Optimum experimental design for Free‐Air Carbon dioxide Enrichment (FACE) studies

This article presents the logical reasoning underlying the optimal design of an experiment. We used Free‐Air Carbon dioxide Enrichment (FACE) experiments to illustrate this trade‐off as such experiments are particularly costly. On a theoretical basis, two‐way nested designs and split‐plot designs have similar power in testing carbon dioxide (CO₂) main effects. If researchers have the choice of adding two replicate rings or two control plots to their experiment, our results show that both options provide a substantial gain in statistical power, with a slightly greater gain in the former case and at reduced financial cost in the latter. The former option, however, provides an insurance against possible ring failure. On an empirical basis, we analysed a preliminary FACE photosynthesis dataset collected at Duke University. The experiment was designed as a split‐plot design to test the effects of growth environment (GROWTH) and measurement CO₂ concentration (MEAS) on photosynthetic rates of loblolly pine. Although a significant effect of MEAS was observed, we failed to detect a significant main effect of GROWTH. Power analysis was used to understand why the GROWTH main effect was not significant. The minimum detectable difference between treatment means that we calculated for GROWTH in this experiment was 4.04 μmol CO₂ m^?2 s^?1 for a statistical power of 0.90, whereas the observed difference was 0.16 μmol CO₂ m^?2 s^?1. Our recommendations for the design of FACE experiments are: (i) consider a second treatment factor with many levels within each ring in order to obtain a split‐plot design that provides a powerful test of interaction between treatment factors; (ii) add control plots, unless financial constrictions disallow for necessary personnel; (3) pool the data of FACE experiments conducted in comparable ecosystems (e.g. forests or grasslands), with two rings per treatment level at each site.     

Relationship between force and intracellular [Ca2+] in tetanized mammalian heart muscle

To determine features of the steady state [Ca2+]-tension relationship in intact heart, we measured steady force and intracellular [Ca2+] ([Ca2+]i) in tetanized ferret papillary muscles. [Ca2+]i was estimated from the luminescence emitted by muscles that had been microinjected with aequorin, a Ca2+-sensitive, bioluminescent protein. We found that by raising extracellular [Ca2+] and/or by exposing muscles to the Ca2+ channel agonist Bay K 8644, tension development could be varied from rest to an apparently saturating level, at which increases in [Ca2+]i produced no further rise in force. 95% of maximal Ca2+-activated force was reached at a [Ca2+]i of 0.85 +/- 0.06 microM (mean +/- SEM; n = 7), which suggests that the sensitivity of the myofilaments to [Ca2+]i is far greater than anticipated from studies of skinned heart preparations (or from previous studies using Ca2+-sensitive microelectrodes in intact heart). Our finding that maximal force was reached by approximately 1 microM also allowed us to calculate that the steady state [Ca2+]i-tension relationship, as it might be observed in intact muscle, should be steep (Hill coefficient of greater than 4), which is consistent with the Hill coefficient estimated from the entire [Ca2+]i-tension relationship derived from families of variably activated tetani (6.08 +/- 0.68; n = 7). Finally, with regard to whether steady state measurements can be applied directly toward understanding physiological contractions, we found that the relation between steady force and [Ca2+]i obtained during tetani was steeper than that between peak force and peak [Ca2+]i observed during physiological twitches.     

cDNA sequence and homologies of the "57-kDa" nucleotide-binding subunit of the vacuolar ATPase from Arabidopsis

Functional and structural similarities among a wide variety of endomembrane H+-ATPases suggest that they form a distinct class with a common origin. Immunological studies (Manolson, M. F., Percy, J. M., Apps, D. K., Xie, X. S., Stone, D. K., and Poole, R. J. (1987) in Proceedings of the Membrane Protein Symposium (Goheen, S. C., ed) pp. 427-434, Bio-Rad, Richmond, CA, and M. F. Manolson, J. M. Percy, D. K. Apps, X. S. Xie, D. K. Stone, M. Harrison, D. J. Clarke, R. J. Poole, unpublished data) support this idea and suggest an evolutionary relationship between the endomembrane and F0F1 ATPases. Further examination of relationships necessitates comparison of protein/nucleic acid sequence data. To this end, we have cloned and sequenced the cDNA encoding the 57-kDa polypeptide of the Arabidopsis vacuolar membrane H+-ATPase. To our knowledge, this is the first report of the sequence of a "57-kDa" subunit for plant or animal endomembrane H+-ATPase. This cDNA encodes a hydrophilic polypeptide containing a putative ATP binding site. Lack of a secretion signal sequence suggests it is not processed through the endoplasmic reticulum but translated on cytosolic ribosomes. Comparison of protein sequences shows the 57-kDa subunit from Arabidopsis to be nearly identical with the corresponding subunit in Neurospora vacuolar membrane H+-ATPase, very similar to the beta subunit of the archaebacterium Sulfolobus, and slightly, but nevertheless significantly, homologous to the alpha and beta subunits of the F0F1-ATPases. These results suggest that these different classes of ATPases have evolved from a common ancestor.     

