Mitochondrial protein phylogeny joins myriapods with chelicerates

The animal phylum Arthropoda is very useful for the study of body plan evolution given its abundance of morphologically diverse species and our profound understanding of Drosophila development. However, there is a lack of consistently resolved phylogenetic relationships between the four extant arthropod subphyla, Hexapoda, Myriapoda, Chelicerata and Crustacea. Recent molecular studies have strongly supported a sister group relationship between Hexapoda and Crustacea, but have not resolved the phylogenetic position of Chelicerata and Myriapoda. Here we sequence the mitochondrial genome of the centipede species Lithobius forficatus and investigate its phylogenetic information content. Molecular phylogenetic analysis of conserved regions from the arthropod mitochondrial proteome yields highly resolved and congruent trees. We also find that a sister group relationship between Myriapoda and Chelicerata is strongly supported. We propose a model to explain the apparently parallel evolution of similar head morphologies in insects and myriapods.     

Identifiability of Finite Mixtures of Multinomial Logit Models with Varying and Fixed Effects

Unique parametrizations of models are very important for parameter interpretation and consistency of estimators. In this paper we analyze the identifiability of a general class of finite mixtures of multinomial logits with varying and fixed effects, which includes the popular multinomial logit and conditional logit models. The application of the general identifiability conditions is demonstrated on several important special cases and relations to previously established results are discussed. The main results are illustrated with a simulation study using artificial data and a marketing dataset of brand choices.     

Computer modeling of high-pressure leaching process of nickel laterite by design of experiments and neural networks

Due to the complex chemical composition of nickel ores, the requests for the decrease of production costs, and the increase of nickel extraction in the existing depletion of high-grade sulfide ores around the world, computer modeling of nickel ore leaching process became a need and a challenge. In this paper, the design of experiments (DOE) theory was used to determine the optimal experimental design plan matrix based on the D optimality criterion. In the high-pressure sulfuric acid leaching (HPSAL) process for nickel laterite in "Rudjinci" ore in Serbia, the temperature, the sulfuric acid to ore ratio, the stirring speed, and the leaching time as the predictor variables, and the degree of nickel extraction as the response have been considered. To model the process, the multiple linear regression (MLR) and response surface method (RSM), together with the two-level and four-factor full factorial central composite design (CCD) plan, were used. The proposed regression models have not been proven adequate. Therefore, the artificial neural network (ANN) approach with the same experimental plan was used in order to reduce operational costs, give a better modeling accuracy, and provide a more successful process optimization. The model is based on the multi-layer neural networks with the back-propagation (BP) learning algorithm and the bipolar sigmoid activation function.     

Primary structure and functional expression from complementary DNA of a brain calcium channel.

The primary structure of a voltage-dependent calcium channel from rabbit brain has been deduced by cloning and sequencing the complementary DNA. Calcium channel activity expressed from the cDNA is dramatically increased by coexpression of the alpha 2 and beta subunits, known to be associated with the dihydropyridine receptor. This channel is a high voltage-activated calcium channel that is insensitive both to nifedipine and to omega-conotoxin. We suggest that it is expressed predominantly in cerebellar Purkinje cells and granule cells.     

An anaerobic mitochondrion that produces hydrogen

Hydrogenosomes are organelles that produce ATP and hydrogen, and are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Although all of these organelles generate hydrogen, the hydrogenosomes from these organisms are structurally and metabolically quite different, just like mitochondria where large differences also exist. These differences have led to a continuing debate about the evolutionary origin of hydrogenosomes. Here we show that the hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis, which thrives in the hindgut of cockroaches, have retained a rudimentary genome encoding components of a mitochondrial electron transport chain. Phylogenetic analyses reveal that those proteins cluster with their homologues from aerobic ciliates. In addition, several nucleus-encoded components of the mitochondrial proteome, such as pyruvate dehydrogenase and complex II, were identified. The N. ovalis hydrogenosome is sensitive to inhibitors of mitochondrial complex I and produces succinate as a major metabolic end product--biochemical traits typical of anaerobic mitochondria. The production of hydrogen, together with the presence of a genome encoding respiratory chain components, and biochemical features characteristic of anaerobic mitochondria, identify the N. ovalis organelle as a missing link between mitochondria and hydrogenosomes.     

