The regional variation of aboveground live biomass in old-growth Amazonian forests

The biomass of tropical forests plays an important role in the global carbon cycle, both as a dynamic reservoir of carbon, and as a source of carbon dioxide to the atmosphere in areas undergoing deforestation. However, the absolute magnitude and environmental determinants of tropical forest biomass are still poorly understood. Here, we present a new synthesis and interpolation of the basal area and aboveground live biomass of old‐growth lowland tropical forests across South America, based on data from 227 forest plots, many previously unpublished. Forest biomass was analyzed in terms of two uncorrelated factors: basal area and mean wood density. Basal area is strongly affected by local landscape factors, but is relatively invariant at regional scale in moist tropical forests, and declines significantly at the dry periphery of the forest zone. Mean wood density is inversely correlated with forest dynamics, being lower in the dynamic forests of western Amazonia and high in the slow‐growing forests of eastern Amazonia. The combination of these two factors results in biomass being highest in the moderately seasonal, slow growing forests of central Amazonia and the Guyanas (up to 350 Mg dry weight ha^?1) and declining to 200–250 Mg dry weight ha^?1 at the western, southern and eastern margins. Overall, we estimate the total aboveground live biomass of intact Amazonian rainforests (area 5.76 × 10⁶ km² in 2000) to be 93±23 Pg C, taking into account lianas and small trees. Including dead biomass and belowground biomass would increase this value by approximately 10% and 21%, respectively, but the spatial variation of these additional terms still needs to be quantified.     

Structural and Biochemical Characterization of the Human Cyclophilin Family of Peptidyl-Prolyl Isomerases

Peptidyl-prolyl isomerases catalyze the conversion between cis and trans isomers of proline. The cyclophilin family of peptidyl-prolyl isomerases is well known for being the target of the immunosuppressive drug cyclosporin, used to combat organ transplant rejection. There is great interest in both the substrate specificity of these enzymes and the design of isoform-selective ligands for them. However, the dearth of available data for individual family members inhibits attempts to design drug specificity; additionally, in order to define physiological functions for the cyclophilins, definitive isoform characterization is required. In the current study, enzymatic activity was assayed for 15 of the 17 human cyclophilin isomerase domains, and binding to the cyclosporin scaffold was tested. In order to rationalize the observed isoform diversity, the high-resolution crystallographic structures of seven cyclophilin domains were determined. These models, combined with seven previously solved cyclophilin isoforms, provide the basis for a family-wide structure∶function analysis. Detailed structural analysis of the human cyclophilin isomerase explains why cyclophilin activity against short peptides is correlated with an ability to ligate cyclosporin and why certain isoforms are not competent for either activity. In addition, we find that regions of the isomerase domain outside the proline-binding surface impart isoform specificity for both in vivo substrates and drug design. We hypothesize that there is a well-defined molecular surface corresponding to the substrate-binding S2 position that is a site of diversity in the cyclophilin family. Computational simulations of substrate binding in this region support our observations. Our data indicate that unique isoform determinants exist that may be exploited for development of selective ligands and suggest that the currently available small-molecule and peptide-based ligands for this class of enzyme are insufficient for isoform specificity.

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Experimental wood addition in streams: effects on organic matter storage and breakdown

1. Channel complexity affects the physical structure, biotic communities and functioning of stream ecosystems. Large wood (LW) is a key element in the creation and maintenance of physically complex stream channels in forested areas. 2. In an attempt to enhance stream habitat quality and ecosystem functioning and to reduce inputs of organic matter to a downstream reservoir, LW was experimentally introduced into four mountain streams in the Basque Country (northern Spain), ranging in channel width from 3 to 13 m. Following a before–after/control–impact (BACI) design, streams were monitored during 1 year prior to wood addition and during 2 years after addition in one control and one experimental reach per stream. 3. Areal cover of benthic organic matter in the entire channel was measured from regular transects and the mass of stored organic matter from random Surber samples. Breakdown of organic matter was assessed in litter bag experiments performed with black alder leaves. When 50% of the initial mass in the bags remained, invertebrates associated with leaf bags were collected. 4. Wood placement produced a 2‐ to 70‐fold increase in the storage of organic matter, especially in thick deposits upstream from wood jams, with values in excess of 2 kg AFDM per m² in the small streams. The accumulation of organic matter produced by wood introduction decreased with increasing stream size. 5. Despite the large increase in the availability of organic matter, litter breakdown rates were unaffected by the experimental reaches, suggesting large increases in the total amount of organic matter consumed at the reach scale. 6. Numbers of invertebrates and shredders per gram of leaf litter did not respond to wood addition. Average body mass of invertebrates associated with leaf litter showed a non‐significant decreasing trend, which might reflect increased recruitment. 7. Although the effects of wood addition can depend on wood stability and stream size, adding LW to restore channel complexity can improve environmental conditions for invertebrate communities and affect stream ecosystem functioning, enhancing the efficiency to use organic matter inputs on a reach scale.     

