Optimizing Metapopulation Sustainability through a Checkerboard Strategy

The persistence of a spatially structured population is determined by the rate of dispersal among habitat patches. If the local dynamic at the subpopulation level is extinction-prone, the system viability is maximal at intermediate connectivity where recolonization is allowed, but full synchronization that enables correlated extinction is forbidden. Here we developed and used an algorithm for agent-based simulations in order to study the persistence of a stochastic metapopulation. The effect of noise is shown to be dramatic, and the dynamics of the spatial population differs substantially from the predictions of deterministic models. This has been validated for the stochastic versions of the logistic map, the Ricker map and the Nicholson-Bailey host-parasitoid system. To analyze the possibility of extinction, previous studies were focused on the attractiveness (Lyapunov exponent) of stable solutions and the structure of their basin of attraction (dependence on initial population size). Our results suggest that these features are of secondary importance in the presence of stochasticity. Instead, optimal sustainability is achieved when decoherence is maximal. Individual-based simulations of metapopulations of different sizes, dimensions and noise types, show that the system''s lifetime peaks when it displays checkerboard spatial patterns. This conclusion is supported by the results of a recently published Drosophila experiment. The checkerboard strategy provides a technique for the manipulation of migration rates (e.g., by constructing corridors) in order to affect the persistence of a metapopulation. It may be used in order to minimize the risk of extinction of an endangered species, or to maximize the efficiency of an eradication campaign.     

Insight into the interaction sites between fatty acid binding proteins and their ligands

Fatty acid binding proteins (FABPs), are evolutionarily conserved small cytoplasmic proteins that occur in many tissue-specific types. One of their primary functions is to facilitate the clearance of the cytoplasmic matrix from free fatty acids and of other detergent-like compounds. Crystallographic studies of FABP proteins have revealed a well defined binding site located deep inside their β-clam structure that is hardly exposed to the bulk solution. However, NMR measurements revealed that, when the protein is equilibrated with its ligands, residues that are clearly located on the outer surface of the protein do interact with the ligand. To clarify this apparent contradiction we applied molecular dynamics simulations to follow the initial steps associated with the FABP–fatty acid interaction using, as a model, the interaction of toad liver basic FABP, or chicken liver bile acid binding protein, with a physiological concentration of palmitate ions. The simulations (~200 ns of accumulated time) show that fatty acid molecules interact, unevenly, with various loci on the protein surface, with the favored regions being the portal and the anti-portal domains. Random encounters with palmitate at these regions led to lasting adsorption to the surface, while encounters at the outer surface of the β-clam were transient. Therefore, we suggest that the protein surface is capable of sequestering free fatty acids from solution, where brief encounters evolve into adsorbed states, which later mature by migration of the ligand into a more specific binding site.     

Early PTSD Symptom Trajectories: Persistence,Recovery, and Response to Treatment: Results from the Jerusalem Trauma Outreach and Prevention Study (J-TOPS)

Context

Uncovering heterogeneities in the progression of early PTSD symptoms can improve our understanding of the disorder''s pathogenesis and prophylaxis.

Objectives

To describe discrete symptom trajectories and examine their relevance for preventive interventions.

Design

Latent Growth Mixture Modeling (LGMM) of data from a randomized controlled study of early treatment. LGMM identifies latent longitudinal trajectories by exploring discrete mixture distributions underlying observable data.

Setting

Hadassah Hospital unselectively receives trauma survivors from Jerusalem and vicinity.

Participants

Adult survivors of potentially traumatic events consecutively admitted to the hospital''s emergency department (ED) were assessed ten days and one-, five-, nine- and fifteen months after ED admission. Participants with data at ten days and at least two additional assessments (n = 957) were included; 125 received cognitive behavioral therapy (CBT) between one and nine months.

Approach

We used LGMM to identify latent parameters of symptom progression and tested the effect of CBT on these parameters. CBT consisted of 12 weekly sessions of either cognitive therapy (n = 41) or prolonged exposure (PE, n = 49), starting 29.8±5.7 days after ED admission, or delayed PE (n = 35) starting at 151.8±42.4 days. CBT effectively reduced PTSD symptoms in the entire sample.

