Aeration for plant root respiration in a tidal marsh

This paper investigates the tidal effects on aeration conditions for plant root respiration in a tidal marsh. We extend the work of Ursino et al. ( 2004) by using a two-phase model for air and water flows in the marsh. Simulations have been conducted to examine directly the link between the airflow dynamics and the aeration condition in the marsh soil. The results show that the effects of entrapped air on water movement in the vadose zone are significant in certain circumstances. Single-phase models based on Richards' equation, which neglect such effects, may not be adequate for quantifying the aeration condition in tidal marsh. The optimal aeration condition, represented by the maximum of the integral magnitude of tidally advected air mass ( TAAM) flux, is found to occur near the tidal creek for the four soil textures simulated. This may explain the observation that some salt marsh plant species grow better near tidal creeks than in the inner marsh areas. Our analyses, based on the two-phase model and predicted TAAM flux magnitude, provide further insight into the positive feedback'' mechanism proposed by Ursino et al. ( 2004). That is, pioneer plants may grow successfully near the creek where the root aeration condition is optimal. The roots of the pioneer plants can soften and loosen the rhizosphere soil, which increases the evapotranspiration rate, the soil porosity, and absolute permeability and weakens the capillary effects. These, in turn, improve further the root aeration conditions and may lead to colonization by plants less resistant to anaerobic conditions.

Impact of changes in natural ultraviolet radiation on pigment composition, physiological and morphological characteristics of the Antarctic moss, Grimmia antarctici

The impact of ambient ultraviolet (UV)-B radiation on the endemic bryophyte, Grimmia antarctici, was studied over 14 months in East Antarctica. Over recent decades, Antarctic plants have been exposed to the largest relative increase in UV-B exposure as a result of ozone depletion. We investigated the effect of reduced UV and visible radiation on the pigment concentrations, surface reflectance and physiological and morphological parameters of this moss. Plexiglass screens were used to provide both reduced UV levels (77%) and a 50% decrease in total radiation. The screen combinations were used to separate UV photoprotective from visible photoprotective strategies, because these bryophytes are growing in relatively high light environments compared with many mosses. G. antarctici was affected negatively by ambient levels of UV radiation. Chlorophyll content was significantly lower in plants grown under near-ambient UV, while the relative proportions of photoprotective carotenoids, especially beta-carotene and zeaxanthin, increased. However, no evidence for the accumulation of UV-B-absorbing pigments in response to UV radiation was observed. Although photosynthetic rates were not affected, there was evidence of UV effects on morphology. Plants that were shaded showed fewer treatment responses and these were similar to the natural variation observed between moss growing on exposed microtopographical ridges and in more sheltered valleys within the turf. Given that other Antarctic bryophytes possess UV-B-absorbing pigments which should offer better protection under ambient UV-B radiation, these findings suggest that G. antarctici may be disadvantaged in some settings under a climate with continuing high levels of springtime UV-B radiation.

A novel cis-acting element, ESP, contributes to high-level endosperm-specific expression in an oat globulin promoter

To examine the genetic controls of endosperm (ES) specificity, several cereal seed storage protein (SSP) promoters were isolated and studied using a transient expression analysis system. An oat globulin promoter (AsGlo1) capable of driving strong ES-specific expression in barley and wheat was identified. Progressive 5' deletions and cis element mutations demonstrated that the mechanism of specificity in the AsGlo1 promoter was distinct from that observed in glutelin and prolamin promoters. A novel interrupted palindromic sequence, ACATGTCAT-CATGT, was required for ES specificity and substantially contributed to expression strength of the AsGlo1 promoter. This sequence was termed the endosperm specificity palindrome (ESP) element. The GCN4 element, which has previously been shown to be required for ES specificity in cereal SSP promoters, had a quantitative role but was not required for tissue specificity. The 960-bp AsGlo1 promoter and a 251-bp deletion containing the ESP element also drove ES-specific expression in stably transformed barley. Reporter gene protein accumulated at very high levels (10% of total soluble protein) in ES tissues of plants transformed with an AsGlo1:GFP construct. Expression strength and tissue specificity were maintained over five transgenic generations. These attributes make the AsGlo1 promoter an ideal promoter for biotechnology applications. In conjunction with previous findings, our data demonstrate that there is more than one genetically distinct mechanism by which ES specificity can be achieved in cereal SSP promoters, and also suggest that there is redundancy between transcriptional and post-transcriptional tissue specificity mechanisms in cereal globulin genes.

