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.     

Nucleation and growth mechanism of ferroelectric domain-wall motion

The motion of domain walls is critical to many applications involving ferroelectric materials, such as fast high-density non-volatile random access memory. In memories of this sort, storing a data bit means increasing the size of one polar region at the expense of another, and hence the movement of a domain wall separating these regions. Experimental measurements of domain growth rates in the well-established ferroelectrics PbTiO3 and BaTiO3 have been performed, but the development of new materials has been hampered by a lack of microscopic understanding of how domain walls move. Despite some success in interpreting domain-wall motion in terms of classical nucleation and growth models, these models were formulated without insight from first-principles-based calculations, and they portray a picture of a large, triangular nucleus that leads to unrealistically large depolarization and nucleation energies. Here we use atomistic molecular dynamics and coarse-grained Monte Carlo simulations to analyse these processes, and demonstrate that the prevailing models are incorrect. Our multi-scale simulations reproduce experimental domain growth rates in PbTiO3 and reveal small, square critical nuclei with a diffuse interface. A simple analytic model is also proposed, relating bulk polarization and gradient energies to wall nucleation and growth, and thus rationalizing all experimental rate measurements in PbTiO3 and BaTiO3.     

Placing late Neanderthals in a climatic context

Attempts to place Palaeolithic finds within a precise climatic framework are complicated by both uncertainty over the radiocarbon calibration beyond about 21,500 14C years bp and the absence of a master calendar chronology for climate events from reference archives such as Greenland ice cores or speleothems. Here we present an alternative approach, in which 14C dates of interest are mapped directly onto the palaeoclimate record of the Cariaco Basin by means of its 14C series, circumventing calendar age model and correlation uncertainties, and placing dated events in the millennial-scale climate context of the last glacial period. This is applied to different sets of dates from levels with Mousterian artefacts, presumably produced by late Neanderthals, from Gorham's Cave in Gibraltar: first, generally accepted estimates of about 32,000 14C years bp for the uppermost Mousterian levels; second, a possible extended Middle Palaeolithic occupation until about 28,000 14C years bp; and third, more contentious evidence for persistence until about 24,000 14C years bp. This study shows that the three sets translate to different scenarios on the role of climate in Neanderthal extinction. The first two correspond to intervals of general climatic instability between stadials and interstadials that characterized most of the Middle Pleniglacial and are not coeval with Heinrich Events. In contrast, if accepted, the youngest date indicates that late Neanderthals may have persisted up to the onset of a major environmental shift, which included an expansion in global ice volume and an increased latitudinal temperature gradient. More generally, our radiocarbon climatostratigraphic approach can be applied to any 'snapshot' date from discontinuous records in a variety of deposits and can become a powerful tool in evaluating the climatic signature of critical intervals in Late Pleistocene human evolution.     

Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia

Chromosomal aberrations are a hallmark of acute lymphoblastic leukaemia (ALL) but alone fail to induce leukaemia. To identify cooperating oncogenic lesions, we performed a genome-wide analysis of leukaemic cells from 242 paediatric ALL patients using high-resolution, single-nucleotide polymorphism arrays and genomic DNA sequencing. Our analyses revealed deletion, amplification, point mutation and structural rearrangement in genes encoding principal regulators of B lymphocyte development and differentiation in 40% of B-progenitor ALL cases. The PAX5 gene was the most frequent target of somatic mutation, being altered in 31.7% of cases. The identified PAX5 mutations resulted in reduced levels of PAX5 protein or the generation of hypomorphic alleles. Deletions were also detected in TCF3 (also known as E2A), EBF1, LEF1, IKZF1 (IKAROS) and IKZF3 (AIOLOS). These findings suggest that direct disruption of pathways controlling B-cell development and differentiation contributes to B-progenitor ALL pathogenesis. Moreover, these data demonstrate the power of high-resolution, genome-wide approaches to identify new molecular lesions in cancer.     

Complex gas hydrate from the Cascadia margin

Natural gas hydrates are a potential source of energy and may play a role in climate change and geological hazards. Most natural gas hydrate appears to be in the form of 'structure I', with methane as the trapped guest molecule, although 'structure II' hydrate has also been identified, with guest molecules such as isobutane and propane, as well as lighter hydrocarbons. A third hydrate structure, 'structure H', which is capable of trapping larger guest molecules, has been produced in the laboratory, but it has not been confirmed that it occurs in the natural environment. Here we characterize the structure, gas content and composition, and distribution of guest molecules in a complex natural hydrate sample recovered from Barkley canyon, on the northern Cascadia margin. We show that the sample contains structure H hydrate, and thus provides direct evidence for the natural occurrence of this hydrate structure. The structure H hydrate is intimately associated with structure II hydrate, and the two structures contain more than 13 different hydrocarbon guest molecules. We also demonstrate that the stability field of the complex gas hydrate lies between those of structure II and structure H hydrates, indicating that this form of hydrate is more stable than structure I and may thus potentially be found in a wider pressure-temperature regime than can methane hydrate deposits.     

Morphological evolution through multiple cis-regulatory mutations at a single gene

One central, and yet unsolved, question in evolutionary biology is the relationship between the genetic variants segregating within species and the causes of morphological differences between species. The classic neo-darwinian view postulates that species differences result from the accumulation of small-effect changes at multiple loci. However, many examples support the possible role of larger abrupt changes in the expression of developmental genes in morphological evolution. Although this evidence might be considered a challenge to a neo-darwinian micromutationist view of evolution, there are currently few examples of the actual genes causing morphological differences between species. Here we examine the genetic basis of a trichome pattern difference between Drosophila species, previously shown to result from the evolution of a single gene, shavenbaby (svb), probably through cis-regulatory changes. We first identified three distinct svb enhancers from D. melanogaster driving reporter gene expression in partly overlapping patterns that together recapitulate endogenous svb expression. All three homologous enhancers from D. sechellia drive expression in modified patterns, in a direction consistent with the evolved svb expression pattern. To test the influence of these enhancers on the actual phenotypic difference, we conducted interspecific genetic mapping at a resolution sufficient to recover multiple intragenic recombinants. This functional analysis revealed that independent genetic regions upstream of svb that overlap the three identified enhancers are collectively required to generate the D. sechellia trichome pattern. Our results demonstrate that the accumulation of multiple small-effect changes at a single locus underlies the evolution of a morphological difference between species. These data support the view that alleles of large effect that distinguish species may sometimes reflect the accumulation of multiple mutations of small effect at select genes.     

Natural history and evolutionary principles of gene duplication in fungi

Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown. With the growing number of sequenced genomes, it is now possible to examine these events in a comprehensive and unbiased manner. Here, we develop a procedure that resolves the evolutionary history of all genes in a large group of species. We apply our procedure to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species. We show that gene duplication and loss is highly constrained by the functional properties and interacting partners of genes. In particular, stress-related genes exhibit many duplications and losses, whereas growth-related genes show selection against such changes. Whole-genome duplication circumvents this constraint and relaxes the dichotomy, resulting in an expanded functional scope of gene duplication. By characterizing the functional fate of duplicate genes we show that duplicated genes rarely diverge with respect to biochemical function, but typically diverge with respect to regulatory control. Surprisingly, paralogous modules of genes rarely arise, even after whole-genome duplication. Rather, gene duplication may drive the modularization of functional networks through specialization, thereby disentangling cellular systems.