Biodiversity and species interactions: extending Lotka–Volterra community theory

A new analysis of the nearly century‐old Lotka–Volterra theory allows us to link species interactions to biodiversity patterns, including: species abundance distributions, estimates of total community size, patterns of community invasibility, and predicted responses to disturbance. Based on a few restrictive assumptions about species interactions, our calculations require only that the community is sufficiently large to allow a mean‐field approximation. We develop this analysis to show how an initial assemblage of species with varying interaction strengths is predicted to sort out into the final community based on the species’ predicted target densities. The sorting process yields predictions of covarying patterns of species abundance, community size, and species interaction strengths. These predictions can be tested using enrichment experiments, examination of latitudinal and productivity gradients, and features of community assembly.     

The mechanism for dioxygen formation in PSII studied by quantum chemical methods.

The availability of an X-ray structure for PSII including the water-oxidizing cluster, where the metal atoms and the amino acids are assigned, has opened up new possibilities to study the mechanism for dioxygen formation. In the present paper the main results of an ongoing hybrid DFT study are presented. The model used follows the structure suggested by the X-ray analysis as closely as possible. After nearly one thousand optimizations of different structures, each one with about 70 atoms, the main features of a water oxidizing mechanism start to emerge. The key intermediate is an oxyl radical state in S(3), stabilized by a weak trans effect to a bridging oxo in the cube. To reach this radical state a structural rearrangement appears necessary, in which one additional bridging oxo is formed between the dangling manganese and a manganese in the cube. The calculated energetics is reasonable but still not fully consistent with a correct mechanism. It is suggested that some part of the structure is not correct, probably the presence of the bicarbonate.     

Functional characterisation of mutations in the ligand-binding domain of the androgen receptor gene in patients with androgen insensitivity syndrome

Five mutations in the ligand-binding domain of the androgen receptor gene were identified in patients with complete (A765T, C784Y, R831X and M895T) or partial (R840G) androgen insensitivity. A765T and R831X have been reported previously whereas the other three mutations are novel. Receptors carrying these mutations were transiently expressed in COS-1 cells, and androgen binding and capacity to transactivate an androgen-responsive reporter gene were assayed. C784Y led to abolished androgen binding and transactivating capacity, R840G and M895T showed reduced specific binding and partial transactivation. The in vitro functions of the R840G and M895T mutants were improved with supraphysiological concentrations of steroid. Received: 10 June 1998 / Accepted: 10 September 1998     

Automated quantification of steatosis: agreement with stereological point counting

Background

Steatosis is routinely assessed histologically in clinical practice and research. Automated image analysis can reduce the effort of quantifying steatosis. Since reproducibility is essential for practical use, we have evaluated different analysis methods in terms of their agreement with stereological point counting (SPC) performed by a hepatologist.

Methods

The evaluation was based on a large and representative data set of 970 histological images from human patients with different liver diseases. Three of the evaluated methods were built on previously published approaches. One method incorporated a new approach to improve the robustness to image variability.

Results

The new method showed the strongest agreement with the expert. At 20× resolution, it reproduced steatosis area fractions with a mean absolute error of 0.011 for absent or mild steatosis and 0.036 for moderate or severe steatosis. At 10× resolution, it was more accurate than and twice as fast as all other methods at 20× resolution. When compared with SPC performed by two additional human observers, its error was substantially lower than one and only slightly above the other observer.

Conclusions

The results suggest that the new method can be a suitable automated replacement for SPC. Before further improvements can be verified, it is necessary to thoroughly assess the variability of SPC between human observers.

     

Invasion under a trade-off between density dependence and maximum growth rate

The invasion of alien species and genotypes is an increasing concern in contemporary ecology. A central question is, what life-history traits enable invasion amidst populations of wild species and conventional cultivars? In order to invade, the initially rare species must perform better than their resident competitors. We conducted a mathematical analysis and simulation of a two-species extension of the Maynard Smith and Slatkin model for population dynamics in discrete time to study the role of density dependence as different types of competition in the invasion of new species. The type of density dependence ranged from scramble to contest competition. This led to intrinsic dynamics of the species range from point equilibrium to cycles and chaos. The traits were treated either as free parameters or constrained by a trade-off resulting from a common fixed strength of density dependence or equilibrium density. Resident and intruder traits had up to ten-fold differences in all of the parameters investigated. Higher equilibrium density of the intruder allowed invasion. Under constrained equilibrium density, an intrinsically stable intruder could invade an unstable resident population. Scramble competition made a population more susceptible to invasion than contest competition (e.g., limitation by light or territory availability). This predicts that a population which is mainly limited by food (or nutrients in plants) is more likely to be invaded than a population limited by a hierarchical competition, such as light among plants. The intruder population may have an effect on the resident population's dynamics, which makes the traditional invasion analysis unable to predict invasion outcome.     