Comparative analysis of translation accuracy in an Escherichia coli and a mammalian cell-free system

The effect of environmental stress on the accuracy of protein synthesis in an Escherichia coli and a rat brain cell-free system was investigated. Poly-U was translated in a rat brain and an E. coli cell-free extract under identical ionic conditions. The fidelity of translation, both in the E. coli and the rat brain extracts, was commensurate with what is known about the accuracy of translation in vivo. The incorporation of phenylalanine (code: UUU) and leucine (code: CUU, UUG or A) was measured at various Mg²⁺ concentrations (3 to 22 mm), various pH's (6.6 to 8.6), various temperatures (23 to 42 °C), and in the presence or absence of 2.4% (v/v) ethanol. It was observed that (i) the accuracy of translation was generally higher in extracts from E. coli than from rat brain, and (ii) relative to that in E. coli, the translation fidelity in rat brain extracts was about 2 times more sensitive to ethanol, at least 5 times more sensitive to temperature, and at least 50 times more sensitive to pH. It was found that this differential sensitivity was not due to a differential behavior of the bacterial and the mammalian aminoacyl-tRNA synthetases under stress, but rather to the process of chain elongation itself. It is concluded that the accuracy of protein synthesis is more resistant to environmental stress in E. coli extracts than in extracts from at least one mammalian tissue.     

The Restoration of Elk (Cervus elaphus) in Ontario, Canada: 1998–2005

In 1997, a plan to restore Elk (Cervus elaphus) to Ontario was approved by the provincial government. The objective of the Ontario elk restoration program, a multipartnered collaboration, was to restore a species that had been extirpated from the province during the 1800s. During 1998–2001, 460 elk were acquired from Elk Island National Park, Alberta, for release in four areas of Ontario. As greater than 90% of the elk were radio collared, monitoring provided detailed information on the dynamics of the four populations. Comprehensive research projects using graduate students were implemented to determine the environmental impact of releasing elk in Ontario. Those studies are in progress or have been completed and include the effect of wolf predation on restored elk, white‐tailed deer and elk resource overlap, the development of genetic profiles for elk, and solutions for elk/human conflicts. Mortality of the released elk averaged 41% (190/460) during 1998–2004 with annual mortality generally declining over time in each release area. The primary causes of elk mortality included wolf predation (25% of mortalities), illegal shooting (13%), stress‐related emaciation (13%) (partially due to the stress of relocation), bacterial infections (7%), and collisions with vehicles (6%). Productivity has been high in one of the release areas with 24–65% of the cows being observed with calves during late winter surveys. However, productivity has been low in two of the northern release areas due to a variety of factors including wolf predation. In some areas, dispersion of elk appeared to be related to the length of time animals were kept in pens prior to release. The precalving population estimate for Ontario in March 2004 was 375–440 elk. A comprehensive program review was conducted in 2003/2004 that included recommendations relating to the future management of elk in Ontario.     

