Overcompensation and population cycles in an ungulate.

Although theoretical studies show that overcompensatory density-dependent mechanisms can potentially generate regular or chaotic fluctuations in animal numbers, the majority of realistic single-species models of invertebrate populations are not overcompensatory enough to cause sustained population cycles. The possibility that overcompensation may generate cycles or chaos in vertebrate populations has seldom been considered. Here we show that highly overcompensatng density-dependent mortality can generate recurrent population crashes consistent with those observed in a naturally limited population of Soay sheep. The observed interval of three or more years between crashes points to sharp 'focusing' of mortality over a narrow range of population density.     

Non-volcanic tremor driven by large transient shear stresses

Non-impulsive seismic radiation or 'tremor' has long been observed at volcanoes and more recently around subduction zones. Although the number of observations of non-volcanic tremor is steadily increasing, the causative mechanism remains unclear. Some have attributed non-volcanic tremor to the movement of fluids, while its coincidence with geodetically observed slow-slip events at regular intervals has led others to consider slip on the plate interface as its cause. Low-frequency earthquakes in Japan, which are believed to make up at least part of non-volcanic tremor, have focal mechanisms and locations that are consistent with tremor being generated by shear slip on the subduction interface. In Cascadia, however, tremor locations appear to be more distributed in depth than in Japan, making them harder to reconcile with a plate interface shear-slip model. Here we identify bursts of tremor that radiated from the Cascadia subduction zone near Vancouver Island, Canada, during the strongest shaking from the moment magnitude M(w) = 7.8, 2002 Denali, Alaska, earthquake. Tremor occurs when the Love wave displacements are to the southwest (the direction of plate convergence of the overriding plate), implying that the Love waves trigger the tremor. We show that these displacements correspond to shear stresses of approximately 40 kPa on the plate interface, which suggests that the effective stress on the plate interface is very low. These observations indicate that tremor and possibly slow slip can be instantaneously induced by shear stress increases on the subduction interface-effectively a frictional failure response to the driving stress.     

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding 'higher' Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H2 metabolism, CO2-reductive acetogenesis and N2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-microl environment can be.     

Verbal and non-verbal intelligence changes in the teenage brain

Intelligence quotient (IQ) is a standardized measure of human intellectual capacity that takes into account a wide range of cognitive skills. IQ is generally considered to be stable across the lifespan, with scores at one time point used to predict educational achievement and employment prospects in later years. Neuroimaging allows us to test whether unexpected longitudinal fluctuations in measured IQ are related to brain development. Here we show that verbal and non-verbal IQ can rise or fall in the teenage years, with these changes in performance validated by their close correlation with changes in local brain structure. A combination of structural and functional imaging showed that verbal IQ changed with grey matter in a region that was activated by speech, whereas non-verbal IQ changed with grey matter in a region that was activated by finger movements. By using longitudinal assessments of the same individuals, we obviated the many sources of variation in brain structure that confound cross-sectional studies. This allowed us to dissociate neural markers for the two types of IQ and to show that general verbal and non-verbal abilities are closely linked to the sensorimotor skills involved in learning. More generally, our results emphasize the possibility that an individual's intellectual capacity relative to their peers can decrease or increase in the teenage years. This would be encouraging to those whose intellectual potential may improve, and would be a warning that early achievers may not maintain their potential.     

Experimental infection of bats with Geomyces destructans causes white-nose syndrome

White-nose syndrome (WNS) has caused recent catastrophic declines among multiple species of bats in eastern North America. The disease's name derives from a visually apparent white growth of the newly discovered fungus Geomyces destructans on the skin (including the muzzle) of hibernating bats. Colonization of skin by this fungus is associated with characteristic cutaneous lesions that are the only consistent pathological finding related to WNS. However, the role of G. destructans in WNS remains controversial because evidence to implicate the fungus as the primary cause of this disease is lacking. The debate is fuelled, in part, by the assumption that fungal infections in mammals are most commonly associated with immune system dysfunction. Additionally, the recent discovery that G. destructans commonly colonizes the skin of bats of Europe, where no unusual bat mortality events have been reported, has generated further speculation that the fungus is an opportunistic pathogen and that other unidentified factors are the primary cause of WNS. Here we demonstrate that exposure of healthy little brown bats (Myotis lucifugus) to pure cultures of G. destructans causes WNS. Live G. destructans was subsequently cultured from diseased bats, successfully fulfilling established criteria for the determination of G. destructans as a primary pathogen. We also confirmed that WNS can be transmitted from infected bats to healthy bats through direct contact. Our results provide the first direct evidence that G. destructans is the causal agent of WNS and that the recent emergence of WNS in North America may represent translocation of the fungus to a region with a naive population of animals. Demonstration of causality is an instrumental step in elucidating the pathogenesis and epidemiology of WNS and in guiding management actions to preserve bat populations against the novel threat posed by this devastating infectious disease.     

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies

Genome-wide association studies (GWAS) have proven to be a powerful method to identify common genetic variants contributing to susceptibility to common diseases. Here, we show that extremely low-coverage sequencing (0.1-0.5×) captures almost as much of the common (>5%) and low-frequency (1-5%) variation across the genome as SNP arrays. As an empirical demonstration, we show that genome-wide SNP genotypes can be inferred at a mean r(2) of 0.71 using off-target data (0.24× average coverage) in a whole-exome study of 909 samples. Using both simulated and real exome-sequencing data sets, we show that association statistics obtained using extremely low-coverage sequencing data attain similar P values at known associated variants as data from genotyping arrays, without an excess of false positives. Within the context of reductions in sample preparation and sequencing costs, funds invested in extremely low-coverage sequencing can yield several times the effective sample size of GWAS based on SNP array data and a commensurate increase in statistical power.     

The landing zone – Ground for model transfer in chemistry

This essay proposes a new notion - the landing zone - in order to identify conceptual features that allow modelers to transfer mathematical tools across disciplinary borders. This discussion refers to the transferable models as ‘templates’. Templates are functions, equations, or computational methods that are capable of being generalized from a particular subject matter. There are formal and conceptual prerequisites for the transfer of a template to a new domain. A landing zone is an ontology that contributes to the satisfaction of these conditions for successful transfer. This paper presents a case study on a model in chemistry - the Quantum Theory of Atoms in Molecules (QTAIM) - that makes use of transferred templates from physics - the virial theorem and the wave function. The landing zone in this case is a new ontological notion, that of the topological atom, which prepares ground for the use of the virial theorem and the wave function in chemistry. The virial theorem requires that there exists in-principle stability to the system that it represents, and the wave function requires transformation in its representation that is justified. The ontology of QTAIM - the landing zone for these templates - grounds the scientific use of these templates in the context of chemistry.