Anthraquinone-based bird repellent for sunflower crops

Non-lethal alternatives are needed to manage bird damage to confectionery and oilseed sunflower crops (Helianthus annuus). Ring-necked pheasants (Phasianus colchicus) can cause localized damage to newly planted sunflower, and blackbirds (Icterids) damage ripening sunflower annually in the United States of America. We conducted seed germination experiments, a repellent efficacy study with ring-necked pheasants and Avipel^® repellent (a.i. 50% 9,10-anthraquinone), and laboratory and field efficacy studies with common grackles (Quiscalus quiscula) and Avipel^®-treated confectionery sunflower. Compared to the germination of seeds not treated with anthraquinone, we observed no negative effects of up to 12,223 ppm, 14,104 ppm, and 11,569 ppm anthraquinone seed treatments for germination of confectionery sunflower, oilseed sunflower, and canola seeds, respectively. Pheasants avoided emergent sunflower seedlings (12 days post-planting) from 15,800 ppm anthraquinone seed treatments during a caged preference test (P = 0.045). We observed a positive concentration–response relationship (P = 0.001) and predicted a threshold concentration (i.e., 80% repellency) of 9200 ppm anthraquinone for common grackles offered Avipel^®-treated confectionery sunflower seeds. Grackles also reliably discriminated between untreated sunflower and seeds treated with 1300 ppm anthraquinone in captivity (P < 0.001). During our field efficacy study for ripening confectionery sunflower, we observed 18% damage among anthraquinone-treated enclosures and 64% damage among untreated enclosures populated with common grackles (P < 0.001). Harvested seed mass averaged 2.54 kg (dry weight) among treated enclosures and 1.24 kg among untreated enclosures (P < 0.001). Our laboratory and field efficacy data provide a reliable basis for planning future field applications of anthraquinone-based repellents for protection of sunflower crops. Supplemental field efficacy studies are necessary for development of an effective avian repellent and management of avian depredation of ripening agricultural crops, including oilseed sunflower.     

Zooplankton interactions in an enclosure experiment: insights from stable isotope analyses

1. Density gradients of cladocerans and copepods were generated in an enclosure experiment to compare the impact on the plankton of a filter feeder (Daphnia hyalina × galeata) with that of more selective feeders (calanoid and cyclopoid copepods). The experiment was conducted in situ over 25 days during spring in a mesotrophic lake, Schöhsee, Germany. 2. The plankton community was monitored regularly. Daphniids were able to graze on the phytoplankton present, which mainly consisted of small (<1000 μm³) species, whereas copepods did not show any impact on algae. 3. At the end of the experiment, Daphnia and remaining cyclopoid copepods were harvested and sorted manually, prior to analyses for stable isotopes of carbon and nitrogen. Daphniids from mesocosms stocked purely with differing densities of Daphnia showed little variability in stable isotope values, whereas those that thrived in enclosure bags together with copepods exhibited lower δ¹³C values. 4. The change in Daphniaδ¹³C indicates a change of food sources, modified by the presence of the copepods: the higher the mean abundance of copepods in the enclosures, the more ¹³C‐depleted the daphniids. Increasing abundance of high nucleic acid (HNA) bacteria in the copepod bags may account for the trend in Daphniaδ¹³C via increased grazing on the bacteria themselves, or via grazing on phytoplankton utilising isotopically light CO₂ from respiratory release. 5. Cyclopoid copepod stable isotope signatures were related to Daphnia and copepod abundances in copepod bags, suggesting that cyclopoids preyed on the available zooplankton.     

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities

Background

To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell lines affected with either HPV16 or HPV18 were assayed at 8 sequential time points for gene expression (mRNA) and gene copy number (DNA) using high-resolution microarrays. Available methods for temporal differential expression analysis are not designed for integrative genomic studies.

Results

Here, we present a method that allows for the identification of differential gene expression associated with DNA copy number changes over time. The temporal variation in gene expression is described by a generalized linear mixed model employing low-rank thin-plate splines. Model parameters are estimated with an empirical Bayes procedure, which exploits integrated nested Laplace approximation for fast computation. Iteratively, posteriors of hyperparameters and model parameters are estimated. The empirical Bayes procedure shrinks multiple dispersion-related parameters. Shrinkage leads to more stable estimates of the model parameters, better control of false positives and improvement of reproducibility. In addition, to make estimates of the DNA copy number more stable, model parameters are also estimated in a multivariate way using triplets of features, imposing a spatial prior for the copy number effect.

Conclusion

With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-327) contains supplementary material, which is available to authorized users.     

