Reference site selection protocols for mine site ecosystem restoration

Reference site selection associated with mining and resource development requires a comprehensive approach so that stakeholders can be confident that restoration efforts have appropriate target ecosystems. Here, we present our process to select reference sites, within a savanna ecosystem, which will be used to develop and assess closure criteria and restoration guidelines for Ranger Mine (Northern Territory, Australia). The selection of reference sites followed five steps involving desktop and field methods. We recommend that restoration projects consider inclusion criteria, randomly select sites from areas matching the chosen criteria, conduct preliminary data analysis, estimate and update sampling effort and precision at several points throughout the project, and invite stakeholder feedback and revision of the process as often as required. This detailed reference site approach appears to be the first to demonstrate how to use available data to reduce bias, address sampling effort and site selection quantitatively, involve stakeholders, and provide useful data, which can be used to calibrate ecological restoration outcomes for savanna ecosystems.     

The Rhesus site

The Rhesus (Rh) blood group system is the most important blood group system in hemolytic disease of the fetus and newborn (HDFN). In clinical transfusions, the D antigen in the Rh blood group system comes third, behind antigens A and B which from ABO blood group system. Over the past decade, molecular technologies have been used to investigate the RHD allele in different ethnic groups. This review first introduces the basic structure of RhD protein and coding genes, then focuses on D-negative, weak D, partial D, DEL, RhD_null variants reported in the Chinese population. To date, more than 460 RHD variants have been reported around the world, but less than 70 RHD variants have been reported in the Chinese population. Further research is needed to identify more RHD polymorphism and establish criteria for blood detection and transfusion guidelines for RHD variants. Only in this way can we better guarantee the safety of blood transfusion and prevent the occurrence of HDFN. With the accumulation of research and clinical data, we should be clearer which RHD variants are to be regarded as RhD negative and which need to be regarded as RhD positive.     

Interference of active site specific reagents in plasminogen-streptokinase active site formation

We have recently observed slow, non-Michaelis-Menten kinetics of activation of native cat plasminogen by catalytic concentrations of streptokinase. In order to understand the reasons for this phenomenon, we undertook to study the formation of the plasminogen-streptokinase activator complex under the same plasminogen activation conditions. The results obtained in this study show that the potential active site in both cat and human plasminogen is capable of binding strongly the specific substrates (S) p-nitrophenyl p-guanidinobenzoate (NPGB) and H-D-valyl-L-leucyl-L-lysyl-p-nitroanilide, through the active site is incapable of hydrolyzing these substrates. Binding studies support these and the following conclusions. Streptokinase binds to this zymogen-substrate complex to create the ternary plasminogen-S-streptokinase complex, which then slowly converts to an acylated plasminogen-streptokinase form. This acylation reaction is 550 times slower than acylation of the preformed plasminogen-streptokinase complex by NPGB. The same reaction also occurs with human plasminogen, though the acylation reaction is 10 times faster than when the cat zymogen is used. NPGB binds specifically to plasminogen but not to streptokinase. These studies proved that inhibition of cat plasminogen activation by streptokinase occurs at the level of activator complex formation. We conclude from our studies that streptokinase binding to both cat and human plasminogen occurs at the potential active site of the zymogen. Consequently, it is probable that plasminogen activation in vivo is inhibited by binding of active site specific inhibitors to plasminogen.     

Discrimination of antigenic site and thiol-inhibitor-sensitive site of hexokinase isoenzymes.

Rabbit antiserum was prepared against hexokinase isoenzyme type I which was purified from rat brain mitochondria. The antiserum inhibited the activity of the mitochondrial hexokinase type I as well as that of the cytosolic type I enzyme prepared from rat brain, kidney and spleen. It did not, however, inhibit the activity of type II hexokinase from muscle and spleen or that of the type III enzyme from spleen. The results suggest that all hexokinase type I isoenzymes may have a common antigenic site irrespective of their sources, though their responses to a thiol inhibitor are different.     

The Muni-Pomadze Ramsar site

The Coastal Wetlands Management Project (CWMP), funded by the Global Environment Facility and implemented by the Ghana Wildlife Department, seeks to preserve the ecological integrity of coastal lagoons that serve as important sites for migratory waterbirds. This report describes the geomorphology, hydrology, soils, water chemistry, and vegetation of the Muni-Pomadze Ramsar site. Muni lagoon is a saline, shallow water lagoon separated from the sea by a sand bar which may be breached occasionally. The bulk of the rainfall in the catchment evaporates or flows as surface runoff into three streams that empty into Muni lagoon. Open water in the lagoon varies seasonally from 100 ha in the dry season to over 1000 ha in the wet season. The natural flora of the site can be divided into four main types; flood plain (including mangrove and wetland vegetation), dune vegetation, riverine vegetation, and terrestrial vegetation on elevated ground. The latter consists of a combination of grasslands, thickets, and Eucalyptus plantations. Fifty-three percent of the site is classified as natural vegetation. An additional 32.5% is agricultural land and 12.6% is residential area for the 11 communities within the site. The main source of employment are farming or fishing. The area surrounding Muni lagoon is used extensively for bushmeat hunting and as the tribal hunting grounds of the Efutu people. Apart from the global importance of the Muni-Pomadze site for biodiversity, management of the site is further justified by its considerable potential for development as an income-generating and educational nature reserve with an eco-cultural theme, managed by the local communities in partnership with the governmental and non-governmental conservation agencies.     

