Computational sequence analysis of matrix metalloproteinases

Matrix metalloproteinases (MMP) play a cardinal role in the breakdown of extracellular matrix involved in a variety of biological and pathological processes. Research on MMPs has classified and characterized these enzymes according to their matrix substrate specificity, gene and protein domain structure, and regulation of activity and expression. However, the discovery of new MMPs has introduced a need for a more comprehensive and systematic method of classification and quantitative comparison of known and newly discovered members. This study compiles a sequence alignment, constructs a dendrogram, and calculates physical data and homology percentage assignments in order to obtain further insight into MMP structure-function relationships. Thorough analysis of MMP primary sequence domains, physical data patterns, and statistical analysis of sequence homology yields higher resolution in the similarities and differences that group MMP members.     

Antiprogestagen RU486 prevents the LH-dependent decrease in the serum concentrations of inhibin in the rat

Summary 1. In the rat, the LH-dependent ovarian progesterone rise mediates several actions of the primary surge of LH on the ovary. This experiment was aimed at elucidating the effects of the antiprogestagen RU486 on the LH-dependent decrease in both the serum concentrations and the ovarian content of inhibin.2. All rats in this experiment were treated with an antagonist of LHRH (1 mg/200 µl saline at 0800 h in proestrus) to supress the endogenous release of LH. One group of rats received 32 µg LH/250 µl saline at 1200 h in proestrus. Other group was given 4 mg RU486/200 µl oil at 0800 h in proestrus. The third group was injected with both RU486 and LH. Rats from the control group were injected with 250 µl saline and 200 µl oil. Animals were decapitated at 1700 h in proestrus and trunk blood and ovaries collected to determine the serum concentrations of LH, FSH, progesterone, 17ß-estradiol and inhibin as well as the ovarian content of inhibin.3. The ovulatory dose of LH in LHRHa-treated rats decreased both the serum concentrations and the ovarian content of inhibin and increased the serum concentrations of FSH. The administration of RU486 blocked the effect of LH on the serum concentrations of inhibin but not that on the ovarian content of inhibin.4. Since the antiprogestagen RU486 blocked the effect of LH on the serum concentrations of inhibin, we conclude that ovarian progesterone, besides mediating the effects of the primary LH surge on the ovulatory process and luteinization, participates in the LH-dependent drop in the serum concentrations of inhibin in proestrous afternoon.     

Stable carbon isotopes as indicators of increased water use efficiency and productivity in white spruce (Picea glauca (Moench) Voss) seedlings

The relationship among water use efficiency (WUE), productivity and carbon isotopic composition (δ¹³C) in white spruce (Picea glauca (Moench) Voss) seedlings was investigated. Sixteen hundred seedlings representing 10 controlled crosses were planted in the field in individual buried sand-filled cylinders. The soil water content in the cylinders was measured using time domain reflectometry over two growing seasons and seedling water use determined by water balance. Two watering treatments were imposed: irrigation and dry land. There was significant (1.6–2.0%c) genetic variation in needle δ¹³C. Ranking of crosses in terms of δ¹³C was generally maintained over watering treatments and there was not a significant genetic versus environmental interaction. There was a positive correlation between δ¹³C and both intrinsic and long-term WUE (more positive δ¹³C with increased WUE) and between δ¹³C and productivity, suggesting a correlation due to variation in photosynthetic capacity. Root to shoot ratios did not increase in water-stressed plants, indicating that responses to drought were primarily at the level of gas exchange, rather than through morphological changes. Our results indicate that it should be possible to use δ¹³C as a surrogate for WUE and to select white spruce genotypes for high WUE without compromising yield.     

