Use of Terrestrial Invertebrates as Indicators of the Ecological Sustainability of Forest Management under the Montreal Process

Twelve nations involved in boreal or temperate forest management are committed to reporting on indicators under the Montreal Process as a mechanism for assessing progress towards sustainable forest management. For fauna, invertebrates are often considered too poorly known and diverse to include in sustainability indicator reporting. The alternative view, that no monitoring of sustainability can be considered adequate without inclusion of some invertebrate species, is espoused in this paper. The microhabitats of soil and litter, foliage and canopy, bark and branch, dead standing trees and coarse woody debris are highlighted as relevant in the context of determining the impacts of forest management on invertebrates and for selecting representative species. It is argued that a selection of those species from each of the key microhabitats that are restricted to later stages of succession should be monitored. This could be complemented by a selection of easily monitored species from a range of functional groups as a means of endeavouring to pick up adverse impacts not foreseen on the basis of present knowledge. In the longer term, habitat indices (developed from predictive models of fauna habitat) should be used to monitor the occurrence of indicator species across the broader landscape, rather than at specific sites where monitoring of species takes place. Most countries would be in a position to select indicator species and commence monitoring for some key microhabitats (e.g. soil and litter). However, further research is needed in many countries before indicator species can be selected for other key microhabitats (e.g. coarse woody debris).     

Novel 2D and 3D multiple-quantum bi-directional HCNCH experiments for the correlation of ribose and base protons/carbons in 13C/15N labeled RNA

Multiple-quantum 2D and 3D bi-directional HCNCH experiments are presented for the correlation of base and ribose protons/carbons in ¹³C/¹⁵N labeled HIV-1 TAR RNA. In both 2D and 3D experiments, the magnetization of H1 is transferred to H6/H8 and H1 through H1-C1-N1/9-C6/8-H6/8 and H1-C1-N1/9-C1-H1 pathways, and the magnetization of H6/8 is transferred to H1 and H6/8 through H6/8-C6/8-N1/9-C1-H1 and H6/8-C6/8-N1/9-C6/8-H6/8 pathways. Chemical shifts of four different nuclei (H1, C1, C6/8 and H6/8) are sampled in the 2D experiment. The correlation of base and ribose protons/carbons is established by the rectangular arrangement of crossover and out-and-back peaks in the proton/carbon correlated spectrum. The rectangular connections can be further resolved using the nitrogen dimension in a ¹H/¹³C/¹⁵N 3D experiment. Furthermore, by taking advantage of the well separated chemical shifts of N1 (pyrimidine) and N9 (purine), the 2D spectrum can be simplified into two sub-spectra based on their base type. Both experiments were tested on a ¹³C/¹⁵N labeled 27-mer HIV-1 TAR RNA containing a UUCG hairpin loop.     

Metabolic behavior of immobilized Candida guilliermondii cells during batch xylitol production from sugarcane bagasse acid hydrolyzate

Candida guilliermondii cells, immobilized in Ca-alginate beads, were used for batch xylitol production from concentrated sugarcane bagasse hydrolyzate. Maximum xylitol concentration (20.6 g/L), volumetric productivity (0.43 g/L. h), and yield (0.47 g/g) obtained after 48 h of fermentation were higher than similar immobilized-cell systems but lower than free-cell cultivation systems. Substrates, products, and biomass concentrations were used in material balances to study the ways in which the different carbon sources were utilized by the yeast cells under microaerobic conditions. The fraction of xylose consumed to produce xylitol reached a maximum value (0.70) after glucose and oxygen depletion while alternative metabolic routes were favored by sub-optimal conditions.     

Effects of resource supplies on the structure and function of microbial communities

The supplies of nutrients, and their elemental stoichiometry, can have significant impacts upon the structure and function of microbial communities. This review focuses on the effects of nutrient supplies on the biodegradation of organic matter, and on the dynamics of host-pathogen interactions. Analyses of data from the literature suggest significant effects of nitrogen:phosphorus supply ratios on the microbial decomposition of organic matter, and it is argued that these stoichiometric effects may have important implications for the fate and fluxes of carbon in natural ecosystems. In addition, it is shown that the supplies of nitrogen and phosphorus to the host can strongly influence the outcome of infections in both terrestrial and aquatic plants, suggesting that resource availability and resource supply ratios potentially may have significant effects on the health of many plant communities. This revised version was published online in August 2006 with corrections to the Cover Date.     