Chromosome counts in the genus Festuca L. section Festuca (Poaceae) in the Iberian Peninsula

Chromosome numbers have been counted in 102 populations belonging to 34 taxa of Festuca L. section Festuca from the Iberian Peninsula. Four of these taxa have been counted for the first time and another three for the first time from the Iberian Peninsula. Furthermore, the levels of ploidy for another three taxa have been obtained for new populations within their distribution area, and for another 18 taxa the ploidy levels have been confirmed. Five levels of ploidy have been established for this section: diploid, tetraploid, hexaploid, octoploid and decaploid. There are 17 diploid taxa, eight tetraploid, three octoploid, two octoploid and one decaploid. The three remaining taxa represent polyploid complexes (one tetra-hexa-octoploid and two hexa-octoploids).     

Agave for tequila and biofuels: an economic assessment and potential opportunities

This paper explores the economic viability of producing biofuels from Agave in Mexico and the potential for it to complement the production of tequila or mescal. We focus on Agave varieties currently being used by the tequila industry to produce two beverages, tequila and mescal, and explore the potential for biofuel production from these plants. Without competing directly with beverage production, we discuss the economic costs and benefits of converting Agave by‐products to liquid fuel as an additional value‐added product and expanding cultivation of Agave on available land. We find that the feedstock cost for biofuel from the Agave piña alone could be more than US$3 L^?1 on average. This is considerably higher than the feedstock costs of corn ethanol and sugarcane ethanol. However, there may be potential to reduce these costs with higher conversion efficiencies or by using sugar present in other parts of the plant. The costs of cellulosic biofuels using the biomass from the entire plant could be lower depending on the conversion efficiency of biomass to fuel and the additional costs of harvesting, collecting and transporting that biomass.     

Biogeographical analysis of two Polypodium species complexes (Polypodiaceae) in Mexico and Central America

We analyzed the geographical and elevational distributions of two Polypodium complexes from Mexico and Central America. Distribution data of nine species of the Polypodium colpodes complex and the Polypodium plesiosorum complex were obtained from almost 1500 herbarium specimens, field collections in Mexico and Costa Rica, and literature studies. The presence of each species was recorded for each Mesoamerican country, in 1° × 1° grid‐cells and biogeographical provinces. The rarity of species was also evaluated. Although the two complexes show extensive overlap, the P. colpodes complex is distributed mainly along the Pacific versant of Mexico and Central America, whereas the P. plesiosorum complex occurs mainly along the Atlantic versant. Those biogeographical provinces with maximum species diversity are Chiapas (seven species), Sierra Madre del Sur (six species), and the Trans‐Mexican Volcanic belt (six species). Grid‐cells with more species are located mainly in the mountains of central‐southern Mexico and northern Central America. Richness does not decrease or increase with latitude. Elevation distributions showed that most Polypodium species are concentrated in the montane interval and three species groups were recognized based on elevational preferences. Polypodium colpodes and P. plesiosorum are the most widely distributed species, whereas Polypodium castaneum and Polypodium flagellare are the only two species that possess the three attributes of rarity (narrow geographical distribution, high habitat specificity, and scarce local populations). Polypodium species of both complexes are present mainly in the montane regions of the study area and show some degree of geographical sympatry, especially in southern Mexico and northern Central America. This overlapping is explained by the elevation tolerance within montane systems and because most species inhabit three or more vegetation types. The distributional patterns of these complexes coincided with the three regional highlands of Mesoamerica, which are separated from each other by the Isthmus of Tehuantepec and by the lowlands of Nicaragua. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Extracellular cyclophilin-A stimulates ERK1/2 phosphorylation in a cell-dependent manner but broadly stimulates nuclear factor kappa B

Background

Although the peptidyl-prolyl isomerase, cyclophilin-A (peptidyl-prolyl isomerase, PPIA), has been studied for decades in the context of its intracellular functions, its extracellular roles as a major contributor to both inflammation and multiple cancers have more recently emerged. A wide range of activities have been ascribed to extracellular PPIA that include induction of cytokine and matrix metalloproteinase (MMP) secretion, which potentially underlie its roles in inflammation and tumorigenesis. However, there have been conflicting reports as to which particular signaling events are under extracellular PPIA regulation, which may be due to either cell-dependent responses and/or the use of commercial preparations recently shown to be highly impure.