A novel conotoxin inhibitor of Kv1.6 channel and nAChR subtypes defines a new superfamily of conotoxins

Using assay-directed fractionation of the venom from the vermivorous cone snail Conus planorbis, we isolated a new conotoxin, designated p114a, with potent activity at both nicotinic acetylcholine receptors and a voltage-gated potassium channel subtype. p114a contains 25 amino acid residues with an amidated C-terminus, an elongated N-terminal tail (six residues), and two disulfide bonds (1-3, 2-4 connectivity) in a novel framework distinct from other conotoxins. The peptide was chemically synthesized, and its three-dimensional structure was demonstrated to be well-defined, with an R-helix and two 3(10)-helices present. Analysis of a cDNA clone encoding the prepropeptide precursor of p114a revealed a novel signal sequence, indicating that p114a belongs to a new gene superfamily, the J-conotoxin superfamily. Five additional peptides in the J-superfamily were identified. Intracranial injection of p114a in mice elicited excitatory symptoms that included shaking, rapid circling, barrel rolling, and seizures. Using the oocyte heterologous expression system, p114a was shown to inhibit both a K+ channel subtype (Kv1.6, IC50) 1.59 mu M) and neuronal (IC50 = 8.7 mu M for alpha 3 beta 4) and neuromuscular (IC50 = 0.54 mu M for alpha 1 beta 1 is an element of delta) subtypes of the nicotinic acetylcholine receptor ( nAChR). Similarities in sequence and structure are apparent between the middle loop of p114a and the second loop of a number of alpha-conotoxins. This is the first conotoxin shown to affect the activity of both voltage-gated and ligand-gated ion channels.

A need for caution in the use of frontal analysis continuous capillary electrophoresis for the determination of ligand binding data

Attention is drawn to a need for caution in the determination of binding data for protein-polyelectrolyte interactions by frontal analysis continuous capillary electrophoresis (FACCE). Because the method is valid only for systems involving comigration of complex(es) and slower-migrating reactant, establishing conformity with that condition is clearly a prerequisite for its application. However, that requirement has not been tested in any published studies thus far. On the basis of calculated FACCE patterns, presented to illustrate features by which such comigration of complex(es) and slower-migrating reactant can be identified, the form of the published pattern for a P-lactoglobulin-poly(styrenesulfonate) mixture does not seem to signify the migration behavior required to justify its consideration in such terms. Additional experimental studies are therefore needed to ascertain the validity of FACCE as a means of determining binding data for the characterization of protein-polyelectrolyte interactions. (c) 2005 Elsevier Inc. All rights reserved.

