Suppression and overexpression of adenosylhomocysteine hydrolase-like protein 1 (AHCYL1) influences zebrafish embryo development A - Possible role for AHCYL1 in inositol phospholipid signaling

Adenosylhomocysteine hydrolase-like protein 1 (AHCYL1) is a novel intracellular protein with similar to 50% protein identity to adenosyl homocysteine hydrolase (AHCY), an important enzyme for metabolizing S-adenosyl-L-homocysteine, the by-product of S-adenosyl-L-homomethionine-dependent methylation. AHCYL1 binds to the inositol 1,4,5-trisphosphate receptor, suggesting that AHCYL1 is involved in intracellular calcium release. We identified two zebrafish AHCYL1 orthologs(zAHCYL1A and -B) by bioinformatics and reverse transcription-PCR. Unlike the ubiquitously present AHCY genes, AHCYL1 genes were only detected in segmented animals, and AHCYL1 proteins were highly conserved among species. Phylogenic analysis suggested that the AHCYL1 gene diverged early from AHCY and evolved independently. Quantitative reverse transcription-PCR showed that zAHCYL1A and -B mRNA expression was regulated differently from the other AHCY-like protein zAHCYL2 and zAHCY during zebrafish embryogenesis. Injection of morpholino antisense oligonucleotides against zAHCYL1A and -B into zebrafish embryos inhibited zAHCYL1A and -B mRNA translation specifically and induced ventralized morphologies. Conversely, human and zebrafish AHCYL1A mRNA injection into zebrafish embryos induced dorsalized morphologies that were similar to those obtained by depleting intracellular calcium with thapsigargin. Human AHCY mRNA injection showed little effect on the embryos. These data suggest that AHCYL1 has a different function from AHCY and plays an important role in embryogenesis by modulating inositol 1,4,5-trisphosphate receptor function for the intracellular calcium release.

Efficient accommodation of local minima in watershed model calibration

The Gauss-Marquardt-Levenberg (GML) method of computer-based parameter estimation, in common with other gradient-based approaches, suffers from the drawback that it may become trapped in local objective function minima, and thus report optimized parameter values that are not, in fact, optimized at all. This can seriously degrade its utility in the calibration of watershed models where local optima abound. Nevertheless, the method also has advantages, chief among these being its model-run efficiency, and its ability to report useful information on parameter sensitivities and covariances as a by-product of its use. It is also easily adapted to maintain this efficiency in the face of potential numerical problems (that adversely affect all parameter estimation methodologies) caused by parameter insensitivity and/or parameter correlation. The present paper presents two algorithmic enhancements to the GML method that retain its strengths, but which overcome its weaknesses in the face of local optima. Using the first of these methods an intelligent search for better parameter sets is conducted in parameter subspaces of decreasing dimensionality when progress of the parameter estimation process is slowed either by numerical instability incurred through problem ill-posedness, or when a local objective function minimum is encountered. The second methodology minimizes the chance of successive GML parameter estimation runs finding the same objective function minimum by starting successive runs at points that are maximally removed from previous parameter trajectories. As well as enhancing the ability of a GML-based method to find the global objective function minimum, the latter technique can also be used to find the locations of many non-global optima (should they exist) in parameter space. This can provide a useful means of inquiring into the well-posedness of a parameter estimation problem, and for detecting the presence of bimodal parameter and predictive probability distributions. The new methodologies are demonstrated by calibrating a Hydrological Simulation Program-FORTRAN (HSPF) model against a time series of daily flows. Comparison with the SCE-UA method in this calibration context demonstrates a high level of comparative model run efficiency for the new method. (c) 2006 Elsevier B.V. All rights reserved.

