Identification and Characterization of a Misfolded Monomeric Serpin Formed at Physiological Temperature

The native serpin state is kinetically trapped. However, under mildly destabilizing conditions, the conformational landscape changes, and a number of nonnative conformations with increased stability can be readily formed. The ability to undergo structural change is due to intrinsic strain within the serpin's tertiary fold, which is utilized for proteinase inhibition but renders the protein susceptible to aberrant folding and self-association. The relationship between these various conformations is poorly understood. Antichymotrypsin (ACT) is an inhibitory serpin that readily forms a number of inactive conformations, induced via either environmental stress or interaction with proteinases. Here we have used a variety of biophysical and structural techniques to characterize the relationship between some of these conformations. Incubation of ACT at physiological temperature results in the formation of a range of conformations, including both polymer and misfolded monomer. The ability to populate these nonnative states and the native conformation reflects an energy landscape that is very sensitive to the solution conditions. X-ray crystallography reveals that the misfolded monomeric conformation is in the delta conformation. Further polymerization and seeding experiments show that the delta conformation is an end point in the misfolding pathway of ACT and not an on-pathway intermediate formed during polymerization. The observation that ACT readily forms this inactive conformation at physiological temperature and pH suggests that it may have a role in both health and disease.     

Assembly and Maturation of the Bacteriophage Lambda Procapsid: gpC Is the Viral Protease

Viral capsids are robust structures designed to protect the genome from environmental insults and deliver it to the host cell. The developmental pathway for complex double-stranded DNA viruses is generally conserved in the prokaryotic and eukaryotic groups and includes a genome packaging step where viral DNA is inserted into a pre-formed procapsid shell. The procapsids self-assemble from monomeric precursors to afford a mature icosahedron that contains a single “portal” structure at a unique vertex; the portal serves as the hole through which DNA enters the procapsid during particle assembly and exits during infection. Bacteriophage λ has served as an ideal model system to study the development of the large double-stranded DNA viruses. Within this context, the λ procapsid assembly pathway has been reported to be uniquely complex involving protein cross-linking and proteolytic maturation events. In this work, we identify and characterize the protease responsible for λ procapsid maturation and present a structural model for a procapsid-bound protease dimer. The procapsid protease possesses autoproteolytic activity, it is required for degradation of the internal “scaffold” protein required for procapsid self-assembly, and it is responsible for proteolysis of the portal complex. Our data demonstrate that these proteolytic maturation events are not required for procapsid assembly or for DNA packaging into the structure, but that proteolysis is essential to late steps in particle assembly and/or in subsequent infection of a host cell. The data suggest that the λ-like proteases and the herpesvirus-like proteases define two distinct viral protease folds that exhibit little sequence or structural homology but that provide identical functions in virus development. The data further indicate that procapsid assembly and maturation are strongly conserved in the prokaryotic and eukaryotic virus groups.     

Leaving the Oil Under the Amazon: Ecuador's Yasuní-ITT Initiative

Oil and gas concessions now cover vast swaths of the western Amazon, including protected areas and indigenous territories. The Yasuní-ITT Initiative, Ecuador's innovative proposal to leave nearly a billion barrels of oil locked beneath Yasuní National Park, is the first major effort to reverse this trend. We provide a concise overview of the initiative, including an in-depth look at its widely lauded goals of protecting biodiversity, respecting indigenous peoples' territory, and combating climate change. We also discuss the proposal's lingering caveats, such as technical questions regarding the generation of financial resources to replace the forgone oil revenue. We conclude that the Yasuní-ITT Initiative is a potentially precedent-setting advance towards avoiding damaging oil and gas development in sensitive areas.     

Game Vertebrate Densities in Hunted and Nonhunted Forest Sites in Manu National Park,Peru

