Canny's compensating pressure theory fails a test

Canny's compensating pressure theory for water transport (American Journal of Botany 85: 897–909) has evolved from the premise that cavitation pressures are only a few tenths of a megapascal negative (approximately −0.3 MPa). In contradiction, “vulnerability curves” indicate that xylem pressures can drop below −3 MPa in some species without causing a loss of hydraulic conductivity. Canny claims these curves do not measure the limits to negative pressure by cavitation, but rather the limits to the compensating tissue pressure that otherwise quickly refills cavitated conduits. Compensating pressure is derived from the turgor pressure of the living cells in the tissue. To test this claim, we compared vulnerability curves of Betula nigra stems given three treatments: (1) living control, (2) killed in a microwave oven, and (3) perfused with a −1.5 MPa (10% w/w) mannitol solution. According to Canny's theory, the microwaved and mannitol curves should show cavitation and loss of conductance beginning at approximately −0.3 MPa because in both cases, the turgor pressure would be eliminated or substantially reduced compared to controls. We also tested the refilling capability of nonstressed stems where compensating pressure would be in full operation and compared this with dead stems with no compensating pressure. According to Canny's interpretation of vulnerability curves, the living stems should refill within 5 min. Results failed to support the compensating tissue theory because (a) all vulnerability curves were identical, reaching a −1.5 MPa threshold before substantial loss of conductance occurred, and (b) killed or living stems had equally slow refilling rates showing no significant increase in conductivity after 30 min. In consequence, the cohesion theory remains the most parsimonious explanation of xylem sap ascent in plants.     

Influence of process operations on shelf-life and microbial population of fresh-cut vegetables

Cut lettuce salads and shredded carrots were prepared according to four different procedures in order to determine the influence of various operations on the shelf-life of these ‘minimally processed’ foods. In particular, the level of active chlorine used or its residue after washing as well as the processing time were considered. The results emphasize the role of free chlorine in reduction of the contamination level and its effectiveness toward Pseudomonadaceae and Enterobacteriaceae. Moreover a 12-h delay without refrigeration, after pre-washing or removal of ends, caused a lengthening of the processing time, enough to allow microbial proliferation and subsequent shortening of shelf-life. Shelf-life extension and the improvement of safety and quality of these products can be obtained by means of adequate processing operations. Received 29 September 1998/ Accepted in revised form 19 July 1999     

Evolutionary Landscapes for the Acquisition of New Ligand Recognition by RNA Aptamers

The evolution of ligand specificity underlies many important problems in biology, from the appearance of drug resistant pathogens to the re-engineering of substrate specificity in enzymes. In studying biomolecules, however, the contributions of macromolecular sequence to binding specificity can be obscured by other selection pressures critical to bioactivity. Evolution of ligand specificity in vitro—unconstrained by confounding biological factors—is addressed here using variants of three flavin-binding RNA aptamers. Mutagenized pools based on the three aptamers were combined and allowed to compete during in vitro selection for GMP-binding activity. The sequences of the resulting selection isolates were diverse, even though most were derived from the same flavin-binding parent. Individual GMP aptamers differed from the parental flavin aptamers by 7 to 26 mutations (20 to 57% overall change). Acquisition of GMP recognition coincided with the loss of FAD (flavin-adenine dinucleotide) recognition in all isolates, despite the absence of a counter-selection to remove FAD-binding RNAs. To examine more precisely the proximity of these two activities within a defined sequence space, the complete set of all intermediate sequences between an FAD-binding aptamer and a GMP-binding aptamer were synthesized and assayed for activity. For this set of sequences, we observe a portion of a neutral network for FAD-binding function separated from GMP-binding function by a distance of three mutations. Furthermore, enzymatic probing of these aptamers revealed gross structural remodeling of the RNA coincident with the switch in ligand recognition. The capacity for neutral drift along an FAD-binding network in such close approach to RNAs with GMP-binding activity illustrates the degree of phenotypic buffering available to a set of closely related RNA sequences—defined as the sets functional tolerance for point mutations—and supports neutral evolutionary theory by demonstrating the facility with which a new phenotype becomes accessible as that buffering threshold is crossed.     

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.     

Start-up of a two-stage bioaugmented anoxic–oxic (A/O) biofilm process treating petrochemical wastewater under different DO concentrations

The traditional two-stage anoxic–oxic (A/O) activated sludge process might be inefficient in pollutants removal and could not ensure the effluent quality. By installing polyurethane foams as carriers and inoculating specialized bacteria in the oxic compartments, the activated sludge systems could be transformed into bioaugmented biofilm processes to enhance the removal efficiency to recalcitrant pollutants. Optimal environment should be provided for the bioaugmented bacteria during systems’ start-up. In the present research, dissolved oxygen (DO) concentration was studied as a crucial environmental factor on the performances of the bioagumented systems. The results indicated that the system adopted lower DO concentration took less time to start-up, performed higher pollutants removal efficiency and stronger resistance to shock loadings compared to the system with higher DO level. This was the first attempt to evaluate the importance of DO concentration on the start-up of the two-stage bioaugmented A/O biofilm process.     

Biofilm stratification during simultaneous nitrification and denitrification (SND) at a biocathode

The aeration of the cathode compartment of bioelectrochemical systems (BESs) was recently shown to promote simultaneous nitrification and denitrification (SND). This study investigates the cathodic metabolism under different operating conditions as well as the structural organization of the cathodic biofilm during SND. Results show that a maximal nitrogen removal efficiency of 86.9 ± 0.5%, and a removal rate of 3.39 ± 0.08 mg N L⁻¹ h⁻¹ could be achieved at a dissolved oxygen (DO) level of 5.73 ± 0.03 mg L⁻¹ in the catholyte. The DO levels used in this study are higher than the thresholds previously reported as detrimental for denitrification. Analysis of the cathodic half-cell potential during batch tests suggested the existence of an oxygen gradient within the biofilm while performing SND. FISH analysis corroborated this finding revealing that the structure of the biofilm included an outer layer occupied by putative nitrifying organisms, and an inner layer where putative denitrifying organisms were most dominant. To our best knowledge this is the first time that nitrifying and denitrifying microorganisms are simultaneously observed in a cathodic biofilm.