Main Outcome Measure

Latent trajectories of PTSD symptoms; effects of CBT on these trajectories.

Results

Three trajectories were identified: Rapid Remitting (rapid decrease in symptoms from 1- to 5-months; 56% of the sample), Slow Remitting (progressive decrease in symptoms over 15 months; 27%) and Non-Remitting (persistently elevated symptoms; 17%). CBT accelerated the recovery of the Slow Remitting class but did not affect the other classes.

Conclusions

The early course of PTSD symptoms is characterized by distinct and diverging response patterns that are centrally relevant to understanding the disorder and preventing its occurrence. Studies of the pathogenesis of PTSD may benefit from using clustered symptom trajectories as their dependent variables.     

X-linked Inhibitor of Apoptosis Protein promotes the degradation of its antagonist, the pro-apoptotic ARTS protein

ARTS (Sept4_i2) is a mitochondrial pro-apoptotic tumor suppressor protein. In response to apoptotic signals, ARTS translocates to the cytosol where it promotes caspase activation through caspase de-repression and proteasome mediated degradation of X-linked Inhibitor of Apoptosis Protein (XIAP). Here we show that XIAP regulates the levels of ARTS by serving as its ubiquitin ligase, thereby providing a potential feedback mechanism to protect against unwanted apoptosis. Using both in vitro and in vivo ubiquitination assays we found that ARTS is directly ubiquitinated by XIAP. Moreover, we found that XIAP-induced ubiquitination and degradation is prevented by removal of the first four amino acids in the N-terminus of ARTS, which contains a single lysine residue at position 3. Thus, this lysine at position 3 is a likely target for ubiquitination by XIAP. Importantly, although the stabilized ARTS lacking its first 4 residues binds XIAP as well as the full length ARTS, it is more potent in promoting apoptosis than the full length ARTS. This suggests that increased stability of ARTS has a significant effect on its ability to induce apoptosis. Collectively, our data reveal a mutual regulatory mechanism by which ARTS and XIAP control each other's levels through the ubiquitin proteasome system.     

Adaptive Flexibility of Oldowan Hominins: Secondary Use of Flakes at Bizat Ruhama,Israel

The lithic assemblage of the Early Pleistocene site of Bizat Ruhama, Israel demonstrates the earliest evidence for systematic secondary knapping of flakes. The site, dated to the Matuyama chron, is one of the earliest primary context Oldowan occurrences in Eurasia. According to the experimental replication of the stone-tool production sequence, the secondary knapping of flakes was a part of a multi-stage operational sequence targeted at the production of small (<2 cm) flakes. This sequence included four stages: acquisition of chert pebbles, production of flakes, deliberate selection of flakes of specific morphologies, and their secondary knapping by free-hand or bipolar methods. The results suggest that flakes with retouch-like scars that were produced during this sequence and which commonly are interpreted as shaped tools are unintentional waste products of the small flake production. The intentional manufacture of very small flakes at Bizat Ruhama was probably an economic response to the raw material constrains. Systematic secondary knapping of flakes has not yet been reported from other Early Pleistocene sites. Systematic secondary knapping for small flake production became increasingly important only in the lithic industries of the second half of the Middle Pleistocene, almost a million years later. The results from Bizat Ruhama indicate that Oldowan stone-tool production sequence was conceptually more complex than previously suggested and offer a new perspective on the capabilities for invention and the adaptive flexibility of the Oldowan hominins.     

