Rook Spring Seed Dispersal in the Agricultural Landscape – Frugivory, Granivory or Accidental Transport?

Seed dispersal seems to be extremely important in agrocoenoses where suitable habitats (patches) are surrounded by an unfavourable environment (matrix). The role of the rook Corvus frugilegus, an omnivorous bird, in seed dispersal was studied in the agricultural landscape of Eastern Poland. We analyzed 739 pellets produced by regurgitation, which were collected under breeding colonies in April, May and June. Our goal was to i) assess the structure of the seed pool in pellets; ii) evaluate the temporal variation in the pellet seed pool on two different time scales; iii) compare the species composition of seeds in pellets and vegetation under the rook nests. Seeds were present in 18 % of pellets; 571 seeds were found, half of them belonging to dry-fruited species, without any obvious adaptations to endozoochory. These seeds could be an additional source of food, or they could have been accidentally swallowed during foraging for other food items. Taking into consideration the abundance of the rook population, we assessed the mean number of seeds transferred by one bird to be from 4 seeds per month in April and up to 160 seeds in June. The most important factor responsible for qualitative and quantitative structure of seed pool in pellets is the time when pellets were regurgitated. The type and availability of food determines the number and species structure of dispersed seeds. The comparison of the species structure of the seed pool in pellets and of the herb layer under the breeding colonies showed that the rook could effectively disperse seeds of weeds, meadow and ruderal species, that could germinate under the dense canopy of trees at the studied sites.     

Atrial natriuretic factor receptor guanylate cyclase signaling: new ATP-regulated transduction motif

ANF-RGC membrane guanylate cyclase is the receptor for the hypotensive peptide hormones, atrial natriuretic factor (ANF) and type B natriuretic peptide (BNP). It is a single transmembrane spanning protein. Binding the hormone to the extracellular domain activates its intracellular catalytic domain. This results in accelerated production of cyclic GMP, a second messenger in controlling blood pressure, cardiac vasculature, and fluid secretion. ATP is the obligatory transducer of the ANF signal. It works through its ATP regulated module, ARM, which is juxtaposed to the C-terminal side of the transmembrane domain. Upon interaction, ATP induces a cascade of temporal and spatial changes in the ARM, which, finally, result in activation of the catalytic module. Although the exact nature and the details of these changes are not known, some of these have been stereographed in the simulated three-dimensional model of the ARM and validated biochemically. Through comprehensive techniques of steady state, time-resolved tryptophan fluorescence and Forster Resonance Energy Transfer (FRET), site-directed and deletion-mutagenesis, and reconstitution, the present study validates and explains the mechanism of the model-based predicted transduction role of the ARM’s structural motif, ⁶⁶⁹WTAPELL⁶⁷⁵. This motif is critical in the ATP-dependent ANF signaling. Molecular modeling shows that ATP binding exposes the ⁶⁶⁹WTAPELL⁶⁷⁵ motif, the exposure, in turn, facilitates its interaction and activation of the catalytic module. These principles of the model have been experimentally validated. This knowledge brings us a step closer to our understanding of the mechanism by which the ATP-dependent spatial changes within the ARM cause ANF signaling of ANF-RGC.     

Long-term effects of drainage and hay-removal on nutrient dynamics and limitation in the Biebrza mires,Poland

To provide a reference for wetlands elsewhere we analysed soil nutrients and the vegetation of floodplains and fens in the relatively undisturbed Biebrza-valley, Poland. Additionally, by studying sites along a water-table gradient, and by comparing pairs of mown and unmown sites, we aimed with exploring long-term effects of drainage and annual hay-removal on nutrient availabilities and vegetation response. In undrained fens and floodplains, N mineralization went slowly (0–30 kg N ha⁻¹ year⁻¹) but it increased strongly with decreasing water table (up to 120 kg N ha⁻¹ year⁻¹). Soil N, P and K pools were small in the undisturbed mires. Drainage had caused a shift from fen to meadow species and the disappearance of bryophytes. Biomass of vascular plants increased with increasing N mineralization and soil P. Annual hay-removal tended to have reduced N mineralization and soil K pools, but it had increased soil P. Moreover, N concentrations in vascular plants were not affected, but P and K concentrations and therefore N:P and N:K ratios tended to be changed. Annual hay-removal had induced a shift from P to K limitation in the severely drained fen, and from P to N limitation in the floodplain. The low nutrient availabilities and productivity of the undisturbed Biebrza mires illustrate the vulnerability of such mires to eutrophication in Poland and elsewhere. In nutrient-enriched areas, hay removal may prevent productivity increase of the vegetation, but also may severely alter N:P:K stoichiometry, induce K-limitation at drained sites, and alter vegetation structure and composition.     