Superfamily active site templates

We show that three-dimensional signatures consisting of only a few functionally important residues can be diagnostic of membership in superfamilies of enzymes. Using the enolase superfamily as a model system, we demonstrate that such a signature, or template, can identify superfamily members in structural databases with high sensitivity and specificity. This is remarkable because superfamilies can be highly diverse, with members catalyzing many different overall reactions; the unifying principle can be a conserved partial reaction or chemical capability. Our definition of a superfamily thus hinges on the disposition of residues involved in a conserved function, rather than on fold similarity alone. A clear advantage of basing structure searches on such active site templates rather than on fold similarity is the specificity with which superfamilies with distinct functional characteristics can be identified within a large set of proteins with the same fold, such as the (beta/alpha)8 barrels. Preliminary results are presented for an additional group of enzymes with a different fold, the haloacid dehalogenase superfamily, suggesting that this approach may be generally useful for assigning reading frames of unknown function to specific superfamilies and thereby allowing inference of some of their functional properties.     

Natural base-pairing interactions between 5' splice site and branch site sequences affect mammalian 5' splice site selection.

In the murine gene encoding the neuronal cell adhesion molecule (NCAM), the integrity of the 5' splice site of exon 18 (E18) is essential for regulation of alternative splicing. To further study the contribution of 5' splice site sequences, we used a simple NCAM pre-mRNA containing a portion of E18 fused to E19 and separated by a shortened intron. This RNA is spliced in vitro to produce five sets of lariat intermediates and products, the most abundant set displaying aberrant migration in acrylamide/urea gels. Base pairing interactions between positions +5 and +8 of the intron and positions -3 and -6 from the branch point were responsible for the faster migration of this set of lariat molecules. To test whether the duplex structure forms earlier and contributes to 5' splice site selection, we used NCAM substrates carrying the 5' splice sites of E17 and E18 in competition for the 3' splice site of E19. Mutations upstream of the major branch site improve E18/E19 splicing in NIH3T3 extracts, whereas compensatory mutations at positions +7 and +8 neutralize the effect of branch site mutations and curtail E18/E19 splicing. Our data suggest that duplex formation occurs early and interferes with the assembly of complexes initiated on the 5' splice site of NCAM E18. This novel type of intron interaction may exist in the introns of other mammalian pre-mRNAs.     

Multiple active site conformations revealed by distant site mutation in ornithine decarboxylase

Ornithine decarboxylase (ODC) is an obligate homodimer that catalyzes the pyridoxal 5'-phosphate-dependent decarboxylation of l-ornithine to putrescine, a vital step in polyamine biosynthesis. A previous mutagenic analysis of the ODC dimer interface identified several residues that were distant from the active site yet had a greater impact on catalytic activity than on dimer stability [Myers, D. P., et al. (2001) Biochemistry 40, 13230-13236]. To better understand the basis of this phenomenon, the structure of the Trypanosoma brucei ODC mutant K294A was determined to 2.15 A resolution in complex with the substrate analogue d-ornithine. This residue is distant from the reactive center (>10 A from the PLP Schiff base), and its mutation reduced catalytic efficiency by 3 kcal/mol. The X-ray structure demonstrates that the mutation increases the disorder of residues Leu-166-Ala-172 (Lys-169 loop), which normally form interactions with Lys-294 across the dimer interface. In turn, the Lys-169 loop forms interactions with the active site, suggesting that the reduced catalytic efficiency is mediated by the decreased stability of this loop. The extent of disorder varies in the four Lys-169 loops in the asymmetric unit, suggesting that the mutation has led to an increase in the population of inactive conformations. The structure also reveals that the mutation has affected the nature of the ligand-bound species. Each of the four active sites contains unusual ligands. The electron density suggests one active site contains a gem-diamine intermediate with d-ornithine; the second has density consistent with a tetrahedral adduct with glycine, and the remaining two contain tetrahedral adducts of PLP, Lys-69, and water (or hydroxide). These data also suggest that the structure is less constrained in the mutant enzyme. The observation of a gem-diamine intermediate provides insight into the conformational changes that occur during the ODC catalytic cycle.     