Ionization and solubility of chitosan solutions related to thermosensitive chitosan/glycerol-phosphate systems

Chitosan is a linear cationic biopolymer composed of glucosamine and N-acetyl-glucosamine that is only soluble in acidic aqueous solutions and precipitates when neutralized. However, it was recently discovered that chitosan dissolved in solutions containing glycerol phosphate was soluble at near neutral pH and produced a sol-gel transition when heated. Understanding this unique thermogelling system requires improved characterization of the ionization and solubility behaviors of chitosan, in particular dependencies on temperature, salt, chitosan concentration, and fD, where fD is the fraction of glucosamine monomers (deacetylated monomers) in chitosan. In the current study we performed temperature-controlled titration and dilution experiments on chitosan solutions with fD of 0.72, 0.85, and 0.98 at concentrations ranging from 1.875 to 30 mM of its glucosamine monomer and with 0 to 150 mM added salt. Light transmittance measurements were performed during titration to indicate precipitation. We found the apparent proton dissociation constant of chitosan, pKap, to (1) decrease strongly with increased temperature, (2) increase strongly with increased salt, (3) increase strongly with increased chitosan concentration in low-salt conditions, and (4) decrease weakly with increasing fD. All of the above influences on chitosan pKap were accurately predicted using a mean-field Poisson-Boltzmann (PB) cylindrical cell model where the only adjustable parameter was the temperature-dependent chitosan intrinsic monomeric dissociation constant pK0(T). The resulting chitosan pK0 values at 25 degrees C were in the range from 6.63 to 6.78 for all chitosans and salt contents tested. The temperature dependence of chitosan ionization was found to strongly reduce pK0(T) by 0.023 units per degrees C, for example, resulting in a reduction of chitosan pK0(T) from 7.1 at 5 degrees C to 6.35 at 37 degrees C for fD of 0.72 in 150 mM salt. A similar temperature-dependent reduction of the pKa of the glucosamine monomer was found (-0.027 units per degrees C) while the pKa of glycerol phosphate did not change significantly with temperature. The latter result suggested that chitosan solutions heated in the presence of glycerol phosphate will become partly neutralized by transferring protons to glycerol phosphate and thereby allow attractive interchain forces to form a physically cross-linked gel under the appropriate conditions. Additionally, the degree of ionization of chitosan when it precipitates upon addition of a strong base was measured to be in the range from 0.25 to 0.55 and was found to (1) be insensitive to temperature, (2) increase strongly with increased salt, and (3) increase strongly with fD. The salt effect was accounted for by the PB model, while the influence of fD appeared to be due to acetyl groups impeding attractive chain-to-chain association to increase solubility and require reduced ionization levels to precipitate.     

The transferable tail: fusion of the N-terminal acidic extension of heparin cofactor II to alpha1-proteinase inhibitor M358R specifically increases the rate of thrombin inhibition

The conversion of the reactive center bond of the serpin alpha1-proteinase inhibitor (alpha1-PI, also known as alpha1-antitrypsin) from Met-Ser to Arg-Ser decreases the rate at which it inhibits neutrophil elastase and endows it with the ability to inhibit thrombin and activated protein C (APC). Another serpin, heparin cofactor II (HCII), contains a unique N-terminal extension that binds thrombin exosite 1. We fused residues 1-75 of HCII to the N-terminus of alpha1-PI M358R, forming an HCII-alpha1-PI chimera (HAPI M358R). It inhibited alpha-thrombin 21-fold faster than alpha1-PI M358R, with second-order rate constants of 2.3 x 10(8) M(-1) min(-1) versus 1.1 x 10(7) M(-1) min(-1), respectively. When gammaT-thrombin, which lacks an intact exosite 1, was substituted for alpha-thrombin, the kinetic advantage of HAPI M358R over alpha1-PI M358R was reduced to 9-fold, whereas APC and trypsin, proteases lacking exosite 1-like regions, were inhibited only 1.3- and 2-fold more rapidly by HAPI M358R than by alpha1-PI M358R, respectively. Maximal enhancement of alpha1-PI M358R activity required the acidic residues found between HCII residues 55 and 75, because no enhancement was observed either by fusion of residues 1-54 alone or by fusion of a mutated HCII acidic extension in which all Glu and Asp residues between positions 55 and 75 were neutralized by mutation. Fusing residues 55-75 to alpha1-PI M358R yielded a relative rate enhancement of only 6-fold, suggesting a need for the full tail region to achieve maximal enhancement. Our results suggest that transfer of the N-terminal acidic extension of HCII to alpha1-PI M358R enhanced its inhibition of thrombin by conferring the ability to bind exosite 1 on HAPI M358R. This enhancement may aid in efforts to tailor this inhibitor for therapeutic use.