Trade-off analysis in the Northern Andes to study the dynamics in agricultural land use.

In this paper we hypothesize that land use change can be induced by non-linearities and thresholds in production systems that impact farmers' decision making. Tradeoffs between environmental and economic indicators is a useful way to represent dynamic properties of agricultural systems. The Tradeoff Analysis (TOA) System is software designed to implement the integrated analysis of tradeoffs in agricultural systems. The TOA methodology is based on spatially explicit econometric simulation models linked to spatially referenced bio-physical simulation models to simulate land use and input decisions. The methodology has been applied for the potato-pasture production system in the Ecuadorian Andes. The land use change literature often describes non-linearity in land use change as a result of sudden changes in the political (e.g. new agricultural policies) or environmental setting (e.g. earthquakes). However, less attention has been paid to the non-linearities in production systems and their consequences for land use change. In this paper, we use the TOA system to study agricultural land use dynamics and to find the underlying processes for non-linearities. Results show that the sources of non-linearities are in the properties of bio-physical processes and in the decision making-process of farmers.

Effects of soil variability and weather conditions on pesticide leaching--a farm-level evaluation.

In line with European regulations, Dutch law imposes an environmental threshold of 0.1 microg L(-1) on pesticide concentrations in ground water. During registration, the risk of exceeding this threshold is assessed through simulations for one or a few standard scenarios that do not reflect spatial variability under field conditions. The introduction of precision agriculture, where soil variability is actively managed, can increase control over pesticide leaching. This study presents a step-wise evaluation of the effects of soil variability and weather conditions on pesticide leaching. The evaluation was conducted on a 100-ha arable farm and aimed at identifying opportunities for precision management. As a first step, a relative risk assessment identified pesticides presenting a relatively high risk to the environment. Second, the effect of weather conditions was analyzed through 20 years of simulations for three distinct soil profiles. Results were summarized in cumulative probability plots to provide a probabilistic characterization of historical weather data. The year matching 90% probability (1981) served as a reference to simulate pesticide leaching from 612 soil profiles. After interpolation, areas where concentrations exceeded the environmental threshold were identified. Out of a total of 19 pesticides, isoproturon [N-dimethyl-N'-(4-(1-methylethyl)phenyl)urea], metribuzin [4-amino-6-tert-butyl-3-(methylthio)-as-triazin-5(4H)-one], and bentazon [2,1,3-benzothiadiazin-4(3H)-one, 3-isopropyl-, 2,2-dioxide] showed the highest risk for leaching. Leaching was strongly affected by soil variability at the within-field, field, and farm levels. Opportunities for precision management were apparent, but depended on the scale level at which environmental thresholds were implemented. When legislation is formulated in this issue, the presented step-wise evaluation can serve as a basis for identification and precision management of high-risk pesticides.

Characterization of the gene encoding quinohaemoprotein ethanol dehydrogenase of Comamonas testosteroni.

The gene encoding quinohaemoprotein ethanol dehydrogenase type I (QH-EDHI) from Comamonas testosteroni has been cloned and sequenced. Comparison of the amino acid sequence deduced from this with that determined for the N-terminal amino acid stretch of purified QH-EDHI, suggests that the gene also contains a leader sequence of 31 residues. Based on this information, the molecular mass of the apo-enzyme, i.e. the enzyme without the cofactors pyrroloquinoline quinone (PQQ) and haem c, and without the Ca2+, appears to be 73 200 Da. Alignment of the deduced amino acid sequence to that of other PQQ-containing dehydrogenases showed that good similarity (up to 43% identity) exists with most of them. This also showed that the amino acid residues presumed to be involved in PQQ and Ca2+ binding and in the typical features of structure and catalysis of methanol dehydrogenase, are conserved at the same positions in QH-EDHI. The C-terminal part of the protein, containing the haem c, exhibited some similarity to cytochromes C553 from cyanobacteria and algae. Correct processing of the qhedh gene appeared to occur in Escherichia coli strain JM 109 in which the gene was placed under control of the lac promoter, as judged from a positive reaction with antibodies raised against authentic QH-EDHI, the size of the protein, the presence of haem c in it, and the specific activity value obtained after reconstitution with PQQ. The qhedh gene seems to form part of an operon which is organized in a way different from that of the genes required for methanol oxidation in methylotrophic bacteria.

Quinohaemoprotein ethanol dehydrogenase from Comamonas testosteroni. Purification, characterization, and reconstitution of the apoenzyme with pyrroloquinoline quinone analogues.