The cost of uniqueness in groundwater model calibration

Calibration of a groundwater model requires that hydraulic properties be estimated throughout a model domain. This generally constitutes an underdetermined inverse problem, for which a Solution can only be found when some kind of regularization device is included in the inversion process. Inclusion of regularization in the calibration process can be implicit, for example through the use of zones of constant parameter value, or explicit, for example through solution of a constrained minimization problem in which parameters are made to respect preferred values, or preferred relationships, to the degree necessary for a unique solution to be obtained. The cost of uniqueness is this: no matter which regularization methodology is employed, the inevitable consequence of its use is a loss of detail in the calibrated field. This, ill turn, can lead to erroneous predictions made by a model that is ostensibly well calibrated. Information made available as a by-product of the regularized inversion process allows the reasons for this loss of detail to be better understood. In particular, it is easily demonstrated that the estimated value for an hydraulic property at any point within a model domain is, in fact, a weighted average of the true hydraulic property over a much larger area. This averaging process causes loss of resolution in the estimated field. Where hydraulic conductivity is the hydraulic property being estimated, high averaging weights exist in areas that are strategically disposed with respect to measurement wells, while other areas may contribute very little to the estimated hydraulic conductivity at any point within the model domain, this possibly making the detection of hydraulic conductivity anomalies in these latter areas almost impossible. A study of the post-calibration parameter field covariance matrix allows further insights into the loss of system detail incurred through the calibration process to be gained. A comparison of pre- and post-calibration parameter covariance matrices shows that the latter often possess a much smaller spectral bandwidth than the former. It is also demonstrated that, as all inevitable consequence of the fact that a calibrated model cannot replicate every detail of the true system, model-to-measurement residuals can show a high degree of spatial correlation, a fact which must be taken into account when assessing these residuals either qualitatively, or quantitatively in the exploration of model predictive uncertainty. These principles are demonstrated using a synthetic case in which spatial parameter definition is based oil pilot points, and calibration is Implemented using both zones of piecewise constancy and constrained minimization regularization. (C) 2005 Elsevier Ltd. All rights reserved.

Optimum coal properties and engineering processes for CO2 geosequestration in Coal

CO2 Geosequestration is seen by many worldwide scientists and engineers as a leading prospective solution to the global warming problem arising from excessive CO2 and other greenhouse gas emissions. CO2 geosequestration in coal seams has two important strategic benefits: the process has an extremely low risk of leakage, due to the adsorbed state of the CO2 and the known reservoir context of essentially-zero leakage into which it is be injected; the second benefit arises from the valuable by-product, clean burning coalbed methane gas. This paper presents the authors’ experience, knowledge and perspective on what coal properties and engineering processes would favour implementing a demonstration or commercial CO2 storage-in-coal project, in Queensland, Australia. As such, it may be considered a template for screening studies to select the optimum coal seam reservoir, and for preliminary studies in designing the injection system and predicting production response to the technology. The paper concludes by examining the current knowledge gaps of CO2 geosequestration in coal, identifying further basic and applied research topics.

Practical and economic advantages of choice feeding systems for laying poultry

Poultry can be managed under different feeding systems, depending on the husbandry skills and the feed available. These systems include the following: (1) a complete dry feed offered as a mash ad libitum; (2) the same feed offered as pellets or crumbles ad libitum; (3) a complete feed with added whole grain; (4) a complete wet feed given once or twice a day; (5) a complete feed offered on a restricted basis; (6) choice feeding. Of all these, an interesting alternative to offering complete diets is choice feeding which can be applied on both a small or large commercial scale. Under choice feeding or free-choice feeding birds are usually offered a choice between three types of feedstuffs: (a) an energy source (e.g. maize, rice bran, sorghum or wheat); (b) a protein source (e.g. soyabean meal, meat meal, fish meal or coconut meal) plus vitamins and minerals and (c), in the case of laying hens, calcium in granular form (i.e. oyster-shell grit). This system differs from the modern commercial practice of offering a complete diet comprising energy and protein sources, ground and mixed together. Under the complete diet system, birds are mainly only able to exercise their appetite for energy. When the environmental temperature varies, the birds either over- or under-consume protein and calcium. The basic principle behind practising choice feeding with laying hens is that individual hens are able to select from the various feed ingredients on offer and compose their own diet, according to their actual needs and production capacity. A choice-feeding system is of particular importance to small poultry producers in developing countries, such as Indonesia, because it can substantially reduce the cost of feed. The system is flexible and can be constructed in such a way that the various needs of a flock of different breeds, including village chickens, under different climates can be met. The system also offers a more effective way to use home-produced grain, such as maize, and by-products, such as rice bran, in developing countries. Because oyster-shell grit is readily available in developing countries at lower cost than limestone, the use of cheaper oyster-shell grit can further benefit small-holders in these countries. These benefits apart, simpler equipment suffices when designing and building a feed mixer on the farm, and transport costs are lower. If whole (unground) grain is used, the intake of which is accompanied by increased efficiency of feed utilisation, the costs of grinding, mixing and many of the handling procedures associated with mash and pellet preparation are eliminated. The choice feedstuffs can all be offered in the current feed distribution systems, either by mixing the ingredients first or by using a bulk bin divided into three compartments.

