Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast

Under laboratory conditions 80% of yeast genes seem not to be essential for viability. This raises the question of what the mechanistic basis for dispensability is, and whether it is the result of selection for buffering or an incidental side product. Here we analyse these issues using an in silico flux model of the yeast metabolic network. The model correctly predicts the knockout fitness effects in 88% of the genes studied and in vivo fluxes. Dispensable genes might be important, but under conditions not yet examined in the laboratory. Our model indicates that this is the dominant explanation for apparent dispensability, accounting for 37-68% of dispensable genes, whereas 15-28% of them are compensated by a duplicate, and only 4-17% are buffered by metabolic network flux reorganization. For over one-half of those not important under nutrient-rich conditions, we can predict conditions when they will be important. As expected, such condition-specific genes have a more restricted phylogenetic distribution. Gene duplicates catalysing the same reaction are not more common for indispensable reactions, suggesting that the reason for their retention is not to provide compensation. Instead their presence is better explained by selection for high enzymatic flux.     

Clarifying the glass-transition behaviour of water by comparison with hyperquenched inorganic glasses

The formation of glasses is normal for substances that remain liquid over a wide temperature range (the 'good glassformers') and can be induced for most liquids if cooling is fast enough to bypass crystallization. During reheating but still below the melting point, good glassformers exhibit glass transitions as they abruptly transform into supercooled liquids, whereas other substances transform directly from the glassy to the crystalline state. Whether water exhibits a glass transition before crystallization has been much debated over five decades. For the last 20 years, the existence of a glass transition at 136 K (ref. 3) has been widely accepted, but the transition exhibits qualities difficult to reconcile with our current knowledge of glass transitions. Here we report detailed calorimetric characterizations of hyperquenched inorganic glasses that, when heated, do not crystallize before reaching their glass transition temperatures. We compare our results to the behaviour of glassy water and find that small endothermic effects, such as the one attributed to the glass transition of water, are only a 'shadow' of the real glass transition occurring at higher temperatures, thus substantiating the conclusion that the glass transition of water cannot be probed directly.     

High-quality electron beams from a laser wakefield accelerator using plasma-channel guiding

Laser-driven accelerators, in which particles are accelerated by the electric field of a plasma wave (the wakefield) driven by an intense laser, have demonstrated accelerating electric fields of hundreds of GV m(-1) (refs 1-3). These fields are thousands of times greater than those achievable in conventional radio-frequency accelerators, spurring interest in laser accelerators as compact next-generation sources of energetic electrons and radiation. To date, however, acceleration distances have been severely limited by the lack of a controllable method for extending the propagation distance of the focused laser pulse. The ensuing short acceleration distance results in low-energy beams with 100 per cent electron energy spread, which limits potential applications. Here we demonstrate a laser accelerator that produces electron beams with an energy spread of a few per cent, low emittance and increased energy (more than 10(9) electrons above 80 MeV). Our technique involves the use of a preformed plasma density channel to guide a relativistically intense laser, resulting in a longer propagation distance. The results open the way for compact and tunable high-brightness sources of electrons and radiation.     

Two new carnivores from an unusual late Tertiary forest biota in eastern North America

Late Cenozoic terrestrial fossil records of North America are biased by a predominance of mid-latitude deposits, mostly in the western half of the continent. Consequently, the biological history of eastern North America, including the eastern deciduous forest, remains largely hidden. Unfortunately, vertebrate fossil sites from this vast region are rare, and few pertain to the critically important late Tertiary period, during which intensified global climatic changes took place. Moreover, strong phylogenetic affinities between the flora of eastern North America and eastern Asia clearly demonstrate formerly contiguous connections, but disparity among shared genera (eastern Asia-eastern North America disjunction) implies significant periods of separation since at least the Miocene epoch. Lacustrine sediments deposited within a former sinkhole in the southern Appalachian Mountains provide a rare example of a late Miocene to early Pliocene terrestrial biota from a forested ecosystem. Here we show that the vertebrate remains contained within this deposit represent a unique combination of North American and Eurasian taxa. A new genus and species of the red (lesser) panda (Pristinailurus bristoli), the earliest and most primitive so far known, was recovered. Also among the fauna are a new species of Eurasian badger (Arctomeles dimolodontus) and the largest concentration of fossil tapirs ever recorded. Cladistical analyses of the two new carnivores strongly suggest immigration events that were earlier than and distinct from previous records, and that the close faunal affinities between eastern North America and eastern Asia in the late Tertiary period are consistent with the contemporaneous botanical record.     