Nest‐site characteristics,breeding success and competitive interactions between two recently sympatric apex predators

An influential period in avian life‐cycles is the annual breeding season, when competition over suitable nesting sites and territories is a key factor that can determine fitness and distribution, especially for species that are highly selective in their nesting habitats. We analysed nest‐site characteristics, breeding success and competitive interactions between two apex predator populations. Whereas the Short‐toed Eagle Circaetus gallicus has nested in the Judean Foothills (Israel) for a long time, the Long‐legged Buzzard Buteo rufinus has only invaded the nesting habitat of the Short‐toed Eagle during their breeding season in the last two decades. These two recently sympatric species have similar nesting ecology and frequently use the same nests. They are therefore expected to compete over nesting sites and territories. We analysed interspecific interactions between these two species by combining information from comprehensive observational, experimental, GIS analysis and remote sensing data, deriving 65 variables to characterize the nest‐sites used and the breeding success in 381 breeding attempts over four consecutive breeding seasons. To assess interspecific and intraspecific territorial behaviour and aggressiveness, stuffed Long‐legged Buzzards and Short‐toed Eagles were presented close to nests. Nest‐site characteristics overlapped substantially between species, and Long‐legged Buzzards occupied 21% of all Short‐toed Eagle nests. Intraspecific aggression rates among Long‐legged Buzzards were higher than their interspecific aggression rates with Short‐toed Eagles and also higher than intraspecific aggression among Short‐toed Eagles. Long‐legged Buzzard and Short‐toed Eagle breeding densities (1.59 ± 0.11 and 2.96 ± 0.11 pairs per 10 km², respectively) are likely to be the highest across their respective breeding distributions, with a maximum productivity of 0.96 ± 0.01 and 0.56 ± 0.05 (young fledged/breeding pair) for Long‐legged Buzzard and Short‐toed Eagle, respectively. Intraspecific interactions among both species play an important role in determining their breeding success and the spatial distribution of nesting sites. Our results suggest that interspecific competition over nesting sites and territories between both species, and the potential dominance of Long‐legged Buzzard, has both direct and indirect impacts on the spatial and demographic distribution of Short‐toed Eagles due to the recent establishment of Long‐legged Buzzard territories in the Judean breeding area.     

Plant classification from bat-like echolocation signals

Classification of plants according to their echoes is an elementary component of bat behavior that plays an important role in spatial orientation and food acquisition. Vegetation echoes are, however, highly complex stochastic signals: from an acoustical point of view, a plant can be thought of as a three-dimensional array of leaves reflecting the emitted bat call. The received echo is therefore a superposition of many reflections. In this work we suggest that the classification of these echoes might not be such a troublesome routine for bats as formerly thought. We present a rather simple approach to classifying signals from a large database of plant echoes that were created by ensonifying plants with a frequency-modulated bat-like ultrasonic pulse. Our algorithm uses the spectrogram of a single echo from which it only uses features that are undoubtedly accessible to bats. We used a standard machine learning algorithm (SVM) to automatically extract suitable linear combinations of time and frequency cues from the spectrograms such that classification with high accuracy is enabled. This demonstrates that ultrasonic echoes are highly informative about the species membership of an ensonified plant, and that this information can be extracted with rather simple, biologically plausible analysis. Thus, our findings provide a new explanatory basis for the poorly understood observed abilities of bats in classifying vegetation and other complex objects.     

A new Thraustochytrid, strain Fng1, isolated from the surface mucus of the hermatypic coral Fungia granulosa

Recent evidence suggests that there is a dynamic microbial biota living on the surface and in the mucus layer of many hermatypic coral species that plays an essential role in coral well-being. Most of the studies published to date emphasize the importance of prokaryotic communities associated with the coral mucus in coral health and disease. In this study, we report the presence of a protist (Fng1) in the mucus of the hermatypic coral Fungia granulosa from the Gulf of Eilat. This protist was identified morphologically and molecularly as belonging to the family Thraustochytridae (phylum Stramenopile, order Labyrinthulida), a group of heterotrophs widely distributed in the marine environment. Morphological examination of this strain revealed a nonmotile organism c. 35 mum in diameter, which is able to thrive on carbon-deprived media, and whose growth and morphology are inoculum dependent. Its fatty acid production profile revealed an array of polyunsaturated fatty acids. A similar protist was also isolated from the mucus of the coral Favia sp. In light of these findings, its possible contribution to the coral holobiont is discussed.