Adaptations of strangler figs to life in the rainforest canopy

Figs are rainforest keystone species. Non-strangler figs establish on the forest floor; strangler figs establish epiphytically, followed by a dramatic transition from epiphyte to free-standing tree that kills its hosts. Free-standing figs display vigorous growth and resource demand suggesting that epiphytic strangler figs require special adaptations to deal with resource limitations imposed by the epiphytic environment. We studied epiphytic and free-standing strangler figs, and non-strangler figs in tropical rainforest and in cultivation, as well as strangler figs in controlled conditions. We investigated whether the transition from epiphyte to free-standing tree is characterised by morphological and physiological plasticity. Epiphyte substrate had higher levels of plant-available ammonium and phosphate, and similar levels of nitrate compared with rainforest soil, suggesting that N and P are initially not limiting resources. A relationship was found between taxonomic groups and plant N physiology; strangler figs, all members of subgenus Urostigma, had mostly low foliar nitrate assimilation rates whereas non-strangler figs, in subgenera Pharmacocycea, Sycidium, Sycomorus or Synoecia, had moderate to high rates. Nitrate is an energetically expensive N source, and low nitrate use may be an adaptation of strangler figs for conserving energy during epiphytic growth. Interestingly, significant amounts of nitrate were stored in fleshy taproot tubers of epiphytic stranglers. Supporting the concept of plasticity, leaves of epiphytic Ficus benjamina L. had lower N and C content per unit leaf area, lower stomatal density and 80% greater specific leaf area than leaves of conspecific free-standing trees. Similarly, glasshouse-grown stranglers strongly increased biomass allocation to roots under water limitation. Epiphytic and free-standing F. benjamina had similar average foliar delta C-13, but epiphytes had more extreme values; this indicates that both groups of plants use the C-3 pathway of CO2 fixation but that water availability is highly variable for epiphytes. We hypothesise that epiphytic figs use fleshy stem tubers to avoid water stress, and that nitrate acts as an osmotic compound in tubers. We conclude that strangler figs are a unique experimental system for studying the transition from rainforest epiphyte to tree, and the genetic and environmental triggers involved.

Epidermal penetration of a therapeutic peptide by lipid conjugation; Stereo-selective peptide availability of a topical diastereomeric lipopeptide

In inflammatory disorders (e.g. psoriasis), local concentrations of human neutrophil elastase (HNE), also known as polymorphonuclear leukocyte elastase (HLE), possibly overwhelm its natural inhibitors leading to extracellular matrix degradation. Elevated levels of HNE have been reported in a variety of inflammatory disorders, including psoriasis. Peptidic HNE inhibitors have a common hydrophobic sequence (Ala-Ala-Pro-Val). This peptide sequence inhibits HNE competitively; however the stratum corneum presents an effective barrier to the delivery of this tetrapeptide across the skin. The current work investigates the delivery of the modified peptide whereby the tetrapeptide was lipidated to enhance its ability to penetrate the stratum The tetrapeptide Was Coupled to a racaemic mixture of a short chain lipoamino acid (LAA) resulting in two diastereomers of the lipoamino acid-modified tetrapeptide. The penetration of the lipopeptide mixture was assessed across human epidermis in vitro. The percentage of applied dose penetrating to the receptor over 8 h following administration was 2.53% for the D-LAA conjugate and 1.47% for the L-diastereomer, compared to 0% for the peptide. The D-diastereomer appears to be relatively stable but the L-diastereomer appears to degrade releasing possibly the tetrapeptide and peptide fragment(s). Therefore the results clearly indicate that coupling the tetrapeptide to a short chain LAA enhances its delivery across human epidermis.

An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination

Several pathogenic strains of Escherichia coli exploit type III secretion to inject effector proteins into human cells, which then subvert eukaryotic cell biology to the bacterium's advantage. We have exploited bioinformatics and experimental approaches to establish that the effector repertoire in the Sakai strain of enterohemorrhagic E. coli (EHEC) O157:H7 is much larger than previously thought. Homology searches led to the identification of > 60 putative effector genes. Thirteen of these were judged to be likely pseudogenes, whereas 49 were judged to be potentially functional. In total, 39 proteins were confirmed experimentally as effectors: 31 through proteomics and 28 through translocation assays. At the protein level, the EHEC effector sequences fall into > 20 families. The largest family, the NleG family, contains 14 members in the Sakai strain alone. EHEC also harbors functional homologs of effectors from plant pathogens (HopPtoH, HopW, AvrA) and from Shigella (OspD, OspE, OspG), and two additional members of the Map/IpgB family. Genes encoding proven or predicted effectors occur in > 20 exchangeable effector loci scattered throughout the chromosome. Crucially, the majority of functional effector genes are encoded by nine exchangeable effector loci that lie within lambdoid prophages. Thus, type III secretion in E. coli is linked to a vast phage metagenome, acting as a crucible for the evolution of pathogenicity.

