Peptide combinatorial libraries identify TSC2 as a death-associated protein kinase (DAPK) death domain-binding protein and reveal a stimulatory role for DAPK in mTORC1 signaling

Death-associated protein kinase (DAPK) is a multidomain enzyme that plays a central role in autophagic and apoptotic signaling, although the protein-protein interactions regulating DAPK functions are not well defined. Peptide aptamer libraries were used to identify the tumor suppressor protein tuberin (TSC2) as a novel DAPK death domain-binding protein, and we evaluated whether DAPK is a positive or negative effector of the TSC2-regulated mammalian target of rapamycin (mTORC1) signaling pathway. Binding studies using death domain miniproteins in vitro and deletion analysis in vivo determined that the death domain of DAPK is the major site for the interaction with TSC2. Recombinant DAPK phosphorylates TSC2 in vitro, and DAPK kinase activity is stimulated by growth factor signaling. Transfection of DAPK promotes phosphorylation of TSC2 in vivo, whereas short interfering RNA-mediated attenuation of DAPK reduces growth factor-stimulated phosphorylation of TSC2. DAPK-dependent phosphorylation leads to TSC1-TSC2 complex dissociation, and consequently manipulation of DAPK by transfection or short interfering RNA demonstrated that DAPK is a positive regulator of mTORC1 in response to growth factor activation. Epistatic studies suggest that DAPK functions downstream from the RAS-MEK-ERK and phosphatidylinositol 3-kinase-AKT growth factor signaling pathways. DAPK(+/-) mouse embryo fibroblasts have attenuated mTORC1 signaling compared with DAPK+/+ counterparts, and overexpression of DAPK in DAPK(+/-) MEFs stimulates mTORC1 activity. These data uncover a novel interaction between DAPK and TSC2 proteins that has revealed a positive link between growth factor stimulation of DAPK and mTORC1 signaling that may ultimately affect autophagy, cell survival, or apoptosis.     

Structural basis for α-conotoxin potency and selectivity

Parkinson’s disease is a debilitating movement disorder characterized by altered levels of α₆β₂1 (1 indicates the possible presence of additional subunits) nicotinic acetylcholine receptors (nAChRs) localized on presynaptic striatal catecholaminergic neurons. α-Conotoxin MII (α-CTx MII) is a highly useful ligand to probe α₆β₂ nAChRs structure and function, but it does not discriminate among closely related α₆1 nAChR subtypes. Modification of the α-CTx MII primary sequence led to the identification of α-CTx MII[E11A], an analog with 500–5300-fold discrimination between α₆1 subtypes found in both human and non-human primates. α-CTx MII[E11A] binds most strongly (femtomolar dissociation constant) to the high affinity α₆ nAChR, a subtype that is selectively lost in Parkinson’s disease. Here, we present the three-dimensional solution structure for α-CTx MII[E11A] as determined by two-dimensional ¹H NMR spectroscopy to 0.13 ± 0.09 ? backbone and 0.45 ± 0.08 ? heavy atom root-mean-square deviation from mean structure. Structural comparisons suggest that the increased hydrophobic area of α-CTx MII[E11A] relative to other members of the α-CTx family may be responsible for its exceptionally high affinity for α6α4β21 nAChR as well as discrimination between α₆β₂ and α₃β₂ containing nAChRs. This finding may enable the rational design of novel peptide analogs that demonstrate enhanced specificity for α₆1 nAChR subunit interfaces and provide a means to better understand nAChR structural determinants that modulate brain dopamine levels and the pathophysiology of Parkinson’s disease.     

Concentration of Disease-Associated Prion Protein with Silicon Dioxide

Reagents that can precipitate the disease-associated prion protein (PrP^Sc) are vital for the development of high sensitivity tests to detect low levels of this disease marker in biological material. Here, a range of minerals are shown to precipitate both ovine cellular prion protein (PrP^C) and ovine scrapie PrP^Sc. The precipitation of prion protein with silicon dioxide is unaffected by PrP^Sc strain or host species and the method can be used to precipitate bovine BSE. This method can reliably concentrate protease-resistant ovine PrP^Sc (PrP^res) derived from 1.69 μg of brain protein from a clinically infected animal diluted into either 50 ml of buffer or 15 ml of plasma. The introduction of a SiO₂ precipitation step into the immunological detection of PrP^res increased detection sensitivity by over 1,500-fold. Minerals such as SiO₂ are readily available, low cost reagents with generic application to the concentration of diseases-associated prion proteins.     

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.