Manu National Park of southern Peru is one of the most renowned protected areas in the world, yet large-bodied vertebrate surveys conducted to date have been restricted to Cocha Cashu Biological Station, a research station covering <0.06 percent of the 1.7 Mha park. Manu Park is occupied by >460 settled Matsigenka Amerindians, 300–400 isolated Matsigenka, and several, little-known groups of isolated hunter–gatherers, yet the impact of these native Amazonians on game vertebrate populations within the park remains poorly understood. On the basis of 1495 km of standardized line-transect censuses, we present density and biomass estimates for 23 mammal, bird, and reptile species for seven lowland and upland forest sites in Manu Park, including Cocha Cashu. We compare these estimates between hunted and nonhunted sites within Manu Park, and with other Neotropical forest sites. Manu Park safeguards some of the most species-rich and highest biomass assemblages of arboreal and terrestrial mammals ever recorded in Neotropical forests, most likely because of its direct Andean influence and high levels of soil fertility. Relative to Barro Colorado Island, seed predators and arboreal folivores in Manu are rare, and generalist frugivores specializing on mature fruit pulp are abundant. The impact of such a qualitative shift in the vertebrate community on the dynamics of plant regeneration, and therefore, on our understanding of tropical plant ecology, must be profound. Despite a number of external threats, Manu Park continues to serve as a baseline against which other Neotropical forests can be gauged. Abstract in Spanish is available at http://www.blackwell-synergy.com/loi/btp .     

Spatial Patterns of Seed Dispersal by White-Faced Capuchins in Costa Rica: Evaluating Distant-Dependent Seed Mortality

Spatial patterns of seed dispersal are the focus of numerous theoretical examinations of endozoochory. Here, we examine the spatial pattern of seed dispersal by white-faced capuchin monkeys Cebus capucinus in Santa Rosa National Park, Costa Rica, and the neighborhood characteristics and distance variables most closely associated with seed survival and germination, and seedling survival and growth in various locations. Overall, distance to the nearest fruiting conspecific tree has the most positive, consistent effect on growth and survival variables, which supports a variation of the Janzen–Connell seed escape hypothesis.     

The pathogenesis of atherosclerosis. An interpretive history of the cholesterol controversy, part IV: the 1984 coronary primary prevention trial ends it--almost

As of the early 1980s, despite the wealth of evidence from experimental animal models, the extensive epidemiologic evidence, the powerful genetic evidence, and the strongly suggestive clinical intervention trial results, most clinicians still remained unpersuaded regarding the relevance of the lipid hypothesis. What was needed was a well-designed, large-scale, long-term, double-blind study demonstrating a statistically significant impact of treatment on coronary heart disease events. The National Institutes of Health (NIH) had laid the groundwork for such a study as early as 1970, but the study was not completed and the results published until 1984. This study, the Coronary Primary Prevention Trial, showed that treatment with a bile acid binding resin reduced major coronary events in hypercholesterolemic men by 19%, with a P value of 0.05. The NIH followed this up with a national Consensus Development Conference on Lowering Blood Cholesterol to Prevent Heart Disease. For the first time, the NIH now went on record advocating screening for hypercholesterolemia and urging aggressive treatment for those at high risk. The Institute initiated a national cooperative program to that end, the National Cholesterol Education Program. For the first time, preventing coronary heart disease became a national public health goal.     

Phosphorus Translocation by Red Deer on a Subalpine Grassland in the Central European Alps

We examined the role of red deer (Cervus elaphus L.) in translocating phosphorus (P) from their preferred grazing sites (short-grass vegetation on subalpine grasslands) to their wider home range in a subalpine grassland ecosystem in the Central European Alps. Phosphorus was used because it is the limiting nutrient in these grasslands. When we compared P removal of aboveground biomass due to grazing with P input due to the deposit of feces on a grid of 268 cells (20 m × 20 m) covering the entire grassland, we detected distinct spatial patterns: the proportion of heavily grazed short-grass vegetation increased with increasing soil-P pool, suggesting that red deer preferably grazed on grid cells with a higher soil-P pool. Biomass consumption related to increased proportion of short-grass vegetation, and therefore P removal, increased with increasing soil-P pool. However, within the two vegetation types (short-grass and tall-grass), consumption was independent from soil-P pool. In addition, P input rates from defecation increased with increasing soil-P pool, resulting in a constant mean net P loss of 0.083 kg ha⁻¹ y⁻¹ (0.03%–0.07% of soil-P pool) independent of both soil-P pool and vegetation type. Thus, there was no P translocation between grid cells with different soil-P pools or between short-grass and tall-grass vegetation. Based on these results, it is likely that the net rate of P loss is too small to explain the observed changes in vegetation composition from tall-herb/meadow communities to short-grass and from tall-grass to short-grass on the grassland since 1917. Instead, we suggest that the grazing patterns of red deer directly induced succession from tall-herb/meadow communities to short-grass vegetation. Yet, it is also possible that long-term net soil-P losses indirectly drive plant succession from short-grass to tall-grass vegetation, because nutrient depletion could reduce grazing pressure in short-grass vegetation and enable the characteristic tall-grass species Carex sempervirens Vill. to establish.     

