Responses of sap flux and stomatal conductance of Pinus taeda L. trees to stepwise reductions in leaf area

Herbivory or artificial foliage removal has been shown to affect gas exchange and canopy water relations. In this study, canopy architecture and water relations in response to progressive defoliation were examined in a stand of 8-year-old loblolly pine (Pinus taeda L.) trees, a shade-intolerant, pioneer species common in the south-eastern USA. Sap flux was measured with constant heat sap flow gauges in order to estimate canopy stomatal conductance (Gs) while foliage in the 6 m high stand was harvested in 1 m increments from the bottom up. Leaf-level stomatal conductance and water potential data were also collected. Profiles of silhouette area ratio and specific leaf area showed no trends with crown height, reflecting an open canopy (leaf area index = 1.55). Therefore, short-term changes in Gs with foliage removal were attributed to hydraulic effects rather than influences of changes in mean microclimate conditions on Gs of remaining foliage. A large increase in Gs was observed during the 6 h pruning period which fully compensated for the reductions in foliage area down to 45%. Canopy stomatal conductance and whole plant liquid phase conductance as calculated from sap flux were both influenced by the rate of growth as indicated by the annual basal area increment.     

Probing Structural Elements of Thermal Stability in Bacterial Oligomeric Alcohol Dehydrogenases. I. Construction and Characterization of Chimeras Consisting of Secondary ADHs from Thermoanaerobacter brockii and Clostridium beijerinckii

Two tetrameric secondary alcohol dehydrogenases (ADHs), one from the mesophile Clostridium beijerinckii (CBADH) and the other from the extreme thermophile Thermoanaerobacter brockii (TBADH), share 75% sequence identity but differ by 26 °C in thermal stability. To explore the role of linear segments of these similar enzymes in maintaining the thermal stability of the thermostable TBADH, a series of 12 CBadh and TBadh chimeric genes and the two parental wild-type genes were expressed in Escherichia coli, and the enzymes were isolated, purified and characterized. The thermal stability of each chimeric enzyme was approximately exponentially proportional to the content of the amino acid sequence of the thermophilic enzyme, indicating that the amino acid residues contributing to the thermal stability of TBADH are distributed along the whole protein molecule. It is suggested that major structural elements of thermal stability may reside among the nine discrepant amino acid residues between the N-terminal 50-amino acid residues of TBADH and CBADH.     

Fungal life in the extremely hypersaline water of the Dead Sea: first records.

The first report, to our knowledge, on the occurrence of filamentous fungi in the hypersaline (340 g salt l-1) Dead Sea is presented. Three species of filamentous fungi from surface water samples of the Dead Sea were isolated: Gymnascella marismortui (Ascomycota), which is described as a new species, Ulocladium chlamydosporum and Penicillium westlingii (Deuteromycota). G. marismortui and U. chlamydosporum grew on media containing up to 50% Dead Sea water. G. marismortui was found to be an obligate halophile growing optimally in the presence of 0.5-2 M NaCl or 10 30% (by volume) of Dead Sea water. Isolated cultures did not grow on agar media without salt, but grew on agar prepared with up to 50% Dead Sea water. This suggests that they may be adapted to life in the extremely stressful hypersaline Dead Sea.     

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.     

Elg1, an alternative subunit of the RFC clamp loader,preferentially interacts with SUMOylated PCNA

Replication‐factor C (RFC) is a protein complex that loads the processivity clamp PCNA onto DNA. Elg1 is a conserved protein with homology to the largest subunit of RFC, but its function remained enigmatic. Here, we show that yeast Elg1 interacts physically and genetically with PCNA, in a manner that depends on PCNA modification, and exhibits preferential affinity for SUMOylated PCNA. This interaction is mediated by three small ubiquitin‐like modifier (SUMO)‐interacting motifs and a PCNA‐interacting protein box close to the N‐terminus of Elg1. These motifs are important for the ability of Elg1 to maintain genomic stability. SUMOylated PCNA is known to recruit the helicase Srs2, and in the absence of Elg1, Srs2 and SUMOylated PCNA accumulate on chromatin. Strains carrying mutations in both ELG1 and SRS2 exhibit a synthetic fitness defect that depends on PCNA modification. Our results underscore the importance of Elg1, Srs2 and SUMOylated PCNA in the maintenance of genomic stability.     

Solution study of engineered quartz binding peptides using replica exchange molecular dynamics

We use replica-exchange molecular dynamics (REMD) to interrogate molecular structures and properties of four engineered dodecapeptides (in solution, in the absence of a surface) that have been shown to bind to quartz with different propensities. We find that all of the strong-binding peptides feature some polyproline type II secondary structure, have less conformational freedom, and feature fewer intrapeptide hydrogen bonds compared with the weak binder. The regions of contiguous proline content in a given sequence appear to play a role in fostering some of these properties of the strong binders. For preliminary insights into quartz binding, we perform lattice-matching studies between a grid corresponding with the quartz (100) surface and the strong-binding peptide REMD structures. Our findings indicate a commonality among the putative contact residues, even for peptide structures with very different backbone conformations. Furthermore, interpeptide interactions in solution are studied. Our preliminary findings indicate that the strong-binder interpeptide contacts are dominated by weak, nonspecific hydrophobic interactions, while the weak-binding peptide shows more variable behavior due to the distribution of charged residues. In summary, the solution structures of peptides appear to be significant. We propose that these differences in their intra- and interpeptide interactions can influence their propensity to bind onto a solid substrate.     

Living with p53, dying of p53

The p53 tumor suppressor protein acts as a major defense against cancer. Among its most distinctive features is the ability to elicit both apoptotic death and cell cycle arrest. In this issue of Cell, Das et al. (2007) and Tanaka et al. (2007) provide new insights into the mechanisms that dictate the life and death decisions of p53.