3-methylcrotonyl-CoA carboxylase deficiency: Clinical, biochemical, enzymatic and molecular studies in 88 individuals

ABSTRACT: BACKGROUND: Isolated 3-methylcrotonyl-CoA carboxylase (MCC) deficiency is an autosomal recessive disorder of leucine metabolism caused by mutations in MCCC1 or MCCC2 encoding the alpha and beta subunit of MCC, respectively. The phenotype is highly variable ranging from acute neonatal onset with fatal outcome to asymptomatic adults. METHODS: We report clinical, biochemical, enzymatic and mutation data of 88 MCC deficient individuals, 53 identified by newborn screening, 26 diagnosed due to clinical symptoms or positive family history and 9 mothers, identified following the positive newborn screening result of their baby. RESULTS: Fifty-seven percent of patients were asymptomatic while 43% showed clinical symptoms, many of which were probably not related to MCC deficiency but due to ascertainment bias. However, 12 patients (5 of 53 identified by newborn screening) presented with acute metabolic decompensations. We identified 15 novel MCCC1 and 16 novel MCCC2 mutant alleles. Additionally, we report expression studies on 3 MCCC1 and 8 MCCC2 mutations and show an overview of all 132 MCCC1 and MCCC2 variants known to date. CONCLUSIONS: Our data confirm that MCC deficiency, despite low penetrance, may lead to a severe clinical phenotype resembling classical organic acidurias. However, neither the genotype nor the biochemical phenotype is helpful in predicting the clinical course.     

Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis

Using sequence data from the 28S ribosomal RNA (rRNA) genes of selected vertebrates, we investigated the effects that constraints imposed by secondary structure have on the phylogenetic analysis of rRNA sequence data. Our analysis indicates that characters from both base-pairing regions (stems) and non-base-pairing regions (loops) contain phylogenetic information, as judged by the level of support of the phylogenetic results compared with a well-established tree based on both morphological and molecular data. The best results (the greatest level of support of well-accepted nodes) were obtained when the complete data set was used. However, some previously supported nodes were resolved using either the stem or loop bases alone. Stem bases sustain a greater number of compensatory mutations than would be expected at random, but the number is < 40% of that expected under a hypothesis of perfect compensation to maintain secondary structure. Therefore, we suggest that in phylogenetic analyses, the weighting of stem characters be reduced by no more than 20%, relative to that of loop characters. In contrast to previous suggestions, we do not recommend weighting of stem positions by one-half, compared with that of loop positions, because this overcompensates for the constraints that selection imposes on the secondary structure of rRNA.      

Histological, histochemical and ultrastructural studies on the bulbus arteriosus of the sticklebacks, Gasterosteus aculeatus and Pungitius pungitius (Pisces: Teleostei)

The bulbar wall has three layers. Its lining consists of squamous-columnar endothelial cells that store neutral mucopolysaccharides and are PAS-positive. They do not contain large amounts of acid phosphatase, acid mucopolysaccharides, glycogen or lipids. A morphometric analysis shows that 32% of the cell volume in Pungitius and 12% in Gasterosteus is occupied by specific granules, 100–600 nm in diameter. According to X-ray probe micro-analysis, these granules bind chromium ions, even though the endothelial cells do not contain catecholamines. Rootlets, packed with plasmalemmal vesicles, extend from the endothelial cells into the middle layer of the bulbus. Here, smooth muscle cells alternate with elastic fibres. The staining reactions of bulbar elastica are compared with those in the mammalian aorta and the ligamentum nuchae. The outer layer of the bulbus is visceral pericardium and beneath its covering mesothelial cells are numerous collagen fibres, non-myelinated nerves, occasional fibroblasts and melanocytes. Scanning electron microscopy shows that the bulbar lining is thrown into longitudinal folds, but that there are no trabeculae subdividing the lumen.
Many features of the bulbus arteriosus may be related to the low systolic pressures of teleosts and to the proximity of their heart and gills. In contrast to mammals, only a small part of the arterial system can act as a windkessel. The bulbus is thus more distensible than the mammalian aorta and must lie within the pericardial cavity so that its greater excursions can be accommodated. Perhaps because the bulbus is so distensible, it has elastic fibres rather than lamellae. This in turn may affect the organization of the smooth muscle cells which do not form "span muscles" as in some mammalian aortae. Like most cells in the bulbus, they are joined to others by desmosomes. Evidently, firm cohesion is important in highly distensible vessels.     

Experimental habituation of aggression in the sea anemone Actinia equina

Behavioural plasticity in Actinia equina (L.) was examined in experimental contests using a range of pedal disc colour phenotypes, which characterize 3 known, ecologically distinct morphs. With repeated pairing of individuals in auto-phenotypic encounters, habituation was easily induced in the 2 mid-shore morphs, but was not obvious in the less aggressive, low-shore form. Subsequent pairing with a different partner revealed that anemones remained aggressive towards a novel opponent. Following novel contact, repairing of the dark red pedal phenotype with the original partner provided some evidence of retention of habituation to a previous opponent, and thus of a specific inducible memory.