The calmodulin-binding site in alpha-fodrin is near the calcium-dependent protease-I cleavage site

Fodrin (brain spectrin) binds calmodulin and is susceptible to proteolysis by calcium-dependent protease I (CDP-I, calcium-activated neutral protease I, or calpain I). Both events involve the central region of the alpha-fodrin subunit, and calmodulin binding enhances the sensitivity of fodrin to CDP-I mediated proteolysis. Fragments of fodrin, generated chemically or proteolytically, which retain calmodulin binding activity have been identified and analyzed by two-dimensional peptide mapping and by direct protein sequencing. Both CDP-I and calmodulin interact with the terminal portion of the eleventh repetitive unit in fodrin, which is at the center of the molecule. CDP-I cleavage occurs between Tyr104 and Gly105 and preserves the calmodulin binding activity of the carboxyl-terminal fragment. In contrast, chymotryptic cleavage at Trp120 reduces the ability of this fragment to bind calmodulin, and tryptic cleavage beyond Trp120 completely eliminates calmodulin binding activity. It is concluded that Ser-Lys-Thr-Ala-Ser-Pro-Trp-Lys-Ser-Ala-Arg-Leu-Met-Val-His-Thr-Val-Ala- Thr- Phe-Asn-Ser-Ile-Lys, a 24-residue peptide which bridges repeats 11 and 12 of brain alpha spectrin contains the high affinity calmodulin binding domain.     

Transport of ABA from the site of biosynthesis to the site of action

There is substantial evidence that abscisic acid (ABA) moves within plants. ABA has been considered as a root-derived signaling molecule that induces stomatal closure in response to dry soil conditions. It has been also reported that ABA synthesized in vegetative tissues is translocated to the seeds. The transport of ABA is an important factor in determining the endogenous concentrations of the hormone at the site of action, and hence, it is an important process in physiological responses. However, the molecular mechanisms that regulate ABA transport are not fully understood. Recent studies using Arabidopsis indicate that ABA is actively synthesized in leaf vascular tissues in response to drought, and that ABA is subsequently transported to the guard cells to close stomata. Identification of the transporters that mediate ABA export from the inside to the outside of the cells at the site of ABA biosynthesis (vascular tissues) and ABA uptake into the cells at the site of action (guard cells), respectively, in this species indicates an active mechanism to regulate ABA transport. Although Arabidopsis represents only one model plant, these findings are useful to discuss common or different regulatory mechanisms among different species and to improve our total understanding of the regulation of ABA transport.     

The PSII calcium site revisited

Oxidation of H₂O by photosystem II is a unique redox reaction in that it requires Ca²⁺ as well as Cl⁻ as obligatory activators/cofactors of the reaction, which is catalyzed by Mn atoms. The properties of the binding site for Ca²⁺ in this reaction resemble those of other Ca²⁺ binding proteins, and recent X-ray structural data confirm that the metal is in fact ligated at least in part by amino acid side chain oxo anions. Removal of Ca²⁺ blocks water oxidation chemistry at an early stage in the cycle of redox reactions that result in O-O bond formation, and the intimate involvement of Ca²⁺ in this reaction that is implied by this result is confirmed by an ever-improving set of crystal structures of the cyanobacterial enzyme. Here, we revisit the photosystem II Ca²⁺ site, in part to discuss the additional information that has appeared since our earlier review of this subject (van Gorkom HJ, Yocum CF In: Wydrzynski TJ, Satoh K (eds) Photosystem II: the light-driven water:plastoquinone oxidoreductase), and also to reexamine earlier data, which lead us to conclude that all S-state transitions require Ca²⁺.     

Active site dynamics of acyl-chymotrypsin

The motions of water molecules, the acyl moiety, the catalytic triad, and the oxyanion binding site of acyl-chymotrypsin were studied by means of a stochastic boundary molecular dynamics simulation. A water molecule that could provide the nucleophilic OH^? for the deacylation stage of the catalysis was found to be trapped between the imidazole ring of His-57 and the carbonyl carbon of the acyl group. It makes a hydrogen bond with the N^ε2 of His-57 and is heldin place through a network of hydrogen-bonded water molecules in theactive site. The water molecule was found as close as 2.8 Å to the carbonyl carbon. This appears to be due to the constraints imposed by nonbonded interaction in the active site. Configurations were found in which one hydrogen of the trapped water shared a bifurcated hydrogen bond with His-57-N^ε2 and Ser-195-0^γ with the water oxygen very close to the carbonyl carbon. The existence of such a water molecule suggests that large movement of the His-57 imidazole ring between positions suitable for providing general-base catalyzed assistance and for providing general-acid catalyzed assistance may notbe required during the reaction. The simulation indicates that the side chains of residues involved in catalysis (i.e., His-57, Ser-195, and Asp-102) are significantly less flexible than other side chains in the protein. The 40% reduction in rms fluctuations is consistent with a comparable reduction calculated from the temperature factors obtained in the X-ray crystal-lographic data of γ-chymotrypsin. The greater rigidity of active site residues seems to result from interconnected hydrogen bonding networks among the residues and between the residues and the solvent water in the active site. © Wiley-Liss, Inc.