Membrane Topology of Human Presenilin-1 in SK-N-SH Cells Determined by Fluorescence Correlation Spectroscopy and Fluorescent Energy Transfer

Presenilin-1 (PS1) protein acts as passive ER Ca²⁺ leak channels that facilitate passive Ca²⁺ leak across ER membrane. Mutations in the gene encoding PS1 protein cause neurodegeneration in the brains of patients with familial Alzheimer’s disease (FAD). FADPS1 mutations abrogate the function of ER Ca²⁺ leak channel activity in human neuroblastoma SK-N-SH cells in vitro (Das et al., J Neurochem 122(3):487–500, 2012) and in mouse embryonic fibroblasts. Consequently, genetic deletion or mutations of the PS1 gene cause calcium (Ca²⁺) signaling abnormalities leading to neurodegeneration in FAD patients. By analogy with other known ion channels it has been proposed that the functional PS1 channels in ER may be multimers of several PS1 subunits. To test this hypothesis, we conjugated the human PS1 protein with an NH₂-terminal YFP-tag and a COOH-terminal CFP-tag. As expected YFP–PS1, and PS1–CFP were found to be expressed on the plasma membranes by TIRF microscopy, and both these fusion proteins increased ER Ca²⁺ leak channel activity similar to PS1 (WT) in SK-N-SH cells, as determined by functional calcium imaging. PS1–CFP was either expressed alone or together with YFP–PS1 into SK-N-SH cell line and the interaction between YFP–PS1 and PS1–CFP was determined by Förster resonance energy transfer analysis. Our results suggest interaction between YFP–PS1 and PS1–CFP confirming the presence of a dimeric or multimeric form of PS1 in SK-N-SH cells. Lateral diffusion of PS1–CFP and YFP–PS1 in the plasma membrane of SK-N-SH cells was measured in the absence or in the presence of glycerol by fluorescence correlation spectroscopy to show that both COOH-terminal and NH₂-terminal of human PS1 are located on the cytoplasmic side of the plasma membrane. Therefore, we conclude that both COOH-terminal and NH₂-terminal of human PS1 may also be oriented on the cytosolic side of ER membrane.     

Nests of Marsh harrier (Circus aeruginosus L.) as refuges of potentially phytopathogenic and zoopathogenic fungi

Birds’ nests may be refuges for various species of fungi including that which are potentially phytopathogenic and zoopathogenic. Among the 2449 isolates of fungi obtained from nests of Marsh harriers 96.8% belonged to filamentous fungi. In total, 37 genera were identified from 63 fungi species. Within the mycobiotas of the examined nests populations of fungi which are potentially pathogenic for humans, homoiothermous animals and plants dominated. Among 63 species, 46 (72%) were potentially pathogenic fungi of which 18 species were potentially phytopathogenic and 32 species were pathogenic for homoiothermous animals. Inter alia species of fungi were found in the Marsh harriers nests: Aspergillus fumigatus, Aspergillus flavus, Scopulariopsis brevicaulis, Chrysosporium keratinophilum and Fusarium poae, Fusarium sporotrichioides. In terms of numbers, dominant in Marsh harrier nests were fungi pathogenic to birds, other homoiothermous animals and humans. On that basis it was concluded that Marsh harrier nests are both a source of fungal infections for that species and one of the links in the epidemiological cycle of opportunistic fungi for humans.     

Different genomic relationship matrices for single-step analysis using phenotypic,pedigree and genomic information

Background

The incorporation of genomic coefficients into the numerator relationship matrix allows estimation of breeding values using all phenotypic, pedigree and genomic information simultaneously. In such a single-step procedure, genomic and pedigree-based relationships have to be compatible. As there are many options to create genomic relationships, there is a question of which is optimal and what the effects of deviations from optimality are.

Methods

Data of litter size (total number born per litter) for 338,346 sows were analyzed. Illumina PorcineSNP60 BeadChip genotypes were available for 1,989. Analyses were carried out with the complete data set and with a subset of genotyped animals and three generations pedigree (5,090 animals). A single-trait animal model was used to estimate variance components and breeding values. Genomic relationship matrices were constructed using allele frequencies equal to 0.5 (G05), equal to the average minor allele frequency (GMF), or equal to observed frequencies (GOF). A genomic matrix considering random ascertainment of allele frequencies was also used (GOF*). A normalized matrix (GN) was obtained to have average diagonal coefficients equal to 1. The genomic matrices were combined with the numerator relationship matrix creating H matrices.