New evidence on the earliest human presence at high northern latitudes in northeast Asia

The timing of early human dispersal to Asia is a central issue in the study of human evolution. Excavations in predominantly lacustrine sediments at Majuangou, Nihewan basin, north China, uncovered four layers of indisputable hominin stone tools. Here we report magnetostratigraphic results that constrain the age of the four artefact layers to an interval of nearly 340,000 yr between the Olduvai subchron and the Cobb Mountain event. The lowest layer, about 1.66 million years old (Myr), provides the oldest record of stone-tool processing of animal tissues in east Asia. The highest layer, at about 1.32 Myr, correlates with the stone tool layer at Xiaochangliang, previously considered the oldest archaeological site in this region. The findings at Majuangou indicate that the oldest known human presence in northeast Asia at 40 degrees N is only slightly younger than that in western Asia. This result implies that a long yet rapid migration from Africa, possibly initiated during a phase of warm climate, enabled early human populations to inhabit northern latitudes of east Asia over a prolonged period.     

Assembly and function of a bacterial genotoxin

The tripartite cytolethal distending toxin (CDT) induces cell cycle arrest and apoptosis in eukaryotic cells. The subunits CdtA and CdtC associate with the nuclease CdtB to form a holotoxin that translocates CdtB into the host cell, where it acts as a genotoxin by creating DNA lesions. Here we show that the crystal structure of the holotoxin from Haemophilus ducreyi reveals that CDT consists of an enzyme of the DNase-I family, bound to two ricin-like lectin domains. CdtA, CdtB and CdtC form a ternary complex with three interdependent molecular interfaces, characterized by globular, as well as extensive non-globular, interactions. The lectin subunits form a deeply grooved, highly aromatic surface that we show to be critical for toxicity. The holotoxin possesses a steric block of the CdtB active site by means of a non-globular extension of the CdtC subunit, and we identify putative DNA binding residues in CdtB that are essential for toxin activity.     

Haematopoietic stem cells adopt mature haematopoietic fates in ischaemic myocardium

Under conditions of tissue injury, myocardial replication and regeneration have been reported. A growing number of investigators have implicated adult bone marrow (BM) in this process, suggesting that marrow serves as a reservoir for cardiac precursor cells. It remains unclear which BM cell(s) can contribute to myocardium, and whether they do so by transdifferentiation or cell fusion. Here, we studied the ability of c-kit-enriched BM cells, Lin- c-kit+ BM cells and c-kit+ Thy1.1(lo) Lin- Sca-1+ long-term reconstituting haematopoietic stem cells to regenerate myocardium in an infarct model. Cells were isolated from transgenic mice expressing green fluorescent protein (GFP) and injected directly into ischaemic myocardium of wild-type mice. Abundant GFP+ cells were detected in the myocardium after 10 days, but by 30 days, few cells were detectable. These GFP+ cells did not express cardiac tissue-specific markers, but rather, most of them expressed the haematopoietic marker CD45 and myeloid marker Gr-1. We also studied the role of circulating cells in the repair of ischaemic myocardium using GFP+-GFP- parabiotic mice. Again, we found no evidence of myocardial regeneration from blood-borne partner-derived cells. Our data suggest that even in the microenvironment of the injured heart, c-kit-enriched BM cells, Lin- c-kit+ BM cells and c-kit+ Thy1.1(lo) Lin- Sca-1+ long-term reconstituting haematopoietic stem cells adopt only traditional haematopoietic fates.