Molecular diversity of arbuscular mycorrhizal fungi and patterns of host association over time and space in a tropical forest

We have used molecular techniques to investigate the diversity and distribution of the arbuscular mycorrhizal (AM) fungi colonizing tree seedling roots in the tropical forest on Barro Colorado Island (BCI), Republic of Panama. In the first year, we sampled newly emergent seedlings of the understory treelet Faramea occidentalis and the canopy emergent Tetragastris panamensis, from mixed seedling carpets at each of two sites. The following year we sampled surviving seedlings from these cohorts. The roots of 48 plants were analysed using AM fungal-specific primers to amplify and clone partial small subunit (SSU) ribosomal RNA gene sequences. Over 1300 clones were screened for random fragment length polymorphism (RFLP) variation and 7% of these were sequenced. Compared with AM fungal communities sampled from temperate habitats using the same method, the overall diversity was high, with a total of 30 AM fungal types identified. Seventeen of these types have not been recorded previously, with the remainder being similar to types reported from temperate habitats. The tropical mycorrhizal population showed significant spatial heterogeneity and nonrandom associations with the different hosts. Moreover there was a strong shift in the mycorrhizal communities over time. AM fungal types that were dominant in the newly germinated seedlings were almost entirely replaced by previously rare types in the surviving seedlings the following year. The high diversity and huge variation detected across time points, sites and hosts, implies that the AM fungal types are ecologically distinct and thus may have the potential to influence recruitment and host composition in tropical forests.     

Genetic differentiation in the winter pine processionary moth (Thaumetopoea pityocampa--wilkinsoni complex), inferred by AFLP and mitochondrial DNA markers

The winter pine processionary moth has become an important pine pest in the last century, as a consequence of the spread of pine cultivation in the Mediterranean region. The pattern of genetic differentiation of this group, that includes two sibling species (Thaumetopoea pityocampa and Th. wilkinsoni), has been studied in nine populations using amplified fragment length polymorphism (AFLP) and single strand conformation polymorphism-sequence analysis (SSCP) of the mitochondrial cytochrome oxidase 1 (COI) and cytochrome oxydase 2 (COII). Results indicate the existence of strong genetic differentiation between the two species that became separated before the Quaternary ice ages. Moreover data indicate that Th. pityocampa has a strong geographical structure, particularly evident at the nuclear level, where all pairwise phiST resulted to be highly significant and individuals from the same population resulted to be strongly clustered when an individual tree was reconstructed. The estimates of the absolute number of migrants between populations (Nm), obtained from mitochondrial and nuclear DNA markers, suggest that gene flow is low and that a gender-related dispersal could occur in this species. The males appear to disperse more than females, contributing to the genetic diversity of populations on a relatively wide range, reducing the risks of inbreeding and the genetic loss associated with bottlenecks occurring in isolated populations.     

Plant water relations at elevated CO2 -- implications for water-limited environments

