Biotechnical Characteristics of Root Systems of Typical Mediterranean Species

Quantifying patterns of fine root dynamics is crucial to the understanding of ecosystem structure and function, and in predicting how ecosystems respond to disturbance. Part of this understanding involves consideration of the carbon lost through root turnover. In the context of the rainfall pattern in the tropics, it was hypothesised that rainfall would strongly influence fine root biomass and longevity. A field study was conducted to determine root biomass, elemental composition and the influence of rainfall on longevity of fine roots in a tropical lowland evergreen rainforest at Danum Valley, Sabah, Malaysia. A combination of root coring, elemental analysis and rhizotron observation methods were used. Fine (less than 2 mm diameter) root biomass was relatively low (1700 kg ha −1) compared with previously described rainforest data. Standing root biomass was positively correlated with preceding rainfall, and the low fine root biomass in the dry season contained higher concentrations of N and lower concentrations of P and K than at other times. Observations on rhizotrons demonstrated that the decrease in fine root biomass in the dry season was a product of both a decrease in fine root length appearance and an increase in fine root length disappearance. Fitting an overall model to root survival time showed significant effects of rainfall preceding root disappearance, with the hazard of root disappearance decreasing by 8 for each 1 mm increase in the average daily (30 day) rainfall preceding root disappearance. While it is acknowledged that other factors have a part to play, this work demonstrates the importance of rainfall and soil moisture in influencing root biomass and root disappearance in this tropical rainforest.     

Analysis of Possible Involvement of Local Bioelectric Responses in Chilling Perception by Higher Plants Exemplified by <Emphasis Type="Italic">Cucurbita pepo</Emphasis>

Macroelectrodes and electrophysiological setup were used in experiments with stems of 15-day-old pumpkin (Cucurbita pepo L.) seedlings for computer-assisted data recording. It is shown that local bioelectric responses induced by graded local chilling are similar to the receptor potentials of animals. These responses increase gradually with stimulus strength and trigger the action potential generation when a temperature threshold is attained. The excitation threshold of cells in seedling stems displays the phenomenon of accommodation. Parameters of local bioelectric responses induced by intermittent cooling can undergo changes similar to sensitization-habituation patterns. The results indicate that local electrical responses may be involved in early stages of cooling perception in cells of higher plants devoid of locomotive functions.     

Engineering proteins with enhanced mechanical stability by force-specific sequence motifs

Use of atomic force microscopy (AFM) has recently led to a better understanding of the molecular mechanisms of the unfolding process by mechanical forces; however, the rational design of novel proteins with specific mechanical strength remains challenging. We have approached this problem from a new perspective that generates linear physical–chemical properties (PCP) motifs from a limited AFM data set. Guided by our linear sequence analysis, we designed and analyzed four new mutants of the titin I1 domain with the goal of increasing the domain's mechanical strength. All four mutants could be cloned and expressed as soluble proteins. AFM data indicate that at least two of the mutants have increased molecular mechanical strength. This observation suggests that the PCP method is useful to graft sequences specific for high mechanical stability to weak proteins to increase their mechanical stability, and represents an additional tool in the design of novel proteins besides steered molecular dynamics calculations, coarse grained simulations, and ?‐value analysis of the transition state. Proteins 2012; © 2011 Wiley Periodicals, Inc.     

Solution NMR Studies of Chlorella Virus DNA Ligase-adenylate

DNA ligases are essential guardians of genome integrity by virtue of their ability to recognize and seal 3′-OH/5′-phosphate nicks in duplex DNA. The substrate binding and three chemical steps of the ligation pathway are coupled to global and local changes in ligase structure, involving both massive protein domain movements and subtle remodeling of atomic contacts in the active site. Here we applied solution NMR spectroscopy to study the conformational dynamics of the Chlorella virus DNA ligase (ChVLig), a minimized eukaryal ATP-dependent ligase consisting of nucleotidyltransferase, OB, and latch domains. Our analysis of backbone ¹⁵N spin relaxation and ¹⁵N,¹H residual dipolar couplings of the covalent ChVLig-AMP intermediate revealed conformational sampling on fast (picosecond to nanosecond) and slow timescales (microsecond to millisecond), indicative of interdomain and intradomain flexibility. We identified local and global changes in ChVLig-AMP structure and dynamics induced by phosphate. In particular, the chemical shift perturbations elicited by phosphate were clustered in the peptide motifs that comprise the active site. We hypothesize that phosphate anion mimics some of the conformational transitions that occur when ligase-adenylate interacts with the nick 5′-phosphate.     

Mechanism of Na‐Ion Storage in Hard Carbon Anodes Revealed by Heteroatom Doping

Hard carbon is the leading candidate anode for commercialization of Na‐ion batteries. Hard carbon has a unique local atomic structure, which is composed of nanodomains of layered rumpled sheets that have short‐range local order resembling graphene within each layer, but complete disorder along the c‐axis between layers. A primary challenge holding back the development of Na‐ion batteries is that a complete understanding of the structure–capacity correlations of Na‐ion storage in hard carbon has remained elusive. This article presents two key discoveries: first, the characteristics of hard carbons structure can be modified systematically by heteroatom doping, and second, that these structural changes greatly affect Na‐ion storage properties, which reveals the mechanisms for Na storage in hard carbon. Specifically, via P or S doping, the interlayer spacing is dilated, which extends the low‐voltage plateau capacity, while increasing the defect concentrations with P or B doping leads to higher sloping sodiation capacity. The combined experimental studies and first principles calculations reveal that it is the Na‐ion‐defect binding that corresponds to the sloping capacity, while the Na intercalation between graphenic layers causes the low‐potential plateau capacity. The understanding suggests a new design principle of hard carbon anode: more reversibly binding defects and dilated turbostratic domains, given that the specific surface area is maintained low.     