Sap flow in wheat under free-air CO2 enrichment

The effects of elevated carbon dioxide (CO₂) concentration on plant water use are best evaluated on plants grown under field conditions and with measurement techniques that do not disturb the natural function of the plant. Heat balance sap flow gauges were used on individual main stems of wheat (Triticum aestivum L. cv Yecora rojo) grown under normal ambient conditions (control) and in a free-air CO₂ enrichment (FACE) system in Arizona with either high (control + high H₂O = CW; FACE + high H₂O = FW) or low (control + low H₂O = CD; FACE + low H₂O = FD) irrigation regimens. Over a 30d period (stem elongation to anthesis), combinations of treatments were monitored with,10–40 gauges per treatment. The effects of increased CO₂ on tiller water use were inconsistent in both the diurnal patterns of sap flow and the statistical analyses of daily sap flow (F_tot). Initial results suggested that the reductions in F_tot, from CO₂ enrichment were small (,0–10%) in relation to the H₂O treatment effect (,20–30%). For a 3d period, F_tot of FW was,19–26% less than that of CW (P = 0.10). Examination of the different sources of variation in the study revealed that the location of gauges within the experimental plots influenced the variance of the sap flow measurements. This variation was probably related to positional variation in subsurface drip lines used to irrigate plots. A sampling design was proposed for use of sap flow gauges in FACE systems with subsurface irrigation that takes into account the main treatment effects of CO₂ enrichment and the other sources of variation identified in this study. Despite the small and often statistically non-significant differences in F_tot between the CW and FW treatments, cumulative water use of the FW treatment at the end of the first three test periods ranged from 7 to 23% lower than that of the CW treatment. Differences in sap flow between FW and CW compared well with treatment differences in evapotranspiration. The results of the study, based on the first reported sap flow measurements of wheat, suggest that irrigation requirements for wheat production, in the present climatic regimen of the south-western US, may be predicted to decrease slightly because of increasing atmospheric CO₂.     

Hydraulic control of stomatal conductance in Douglas fir [Pseudotsuga menziesii (Mirb.) Franco] and alder [Alnus rubra (Bong)] seedlings

Experiments were conducted on 1-year-old Douglas fir [Pseudotsuga menziesii (Mirb.) Franco] and 2- to 3-month-old alder [Alnus rubra (Bong)] seedlings growing in drying soils to determine the relative influence of root and leaf water status on stomatal conductance (g_c). The water status of shoots was manipulated independently of that of the roots using a pressure chamber that enclosed the root system. Pressurizing the chamber increases the turgor of cells in the shoot but not in the roots. Seedling shoots were enclosed in a whole-plant cuvette and transpiration and net photosynthesis rates measured continuously. In both species, stomatal closure in response to soil drying was progressively reversed with increasing pressurization. Responses occurred within minutes of pressurization and measurements almost immediately returned to pre-pressurization levels when the pressure was released. Even in wet soils there was a significant increase in g_c with pressurization. In Douglas fir, the stomatal response to pressurization was the same for seedlings grown in dry soils for up to 120 d as for those subjected to drought stress over 40 to 60 d. The stomatal conductance of both Douglas fir and alder seedlings was less sensitive to root chamber pressure at higher vapour pressure deficits (D), and stomatal closure in response to increasing D from 1.04 to 2.06 kPa was only partially reversed by pressurization. Our results are in contrast to those of other studies on herbaceous species, even though we followed the same experimental approach. They suggest that it is not always appropriate to invoke a ‘feedforward’ model of short-term stomatal response to soil drying, whereby chemical messengers from the roots bring about stomatal closure.     

Carbon isotope fractionation in tree ring early and late wood in relation to intra-growing season water balance

We determined the stable carbon isotope composition (δ^1.3C) of cellulose extracted from early and late wood in Douglas fir [Pseudotsuga menziexii (Mirb.) Franco] tree rings. Data were obtained for the period 1962 to 1981, at the start of which the trees were 20 years old. A water balance model was used to calculate daily stand transpiration and water deficit. The model incorporates site factors (soil water availability, slope and aspect) and environmental variables (solar radiation, air temperature and rainfall). There was far greater variability in late wood than in early wood δ^1.3C. In wet years, late wood δ^1.3C was significantly lighter (by as much as 2δ) than early wood δ^1.3C but in dry years this difference was reversed. Differences between spring and summer cumulative transpiration accounted for almost 60δ of the variability in differences between early and late wood δ^1.3C. We found excellent correspondence between summer cumulative transpiration and late wood δ^1.3C, with estimates of transpiration accounting for up to 93% of the variability in δ^1.3C. Correlations between early wood δ^1.3C and spring transpiration were generally poor (r2<0.4), but we were able to identify those exceptional years in which there had been a very dry spring. Our results indicate that, while tree ring δ^1.3C correlates reasonably well with basal area increment, it is a far better indicator of inter- and intra-annual variability in water availability than radial growth.     

Altered drug translocation mediated by the MDR protein: Direct,indirect, or both?

