Population dynamics of three songbird species in a nestbox population in Central Europe show effects of density,climate and competitive interactions

Unravelling the contributions of density‐dependent and density‐independent factors in determining species population dynamics is a challenge, especially if the two factors interact. One approach is to apply stochastic population models to long‐term data, yet few studies have included interactions between density‐dependent and density‐independent factors, or explored more than one type of stochastic population model. However, both are important because model choice critically affects inference on population dynamics and stability. Here, we used a multiple models approach and applied log‐linear and non‐linear stochastic population models to time series (spanning 29 years) on the population growth rates of Blue Tits Cyanistes caeruleus, Great Tits Parus major and Pied Flycatchers Ficedula hypoleuca breeding in two nestbox populations in southern Germany. We focused on the roles of climate conditions and intra‐ and interspecific competition in determining population growth rates. Density dependence was evident in all populations. For Blue Tits in one population and for Great Tits in both populations, addition of a density‐independent factor improved model fit. At one location, Blue Tit population growth rate increased following warmer winters, whereas Great Tit population growth rates decreased following warmer springs. Importantly, Great Tit population growth rate also decreased following years of high Blue Tit abundance, but not vice versa. This finding is consistent with asymmetric interspecific competition and implies that competition could carry over to influence population dynamics. At the other location, Great Tit population growth rate decreased following years of high Pied Flycatcher abundance but only when Great Tit population numbers were low, illustrating that the roles of density‐dependent and density‐independent factors are not necessarily mutually exclusive. The dynamics of this Great Tit population, in contrast to the other populations, were unstable and chaotic, raising the question of whether interactions between density‐dependent and density‐independent factors play a role in determining the (in) stability of the dynamics of species populations.     

Validating and improving elastic network models with molecular dynamics simulations

Elastic network models (ENMs) are a class of simple models intended to represent the collective motions of proteins. In contrast to all‐atom molecular dynamics simulations, the low computational investment required to use an ENM makes them ideal for speculative hypothesis‐testing situations. Historically, ENMs have been validated via comparison to crystallographic B‐factors, but this comparison is relatively low‐resolution and only tests the predictions of relative flexibility. In this work, we systematically validate and optimize a number of ENM‐type models by quantitatively comparing their predictions to microsecond‐scale all‐atom simulations of three different G protein coupled receptors. We show that, despite their apparent simplicity, well‐optimized ENMs perform remarkably well, reproducing the protein fluctuations with an accuracy comparable to what one would expect from all‐atom simulations run for several hundred nanoseconds. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

The Nicotiana attenuata LECTIN RECEPTOR KINASE 1 is involved in the perception of insect feeding

The Nicotiana attenuata LECTIN RECEPTOR KINASE 1 (LecRK1) has been recently identified as a component of the mechanism used by plants to suppress the Manduca sexta-triggered accumulation of salicylic acid (SA). The suppression of the SA burst by LecRK1 allows for the unfettered induction of jasmonic acid (JA)-mediated defense responses against M. sexta herbivory. LecRK1 contains a multi-domain extracellular region composed of a G-type Lectin domain and a PAN-AP domain separated by a variable sequence with low similarity to an EGF domain. The LecRK1 intracellular region is composed of a single domain structure with predicted Ser/Thr protein kinase activity. The multi-domain structure of the extracellular region of LecRK1 adds a level of complexity in terms of the potential ligands that this receptor protein could recognize.     

