Structure of CcmG/DsbE at 1.14 angstrom resolution: High-fidelity reducing activity in an indiscriminately oxidizing environment

CcmG is unlike other periplasmic thioredoxin (TRX)like proteins in that it has a specific reducing activity in an oxidizing environment and a high fidelity of interaction. These two unusual properties are required for its role in c-type cytochrome maturation. The crystal structure of CcmG reveals a modified TRX fold with an unusually acidic active site and a groove formed from two inserts in the fold. Deletion of one of the groove-forming inserts disrupts c-type cytochrome formation. Two unique structural features of CcmG-an acidic active site and an adjacent groove-appear to be necessary to convert an indiscriminately binding scaffold, the TRX fold, into a highly specific redox protein.

Adoption and maintenance of contour bunds and hedgerows in a dynamic environment - Experience in the Philippine uplands

The widespread adoption of soil conservation technologies by farmers (notably contour hedgerows) observed in Guba, Cebu City, Philippines, is not often observed elsewhere In the country. Adoption of these technologies was because of the interaction of such phenomena as site-specific factors, appropriate extension systems, and technologies. However, lack of hedgerow maintenance, decreasing hedgerow quality, and disappearance of hedgerows raised concerns about sustainability. The dynamic nature of upland farming systems suggests the need for a location-specific farming system development framework, which provides farmers with ongoing extension for continual promotion of appropriate conservation practices.

Mental health: How well are occupational therapists equipped for a changed practice environment?

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Using crop simulation to generate genotype by environment interaction effects for sorghum in water-limited environments

Multi-environment trials (METs) used to evaluate breeding lines vary in the number of years that they sample. We used a cropping systems model to simulate the target population of environments (TPE) for 6 locations over 108 years for 54 'near-isolines' of sorghum in north-eastern Australia. For a single reference genotype, each of 547 trials was clustered into 1 of 3 'drought environment types' (DETs) based on a seasonal water stress index. Within sequential METs of 2 years duration, the frequencies of these drought patterns often differed substantially from those derived for the entire TPE. This was reflected in variation in the mean yield of the reference genotype. For the TPE and for 2-year METs, restricted maximum likelihood methods were used to estimate components of genotypic and genotype by environment variance. These also varied substantially, although not in direct correlation with frequency of occurrence of different DETs over a 2-year period. Combined analysis over different numbers of seasons demonstrated the expected improvement in the correlation between MET estimates of genotype performance and the overall genotype averages as the number of seasons in the MET was increased.

Recoverable reserves and support effects when optimizing open pit mine designs

Orebody modelling, support effects and the estimation of recoverable reserves are key parts of open pit optimization studies. A case study is presented on the estimation of recoverable reserves using an implementation of indicator kriging where metal quantity is used to select cutoffs, and support corrections founded on a conditional simulation approach. Mining selectivity is explored in the subsequent optimization study to compare results from indicator kriging of grade estimates on a regular size blocks and indicator kriging estimates on small size blocks. The use of indicator kriging models adjusted for a given selectivity and the use of grade proportions in each block for the optimization study, provide a presentation of the expected ore recovery for a predefined level of selectivity. The case study shows that indicator kriging estimation with full accounting of block grade distributions generates substantially better results in the pit optimization study. In addition, the adverse effects of small blocks and over-smoothing on optimization results are illustrated.

The effect of sodium chloride supplementation on the milk production of grazing Holstein Friesian cows during summer and autumn in a humid sub-tropical environment

Two studies were conducted to examine the effects of including NaCl at various rates in grain-based supplements for Friesian cows grazing established, dominant (>90%), rainfed kikuyu (Pennisetum clandestinum cv. Common) pastures during summer and autumn in a humid sub-tropical environment. In study 1 (19 January-27 March 1998), 48 cows (36 multiparous, 12 primiparous; 27-96 days postpartum) were allocated to one of four groups based on genetic merit, milk production, liveweight (LW) and days postpartum. They were fed (2.7 kg dry matter (DM) per cow, twice-a-day) one of four isoenergetic and isonitrogenous barley grain-based concentrates containing NaCl at concentrations (% as-fed) of either 0 (SC1), 1.1 (SC2), 2.2 (SC3) or 3.3 (SC4). Maximum temperature humidity index (THImax) was greater than or equal to78 during 50% of the experimental period. Concentrate NaCl content had no effect (P>0.05) on daily milk yield or LW change but daily yields of 4% fat corrected milk (FCM), fat and protein were higher (P0.05) among treatments at 7.6+/-1.24 kg DM per cow. In study 2 (18 January 1999-1 March 1999), 48 cows (32 pluriparous, 16 primiparous: 32-160 days postpartum) were fed (2.7 kg DM per cow twice-a-day) one of two isoenergetic and isonitrogenous barley grain-based concentrates containing NaCl at concentrations (% as-fed) of 0 (control) or 2.2 (HSC). THImax was greater than or equal to78 during 34% of days in the experimental period. Yields of milk, FCM, fat and protein were lower (P0.05) by concentrate NaCl content. These studies indicate that NaCl supplementation can be beneficial in terms of milk production during warm, humid conditions as opposed to milder conditions. (C) 2002 Elsevier Science B.V. All rights reserved.

