Post‐fire tree establishment patterns at the alpine treeline ecotone: Mount Rainier National Park,Washington, USA

Questions: Does tree establishment: (1) occur at a treeline depressed by fire, (2) cause the forest line to ascend upslope, and/or (3) alter landscape heterogeneity? (4) What abiotic and biotic local site conditions are most important in structuring establishment patterns? (5) Does the abiotic setting become more important with increasing upslope distance from the forest line? Location: Western slopes of Mount Rainier, USA. Methods: We performed classification analysis of 1970 satellite imagery and 2003 aerial photography to delineate establishment. Local site conditions were calculated from a LIDAR‐based DEM, ancillary climate data, and 1970 tree locations in a GIS. We used logistic regression on a spatially weighted landscape matrix to rank variables. Results: Considerable establishment after 1970 caused forest line elevation to increase over 150 m in specific locations. Landscape heterogeneity increased with distance from the 1970 forest line. At a broad spatial context, we found establishment was most common near existing trees (0‐50 m) and at low elevations (1250‐1350 m). Slope aspect (W, NW, N, NE, and E), slope angle (40‐60°), and other abiotic factors emerged as important predictors of establishment with increasing upslope distance from the forest line to restricted spatial extents. Conclusions: Favorable climatic conditions likely triggered widespread tree establishment. Readily available seed probably enhanced establishment rates near sexually mature trees, particularly in the less stressful environment at low elevations. The mass effect of nearly ubiquitous establishment in these areas may have obscured the importance of the abiotic setting to restricted spatial extents. Topographic variability apparently produced favorable sites that facilitated opportunistic establishment with increasing upslope distance from the forest line, thereby enabling additional trees to invade the alpine tundra.     

Rethinking the common garden in invasion research

In common garden experiments, a number of genotypes are raised in a common environment in order to quantify the genetic component of phenotypic variation. Common gardens are thus ideally suited for disentangling how genetic and environmental factors contribute to the success of invasive species in their new non-native range. Although common garden experiments are increasingly employed in the study of invasive species, there has been little discussion about how these experiments should be designed for greatest utility. We argue that this has delayed progress in developing a general theory of invasion biology. We suggest a minimum optimal design (MOD) for common garden studies that target the ecological and evolutionary processes leading to phenotypic differentiation between native and invasive ranges. This involves four elements: (A) multiple, strategically sited garden locations, involving at the very least four gardens (2 in the native range and 2 in the invaded range); (B) careful consideration of the genetic design of the experiment; (C) standardization of experimental protocols across all gardens; and (D) care to ensure the biosafety of the experiment. Our understanding of the evolutionary ecology of biological invasions will be greatly enhanced by common garden studies, if and only if they are designed in a more systematic fashion, incorporating at the very least the MOD suggested here.     

Papuacedrus (Cupressaceae) in Eocene Patagonia: A new fossil link to Australasian rainforests

The 51.9 Ma Laguna del Hunco (LH) and 47.5 Ma Río Pichileufú (RP) floras from Patagonia, Argentina are unusually rich, angiosperm-dominated assemblages with living relatives in the low-latitude West Pacific, neotropics, and temperate southern latitudes. The diverse gymnosperms in these floras are important for Gondwanan biogeographic history and paleoclimatic interpretations. "Libocedrus" prechilensis Berry 1938 (Cupressaceae), previously known only from the holotype (RP), a vegetative branch, is revised here based on new material from both localities, including a seed cone attached to a shoot with cuticle (LH). Characters of these fossils are diagnostic of monotypic Papuacedrus (highlands of New Guinea and Moluccas). Living P. papuana is most abundant in cloud forests receiving up to 4 m rainfall annually, whereas Austrocedrus (Libocedrus) chilensis, the basis of comparison when the fossil species was named, inhabits dry, cold steppe margins to mediterranean climates in southern South America. We establish Papuacedrus prechilensis comb. nov., which simultaneously invalidates a southern South American connection for the fossil floras and reveals a link to West Pacific montane rainforests. Combined evidence indicates a biome similar to extant subtropical, or tropical montane, rainforests that persisted for at least 4.4 Myr, linking elevated floral richness to abundant rainfall.     