Results

In G05 and GMF, both diagonal and off-diagonal elements were on average greater than the pedigree-based coefficients. In GOF and GOF*, the average diagonal elements were smaller than pedigree-based coefficients. The mean of off-diagonal coefficients was zero in GOF and GOF*. Choices of G with average diagonal coefficients different from 1 led to greater estimates of additive variance in the smaller data set. The correlation between EBV and genomic EBV (n = 1,989) were: 0.79 using G05, 0.79 using GMF, 0.78 using GOF, 0.79 using GOF*, and 0.78 using GN. Accuracies calculated by inversion increased with all genomic matrices. The accuracies of genomic-assisted EBV were inflated in all cases except when GN was used.

Conclusions

Parameter estimates may be biased if the genomic relationship coefficients are in a different scale than pedigree-based coefficients. A reasonable scaling may be obtained by using observed allele frequencies and re-scaling the genomic relationship matrix to obtain average diagonal elements of 1.     

Fluorescence intensity decays of 2-aminopurine solutions: lifetime distribution approach

The fluorescent adenine analog 2-aminopurine (2AP) has been used extensively to monitor conformational changes and macromolecular binding events involving nucleic acids because its fluorescence properties are highly sensitive to changes in chemical environment. Furthermore, site-specific incorporation of 2AP permits local DNA and RNA conformational events to be discriminated from the global structural changes monitored by UV-Vis spectroscopy and circular dichroism. However, although the steady-state fluorescence properties of 2AP have been well defined in diverse settings, interpretation of 2AP fluorescence lifetime parameters has been hampered by the heterogeneous nature of multiexponential 2AP intensity decays observed across populations of microenvironments. To resolve this problem, we tested the utility of multiexponential versus continuous Lorentzian lifetime distribution models to describe fluorescence intensity decays from 2AP in diverse chemical backgrounds and within the context of RNA. Heterogeneity was introduced into 2AP intensity decays by mixing solvents of differing polarities or by adding quenchers under high viscosity to evaluate the transient effect. Heterogeneity of 2AP fluorescence within the context of a synthetic RNA hairpin was introduced by structural remodeling using a magnesium salt. In each case except folded RNA (which required a bimodal distribution), 2AP lifetime properties were well described by single Lorentzian distribution functions, abrogating the need to introduce additional discrete lifetime subpopulations. Rather, heterogeneity in fluorescence decay processes was accommodated by the breadth of each distribution. This approach also permitted solvent relaxation effects on 2AP emission to be assessed by comparing lifetime distributions at multiple wavelengths. Together, these studies provide a new perspective for the interpretation of 2AP fluorescence lifetime properties that will further the utility of this fluorophore in analyses of the complex and heterogeneous structural microenvironments associated with nucleic acids.     

Fluorescence spectral properties of cyanine dye-labeled DNA oligomers on surfaces coated with silver particles

We examined the fluorescence spectral properties of DNA oligomers, labeled with Cy3 or Cy5, when bound to quartz surfaces coated with metallic silver particles. Prior to binding of labeled DNA the surfaces were treated with polylysine or 3-aminopropyl triethoxysilane or were coated with avidin for binding of biotinylated oligomers. The fluorescence intensities were increased an average of 8-fold on these surfaces. Despite the increased emission intensity, the photostability of the labeled DNA was the same or higher on the silver-coated surfaces than on the uncoated slides. The time-integrated intensities, that is the area under the intensity plots with continuous illumination, increased an average of 6-fold. In all cases the lifetimes were dramatically shortened on the silver particles, indicating an over 100-fold increase in the radiative decay rates. These results suggest the use of substrates containing silver particles for increased sensitivity of DNA detection on DNA arrays.     

Effects of metallic silver island films on resonance energy transfer between N,N'-(dipropyl)-tetramethyl- indocarbocyanine (Cy3)- and N,N'-(dipropyl)-tetramethyl- indodicarbocyanine (Cy5)-labeled DNA

Resonance energy transfer (RET) is typically limited to distances below 60 A, which can be too short for some biomedical assays. We examined a new method for increasing the RET distances by placing donor- and acceptor-labeled DNA oligomers between two slides coated with metallic silver particles. A N,N'-(dipropyl)-tetramethylindocarbocyanine donor and a N,N'-(dipropyl)-tetramethylindodicarbocyanine acceptor were covalently bound to opposite 5' ends of complementary 23 base pair DNA oligomers. The transfer efficiency was 25% in the absence of silver particles or if only one slide was silvered, and it increased to an average value near 64% between two silvered slides. The average value of the Forster distance increased from 58 to 77 A. The energy transfer data were analyzed with a model assuming two populations of donor-acceptor pairs: unaffected and affected by silver island films. In an affected fraction of about 28%, the apparent energy transfer efficiency is near 87% and the Forster distance increases to 119 A. These results suggest the use of metallic silver particles to increase the distances over which RET occurs in biomedical and biotechnology assays.