Review of elevated atmospheric CO2 effects on agro-ecosystems: residue decomposition processes and soil C storage

A series of studies using major crops (cotton [Gossypium hirsutum L.], wheat [Triticum aestivum L.], grain sorghum [Sorghum bicolor (L.) Moench.] and soybean [Glycine max (L.) Merr.]) were reviewed to examine the impact of elevated atmospheric CO₂ on crop residue decomposition within agro-ecosystems. Experiments evaluated utilized plant and soil material collected from CO₂ study sites using Free Air CO₂ Enrichment (FACE) and open top chambers (OTC). A incubation study of FACE residue revealed that CO₂-induced changes in cotton residue composition could alter decomposition processes, with a decrease in N mineralization observed with FACE, which was dependent on plant organ and soil series. Incubation studies utilizing plant material grown in OTC considered CO₂-induced changes in relation to quantity and quality of crop residue for two species, soybean and grain sorghum. As with cotton, N mineralization was reduced with elevated CO₂ in both species, however, difference in both quantity and quality of residue impacted patterns of C mineralization. Over the short-term (14 d), little difference was observed for CO₂ treatments in soybean, but C mineralization was reduced with elevated CO₂ in grain sorghum. For longer incubation periods (60 d), a significant reduction in CO₂-C mineralized per g of residue added was observed with the elevated atmospheric CO₂ treatment in both crop species. Results from incubation studies agreed with those from the OTC field observations for both measurements of short-term CO₂ efflux following spring tillage and the cumulative effect of elevated CO₂ (> 2 years) in this study. Observations from field and laboratory studies indicate that with elevated atmospheric CO₂, the rate of plant residue decomposition may be limited by N and the release of N from decomposing plant material may be slowed. This indicates that understanding N cycling as affected by elevated CO₂ is fundamental to understanding the potential for soil C storage on a global scale. This revised version was published online in June 2006 with corrections to the Cover Date.     

Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3

DEAD-box proteins utilize ATP to bind and remodel RNA and RNA-protein complexes. All DEAD-box proteins share a conserved core that consists of two RecA-like domains. The core is flanked by subfamily-specific extensions of idiosyncratic function. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest as members function during protein translation, are essential for viability, and are frequently altered in human malignancies. Here, we define the function of the subfamily-specific extensions of the human DEAD-box protein DDX3. We describe the crystal structure of the subfamily-specific core of wild-type DDX3 at 2.2 Å resolution, alone and in the presence of AMP or nonhydrolyzable ATP. These structures illustrate a unique interdomain interaction between the two ATPase domains in which the C-terminal domain clashes with the RNA-binding surface. Destabilizing this interaction accelerates RNA duplex unwinding, suggesting that it is present in solution and inhibitory for catalysis. We use this core fragment of DDX3 to test the function of two recurrent medulloblastoma variants of DDX3 and find that both inactivate the protein in vitro and in vivo. Taken together, these results redefine the structural and functional core of the DDX3 subfamily of DEAD-box proteins.     

Identification and characterization of key substructures involved in the early folding events of a (beta/alpha)8-barrel protein as studied by experimental and computational methods

A number of studies have examined the structural properties of late folding intermediates of (beta/alpha)8-barrel proteins involved in tryptophan biosynthesis, whereas there is little information available about the early folding events of these proteins. To identify the contiguous polypeptide segments important to the folding of the (beta/alpha)8-barrel protein Escherichia coli N-(5'-phosphoribosyl)anthranilate isomerase, we structurally characterized fragments and circularly permuted forms of the protein. We also simulated thermal unfolding of the protein using molecular dynamics. Our fragmentation experiments demonstrate that the isolated (beta/alpha)(1-4)beta5 fragment is almost as stable as the full-length protein. The far and near-UV CD spectra of this fragment are indicative of native-like secondary and tertiary structures. Structural analysis of the circularly permutated proteins shows that if the protein is cleaved within the two N-terminal betaalpha modules, the amount of secondary structure is unaffected, whereas, when cleaved within the central (beta/alpha)(3-4)beta5 segment, the protein simply cannot fold. An ensemble of the denatured structures produced by thermal unfolding simulations contains a persistent local structure comprised of beta3, beta4 and beta5. The presence of this three-stranded beta-barrel suggests that it may be an important early-stage folding intermediate. Interactions found in (beta/alpha)(3-4)beta5 may be essential for the early events of ePRAI folding if they provide a nucleation site that directs folding.     

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.

The flexibility of different regions of HIV-1 protease was examined by using a database consisting of 73 X-ray structures that differ in terms of sequence, ligands or both. The root-mean-square differences of the backbone for the set of structures were shown to have the same variation with residue number as those obtained from molecular dynamics simulations, normal mode analyses and X-ray B-factors. This supports the idea that observed structural changes provide a measure of the inherent flexibility of the protein, although specific interactions between the protease and the ligand play a secondary role. The results suggest that the potential energy surface of the HIV-1 protease is characterized by many local minima with small energetic differences, some of which are sampled by the different X-ray structures of the HIV-1 protease complexes. Interdomain correlated motions were calculated from the structural fluctuations and the results were also in agreement with molecular dynamics simulations and normal mode analyses. Implications of the results for the drug-resistance engendered by mutations are discussed briefly.