An Unusual Recent Expansion of the C-Terminal Domain of RNA Polymerase II in Primate Malaria Parasites Features a Motif Otherwise Found Only in Mammalian Polymerases

The tail of the enzyme RNA polymerase II is responsible for integrating the diverse events of gene expression in eukaryotes and is indispensable for life in yeast, fruit flies, and mice. The tail features a C-terminal domain (CTD), which is comprised of tandemly repeated Y₁-S₂-P₃-T₄-S₅-P₆-S₇ amino acid heptads that are highly conserved across evolutionary lineages, with all mammalian polymerases featuring 52 identical heptad repeats. However, the composition and function of protozoan CTDs remain less well understood. We find that malaria parasites (genus Plasmodium) display an unprecedented plasticity within the length and composition of their CTDs. The CTD in malaria parasites which infect human and nonhuman primates has expanded compared to closely related species that infect rodents or birds. In addition, this variability extends to different isolates within a single species, such as isolates of the human malaria parasite, Plasmodium falciparum. Our results indicate that expanded CTD heptads in malaria parasites correlates with parasitism of primates and provide the first demonstration of polymorphism of the RNA polymerase II CTD within a single species. The expanded set of CTD heptads feature lysine in the seventh position (Y₁-S₂-P₃-T₄-S₅-P₆-K₇), a sequence only seen otherwise in the distal portion of mammalian polymerases. These observations raise new questions for the radiation of malaria parasites into diverse hosts and for the molecular evolution of RNA polymerase II.     

Skeletal Muscle AMP-activated Protein Kinase Is Essential for the Metabolic Response to Exercise in Vivo