The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre

Hydrogenases are abundant enzymes that catalyse the reversible interconversion of H(2) into protons and electrons at high rates. Those hydrogenases maintaining their activity in the presence of O(2) are considered to be central to H(2)-based technologies, such as enzymatic fuel cells and for light-driven H(2) production. Despite comprehensive genetic, biochemical, electrochemical and spectroscopic investigations, the molecular background allowing a structural interpretation of how the catalytic centre is protected from irreversible inactivation by O(2) has remained unclear. Here we present the crystal structure of an O(2)-tolerant [NiFe]-hydrogenase from the aerobic H(2) oxidizer Ralstonia eutropha H16 at 1.5?? resolution. The heterodimeric enzyme consists of a large subunit harbouring the catalytic centre in the H(2)-reduced state and a small subunit containing an electron relay consisting of three different iron-sulphur clusters. The cluster proximal to the active site displays an unprecedented [4Fe-3S] structure and is coordinated by six cysteines. According to the current model, this cofactor operates as an electronic switch depending on the nature of the gas molecule approaching the active site. It serves as an electron acceptor in the course of H(2) oxidation and as an electron-delivering device upon O(2) attack at the active site. This dual function is supported by the capability of the novel iron-sulphur cluster to adopt three redox states at physiological redox potentials. The second structural feature is a network of extended water cavities that may act as a channel facilitating the removal of water produced at the [NiFe] active site. These discoveries will have an impact on the design of biological and chemical H(2)-converting catalysts that are capable of cycling H(2) in air.     

Use of ionic liquid in leaching process of brass wastes for copper and zinc recovery

Brass ash from the industrial brass manufacturer in Turkey was leached using the solutions of ionic liquid (IL) 1-butyl-3-methyl-imidazolium hydrogen sulfate ([bmim]HSO₄) at ambient pressure in the presence of hydrogen peroxide (H₂O₂) and potassium peroxymonosulfate (oxone) as the oxidants. Parameters affecting leaching efficiency, such as dissolution time, IL concentration, and oxidizing agent addition, were investigated. The results show that [bmim]HSO₄ is an efficient IL for the brass ash leaching, providing the dissolution efficiencies of 99% for Zn and 24.82% for Cu at a concentration of 50vol% [bmim]HSO₄ in the aqueous solution without any oxidant. However, more than 99% of zinc and 82% of copper are leached by the addition of 50vol% H₂O₂ to the [bmim]HSO₄ solution. Nevertheless, the oxone does not show the promising oxidant behavior in leaching using [bmim]HSO₄.     

A conspicuous nickel protein in microbial mats that oxidize methane anaerobically

Anaerobic oxidation of methane (AOM) in marine sediments is an important microbial process in the global carbon cycle and in control of greenhouse gas emission. The responsible organisms supposedly reverse the reactions of methanogenesis, but cultures providing biochemical proof of this have not been isolated. Here we searched for AOM-associated cell components in microbial mats from anoxic methane seeps in the Black Sea. These mats catalyse AOM rather than carry out methanogenesis. We extracted a prominent nickel compound displaying the same absorption spectrum as the nickel cofactor F430 of methyl-coenzyme M reductase, the terminal enzyme of methanogenesis; however, the nickel compound exhibited a higher molecular mass than F430. The apparent variant of F(430) was part of an abundant protein that was purified from the mat and that consists of three different subunits. Determined amino-terminal amino acid sequences matched a gene locus cloned from the mat. Sequence analyses revealed similarities to methyl-coenzyme M reductase from methanogenic archaea. The abundance of the nickel protein (7% of extracted proteins) in the mat suggests an important role in AOM.