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.     

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.     

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.     

The extent of linkage disequilibrium in Arabidopsis thaliana.

Linkage disequilibrium (LD), the nonrandom occurrence of alleles in haplotypes, has long been of interest to population geneticists. Recently, the rapidly increasing availability of genomic polymorphism data has fueled interest in LD as a tool for fine-scale mapping, in particular for human disease loci. The chromosomal extent of LD is crucial in this context, because it determines how dense a map must be for associations to be detected and, conversely, limits how finely loci may be mapped. Arabidopsis thaliana is expected to harbor unusually extensive LD because of its high degree of selfing. Several polymorphism studies have found very strong LD within individual loci, but also evidence of some recombination. Here we investigate the pattern of LD on a genomic scale and show that in global samples, LD decays within approximately 1 cM, or 250 kb. We also show that LD in local populations may be much stronger than that of global populations, presumably as a result of founder events. The combination of a relatively high level of polymorphism and extensive haplotype structure bodes well for developing a genome-wide LD map in A. thaliana.     

The earliest known eutherian mammal

The skeleton of a eutherian (placental) mammal has been discovered from the Lower Cretaceous Yixian Formation of northeastern China. We estimate its age to be about 125 million years (Myr), extending the date of the oldest eutherian records with skull and skeleton by about 40 50 Myr. Our analyses place the new fossil at the root of the eutherian tree and among the four other known Early Cretaceous eutherians, and suggest an earlier and greater diversification of stem eutherians that occurred well before the molecular estimate for the diversification of extant placental superorders (104 64 Myr). The new eutherian has limb and foot features that are known only from scansorial (climbing) and arboreal (tree-living) extant mammals, in contrast to the terrestrial or cursorial (running) features of other Cretaceous eutherians. This suggests that the earliest eutherian lineages developed different locomotory adaptations, facilitating their spread to diverse niches in the Cretaceous.     

Distribution and status of the yellow-faced pocket gopher in Kansas

Previous research suggests that the yellow-faced pocket gopher ( Cratogeomys castanops ) occupies a restricted range in western Kansas that is surrounded by the range of the plains pocket gopher ( Geomys bursarius ), which is regarded as a superior competitor. To determine whether the plains pocket gopher has encroached on the range of the yellow-faced pocket gopher in the past 35 years and to better understand the geographic relationships of these species, we trapped pocket gophers in western Kansas and collected soil texture and land cover data. We used ArcView 3.2 to map the distributions of these species in the study area, as well as the kinds of soil and land cover found in their potential home ranges. Although the distributions of the 2 species overlap, they are strictly parapatric. The apparent cause of this parapatric relationship is differential tolerance of soil textures. The distribution of the yellow-faced pocket gopher in Kansas is limited to just 7 counties divided into 2 populations, both surrounded by the distribution of the plains pocket gopher. We found no evidence that the range of the plains pocket gopher has expanded at the expense of the yellow-faced pocket gopher in the past 35 years. Thus, although the yellow-faced pocket gopher remains a “species of greatest conservation need” in Kansas because of agricultural threats, it evidently is not imperiled at this time.     

A steady-state superradiant laser with less than one intracavity photon

The spectral purity of an oscillator is central to many applications, such as detecting gravity waves, defining the second, ground-state cooling and quantum manipulation of nanomechanical objects, and quantum computation. Recent proposals suggest that laser oscillators which use very narrow optical transitions in atoms can be orders of magnitude more spectrally pure than present lasers. Lasers of this high spectral purity are predicted to operate deep in the 'bad-cavity', or superradiant, regime, where the bare atomic linewidth is much less than the cavity linewidth. Here we demonstrate a Raman superradiant laser source in which spontaneous synchronization of more than one million rubidium-87 atomic dipoles is continuously sustained by less than 0.2 photons on average inside the optical cavity. By operating at low intracavity photon number, we demonstrate isolation of the collective atomic dipole from the environment by a factor of more than ten thousand, as characterized by cavity frequency pulling measurements. The emitted light has a frequency linewidth, measured relative to the Raman dressing laser, that is less than that of single-particle decoherence linewidths and more than ten thousand times less than the quantum linewidth limit typically applied to 'good-cavity' optical lasers, for which the cavity linewidth is much less than the atomic linewidth. These results demonstrate several key predictions for future superradiant lasers, which could be used to improve the stability of passive atomic clocks and which may lead to new searches for physics beyond the standard model.     

Prion-like behaviour and tau-dependent cytotoxicity of pyroglutamylated amyloid-β

Extracellular plaques of amyloid-β and intraneuronal neurofibrillary tangles made from tau are the histopathological signatures of Alzheimer's disease. Plaques comprise amyloid-β fibrils that assemble from monomeric and oligomeric intermediates, and are prognostic indicators of Alzheimer's disease. Despite the importance of plaques to Alzheimer's disease, oligomers are considered to be the principal toxic forms of amyloid-β. Interestingly, many adverse responses to amyloid-β, such as cytotoxicity, microtubule loss, impaired memory and learning, and neuritic degeneration, are greatly amplified by tau expression. Amino-terminally truncated, pyroglutamylated (pE) forms of amyloid-β are strongly associated with Alzheimer's disease, are more toxic than amyloid-β, residues 1-42 (Aβ(1-42)) and Aβ(1-40), and have been proposed as initiators of Alzheimer's disease pathogenesis. Here we report a mechanism by which pE-Aβ may trigger Alzheimer's disease. Aβ(3(pE)-42) co-oligomerizes with excess Aβ(1-42) to form metastable low-n oligomers (LNOs) that are structurally distinct and far more cytotoxic to cultured neurons than comparable LNOs made from Aβ(1-42) alone. Tau is required for cytotoxicity, and LNOs comprising 5% Aβ(3(pE)-42) plus 95% Aβ(1-42) (5% pE-Aβ) seed new cytotoxic LNOs through multiple serial dilutions into Aβ(1-42) monomers in the absence of additional Aβ(3(pE)-42). LNOs isolated from human Alzheimer's disease brain contained Aβ(3(pE)-42), and enhanced Aβ(3(pE)-42) formation in mice triggered neuron loss and gliosis at 3 months, but not in a tau-null background. We conclude that Aβ(3(pE)-42) confers tau-dependent neuronal death and causes template-induced misfolding of Aβ(1-42) into structurally distinct LNOs that propagate by a prion-like mechanism. Our results raise the possibility that Aβ(3(pE)-42) acts similarly at a primary step in Alzheimer's disease pathogenesis.