Structure of mammalian AMPK and its regulation by ADP

The heterotrimeric AMP-activated protein kinase (AMPK) has a key role in regulating cellular energy metabolism; in response to a fall in intracellular ATP levels it activates energy-producing pathways and inhibits energy-consuming processes. AMPK has been implicated in a number of diseases related to energy metabolism including type 2 diabetes, obesity and, most recently, cancer. AMPK is converted from an inactive form to a catalytically competent form by phosphorylation of the activation loop within the kinase domain: AMP binding to the γ-regulatory domain promotes phosphorylation by the upstream kinase, protects the enzyme against dephosphorylation, as well as causing allosteric activation. Here we show that ADP binding to just one of the two exchangeable AXP (AMP/ADP/ATP) binding sites on the regulatory domain protects the enzyme from dephosphorylation, although it does not lead to allosteric activation. Our studies show that active mammalian AMPK displays significantly tighter binding to ADP than to Mg-ATP, explaining how the enzyme is regulated under physiological conditions where the concentration of Mg-ATP is higher than that of ADP and much higher than that of AMP. We have determined the crystal structure of an active AMPK complex. The structure shows how the activation loop of the kinase domain is stabilized by the regulatory domain and how the kinase linker region interacts with the regulatory nucleotide-binding site that mediates protection against dephosphorylation. From our biochemical and structural data we develop a model for how the energy status of a cell regulates AMPK activity.     

Bidirectional resection of DNA double-strand breaks by Mre11 and Exo1

Repair of DNA double-strand breaks (DSBs) by homologous recombination requires resection of 5'-termini to generate 3'-single-strand DNA tails. Key components of this reaction are exonuclease 1 and the bifunctional endo/exonuclease, Mre11 (refs 2-4). Mre11 endonuclease activity is critical when DSB termini are blocked by bound protein--such as by the DNA end-joining complex, topoisomerases or the meiotic transesterase Spo11 (refs 7-13)--but a specific function for the Mre11 3'-5' exonuclease activity has remained elusive. Here we use Saccharomyces cerevisiae to reveal a role for the Mre11 exonuclease during the resection of Spo11-linked 5'-DNA termini in vivo. We show that the residual resection observed in Exo1-mutant cells is dependent on Mre11, and that both exonuclease activities are required for efficient DSB repair. Previous work has indicated that resection traverses unidirectionally. Using a combination of physical assays for 5'-end processing, our results indicate an alternative mechanism involving bidirectional resection. First, Mre11 nicks the strand to be resected up to 300 nucleotides from the 5'-terminus of the DSB--much further away than previously assumed. Second, this nick enables resection in a bidirectional manner, using Exo1 in the 5'-3' direction away from the DSB, and Mre11 in the 3'-5' direction towards the DSB end. Mre11 exonuclease activity also confers resistance to DNA damage in cycling cells, suggesting that Mre11-catalysed resection may be a general feature of various DNA repair pathways.     

Zero outward flow velocity for plasma in a heliosheath transition layer

Voyager 1 has been in the reservoir of energetic ions and electrons that constitutes the heliosheath since it crossed the solar wind termination shock on 16 December 2004 at a distance from the Sun of 94 astronomical units (1?AU = 1.5?×?10(8)?km). It is now ～22?AU past the termination shock crossing. The bulk velocity of the plasma in the radial-transverse plane has been determined using measurements of the anisotropy of the convected energetic ion distribution. Here we report that the radial component of the velocity has been decreasing almost linearly over the past three years, from ～70?km?s(-1) to ～0?km?s(-1), where it has remained for the past eight months. It now seems that Voyager 1 has entered a finite transition layer of zero-radial-velocity plasma flow, indicating that the spacecraft may be close to the heliopause, the border between the heliosheath and the interstellar plasma. The existence of a flow transition layer in the heliosheath contradicts current predictions--generally assumed by conceptual models--of a sharp discontinuity at the heliopause.     

The genome of the green anole lizard and a comparative analysis with birds and mammals

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.     

