NAADP mobilizes Ca2+ from a thapsigargin-sensitive store in the nuclear envelope by activating ryanodine receptors

Ca2+ release from the envelope of isolated pancreatic acinar nuclei could be activated by nicotinic acid adenine dinucleotide phosphate (NAADP) as well as by inositol 1,4,5-trisphosphate (IP3) and cyclic ADP-ribose (cADPR). Each of these agents reduced the Ca2+ concentration inside the nuclear envelope, and this was associated with a transient rise in the nucleoplasmic Ca2+ concentration. NAADP released Ca2+ from the same thapsigargin-sensitive pool as IP3. The NAADP action was specific because, for example, nicotineamide adenine dinucleotide phosphate was ineffective. The Ca2+ release was unaffected by procedures interfering with acidic organelles (bafilomycin, brefeldin, and nigericin). Ryanodine blocked the Ca2+-releasing effects of NAADP, cADPR, and caffeine, but not IP3. Ruthenium red also blocked the NAADP-elicited Ca2+ release. IP3 receptor blockade did not inhibit the Ca2+ release elicited by NAADP or cADPR. The nuclear envelope contains ryanodine and IP3 receptors that can be activated separately and independently; the ryanodine receptors by either NAADP or cADPR, and the IP3 receptors by IP3.     

Stable Golgi-mitochondria complexes and formation of Golgi Ca(2+) gradients in pancreatic acinar cells

We have determined the localization of the Golgi with respect to other organelles in living pancreatic acinar cells and the importance of this localization to the establishment of Ca(2+) gradients over the Golgi. Using confocal microscopy and the Golgi-specific fluorescent probe 6-((N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)hexanoyl)sphingosine, we found Golgi structures localizing to the outer edge of the secretory granular region of individual acinar cells. We also assessed Golgi positioning in acinar cells located within intact pancreatic tissue using two-photon microscopy and found a similar localization. The mitochondria segregate the Golgi from lateral regions of the plasma membrane, the nucleus, and the basal part of the cytoplasm. The Golgi is therefore placed between the principal Ca(2+) release sites in the apical region of the cell and the important Ca(2+) sink formed by the peri-granular mitochondria. During acetylcholine-induced cytosolic Ca(2+) signals in the apical region, large Ca(2+) gradients form over the Golgi (decreasing from trans- to cis-Golgi). We further describe a novel, close interaction of the peri-granular mitochondria and the Golgi apparatus. The mitochondria and the Golgi structures form very close contacts, and these contacts remain stable over time. When the cell is forced to swell, the Golgi and mitochondria remain juxtaposed up to the point of cell lysis. The strategic position of the Golgi (closer to release sites than the bulk of the mitochondrial belt) makes this organelle receptive to local apical Ca(2+) transients. In addition the Golgi is ideally placed to be preferentially supplied by ATP from adjacent mitochondria.     

Production of functional antibodies generated in a nonlytic insect cell expression system

A monoclonal antibody directed against the type 2 adenovirus (Ad2) penton base protein was cloned and expressed in Spodoptera frugiperda (Sf9) cells using a nonlytic vector system. The coding sequences for the immunoglobulin light and heavy chains were placed under the control of the Orgyia pseudotsugata multicapsid nucleopolyhedrosis virus immediate-early 2 (OpIE2) promoter. Transfected Sf9 cells continuously secreted the antibody which retained the ability to recognize both native and recombinant Ad2 penton base proteins. Bifunctional penton base antibodies were also generated by fusing a gene for a growth factor or a cytokine at the 3' end of the Ig constant heavy chain domain. The quantity and activity of recombinant antibodies generated in the nonlytic insect cell system could be determined relatively quickly compared to other expression systems. Moreover, these recombinant proteins were not subjected to proteolytic degradation as frequently occurs during baculovirus-mediated cell lysis and the levels of recombinant antibodies produced in the nonlytic system were comparable to those reported for cytolytic baculovirus vectors.     

Density compensation in neotropical primate communities: evidence from 56 hunted and nonhunted Amazonian forests of varying productivity

Density compensation is a community-level phenomenon in which increases in the abundance of some species may offset the population decline, extirpation, or absence of other potentially interacting competitors. In this paper we examine the evidence for density compensation in neotropical primate assemblages using data from 56 hunted and nonhunted, but otherwise undisturbed, forest sites of Amazonia and the Guianan shields from which population density estimates are available for all diurnal primate species. We found good evidence of density compensation of the residual assemblage of nonhunted mid-sized species where the large-bodied (ateline) species had been severely reduced in numbers or driven to local extinction by subsistence hunters. Only weak evidence for density compensation, however, was detected in small-bodied species. These conclusions are based on the effects of ordinal measures of hunting pressure on the aggregate primate biomass across different size classes after controlling for the effects of forest type and productivity. These results are interpreted primarily in relation to patterns of niche partitioning between different primate functional groups or ecospecies. This study suggests that while overhunting drastically reduces the average body size in multi-species assemblages of forest vertebrates, depletion of large-bodied species is only partially offset (i.e. undercompensated) by smaller taxa. Received: 2 November 1998 / Accepted: 8 September 1999     