Fibrosis and progression of Autosomal Dominant Polycystic Kidney Disease (ADPKD)

The age on onset of decline in renal function and end-stage renal disease (ESRD) in autosomal polycystic kidney disease (ADPKD) is highly variable and there are currently no prognostic tools to identify patients who will progress rapidly to ESRD. In ADPKD, expansion of cysts and loss of renal function are associated with progressive fibrosis. Similar to the correlation between tubulointerstitial fibrosis and progression of chronic kidney disease (CKD), in ADPKD, fibrosis has been identified as the most significant manifestation associated with an increased rate of progression to ESRD. Fibrosis in CKD has been studied extensively. In contrast, little is known about the mechanisms underlying progressive scarring in ADPKD although some commonality may be anticipated. Current data suggest that fibrosis associated with ADPKD shares at least some of the “classical” features of fibrosis in CKD (increased interstitial collagens, changes in matrix metalloproteinases (MMPs), over-expression of tissue inhibitor of metalloproteinase-1 (TIMP-1), over-expression of plasminogen activator inhibitor-1 (PAI-1) and increased transforming growth factor beta (TGFβ) but that there are also some unique and stage-specific features. Epithelial changes appear to precede and to drive interstitial changes leading to the proposal that development of fibrosis in ADPKD is biphasic with alterations in cystic epithelia precipitating changes in interstitial fibroblasts and that reciprocal interactions between these cell types drives progressive accumulation of extracellular matrix (ECM). Since fibrosis is a major component of ADPKD it follows that preventing or slowing fibrosis should retard disease progression with obvious therapeutic benefits. The development of effective anti-fibrotic strategies in ADPKD is dependent on understanding the precise mechanisms underlying initiation and progression of fibrosis in ADPKD and the role of the intrinsic genetic defect in these processes. This article is part of a Special Issue entitled: Polycystic Kidney Disease.     

Fragmented living: Behavioural ecology of primates in a forest fragment in the Lopé Reserve, Gabon

A 17-month study was made of the primates using a 9-ha “island” of forest, surrounded by savanna, in the northern part of the Lopé Reserve, Gabon. One group ofCercopithecus cephus (plus a young maleCercopithecus nictitans who was in permanent association with them) were resident in the fragment and groups of five other species of primates made visits during 127 days of observation:Pan troglodytes, 15 visits;Cercocebus albigena, 10;Colobus satanas, 3;Cercopithecus nictitans, 2;C. pogonias, 1. Visits were also made by lone males of three species,C. nictitans, Cercocebus albigena, andMandrillus sphinx. The eighth species of diurnal primate present at Lopé,Gorilla g. gorilla, did not visit the fragment during the study. Compared to conspecific groups in neighbouring continuous forest, primates in the fragment ate less fruit, seeds and flowers and more insects and leaves. The local population density of primates resident in the fragment was equivalent to that of the neighbouring continuous forest where all eight species occur, despite the diversity and abundance of fruit being less in the fragment. The costs imposed on the resident group by the reduced diversity and availability of preferred fruit foods appeared to be offset by a number of benefits that increased individual feeding efficiency for monkeys residing within a single fragment. These included lower travel costs, reduced feeding competition between individuals through group fission, and excellent knowledge of the location and quality of food resources in the small home range. It is also possible that the overall negative impact of inter-specific feeding competition was lower in fragments than in continuous forest and that micro-habitat differences resulted in an increased availability of palatable insect and leaf fallback foods in the fragment.     

Ontogenetic Variation in the Diurnal Food and Habitat Associations of an Endemic and an Exotic Fish in Floodplain Ponds: Consequences for Niche Partitioning

In floodplain ponds with low piscivore abundance, both endemic Midgley's gudgeons, Hypseleotris sp. 5, and exotic mosquitofish, Gambusia holbrooki, showed significant ontogenetic variation in the use of food and space. Small gudgeons were generally associated with surface and benthic habitats, then restricted their distribution to benthic habitats at a size of approximately 24mm (standard length). The ontogenetic variation in mosquitofish habitat use was less discrete, and could be described as a tendency for larger individuals to be associated with the bottom of the littoral macrophyte beds than with the surface of the macrophyte beds or surface of the limnetic zone. Small gudgeons exhibited high spatial overlap with mosquitofish within the surface habitats of the ponds. All size-class/species comparisons showed significant partitioning of food resources, however, the diets of small gudgeons and mosquitofish were very similar. Therefore, juvenile gudgeons may have to pass through a similar spatial and trophic niche to introduced mosquitofish before recruiting to the adult stage. Possible mechanisms driving the ontogenetic variation in gudgeon and mosquitofish habitat use are discussed. This paper demonstrates that ontogenetic niche shifts at fine spatial scales can affect our interpretation of interactions between native and introduced fishes.     