History of science and its utopian reconstructions

In recent years explicitly utopian visions have reappeared across the political spectrum. To a surprising degree these visions have drawn on histories and science and technology. What should scholars of Science and Technology Studies (STS) and History and Philosophy of Science (HPS) make of these developments? The concept of utopia has often been treated with considerable distrust in these fields, as an indication of closed end-directed blueprints, or as an indication of fantasies of limitless technological improvement and purification of categories. Alongside this uneasiness, however, HPS and STS scholars have also projected transformative ambitions, seeking to recover from the past different ways of knowing and relating to the human and non-human world. By engaging with critiques of utopia from thinkers including Karl Popper, Otto Neurath, Bruno Latour, Isabelle Stengers and Donna Haraway, and exploring some of the utopian strands which have recurred in studies of science and technology—including the longing for integration, the association of science with planning, and the ways in which feminist scholars have envisaged alternative forms of science—we can understand the ongoing, and often unrecognised, utopian dimensions of HPS and STS.     

Differential phytosociological interactions involving male and female Atriplex bonnevillensis

Wind-pollinated dioecious plants often exhibit spatial segregation of the sexes. This partial niche separation has most often been explored using abiotic niche axes. However, if the sexes are truly separated in space, then they are apt to encounter different plant species that may heavily affect growth and reproduction. Also, to the extent that their niches differ, the sexes may respond differently to the same co-occurring species. Here we examine interspecific interactions that influence male and female reproductive potential in Atriplex bonnevillensis. Using Emlen’s interaction assessment, a technique which assesses species interactions based on cover classes, we show that Salsola species compete significantly with females but not males, while Halogeton glomeratus competes with males but not females. The effect of competition only became apparent when we corrected for site-specific fertility. These results imply that differential competition must be considered when studying dioecious plants that display spatial segregation of the sexes.     

Correlation of neighborhood relationships, carbon assimilation, and water status of sagebrush seedlings establishing after fire

Interactions of Artemisia tridentata ssp. vaseyana (mountain big sagebrush) and neighboring herbs may affect community development following fire in sagebrush steppe. Dry mass, photosynthesis, and water relations were measured for seedlings of A. tridentata ssp. vaseyana occurring at different distances from neighboring herbs in the initial growing seasons following fire, when herbs dominate plant community cover. Seedling mass significantly increased as distance to neighboring herbs increased, although a low r 2 indicated that mass was also affected by other sources of variation. Carbon assimilation ( A net ) was also greater for A. tridentata ssp. vaseyana seedlings in microsites farther from herbs, except during those sampling dates when A net and water availability were at low levels. Contrary to our expectations, water status of seedlings was not correlated with their distances to neighboring herbs, and supplemental watering did not affect the slope of the relationship between seedling mass and distance to neighboring herbs. These findings suggest that negative relationships between A. tridentata ssp. vaseyana seedlings and herbs establishing after fire are not likely due to competition over water and may instead result from interactions over factors not measured here (e.g., nutrients).     

Douglas-fir tussock moth ( Orgyia pseudotsugata McDunnough) on subalpine fir in northern Utah

Douglas-fir tussock moth ( Orgyia pseudotsugata McDunnough) defoliation was detected by aerial survey on three areas of the Wasatch-Cache National Forest in 1990 and 1991. These are the first documented tussock moth outbreaks in Utah. Ground surveys revealed that subalpine fir ( Abies lasiocarpa [Hook.] Nutt.) was heavily defoliated during the outbreak. Douglas-fir ( Pseudotsuga menziesii [Mirb.] Franco), though minor component in the affected areas, had noticeably less defoliation and mortality. Adjacent stands of Douglas-fir had little or no visible tussock moth activity. Defoliation on subalpine fir was typically found evenly distributed throughout the crown rather than concentrated at the top. Ninety-four percent of subalpine fir with defoliation ratings of 90% or more were killed. Top-kill occurred on nearly one-half of subalpine firs defoliated 25-89%. Heavy defoliated trees tended to occur in pockets bounded by areas of light defoliation. After three consecutive years of defoliation, tussock moth populations collapsed. No life stages were detected in 1993 from visual inspections of foliage or in pheromone traps.