Expression of the calcitonin receptor, calcitonin receptor-like receptor, and receptor activity modifying proteins during osteoclast differentiation

The expressions of the calcitonin receptor (CTR), the calcitonin receptor-like receptor (CLR), the receptor activity-modifying proteins (RAMP) 1-3, and of the receptor component protein (RCP) have been studied in mouse bone marrow macrophages (BMM) during osteoclast differentiation, induced by treatment with M-CSF and RANKL. Analyses of mRNA showed that CLR and RAMP1-3, but not CTR, were expressed in M-CSF stimulated BMM. RANKL gradually increased CTR mRNA, transiently enhanced CLR and transiently decreased RAMP1 mRNA, but did not affect RAMP2, RAMP3, or RCP mRNA. However, RANKL did not affect protein levels of CLR or RAMP1-3 as assessed by Western blots or FACS analyses, whereas immunocytochemistry showed enhanced CTR protein. Analyses of cAMP production showed that BMM cells expressed functional receptors for calcitonin gene-related peptide (CGRP), amylin, adrenomedullin, and intermedin, but not for calcitonin and calcitonin receptor stimulating peptide (CRSP), but that RANKL induced the expression of receptors for calcitonin and CRSP as well. Calcitonin, CGRP, amylin, adrenomedullin, intermedin, and CRSP all down regulated the CTR mRNA, but none of the peptides caused any effects on the expression of CLR or any of the RAMPs. Our data show that BMM cells express receptors for CGRP, amylin, adrenomedullin, and intermedin and that RANKL induces the formation of receptors for calcitonin and CRSP in these cells. We also show, for the first time, that the CTR is not only down regulated by signaling through the CTR but also by the peptides signaling through CLR/RAMPs.     

The Pseudomonas syringae type III effector HopAM1 enhances virulence on water-stressed plants

Pseudomonas syringae strains deliver diverse type III effector proteins into host cells, where they can act as virulence factors. Although the functions of the majority of type III effectors are unknown, several have been shown to interfere with plant basal defense mechanisms. Type III effectors also could contribute to bacterial virulence by enhancing nutrient uptake and pathogen adaptation to the environment of the host plant. We demonstrate that the type III effector HopAM1 (formerly known as AvrPpiB) enhances the virulence of a weak pathogen in plants that are grown under drought stress. This is the first report of a type III effector that aids pathogen adaptation to water availability in the host plant. Expression of HopAM1 makes transgenic Ws-0 Arabidopsis hypersensitive to abscisic acid (ABA) for stomatal closure and germination arrest. Conditional expression of HopAM1 in Arabidopsis also suppresses basal defenses. ABA responses overlap with defense responses and ABA has been shown to suppress defense against P. syringae pathogens. We propose that HopAM1 aids P. syringae virulence by manipulation of ABA responses that suppress defense responses. In addition, host ABA responses enhanced by type III delivery of HopAM1 protect developing bacterial colonies inside leaves from osmotic stress.     

A new cajaro catfish (Siluriformes: Pimelodidae:Phractocephalus) from the Late Miocene of southwestern Amazonia and its relationship to °Phractocephalus nassi of the Urumaco Formation

A new fossil species of the living catfish genusPhractocephalus is described from fluvial Sediments of late Miocene age in Acre State, Brazil and the Madre de Dios region, Peru. †Phractocephalus acreornatus n. sp., is known from a complete neurocranium with associated Weberian complex vertebrae and posttemporal-supracleithra, and several isolated skeletal elements. °Phractocephalus acreornatus is diagnosed by the following combination of characters: 1) anterior half of supraoccipital, frontals and sometimes mesethmoid with coarse parallel ridges and sulci in addition to reticulating ridges and subcircular pits; 2) mesethmoid very broad and coarsely ornamented; 3) lateral ethmoid projecting anteriorly above palatine condyle into olfactory capsule, its anterolateral margin convex and fluted, and its orbital notch reduced; 4) supraoccipital process long, concealing Weberian vertebrae in dorsal view; 5) opercle covered with rough, reticulating ridges and pits; 6) interopercle relatively deep, its outer side coarsely ornamented; 7) pectoral spine shaft ornamented with reticulating ridges and pits. Variability of the form of the much expanded supraoccipital process inPhractocephalus is evaluated for its taxonomic significance. Although °P.acreornatus is distinct from both modernP. hemloliopterus and fossil °P. nassi, like most Miocene fossil fishes from South America, this extinct species is closely similar to its relatives. Available characters provide evidence for a close relationship between °P. acreornatus and °P. nassi from the Urumaco Formation, Venezuela. The provenance of these late Miocene catfishes in lowland western Amazonia and north-central South America is congruent with paleogeographic modeis positing a large, north flowing “Paleo-Amazon-Orinoco” river System in the Andean foreland basin during the Neogene.