A general method to quantify quasi-equivalence in icosahedral viruses

A quantitative, atom-based, method is described for comparing protein subunit interfaces in icosahedral virus capsids with quasi-equivalent surface lattices. An integrated, normalized value (between 0 and 1) based on equivalent residue contacts (Q-score) is computed for every pair of subunit interactions and scores that are significantly above zero readily identify interfaces that are quasi-equivalent to each other. The method was applied to all quasi-equivalent capsid structures (T=3, 4, 7 and 13) in the Protein Data Bank and the Q-scores were interpreted in terms of their structural underpinnings. The analysis allowed classification of T=3 structures into three groups with architectures that resemble different polyhedra with icosahedral symmetry. The preference of subunits to form dimers in the T=4 human Hepatitis B virus capsid (HBV) was clearly reflected in high Q-scores of quasi-equivalent dimers. Interesting differences between the classical T=7 capsid and polyoma-like capsids were also identified. Application of the method to the outer-shell of the T=13 Blue tongue virus core (BTVC) highlighted the modest distortion between the interfaces of the general trimers and the strict trimers of VP7 subunits. Furthermore, the method identified the quasi 2-fold symmetry in the inner capsids of the BTV and reovirus cores. The results show that the Q-scores of various quasi-symmetries represent a "fingerprint" for a particular virus capsid architecture allowing particle classification into groups based on their underlying structural and geometric features.     

Differential induction of regulatory genes during mesoderm formation in Xenopus laevis embryos

Mesoderm development in Xenopus laevis depends on inductive cell interactions mediated by diffusible molecules. The mesoderm inducer activin is capable of redirecting the development of animal explants both morphologically and biochemically. We have studied the induction of four regulatory genes, Mix. 1, goosecoid (gsc), Xlim-1 and Xbra in such explants by activin, and the influence of other factors on this induction. Activin induction of gsc is strongly enhanced by dorsalization of the embryo by LiCl, while expression of the other genes is only slightly enhanced. The protein synthesis inhibitor cycloheximide (CHX) inhibits the activin-dependent induction of Xbra partially, while induction of Mix. 1 and Xlim- 1 is essentially unaffected. In contrast, gsc shows strong superinduction in the presence of activin and CHX, and can be induced in animal explants by CHX alone. Induction and superinduction by CHX have previously been observed for immediate early genes in a variety of systems, notably for the activation of c-fos expression by serum stimulation, but have not been reported in early amphibian embryos. © 1993Wiley-Liss, Inc.     

LuTHy: a double‐readout bioluminescence‐based two‐hybrid technology for quantitative mapping of protein–protein interactions in mammalian cells

Information on protein–protein interactions (PPIs) is of critical importance for studying complex biological systems and developing therapeutic strategies. Here, we present a double‐readout bioluminescence‐based two‐hybrid technology, termed LuTHy, which provides two quantitative scores in one experimental procedure when testing binary interactions. PPIs are first monitored in cells by quantification of bioluminescence resonance energy transfer (BRET) and, following cell lysis, are again quantitatively assessed by luminescence‐based co‐precipitation (LuC). The double‐readout procedure detects interactions with higher sensitivity than traditional single‐readout methods and is broadly applicable, for example, for detecting the effects of small molecules or disease‐causing mutations on PPIs. Applying LuTHy in a focused screen, we identified 42 interactions for the presynaptic chaperone CSPα, causative to adult‐onset neuronal ceroid lipofuscinosis (ANCL), a progressive neurodegenerative disease. Nearly 50% of PPIs were found to be affected when studying the effect of the disease‐causing missense mutations L115R and ?L116 in CSPα with LuTHy. Our study presents a robust, sensitive research tool with high utility for investigating the molecular mechanisms by which disease‐associated mutations impair protein activity in biological systems.