Engineering closure of an open pit gold operation in a semi-arid climate

Along with material characteristics and geometry, the climate in which a mine is located can have a dramatic effect on the appropriate options for rehabilitation. The paper outlines the setting, mining, milling and waste disposal at Kidston Gold Mine's open pit operations in the semi-arid climate of North Queensland, Australia, before focusing on the engineering aspects of the rehabilitation of Kidston. The mine took a holistic and proactive approach to rehabilitation, and was prepared to demonstrate a number of innovative approaches, which are described in the paper. Engineering issues that had to be addressed included the geotechnical stability and deformation of waste rock dumps, including a 240 m high in-pit dump: the construction and performance monitoring of a “store and release” cover over potentially acid forming mineralised waste rock; erosion from the side slopes of the waste rock dumps; the in-pit co-disposal of waste rock and thickened tailings; the geotechnical stability of the tailings dam wall; the potential for erosion of bare tailings; the water balance of the tailings dam; direct revegetation of the tailings; and the pit hydrology. The rehabilitation of the mine represents an important benchmark in mine site rehabilitation best practice, from which lessons applicable worldwide can be shared.

The E(NK) model: extending the NK model to incorporate gene-by-environment interactions and epistasis for diploid genomes

The haploid NK model developed by Kauffman can be extended to diploid genomes and to incorporate gene-by-environment interaction effects in combination with epistasis. To provide the flexibility to include a wide range of forms of gene-by-environment interactions, a target population of environment types (TPE) is defined. The TPE consists of a set of E different environment types, each with their own frequency of occurrence. Each environment type conditions a different NK gene network structure or series of gene effects for a given network structure, providing the framework for defining gene-by-environment interactions. Thus, different NK models can be partially or completely nested within the E environment types of a TPE, giving rise to the E(NK) model for a biological system. With this model it is possible to examine how populations of genotypes evolve in context with properties of the environment that influence the contributions of genes to the fitness values of genotypes. We are using the E(NK) model to investigate how both epistasis and gene-by-environment interactions influence the genetic improvement of quantitative traits by plant breeding strategies applied to agricultural systems. © 2002 Wiley Periodicals, Inc.

Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission

If open reading frames (ORFs) have been transmitted primarily by vertical descent, the distributional profile of orthologues of each ORF should be congruent with the organismal tree or a subtree thereof. Distributional patterns not reconciled parsimoniously with tree-like descent and loss are prima facie evidence of lateral gene transfer. Herein, a rigorous criterion for recognizing ORF distributions is described and implemented; it does not require the inference of phylogenetic trees, nor does it assume any specific tree. Because lineage-specific differences in rates of sequence change can also generate unexpected distributional patterns, rate artefacts, were controlled for by requiring pairwise matches between ORFs to exceed a rigorous inclusion threshold, but absence of a match was assessed against a more-permissive exclusion threshold. Applying this dual-threshold criterion to cross-domain and cross-phylum distributional patterns for ORFs in 23 bacterial genomes, a relative abundance of ORFs was observed that find a match in exactly seven other bacterial phyla; 94-99% of these ORFs also find matches among the Archaea and/or Eukarya. In the larger (and some smaller) bacterial genomes, ORFs that find matches in exactly one other bacterial phylum are also relatively abundant, but fewer of these have non-bacterial homologues; most of their matches within the Bacteria are to the Proteobacteria and/or Firmicutes, which cannot be sister lineages to all bacteria. ORFs that are neither distributed universally among the Bacteria, nor necessarily shared with topologically adjacent lineages, are preferentially enriched in large bacterial genomes.