Long-term exposure of plants to elevated [CO2] leads to a number of growth and physiological effects, many of which are interpreted in the context of ameliorating the negative impacts of drought. However, despite considerable study, a clear picture in terms of the influence of elevated [CO2] on plant water relations and the role that these effects play in determining the response of plants to elevated [CO2] under water-limited conditions has been slow to emerge. In this paper, four areas of research are examined that represent critical, yet uncertain, themes related to the response of plants to elevated [CO2] and drought. These include (1) fine-root proliferation and implications for whole-plant water uptake; (2) enhanced water-use efficiency and consequences for drought tolerance; (3) reductions in stomatal conductance and impacts on leaf water potential; and (4) solute accumulation, osmotic adjustment and dehydration tolerance of leaves. A survey of the literature indicates that the growth of plants at elevated [CO2] can lead to conditions whereby plants maintain higher (less negative) leaf water potentials. The mechanisms that contribute to this effect are not fully known, although CO2-induced reductions in stomatal conductance, increases in whole-plant hydraulic conductance and osmotic adjustment may be important. Less understood are the interactive effects of elevated [CO2] and drought on fine-root production and water-use efficiency, and the contribution of these processes to plant growth in water-limited environments. Increases in water-use efficiency and reductions in water use can contribute to enhanced soil water content under elevated [CO2]. Herbaceous crops and grasslands are most responsive in this regard. The conservation of soil water at elevated [CO2] in other systems has been less studied, but in terms of maintaining growth or carbon gain during drought, the benefits of CO2-induced improvements in soil water content appear relatively minor. Nonetheless, because even small effects of elevated [CO2] on plant and soil water relations can have important implications for ecosystems, we conclude that this area of research deserves continued investigation. Future studies that focus on cellular mechanisms of plant response to elevated [CO2] and drought are needed, as are whole-plant investigations that emphasize the integration of processes throughout the soil--plant--atmosphere continuum. We suggest that the hydraulic principles that govern water transport provide an integrating framework that would allow CO2-induced changes in stomatal conductance, leaf water potential, root growth and other processes to be uniquely evaluated within the context of whole-plant hydraulic conductance and water transport efficiency.     

Evaluation of C-H cdots,three dots,centered O hydrogen bonds in native and misfolded proteins

Non-traditional C-H cdots, three dots, centered Y hydrogen bonds, in which a carbon atom acts as the hydrogen donor and an electronegative atom Y (Y=N, O or S) acts as the acceptor, have been reported in proteins, but their importance in protein structures is not well established. Here, we present the results of three computational tests that examine the significance of C-H cdots, three dots, centered Y bonds involving the C(alpha) in proteins. First, we compared the number of C(alpha)-H cdots, three dots, centered Y bonds in native structures with two sets of compact, energy-minimized decoy structures. The decoy structures contain about as many C(alpha)-H cdots, three dots, centered Y bonds as the native structures, indicating that the constraints of chain connectivity and compactness can lead to incidental formation of C(alpha)-H cdots, three dots, centered Y bonds. Secondly, we examined whether short C(alpha)-H cdots, three dots, centered Y bonds have a tendency to be linear, as is expected for a cohesive hydrogen-bonding interaction. The native structures do show this trend, but so does one of the decoy sets, suggesting that this criterion is also not sufficient to indicate a stabilizing interaction. Finally, we examined the preference for C(alpha)-H cdots, three dots, centered Y bond donors to be near to strong hydrogen bond acceptors. In the native proteins, the alpha protons attract strong acceptors like oxygen atoms more than weak acceptors. In contrast, hydrogen bond donors in the decoy structures do not distinguish between strong and weak acceptors. Thus, any individual C(alpha)-H cdots, three dots, centered Y bond may be fortuitous and occur due to the polypeptide connectivity and compactness. Taken collectively, however, C(alpha)-H cdots, three dots, centered Y bonds provide a weakly cohesive force that stabilizes proteins.     

Quantification of the influence of HPrSer46P on CcpA-cre interaction

Carbon catabolite repression (CCR) of the Bacillus megateriumxyl operon is dependent on the catabolite responsive element cre, the catabolite control protein (CcpA) and the histidine-containing phosphocarrier protein phosphorylated at the serine 46 residue (HPrSer46P). The latter is formed in the presence of glucose and mediates CCR via CcpA. We present evidence for the presence of HPrSer46P in a ternary complex with CcpA and cre. We also demonstrate increased stability of this complex compared to the CcpA-cre complex by electrophoretic mobility shift analysis (EMSA). This stabilization by HPrSer46P is the same for the xyl cre and an improved cre. Thus, HPrSer46P is a co-repressor for CcpA. In addition, surface plasmon resonance (SPR) experiments yielded binding constants of CcpA and the CcpA-HPrSer46P complex with cre. HPrSer46P stimulated CcpA binding to cre 50-fold. The binding constant is 4.9(+/- 0.5) x 10(6) M(-1). Non-phosphorylated HPr did not affect the complex formation between CcpA and cre. Previously proposed effects by glucose-6-phosphate, fructose-1,6-diphosphate and NADP on CcpA-cre or CcpA-HPrSer46P-cre formation were not found in EMSA and SPR experiments.