The timing of birds' breeding seasons: a review of experiments that manipulated timing of breeding

Reproductive success usually declines in the course of the season, which may be a direct effect of breeding time, an effect of quality (individuals with high phenotypic or environmental quality breeding early), or a combination of the two. Being able to distinguish between these possibilities is crucial when trying to understand individual variation in annual routines, for instance when to breed, moult and migrate. We review experiments with free-living birds performed to distinguish between the 'timing' and 'quality' hypothesis. 'Clean' manipulation of breeding time seems impossible, and we therefore discuss strong and weak points of different manipulation techniques. We find that the qualitative results were independent of manipulation technique (inducing replacement clutches versus cross-fostering early and late clutches). Given that the two techniques differ strongly in demands made on the birds, this suggests that potential experimental biases are limited. Overall, the evidence indicated that date and quality are both important, depending on fitness component and species, although evidence for the date hypothesis was found more frequently. We expected both effects to be prevalent, since only if date per se is important, does an incentive exist for high-quality birds to breed early. We discuss mechanisms mediating the seasonal decline in reproductive success, and distinguish between effects of absolute date and relative date, for instance timing relative to seasonal environmental fluctuations or conspecifics. The latter is important at least in some cases, suggesting that the optimal breeding time may be frequency dependent, but this has been little studied. A recurring pattern among cross-fostering studies was that delay experiments provided evidence for the quality hypothesis, while advance experiments provided evidence for the date hypothesis. This indicates that late pairs are constrained from producing a clutch earlier in the season, presumably by the fitness costs this would entail. This provides us with a paradox: evidence for the date hypothesis leads us to conclude that quality is important for the ability to breed early.     

Improving consensus structure by eliminating averaging artifacts

Background  

Common structural biology methods (i.e., NMR and molecular dynamics) often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA) is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, including unphysical bond lengths and angles.     

Bacterial colonization of a fumigated alkaline saline soil

After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m^?1, and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8 %) compared to the unfumigated soil (34.2 %), while that of the Bacteroidetes decreased from 16.2 % in the unfumigated soil to 8.8 % in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7 % in the unfumigated soil to 25.7 %. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.     

Great tits growing old: selective disappearance and the partitioning of senescence to stages within the breeding cycle

Deterioration of reproductive traits with age is observed in an increasing number of species. Although such deterioration is often attributed to reproductive senescence, a within-individual decline in reproductive success with age, few studies on wild animals have focused on direct fitness measures while accounting for selective disappearance and terminal effects, and to our knowledge none have determined how senescence effects arise from underlying reproductive traits. We show for female great tits that such an approach helps understanding of the onset, impact and architecture of senescence. Cross-sectional analysis of 49 years of breeding data shows annual recruit production to decline from 3.5 years of age, this decline affecting 9 per cent of females each year. Longitudinal analyses, however, show that selective disappearance of poor-quality breeders partly masks senescence, which in fact starts at 2.8 years and affects 21 per cent of females each year. There is no evidence for abrupt terminal effects. Analyses of underlying traits show no deterioration in clutch size, but significant declines in brood size and fledgling number. Furthermore, these traits contribute −9, 12 and 39 per cent to the senescent decline in recruit production, respectively. Besides providing detailed knowledge of the patterns and architecture of senescence in a natural population, these results illustrate the importance of modelling individual variation, and facilitate study of the underlying mechanisms of senescence.     

Biohydrogenation of linoleic acid by Clostridium sporogenes, Clostridium bifermentans, Clostridium sordellii and Bacteroides sp.

Abstract Several strains of Clostridium bifermentans, Clostridium sporogenes and Clostridium sordellit and one strain of Bacteroides sp. hydrogenate linoleic acid into transvaccenic acid in vitro following the same pathway. Linoleic acid (18:2; 9- cis , 12- cis ) was first isomerised into 9- cis , 11- trans -octadecadienoic acid, after which the 9- cis double bond was reduced. These species also hydrogenated linoleic acid into an octadecenoic acid in vivo when mono-associated with gnotobiotic rats. Several other species of Clostridium and Bacteroides did not hydrogenate linoleic acid.     

A microfluidic competitive immuno-aggregation assay for high sensitivity cell secretome detection

We report a high-sensitivity cell secretome detection method using competitive immuno-aggregation and a micro-Coulter counter. A target cell secretome protein competes with anti-biotin-coated microparticles (MPs) to bind with a biotinylated antibody (Ab), causing decreased aggregation of the functionalized MPs and formation of a mixture of MPs and aggregates. In comparison, without the target cell secretome protein, more microparticles are functionalized, and more aggregates are formed. Thus, a decrease in the average volume of functionalized microparticles/aggregates indicates an increase in cell secretome concentration. This volume change is measured by the micro-Coulter counter, which is used to quantitatively estimate the cell secretome concentration. Vascular endothelial growth factor (VEGF), one of the key cell secretome proteins that regulate angiogenesis and vascular permeabilization, was used as the target protein to demonstrate the sensing principle. A standard calibration curve was generated by testing samples with various VEGF concentrations. A detection range from 0.01 ng/mL to 100.00 ng/mL was achieved. We further demonstrated the quantification of VEGF concentration in exogenous samples collected from the secretome of human mesenchymal stem cells (hMSCs) at different incubation times. The results from the assay agree well with the results of a parallel enzyme-linked immunoabsorbent assay (ELISA) test, indicating the specificity and reliability of the competitive immuno-aggregation assay. With its simple structure and easy sample preparation, this assay not only enables high sensitivity detection of VEGF but also can be readily extended to other types of cell secretome analysis as long as the specific Ab is known.     

5-Fluoronicotine,noranhydroecgonine, and pyridyl-methylpyrrolidine release acetylcholine and biogenic amines in rat cortex in vivo

The effects of nicotinic receptor agonists 5-fluoronicotine, noranhydroecgonine and pyridyl-methylpyrrolidine on the cortical release of acetylcholine (ACh), norepinephrine (NE), dopamine (DA) and serotonin (5-HT) were investigated with microdialysis in rat. 5-Fluoronicotine significantly elevated ACh to 76% above basal values and DA to 69% above baseline. Pyridyl-methylpyrrolidine significantly increased the release of ACh to 39% above basal values and NE to 63% above baseline. Noranhydroecgonine significantly elevated NE to 64% above basal values and DA to 147% above baseline. 5-Fluoronicotine did not affect NE release; pyridylmethylpyrrolidine did not alter DA release; and noranhydroecgonine did not significantly elevate ACh release. None of these agonists increased the release of 5-HT. All responses were blocked by prior administration of mecamylamine, a nicotinic receptor antagonist. The distinctive neurotransmitter-related profiles for the three agonists are suggestive of activity at subtypes of nicotinic receptors, an effect that may be related to the structural diversity of these compounds.