Axillary bud outgrowth: sending a message

Mutants that branch profusely in the presence of a growing shoot tip have highlighted the role of graft-transmissible signals that are produced in roots and stem. Orthologous genes in Arabidopsis, pea and petunia are involved in the transmission of a novel long-distance message. These genes show varying degrees of regulation by auxin and an auxin-independent feedback system, and encode enzymes that might act on carotenoid-like substrates. Axillary bud outgrowth is under homeostatic control, involving developmental stages or checkpoints. Perturbation of the long-range messaging and auxin depletion does not guarantee that bud outgrowth will ensue at a particular node.

Chemical synthesis and structure elucidation of bovine kappa-casein (1-44)

The caseins (alpha(s1), alpha(s2), beta, and kappa) are phosphoproteins present in bovine milk that have been studied for over a century and whose structures remain obscure. Here we describe the chemical synthesis and structure elucidation of the N-terminal segment (1-44) of bovine K-casein, the protein which maintains the micellar structure of the caseins. K-Casein (1-44) was synthesised by highly optimised Boc solid-phase peptide chemistry and characterised by mass spectrometry. Structure elucidation was carried out by circular dichroism and nuclear magnetic resonance spectroscopy. CD analysis demonstrated that the segment was ill defined in aqueous medium but in 30% trifluoroethanol it exhibited considerable helical structure. Further, NMR analysis showed the presence of a helical segment containing 26 residues which extends from Pro(8) to Arg(34). This is the first report which demonstrates extensive secondary structure within the casein class of proteins. (c) 2006 Elsevier Inc. All rights reserved.

Differences in plant function in phosphorus- and nitrogen-limited mangrove ecosystems

Mangrove ecosystems can be either nitrogen (N) or phosphorus (P) limited and are therefore vulnerable to nutrient pollution. Nutrient enrichment with either N or P may have differing effects on ecosystems because of underlying differences in plant physiological responses to these nutrients in either N- or P-limited settings. Using a common mangrove species, Avicennia germinans, in sites where growth was either N or P limited, we investigated differing physiological responses to N and P limitation and fertilization. We tested the hypothesis that water uptake and transport, and hydraulic architecture, were the main processes limiting productivity at the P-limited site, but that this was not the case at the N-limited site. We found that plants at the P-deficient site had lower leaf water potential, stomatal conductance and photosynthetic carbon-assimilation rates, and less conductive xylem, than those at the N-limited site. These differences were greatly reduced with P fertilization at the P-limited site. By contrast, fertilization with N at the N-limited site had little effect on either photosynthetic or hydraulic traits. We conclude that growth in N- and P-limited sites differentially affect the hydraulic pathways of mangroves. Plants experiencing P limitation appear to be water deficient and undergo more pronounced changes in structure and function with relief of nutrient deficiency than those in N-limited ecosystems.

Effects of litter and fine root composition on their decomposition in a Rhodic Paleustalf under different land uses

Plant litter and fine roots are important in maintaining soil organic carbon (C) levels as well as for nutrient cycling. The decomposition of surface-placed litter and fine roots of wheat ( Triticum aestivum ), lucerne ( Medicago sativa ), buffel grass ( Cenchrus ciliaris ), and mulga ( Acacia aneura ), placed at 10-cm and 30-cm depths, was studied in the field in a Rhodic Paleustalf. After 2 years, = 60% of mulga roots and twigs remained undecomposed. The rate of decomposition varied from 4.2 year -1 for wheat roots to 0.22 year -1 for mulga twigs, which was significantly correlated with the lignin concentration of both tops and roots. Aryl+O-aryl C concentration, as measured by 13 C nuclear magnetic resonance spectroscopy, was also significantly correlated with the decomposition parameters, although with a lower R 2 value than the lignin concentration. Thus, lignin concentration provides a good predictor of litter and fine root decomposition in the field.

Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E-coli genome

High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms. (c) 2005 Elsevier Ltd. All rights reserved.