides coded in the theoretical proteomes of Mycobacterium smegmatis (37) and Deinococcus deserti (21) with a total of 342 and 278 validations, respectively.An interesting chromatographic method to fractionate peptide mixtures for gel-free high-throughput proteome analysis has been developed over the last years and applied to various topics (43, 44). This technique, known as COmbined FRActional DIagonal Chromatography (COFRADIC), uses a double chromatographic separation with a chemical reaction in between to change the physico-chemical properties of the extraneous peptides to be resolved from the peptides of interest. Its previous applications include the separation of methionine-containing peptides (43), N-terminal peptide enrichment (45, 46), sulfur amino acid-containing peptides (47), and phosphorylated peptides (48). COFRADIC was identified as the best method for identification of N-terminal peptides of two archaea, resulting in the identification of 240 polypeptides (9% of the theoretical proteome) for Halobacterium salinarum and 220 (8%) for Natronomonas pharaonis (24).Taking advantage of both the specificity of TMPP labeling, the resolving power of COFRADIC for enrichment, and the increase in information through the use of multiple proteases, we performed the proteogenomic analysis of a marine bacterium from the Roseobacter clade, namely Roseobacter denitrificans OCh114. This novel approach allowed us to validate and correct 534 unique proteins (13% of the theoretical proteome) with TMPP-labeled N-terminal signatures obtained using high-resolution tandem mass spectrometry. We corrected 41 annotations and detected five new open reading frames in the R. denitrificans genome. We further identified eight distinct proteins showing direct evidence for multiple start sites.     

Sequence analysis and receptor specificity of the hemagglutinin of a recent influenza H2N2 virus isolated from chicken in North America

Influenza viruses bind host cells following an interaction between the viral hemagglutinin (HA) protein and host cell sialylated glycoproteins and glycolipids. Differences in binding affinities of the HAs for different types of sialic acid linkages (α2-3 vs. α2-6) contribute to determining the host range of an influenza virus. The ability of an avian influenza virus HA to bind the human form of the receptor may be one requirement for an avian virus to propagate in the human population. In this paper, we describe the characterization of the HA from an H2N2 virus isolated from a Pennsylvania chicken farm in 2004. Sequence analysis revealed that this HA is a member of the Eurasian clade, and receptor binding studies show that it maintains its specificity for the avian influenza virus α2-3 linked sialic acid receptor.     

Renal nerves and nNOS: roles in natriuresis of acute isovolumetric sodium loading in conscious rats

It was hypothesized that renal sympathetic nerve activity (RSNA) and neuronal nitric oxide synthase (nNOS) are involved in the acute inhibition of renin secretion and the natriuresis following slow NaCl loading (NaLoad) and that RSNA participates in the regulation of arterial blood pressure (MABP). This was tested by NaLoad after chronic renal denervation with and without inhibition of nNOS by S-methyl-thiocitrulline (SMTC). In addition, the acute effects of renal denervation on MABP and sodium balance were assessed. Rats were investigated in the conscious, catheterized state, in metabolic cages, and acutely during anesthesia. NaLoad was performed over 2 h by intravenous infusion of hypertonic solution (50 micromol.min(-1).kg body mass(-1)) at constant body volume conditions. SMTC was coinfused in amounts (20 microg.min(-1).kg(-1)) reported to selectively inhibit nNOS. Directly measured MABPs of acutely and chronically denervated rats were less than control (15% and 9%, respectively, P < 0.005). Plasma renin concentration (PRC) was reduced by renal denervation (14.5 +/- 0.2 vs. 19.3 +/- 1.3 mIU/l, P < 0.005) and by nNOS inhibition (12.4 +/- 2.3 vs. 19.6 +/- 1.6 mlU/l, P < 0.005). NaLoad reduced PRC (P < 0.05) and elevated MABP modestly (P < 0.05) and increased sodium excretion six-fold, irrespective of renal denervation and SMTC. The metabolic data demonstrated that renal denervation lowered sodium balance during the first days after denervation (P < 0.001). These data show that renal denervation decreases MABP and renin secretion. However, neither renal denervation nor nNOS inhibition affects either the renin down-regulation or the natriuretic response to acute sodium loading. Acute sodium-driven renin regulation seems independent of RSNA and nNOS under the present conditions.     

Bedraggled, a putative transporter, influences the tissue polarity complex during the R3/R4 fate decision in the Drosophila eye

The tissue polarity pathway is required for the establishment of epithelial polarity in a variety of vertebrate and invertebrate organs. Core tissue polarity proteins act in a dynamically regulated complex to direct the polarization of the Drosophila eye. We report the identification and characterization of bedraggled (bdg), a novel gene that regulates one output of the tissue polarity pathway--the establishment of the R3/R4 photoreceptor fates. bdg encodes a novel, putative transporter protein and interacts genetically with all of the core polarity genes to influence the specification of the R3 and R4 cell fates. Finally, bdg is required for both viability and the initial stages of imaginal disc development.     

The effects of geographic origin and antibiotic treatment on the gut symbiotic communities of Bactrocera oleae populations

The olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), is the major insect pest of olive orchards (Olea europaea L.), causing extensive damages on cultivated olive crops worldwide. Due to its economic importance, it has been the target species for a variety of population control approaches including the sterile insect technique (SIT). However, the inefficiency of the current mass‐rearing techniques impedes the successful application of area‐wide integrated pest management programs with an SIT component. It has been shown that insect mass rearing and quality of sterile insects can be improved by the manipulation of the insect gut microbiota and probiotic applications. In order to exploit the gut bacteria, it is important to investigate the structure of the gut microbial community. In the current study, we characterized the gut bacterial profile of two wild olive fruit fly populations introduced in laboratory conditions using next generation sequencing of two regions of the 16S rRNA gene. We compared the microbiota profiles regarding the geographic origin of the samples. Additionally, we investigated potential changes in the gut bacteria community before and after the first exposure of the wild adult flies to artificial adult diet with and without antibiotics. Various genera – such as Erwinia, Providencia, Enterobacter, and Klebsiella – were detected for the first time in B. oleae. The most dominant species was Candidatus Erwinia dacicola Capuzzo et al. and it was not affected by the antibiotics in the artificial adult diet used in the first generation of laboratory rearing. Geographic origin affected the overall structure of the gut community of the olive fruit fly, but antibiotic treatment in the first generation did not significantly alter the gut microbiota community.