Total and phytate-phosphorus contents and phytase activity of Australian-sourced feed ingredients for pigs and poultry

A total of 160 samples of 20 Australian-sourced feed ingredients of plant origin for pigs and poultry was analysed for total phosphorus and phytate-phosphorus contents and endogenous phytase activity. The majority of total P was present as phytate-phosphorus, and these concentrations were significantly correlated in 9 feed ingredients. The endogenous phytase activity in tested feed ingredients was negligible other than for wheat, its by-products and barley. Phytate-phosphorus was determined by a standard 'ferric chloride precipitation' method, which was satisfactory for individual feed ingredients, with the exception of lupins and faba beans. It appears that phytate is more difficult to extract from these two feedstuffs, possibly because of the affinity of phytate for protein. Ferric chloride precipitation methods are not suitable for phytate-phosphorus determinations of complete feed samples containing other sources of phosphorus, which is a distinct limitation. A lesser limitation is that these methods cannot distinguish between the various esters of myo-inositol phosphate present. Given the variation of phytate contents within ingredients, particularly wheat, the desirability of determining dietary substrate levels is emphasised to take full advantage of including exogenous phytases in pig and poultry diets to reduce phosphorus excretion and abate phosphorus pollution.

Application of nox-restriction fragment length polymorphism for the differentiation of Brachyspira intestinal spirochetes isolated from pigs and poultry in Australia

Sixty-nine intestinal spirochetes isolated from pigs and poultry in eastern Australia were selected to evaluate the effectiveness of a species-specific PCR-based restriction fragment length polymorphism (RFLP) analysis of the Brachyspira nox gene. For comparative purposes, all isolates were subjected to species-specific PCRs for the pathogenic species Brachyspira hyodysenteriae and Brachyspira pilosicoli, and selected isolates were examined further by sequence analysis of the nox and 16S ribosomal RNA genes. Modifications to the original nox-RFLP method included direct inoculation of bacterial cells into the amplification mixture and purification of the PCR product, which further optimized the nox-RFLP for use in a veterinary diagnostic laboratory, producing sufficient product for both species identification and future comparisons. Although some novel profiles that prevented definitive identification were observed, the nox-RFLP method successfully classified 45 of 51 (88%) porcine and 15 of 18 (83%) avian isolates into 5 of the 6 recognized species of Brachyspira. This protocol represents a significant improvement over conventional methods currently used in veterinary diagnostic laboratories for rapid specific identification of Brachyspira spp. isolated from both pigs and poultry.

Matching poultry production with available feed resources: issues and constraints

Corn and soyabeans may not be available in many countries particularly those which do not have sufficient foreign currency or the capacity to grow them. This paper outlines strategies that may be important under these circumstances. Alternative feedstuffs and various feeding systems may be used to support poultry production. Alternative ingredients such as rice bran, pearl millet, cottonseed meal and grain legumes are discussed. Evidence is presented showing that amino acid requirements of layers and broilers may be too generous particularly in countries where climate, management and disease can impose production constraints. The ability of finishing broilers to perform well on very low-energy diets allows the inclusion of alternative feeds and by-products into formulations. Very low protein diets based on cereals and free amino acids can be used for layers without loss of performance. Self-selection of feedstuffs may be an important strategy in reducing feed costs of broilers and layers. The concept of matching production with available feed resources may compromise broiler growth and egg production, but in many countries this may be the most economical choice. Countries in the humid tropics usually have reduced poultry performance. The effects of high temperature and humidity are difficult to overcome. The vexed questions of the escalation in the price of fossil fuel and the outbreak of avian influenza, both seemingly without a solution, are clouds hanging over an otherwise buoyant industry.

Quantum symmetries and the Weyl–Wigner product of group representations

In the usual formulation of quantum mechanics, groups of automorphisms of quantum states have ray representations by unitary and antiunitary operators on complex Hilbert space, in accordance with Wigner's theorem. In the phase-space formulation, they have real, true unitary representations in the space of square-integrable functions on phase space. Each such phase-space representation is a Weyl–Wigner product of the corresponding Hilbert space representation with its contragredient, and these can be recovered by 'factorizing' the Weyl–Wigner product. However, not every real, unitary representation on phase space corresponds to a group of automorphisms, so not every such representation is in the form of a Weyl–Wigner product and can be factorized. The conditions under which this is possible are examined. Examples are presented.