Variations in Amazon forest productivity correlated with foliar nutrients and modelled rates of photosynthetic carbon supply

The rate of above-ground woody biomass production, W(P), in some western Amazon forests exceeds those in the east by a factor of 2 or more. Underlying causes may include climate, soil nutrient limitations and species composition. In this modelling paper, we explore the implications of allowing key nutrients such as N and P to constrain the photosynthesis of Amazon forests, and also we examine the relationship between modelled rates of photosynthesis and the observed gradients in W(P). We use a model with current understanding of the underpinning biochemical processes as affected by nutrient availability to assess: (i) the degree to which observed spatial variations in foliar [N] and [P] across Amazonia affect stand-level photosynthesis; and (ii) how these variations in forest photosynthetic carbon acquisition relate to the observed geographical patterns of stem growth across the Amazon Basin. We find nutrient availability to exert a strong effect on photosynthetic carbon gain across the Basin and to be a likely important contributor to the observed gradient in W(P). Phosphorus emerges as more important than nitrogen in accounting for the observed variations in productivity. Implications of these findings are discussed in the context of future tropical forests under a changing climate.     

Quantifying density dependence in a bird population using human disturbance

Although density dependence has long been recognised as vital to population regulation, there have been relatively few studies demonstrating it spatially in wildlife populations, often due to the confounding effects of variation in habitat quality. We report on a study of woodlarks Lullula arborea, a species of European conservation concern, breeding on lowland heath in Dorset, England. We take the novel approach of utilising the birds’ response to human disturbance, which resulted in much of the variation in density but had no direct impact on demographic rates. Within years, in sites with greater density there were smaller mean chick masses, lower post-fledging survival, and higher rates of nestling mortality attributed to starvation. The effects on clutch size and fledging success were confounded by the area of grassland within a site. There was no effect on brood size. Density dependence also operated within sites between years: as density increased there were reductions in mean chick mass and post-fledging survival, while nestling mortality attributed to starvation increased. Density-dependent effects on clutch size were only weakly regulatory, whereas density-dependent starvation and post-fledging mortality rates contributed strongly to differences in overall breeding output. Heavier chicks (when 7 days old) were significantly more likely to fledge and less likely to starve. Broods with heavier chicks were more likely to supply recruits to the breeding population. Nestling mass was not a factor in survival in the immediate post-fledging period, suggesting that density-dependent processes act independently on this stage. We conclude that the number of birds per hectare of suitable habitat is a valid means of expressing density, and that habitat acts as a surrogate for food abundance through which density dependence operates on the woodlark population.     

Placement,survival and predator identity of Eurasian Curlew Numenius arquata nests on lowland grass-heath

ABSTRACT

Capsule

Within the UK’s largest lowland Eurasian Curlew Numenius arquata population, curlew preferentially nested on physically disturbed (treated) than undisturbed (control) grassland, and low nest survival rates were primarily attributable to predation by Red Fox Vulpes vulpes.     

Impact of variance components on reliability of absolute quantification using digital PCR

Background

Digital polymerase chain reaction (dPCR) is an increasingly popular technology for detecting and quantifying target nucleic acids. Its advertised strength is high precision absolute quantification without needing reference curves. The standard data analytic approach follows a seemingly straightforward theoretical framework but ignores sources of variation in the data generating process. These stem from both technical and biological factors, where we distinguish features that are 1) hard-wired in the equipment, 2) user-dependent and 3) provided by manufacturers but may be adapted by the user. The impact of the corresponding variance components on the accuracy and precision of target concentration estimators presented in the literature is studied through simulation.

Results

We reveal how system-specific technical factors influence accuracy as well as precision of concentration estimates. We find that a well-chosen sample dilution level and modifiable settings such as the fluorescence cut-off for target copy detection have a substantial impact on reliability and can be adapted to the sample analysed in ways that matter. User-dependent technical variation, including pipette inaccuracy and specific sources of sample heterogeneity, leads to a steep increase in uncertainty of estimated concentrations. Users can discover this through replicate experiments and derived variance estimation. Finally, the detection performance can be improved by optimizing the fluorescence intensity cut point as suboptimal thresholds reduce the accuracy of concentration estimates considerably.

Conclusions

Like any other technology, dPCR is subject to variation induced by natural perturbations, systematic settings as well as user-dependent protocols. Corresponding uncertainty may be controlled with an adapted experimental design. Our findings point to modifiable key sources of uncertainty that form an important starting point for the development of guidelines on dPCR design and data analysis with correct precision bounds. Besides clever choices of sample dilution levels, experiment-specific tuning of machine settings can greatly improve results. Well-chosen data-driven fluorescence intensity thresholds in particular result in major improvements in target presence detection. We call on manufacturers to provide sufficiently detailed output data that allows users to maximize the potential of the method in their setting and obtain high precision and accuracy for their experiments.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-283) contains supplementary material, which is available to authorized users.