Methods

We have produced and validated the purity of recombinant PPIA in order to subject it to a comparative analysis between different cell types. Specifically, we have used a combination of multiple methods such as luciferase reporter screens, translocation assays, phosphorylation assays, and nuclear magnetic resonance to compare extracellular PPIA activities in several different cell lines that included epithelial and monocytic cells.

Results

Our findings have revealed that extracellular PPIA activity is cell type-dependent and that PPIA signals via multiple cellular receptors beyond the single transmembrane receptor previously identified, Extracellular Matrix MetalloPRoteinase Inducer (EMMPRIN). Finally, while our studies provide important insight into the cell-specific responses, they also indicate that there are consistent responses such as nuclear factor kappa B (NFκB) signaling induced in all cell lines tested.

Conclusions

We conclude that although extracellular PPIA activates several common pathways, it also targets different receptors in different cell types, resulting in a complex, integrated signaling network that is cell type-specific.     

Natural Occurrence of Pepino mosaic virus in Lycopersicon Species in Central and Southern Peru

Pepino mosaic virus (PepMV), a potexvirus first described in 1980 from pepino ( Solanum muricatum ) plants cultivated in Peru, was isolated from diseased tomato plants in the Netherlands in 1999, and is now the cause of an emerging tomato disease in Europe. In a survey of central and southern Peru, 65 wild and four cultivated populations of Lycopersicon , as well as six populations of other species of Solanaceae , were tested for the presence of PepMV and six other viruses. Of the Lycopersicon population sampled, 23 (35.4%) reacted positively in double antibody sandwich (DAS)-enzyme-linked immunosorbent assay (ELISA) with antisera to PepMV. DAS-ELISA tests for PepMV of other solanaceous species were negative, except for one sample of pepino ( Solanum muricatum ). Mechanical inoculation of susceptible Lycopersicon esculentum cv. NE-1 plants with crude sap extracts of 20 of these samples confirmed that 15 of them (from the Departments of Apurimac, Arequipa and Moquegua) were infected with PepMV; these inoculated plants were also DAS-ELISA positive and, in most cases, developed symptoms. Thirteen of the infective extracts were obtained from plants of wild Lycopersicon species (three L. chilense , three L. chmielewskii , two L. parviflorum and five L. peruvianum ) and one each from the cultivated species L. esculentum and S. muricatum . The wild Lycopersicon species are newly reported natural hosts of PepMV. Tests for the other six viruses were negative, except that two samples contained Tomato mosaic virus . Thus, PepMV occurs in Lycopersicon species in central and southern Peru, even in isolated wild populations. These results indicate that the virus is not new to the region and has an efficient mechanism of natural transmission.     

Mesodynamics in the SARS nucleocapsid measured by NMR field cycling

Protein motions on all timescales faster than molecular tumbling are encoded in the spectral density. The dissection of complex protein dynamics is typically performed using relaxation rates determined at high and ultra-high field. Here we expand this range of the spectral density to low fields through field cycling using the nucleocapsid protein of the SARS coronavirus as a model system. The field-cycling approach enables site-specific measurements of R ₁ at low fields with the sensitivity and resolution of a high-field magnet. These data, together with high-field relaxation and heteronuclear NOE, provide evidence for correlated rigid-body motions of the entire β-hairpin, and corresponding motions of adjacent loops with a time constant of 0.8 ns (mesodynamics). MD simulations substantiate these findings and provide direct verification of the time scale and collective nature of these motions.     

Streptococcus pneumoniae IgA1 protease: A metalloprotease that can catalyze in a split manner in vitro

IgA1 proteases (IgA1P) from diverse pathogenic bacteria specifically cleave human immunoglobulin A1 (IgA1) at the hinge region, thereby thwarting protective host immune responses. Streptococcus pneumoniae (S. pneumoniae) IgA1P shares no sequence conservation with serine or cysteine types of IgA1Ps or other known proteins, other than a conserved HExxH Zn‐binding motif (1604‐1608) found in metalloproteases. We have developed a novel expression system to produce the mature S. pneumoniae IgA1P and we have discovered that this form is both attached to the bacterial cell surface and released in its full form. Our data demonstrate that the S. pneumoniae IgA1P comprises two distinct regions that associate to form an active metalloprotease, the first such example of a metalloprotease that can be split in vitro and recombined to form an active enzyme. By capitalizing on this novel domain architecture, we show that the N‐terminal region of S. pneumoniae IgA1P comprises the primary binding region for IgA1, although the C‐terminal region of S. pneumoniae IgA1P is necessary for cleavage of IgA1. Our findings lend insight into the protein domain architecture of the S. pneumoniae IgA1P and function of this important virulence factor for S. pneumoniae infection.