AMP-activated protein kinase (AMPK) has been postulated as a super-metabolic regulator, thought to exert numerous effects on skeletal muscle function, metabolism, and enzymatic signaling. Despite these assertions, little is known regarding the direct role(s) of AMPK in vivo, and results obtained in vitro or in situ are conflicting. Using a chronically catheterized mouse model (carotid artery and jugular vein), we show that AMPK regulates skeletal muscle metabolism in vivo at several levels, with the result that a deficit in AMPK activity markedly impairs exercise tolerance. Compared with wild-type littermates at the same relative exercise capacity, vascular glucose delivery and skeletal muscle glucose uptake were impaired; skeletal muscle ATP degradation was accelerated, and arterial lactate concentrations were increased in mice expressing a kinase-dead AMPKα2 subunit (α2-KD) in skeletal muscle. Nitric-oxide synthase (NOS) activity was significantly impaired at rest and in response to exercise in α2-KD mice; expression of neuronal NOS (NOSμ) was also reduced. Moreover, complex I and IV activities of the electron transport chain were impaired 32 ± 8 and 50 ± 7%, respectively, in skeletal muscle of α2-KD mice (p < 0.05 versus wild type), indicative of impaired mitochondrial function. Thus, AMPK regulates neuronal NOSμ expression, NOS activity, and mitochondrial function in skeletal muscle. In addition, these results clarify the role of AMPK in the control of muscle glucose uptake during exercise. Collectively, these findings demonstrate that AMPK is central to substrate metabolism in vivo, which has important implications for exercise tolerance in health and certain disease states characterized by impaired AMPK activation in skeletal muscle.The ubiquitously expressed serine/threonine AMP-activated protein kinase (AMPK)² is an αβγ heterotrimer postulated to play a key role in the response to energetic stress (1, 2), because of its sensitivity to increased cellular AMP levels (3). Pharmacological activation of AMPK (primarily via the AMP analogue ZMP) increases catabolic processes such as GLUT4 translocation (4, 5), glucose uptake (6, 7), long chain fatty acid (LCFA) uptake (8), and substrate oxidation (6). Concomitantly, pharmacological activation of AMPK inhibits anabolic processes, and in skeletal muscle genetic reduction of the catalytic AMPKα2 subunit eliminates these pharmacological effects (9–12). Thus, AMPK has been proposed to act as a metabolic master switch (2, 13, 14). Physiologically, exercise at intensities sufficient to increase free cytosolic AMP (AMP_free) levels is a potent stimulus of AMPK, preferentially activating AMPKα2 in skeletal muscle (15–17). The metabolic profile of skeletal muscle during moderate to high intensity exercise is remarkably similar to skeletal muscle in which AMPK has been pharmacologically activated (i.e. increases in catabolic processes). This is consistent with the hypothesis that AMPK activation is required for the metabolic response to increased cellular stress. Given this, it is surprising that the direct role(s) of skeletal muscle AMPK during exercise under physiological in vivo conditions is unknown.A number of studies have tried to attribute causality to the AMPK and metabolic responses to exercise using transgenic models. In mouse models in which AMPKα2 protein expression and/or activity has been impaired, contractions performed in isolated skeletal muscle in vitro, ex vivo, or in situ have demonstrated that skeletal muscle glucose uptake (MGU) is normal (9, 10), partially impaired (11, 18), or ablated (19). Furthermore, ex vivo skeletal muscle LCFA uptake and oxidation in response to contraction appears to be AMPK-independent (20, 21). A key limitation of these studies is that the experimental models were not physiological. Under in vivo conditions, mice expressing a kinase-dead (18) or inactive (22) AMPKα2 subunit in cardiac and skeletal muscle have impaired voluntary and maximal physical activity, respectively, indicative of a physiological role for AMPK during exercise. In this context, obese non-diabetic and diabetic individuals have impaired skeletal muscle AMPK activation during moderate intensity exercise (23) as well as during the post-exercise period (24), yet the contribution of this impairment to the disease state is unclear. Thus, in vivo studies are essential to define the role of AMPK in skeletal muscle during exercise.Physical exercise of a moderate intensity is an effective adjunct treatment for chronic metabolic diseases such as obesity and type 2 diabetes (25). Given the importance of elucidating the molecular mechanism(s) regulating skeletal muscle substrate metabolism during exercise and the putative role of AMPK as a critical mediator in this process, we tested the hypothesis that AMPKα2 is functionally linked to substrate metabolism in vivo.     

Evasion and disruption of innate immune signalling by hepatitis C and West Nile viruses

Signalling pathways leading to type I interferon production are the first line of defence employed by the host to combat viruses, and represent a barrier that an invading virus must overcome in order to establish infection. In this review we highlight the ability of two members of the Flaviviridae, a globally distributed family of RNA viruses that represent a significant public health concern, to disrupt and evade these defences. Hepatitis C virus is a hepatotropic virus, infecting greater than 170 million people worldwide, while West Nile virus is a neurotropic virus that causes encephalitis in humans and horses. While these viruses cause distinct disease phenotypes, the ability of pathogenic strains to modulate the innate immune response is a key factor in influencing disease outcome. Both viruses have evolved unique strategies to target various aspects of type I interferon induction and signalling in order to prevent viral clearance and to promote virus replication.     

A statistical framework to evaluate virtual screening

Background  

Receiver operating characteristic (ROC) curve is widely used to evaluate virtual screening (VS) studies. However, the method fails to address the "early recognition" problem specific to VS. Although many other metrics, such as RIE, BEDROC, and pROC that emphasize "early recognition" have been proposed, there are no rigorous statistical guidelines for determining the thresholds and performing significance tests. Also no comparisons have been made between these metrics under a statistical framework to better understand their performances.     

Comparison of small n statistical tests of differential expression applied to microarrays

Background  

DNA microarrays provide data for genome wide patterns of expression between observation classes. Microarray studies often have small samples sizes, however, due to cost constraints or specimen availability. This can lead to poor random error estimates and inaccurate statistical tests of differential expression. We compare the performance of the standard t-test, fold change, and four small n statistical test methods designed to circumvent these problems. We report results of various normalization methods for empirical microarray data and of various random error models for simulated data.