Pilot-scale extraction of PHB from recombinant E-coli by homogenization and centrifugation

A new method of poly-beta-hydroxybutyrate (PHB) extraction from recombinant E. coli is proposed, using homogenization and centrifugation coupled with sodium hypochlorite treatment. The size of PHB granules and cell debris in homogenates was characterised as a function of the number of homogenization passes. Simulation was used to develop the PHB and cell debris fractionation system, enabling numerical examination of the effects of repeated homogenization and centrifuge-feedrate variation. The simulation provided a good prediction of experimental performance. Sodium hypochlorite treatment was necessary to optimise PHB fractionation. A PHB recovery of 80% at a purity of 96.5% was obtained with the final optimised process. Protein and DNA contained in the resultant product were negligible. The developed process holds promise for significantly reducing the recovery cost associated with PHB manufacture.

Murine DEP-1, a receptor protein tyrosine phosphatase, is expressed in macrophages and is regulated by CSF-1 and LPS

The spectrum of protein tyrosine phosphatases (PTPs) expressed in bone marrow-derived murine macrophages (BMMs) was examined using reverse transcriptase-polymerase chain reaction. Ten different PTP cDNAs were isolated and in this study we focus on mDEP-1, a type III receptor PTP. Three mDEP-1 transcripts were expressed in primary macrophages and macrophage cell lines and were induced during macrophage differentiation of M1 myeloid leukemia cells. A valiant mRNA Tvas identified that encodes an alternate carboxyl-terminus and 3' UTR. The expression of mDEP-1 was down-regulated by CSF-1 (macrophage colony-stimulating factor) and up-regulated by bacterial lipopolysaccharide, an important physiological regulator of macrophage function that opposes CSF-1 action. Whole mount irt situ hybridization, and immunolocalization of the protein, confirmed that mDEP-1 is expressed by a subset of embryonic macrophages in the liver and mesenchyme. mDEP-1 was also detected in the eye and peripheral nervous system of the developing embryo. Attempts to express mDEP-1 constitutively in the macrophage cell line RAW264 were unsuccessful, with results suggesting that the gene product inhibits cell proliferation.

The solution structure of a copper(II) compound of a new cyclic octapeptide by EPR spectroscopy and force field calculations

A new cyclic octapeptide, cyclo(Ile-Ser-(Gly)Thz-Ile-Thr-(Gly)Thz) (PatN), related to patellamide A, has been synthesized and reacted with copper(II) and base to form mono- and dinuclear complexes. The coordination environments around copper(TI) have been characterized by EPR spectroscopy. The solution structure of the thermodynamically most stable product, a purple dicopper(TI) compound, has been examined by simulating weakly dipole-dipole coupled EPR spectra based upon structural parameters obtained from force field (MM and MD) calculations. The MM-EPR method produces a saddle-shaped structure for [Cu-2(PatN)(OH2)(6)] that is similar to the known solution structure of patellamide A and the known solid-state structure of [Cu-2(AscidH(2))CO3(OH2)(2)]. Compared with the latter, [Cu-2(PatN)] has no carbonate bridge and a significantly flatter topology. The MM-EPR approach to solution-structure determination for paramagnetic metallopeptides may find wide applications to other metallopeptides and metalloproteins.

Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease

High-resolution crystal structures are described for seven macrocycles complexed with HIV-1 protease (HIVPR). The macrocycles possess two amides and an aromatic group within 15-17 membered rings designed to replace N- or C-terminal tripeptides from peptidic inhibitors of HIVPR. Appended to each macrocycle is a transition state isostere and either an acyclic peptide, nonpeptide, or another macrocycle. These cyclic analogues are potent inhibitors of HIVPR, and the crystal structures show them to be structural mimics of acyclic peptides, binding in the active site of HIVPR via the same interactions. Each macrocycle is restrained to adopt a P-strand conformation which is preorganized for protease binding. An unusual feature of the binding of C-terminal macrocyclic inhibitors is the interaction between a positively charged secondary amine and a catalytic aspartate of HIVPR. A bicyclic inhibitor binds similarly through its secondary amine that lies between its component N-terminal and C-terminal macrocycles. In contrast, the corresponding tertiary amine of the N-terminal macrocycles does not interact with the catalytic aspartates. The amine-aspartate interaction induces a 1.5 Angstrom N-terminal translation of the inhibitors in the active site and is accompanied by weakened interactions with a water molecule that bridges the ligand to the enzyme, as well as static disorder in enzyme flap residues. This flexibility may facilitate peptide cleavage and product dissociation during catalysis. Proteases [Aba(67,95)]HIVPR and [Lys(7),Ile(33),Aba(67,95)]- HIVPR used in this work were shown to have very similar crystal structures.