Pyrroloquinoline-quinone(PQQ)-free quinohaemoprotein ethanol dehydrogenase (QH-EDH) apoenzyme was isolated from ethanol-grown Comamonas testosteroni. The purified apoenzyme, showing a single band of 71 kDa on native gel electrophoresis, could be only partially converted into active holoenzyme by addition of PQQ in the presence of calcium ions. In addition to a band with a molecular mass of 71 kDa, additional bands of 51 kDa and 25 kDa were observed with SDS/PAGE. Analysis of the N-terminal sequences of the bands and comparison with the DNA sequence of the gene, suggested that the latter two originate from the former one, due to scission occurring at a specific site between two vicinal residues in the protein chain. The extent of scission appeared to increase during growth of the organism. After addition of PQQ to apoenzyme, holoenzyme and nicked, inactive enzyme could be separated. Holoenzyme prepared in this way was found to contain equimolar amounts of PQQ, Ca2+ and covalently bound haem. EPR spectra of fully oxidized apo-QH-EDH and holo-QH-EDH showed g values typical for low-spin haem c proteins. In partially oxidized holo-QH-EDH an organic radical signal attributed to the semiquinone form of PQQ was observed. Binding of PQQ leads to conformational changes, as reflected by changes of spectral and chromatographic properties. Reconstitution of apoenzyme with PQQ analogues resulted in a decreased activity and enantioselectivity for the oxidation of chiral alcohols. Compared with PQQ, analogues with a large substituent had a lower affinity for the apoenzyme. Results with other analogues indicated that possession of the o-quinone/o-quinol moiety is not essential for binding but it is for activity.

Variation in induction of chromosomal beta-lactamase expression in strains of Enterobacter cloacae.

Eight strains of Enterobacter cloacae with varying patterns of susceptibility to beta-lactam antibiotics were studied to compare the inducibility and expression of their beta-lactamase genes. These strains included two isolates from one patient, which differed in their susceptibility to cefamandole. A resistant strain constitutively produced large amounts of beta-lactamase; a sensitive strain produced an inducible beta-lactamase. Study of induction and growth characteristics of all strains revealed that the induction and the expression of inducible beta-lactamase genes may vary considerably among strains of E. cloacae.

Molecular characterization of an Enterobacter cloacae outer membrane protein (OmpX).

A chromosomal gene of Enterobacter cloacae encoding an outer membrane protein (OmpX) has been cloned. Overproduction of the OmpX protein decreased the quantity of porins in the outer membrane of the parental strain and of Escherichia coli HB101. The ompX gene was located by insertions of the gamma delta sequence into the recombinant plasmid. The polarity of the gene was determined by in vitro transcription and translation of the gamma delta-containing plasmids. The nucleotide sequence of the ompX gene was elucidated by using both inverted terminal repeats of the gamma delta sequence as starting points for M13 dideoxy sequencing. The gene was found to encode a precursor of the OmpX protein consisting of 172 amino acid residues with a molecular mass of 18.6 kDa. The protein contains an N-terminal signal sequence of 23 amino acid residues. The exact cleavage point was established by sequencing the N-terminal part of the mature protein. The OmpX protein has several characteristics in common with outer membrane proteins of gram-negative bacteria. The protein is rather hydrophilic and is devoid of long hydrophobic stretches. On the basis of these results, we present a model for the OmpX protein folding in an outer membrane.

Biological characterization of an Enterobacter cloacae outer membrane protein (OmpX).

We have described a gene coding for an Enterobacter cloacae protein, provisionally called OmpX (J. Stoorvogel, M. J. A. W. M. van Bussel, J. Tommassen, and J. A. M. van de Klundert, J. Bacteriol. 173:156-160, 1991). In the work reported here, OmpX was localized in the cell envelope by means of sucrose gradient fractionation of membrane vesicles. Overproduction of OmpX in Escherichia coli from a multicopy plasmid resulted in a reduction in the amount of OmpF. No accumulation of OmpF, of its uncleft precursor, or of its degradation products could be detected in various cell fractions by Western immunoblot analysis using monoclonal antibodies produced in response to OmpF. A decrease in the rate of synthesis of ompF mRNA was indicated by a beta-galactosidase assay in an ompF-lacZ fusion strain containing the cloned ompX gene and by Northern (RNA) blot analysis. These results indicate that the inhibition is at the level of transcription. Colony hybridization, using an internal ompX fragment as a probe, showed a widespread distribution of the ompX gene among clinical isolates of members of the family Enterobacteriaceae. To study the function of the OmpX protein and its role in the regulation of porin protein synthesis, the ompX gene was deleted from the Enterobacter cloacae chromosome and replaced by the aphA gene. The absence of the ompX gene had no apparent effect on cell growth or on the regulation of the porin proteins.

Effect of lexA and ssb genes, present on a uvrA recombinant plasmid, on the UV survival of Escherichia coli K-12.

The recombinant plasmid pJA01 contains, besides the uvrA gene, the genes lexA, ubiA and ssb. This plasmid does not fully complement a uvrA mutation in a Rec+ background. Plasmids which contain the uvrA and ssg genes, but not the lexA gene, show a higher but still only partial complementation. Full complementation achieved when the ssb gene us inactivated by insertion of Tn5. Furthermore, it appears that the presence of the ssb gene on a multicopy plasmid sensitizes wild-type cells to UV light. The effect of Ssb (single-strand DNA binding protein) overproduction on UV survival is discussed.