Overexpression of the MDR protein, or p-glycoprotein (p-GP), in cells leads to decreased initial rates of accumulation and altered intracellular retention of chemotherapeutic drugs and a variety of other compounds. Thus, increased expression of the protein is related to increased drug resistance. Since several homologues of the MDR protein (CRP, ltpGPA, PDR5, sapABCDF) are also involved in conferring drug resistance phenomena in microorganisms, elucidating the function of the MDR protein at a molecular level will have important general applications. Although MDR protein function has been studied for nearly 20 years, interpretation of most data is complicated by the drug-selection conditions used to create model MDR cell lines. Precisely what level of resistance to particular drugs is conferred by a given amount of MDR protein, as well as a variety of other critical issues, are not yet resolved. Data from a number of laboratories has been gathered in support of at least four different models for the MDR protein. One model is that the protein uses the energy released from ATP hydrolysis to directly translocate drugs out of cells in some fashion. Another is that MDR protein overexpression perturbs electrical membrane potential () and/or intracellular pH (pH_i) and therebyindirectly alters translocation and intracellular retention of hydrophobic drugs that are cationic, weakly basic, and/or that react with intracellular targets in a pH_i, or -dependent manner. A third model proposes that the protein alternates between drug pump and Cl^– channel (or channel regulator) conformations, implying that both direct and indirect mechanisms of altered drug translocation may be catalyzed by MDR protein. A fourth is that the protein acts as an ATP channel. Our recent work has tested predictions of these models via kinetic analysis of drug transport and single-cell photometry analysis of pH_i, , and volume regulation in novel MDR and CFTR transfectants that have not been exposed to chemotherapeutic drugs prior to analysis. This paper reviews these data and previous work from other laboratories, as well as relevant transport physiology concepts, and summarizes how they either support or contradict the different models for MDR protein function.     

Inhibitor binding to isolated chloroplast cytochrome bf complex

Effects of three inhibitors of quinol oxidation in the chloroplast cytochrome bf complex (stigmatellin, tridecylstigmatellin and dibromothymoquinone) were studied in an isolated system comprising Photosystem I (PS I) particles, plastocyanin (PC) and cytochrome bf complex, in the absence of quinol or quinone. Addition of these inhibitors increased the extent of cytochrome f oxidation after a laser flash created oxidised PS I reaction centre (P700) and PC, and decreased somewhat the extent of PC oxidation. The re-reduction of oxidised P700 was more complete than when inhibitor was absent. The data were simulated with reactions which included the putative reduction of cytochrome f by the Rieske centre (FeS) and different rate-coefficients according as to whether inhibitor was bound to the bf complex or not. It was concluded that under the conditions studied the Rieske centre donated electrons to oxidised cytochrome f and plastocyanin with an average rate coefficient of 35 s^–1. This electron transfer was prevented by any of the three inhibitors, which also increased the equilibrium coefficient for the cytochrome f/PC reaction by a maximum factor of two. This increase corresponded to a decrease in the back reaction coefficient and an increase in the forward rate. The equilibrium coefficient for the reduction of oxidised P700 by PC was about 2 in the absence of inhibitor but increased to about 20 in their presence, but only if cytochrome bf complex was additionally present. This was attributed to the transient formation of complexes between P700 with bound plastocyanin, and bf complex. The operative mid-point potential of FeS, if that of cytochrome f is 370 mV, was 390 mV. Deviations in midpoint potentials (P700/plastocyanin) from solution values were attributed to the bound state of the reactants. Estimates were made of the binding coefficient of each of the three inhibitors to p-sites in the cytochrome bf complex in the absence of competing quinol. A stoichiometry of two inhibitors per bf dimer was necessary to cause the above changes in reduction potential of cyt f and PC. A result of one inhibitor per dimer was statistically unlikely, particularly in the case of tridecylstigmatellin.Abbreviations Cyt- cytochrome - DBMIB(H₂)- 2,5-dibromo-3--ethyl-6-isopropyl-p-benzoquinone (reduced) - E _m- midpoint reduction potential of a couple relative to the standard hydrogen electrode - e-t- electron transfer - FeS (or R)- Rieske iron-sulphur centre - HEPES- N-2-hydroxyethylpiperazine-N-2-ethanesulphonic acid - Mega-9- nonoyl-N-methylglucamide - n-site (Q_r-site)- quinone reduction site in cytochrome bf complex - PC- plastocyanin - p-site (Q_o-site)- quinol oxidation site in cytochrome bf complex - PQ- plastoquinone - PSI- Photosystem I - P700- reaction centre in Photosystem I - TDS- tridecyl stigmatellin     

Halcyon days with Bill Arnold

The circumstances that led to the discovery that plants luminesce after they are illuminated are described, as are other discoveries that would not have been possible were it not for the fortuitous association I had with my dear and most admirable friend, W.A. Arnold, to whom this special issue is dedicated.