The Influence of Previous Mountain Pine Beetle (Dendroctonus ponderosae) Activity on the 1988 Yellowstone Fires

We examined the historical record of mountain pine beetle (Dendroctonus ponderosae Hopkins) activity within Yellowstone National Park, Wyoming, for the 25-years period leading up to the 1988 Yellowstone fires (1963–86) to determine how prior beetle activity and the resulting tree mortality affected the spatial pattern of the 1988 Yellowstone fires. To obtain accurate estimates of our model parameters, we used a Markov chain Monte Carlo method to account for the high degree of spatial autocorrelation inherent to forest fires. Our final model included three statistically significant variables: drought, aspect, and sustained mountain pine beetle activity in the period 1972–75. Of the two major mountain pine beetle outbreaks that preceded the 1988 fires, the earlier outbreak (1972–75) was significantly correlated with the burn pattern, whereas the more recent one (1980–83) was not. Although regional drought and high winds were responsible for the large scale of this event, the analysis indicates that mountain pine beetle activity in the mid-1970s increased the odds of burning in 1988 by 11% over unaffected areas. Although relatively small in magnitude, this effect, combined with the effects of aspect and spatial variation in drought, had a dramatic impact on the spatial pattern of burned and unburned areas in 1988.     

Endolithic photosynthetic communities within ancient and recent travertine deposits in Yellowstone National Park

Molecular and culture based methods were used to survey endolithic, photosynthetic communities from hot spring-formed travertine rocks of various ages, ranging from<10 to greater than 300,000 years. Much of this travertine contained a 1-3-mm-thick greenish band composed mainly of cyanobacteria 1-5 mm below the rock surface. The travertine rocks experienced desiccation in summer and freezing in winter. A total of 83 environmental 16S rRNA gene sequences were obtained from clone libraries and denaturing gradient gel electrophoresis. Small subunit rRNA gene sequences and cell morphology were determined for 36 cyanobacterial culture isolates from these samples. Phylogenetic analysis showed that the 16S rRNA gene sequences fell into 15 distinct clusters, including several novel lineages of cyanobacteria.     

哀牢山国家级自然保护区南华片三种雉类春季取食地利用比较

探讨亲缘关系密切、营养关系相似的物种间的共存机制,是群落生态学的研究热点之一。研究结果有助于了解同域物种的资源利用特点和分化方式,对于地区生物多样性的保育工作亦具有指导意义。黑颈长尾雉(Syrmaticushumiae)、白鹇(Lophuranycthemera)和红喉山鹧鸪(Arborophilarufogularis)为哀牢山国家自然保护区南华片区同域分布的3种雉类,它们亲缘关系较近,食性相似。比较三者春季取食地18个生态因子生态位宽度和重叠指数,结果显示,黑颈长尾雉广适性(生态位宽度值>0·8)的取食地因子最少(1个),专一性(生态位宽度<0·8)因子最多(4个);白鹇居中(3个和2个);红喉山鹧鸪与黑颈长尾雉恰好相反(6个和0个)。黑颈长尾雉与白鹇生态位重叠指数≥0·5的因子数(5个)多于黑颈长尾雉与红喉山鹧鸪的(2个)和白鹇与红喉山鹧鸪的(4个);灌木层盖度、草本层盖度和种子密度的生态位重叠指数在3种雉类间均较大。单因素方差分析结果表明,3种雉类在坡向、乔木密度、草本层盖度、种子密度和土壤动物等5个因子均无差异;在距空旷地距离、距道路距离和灌木层盖度等3个因子均有差异;而其余因子则是在不同的两个物种之间有差异。主成分分析结果显示,黑颈长尾雉取食地前7个主成分的累计信息量达85·6%,白鹇的前6个达86·0%,红喉山鹧鸪的前5个达79·0%。影响这三种雉类取食地选择的因子主要集中于前3个主成分。3种雉类间取食地因子差异状态呈镶嵌分布,意味着种间生态位呈分化状态。各物种优先选择的因子组合不同,各因子的重要程度亦不一。