Preliminary approach to neutron instrument selecction at ESSB-Bilbao based on experience at ISIS molecular spectroscopy group

Collaborative efforts between the Neutronics and Target Design Group at the Instituto de Fusión Nuclear and the Molecular Spectroscopy Group at the ISIS Pulsed Neutron and Muon Source date back to 2012 in the context of the ESS-Bilbao project. The rationale for these joint activities was twofold, namely: to assess the realm of applicability of the low-energy neutron source proposed by ESS-Bilbao - for details; and to explore instrument capabilities for pulsed-neutron techniques in the range 0.05-3 ms, a time range where ESS-Bilbao and ISIS could offer a significant degree of synergy and complementarity. As part of this collaboration, J.P. de Vicente has spent a three-month period within the ISIS Molecular Spectroscopy Group, to gain hands-on experience on the practical aspects of neutron-instrument design and the requisite neutron-transport simulations. To date, these activities have resulted in a joint MEng thesis as well as a number of publications and contributions to national and international conferences. Building upon these previous works, the primary aim of this report is to provide a self-contained discussion of general criteria for instrument selection at ESS-Bilbao, the first accelerator-driven, low-energy neutron source designed in Spain. To this end, Chapter 1 provides a brief overview of the current design parameters of the accelerator and target station. Neutron moderation is covered in Chapter 2, where we take a closer look at two possible target-moderator-reflector configurations and pay special attention to the spectral and temporal characteristics of the resulting neutron pulses. This discussion provides a necessary starting point to assess the operation of ESSB in short- and long-pulse modes. These considerations are further explored in Chapter 3, dealing with the primary characteristics of ESS-Bilbao as a short- or long-pulse facility in terms of accessible dynamic range and spectral resolution. Other practical aspects including background suppression and the use of fast choppers are also discussed. The guiding principles introduced in the first three chapters are put to use in Chapter 4 where we analyse in some detail the capabilities of a small-angle scattering instrument, as well as how specific scientific requirements can be mapped onto the optimal use of ESS-Bilbao for condensed-matter research. Part 2 of the report contains additional supporting documentation, including a description of the ESSB McStas component, a detailed characterisation of moderator response and neutron pulses, and estimates ofparameters associated with the design and operation of neutron choppers. In closing this brief foreword, we wish to thank both ESS-Bilbao and ISIS for their continuing encouragement and support along the way.

Biodiversidad de frijol (Phaseolus vulgaris L.) en Honduras. Caracterización agromorfológica, molecular y ecogeográfica

En el presente trabajo se ha llevado a cabo un estudio de la biodiversidad del frijol común (Phaseolus vulgaris L.) en Honduras, que es el segundo de los cultivos de granos básicos en importancia. Dicho estudio se ha realizado mediante una caracterización agromorfológica, molecular y ecogeográfica en una selección de 300 accesiones conservadas en el banco de germoplasma ubicado en la Escuela Agrícola Panamericana (EAP) El Zamorano, y que se colectaron en 13 departamentos del país durante el periodo de 1990 a 1994. Estas accesiones fueron colectadas cuatro años antes del acontecimiento del huracán Mitch, el cual a su paso afectó al 96% del área total cultivable en su momento, lo cual nos hace considerar que la biodiversidad de razas locales (landraces) de frijol común existentes in situ fueron severamente afectadas. Los trabajos dirigidos a analizar la biodiversidad de razas locales de frijol común en Honduras son escasos, y este trabajo se constituye como el primero que incluye una amplia muestra a ser estudiada a través de una caracterización en tres aspectos complementarios (agromorfológico, molecular y ecogeográfico). Se evaluaron 32 caracteres agromorfológicos, 12 cuantitativos y 20 cualitativos, en distintas partes de la planta. Se establecieron las correlaciones entre los caracteres agromorfológicos y se elaboró un dendrograma con los mismos, en el que se formaron ocho grupos, en parte relacionados principalmente con los colores y tamaños de la semilla. Mediante el análisis de componentes principales se estudiaron los caracteres de más peso en cada uno de los tres primeros componentes. Asimismo, se estudiaron las correlaciones entre caracteres, siendo las más altas la longitud y anchura de la hoja, días a madurez y a cosecha y longitud y peso de semilla. Por otra parte, el mapa de diversidad agromorfológica mostró la existencia de tres zonas con mayor diversidad: en el oeste (en los departamentos de Santa Bárbara, Lempira y Copán), en el centro-norte (en los departamentos de Francisco Morazán, Yoro y Atlántida) y en el sur (en el departamento de El Paraíso y al sur de Francisco Morazán). Para la caracterización molecular partimos de 12 marcadores de tipo microsatélite, evaluados en 54 accesiones, que fueron elegidas por constituir grupos que compartían un mismo nombre local. Finalmente, se seleccionaron los cuatro microsatélites (BM53, GATS91, BM211 y PV-AT007) que resultaron ser más polimórficos e informativos para el análisis de las 300 accesiones, con los que se detectaron un total de 119 alelos (21 de ellos únicos o privados de accesión) y 256 patrones alélicos diferentes. Para estudiar la estructura y relaciones genéticas en las 300 accesiones se incluyeron en el análisis tres controles o accesiones de referencia, pertenecientes dos de ellas al acervo genético Andino y una al Mesoamericano. En el dendrograma se obtuvieron 25 grupos de accesiones con idénticas combinaciones de alelos. Al comparar este dendrograma con el de caracteres agromorfológicos se observaron diversos grupos con marcada similitud en ambos. Un total de 118 accesiones resultaron ser homogéneas y homocigóticas, a la vez que representativas del grupo de 300 accesiones, por lo que se analizaron con más detalle. El análisis de la estructura genética definió la formación de dos grupos, supuestamente relacionados con los acervos genéticos Andino (48) y Mesoamericano (61), y un reducido número de accesiones (9) que podrían tener un origen híbrido, debido a la existencia de un cierto grado de introgresión entre ambos acervos. La diferenciación genética entre ambos grupos fue del 13,3%. Asimismo, 66 de los 82 alelos detectados fueron privados de grupo, 30 del supuesto grupo Andino y 36 del Mesoamericano. Con relación al mapa de diversidad molecular, presentó una distribución bastante similar al de la diversidad agromorfológica, detectándose también las zonas de mayor diversidad genética en el oeste (en los departamentos de Lempira y Santa Bárbara), en el centro-norte (en los departamentos de Yoro y Atlántida) y en el sur (en el departamento de El Paraíso y al sur de Francisco Morazán). Para la caracterización ecogeográfica se seleccionaron variables de tipo bioclimático (2), geofísico (2) y edáfico (8), y mediante el método de agrupamiento de partición alrededor de los medoides, la combinación de los grupos con cada uno de los tres tipos de variables definió un total de 32 categorías ecogeográficas en el país, detectándose accesiones en 16 de ellas. La distribución de las accesiones previsiblemente esté relacionada con la existencia de condiciones más favorables al cultivo de frijol. En el mapa de diversidad ecogeográfica, nuevamente, se observaron varias zonas con alta diversidad tanto en el oeste, como en el centro-norte y en el sur del país. Como consecuencia del estudio realizado, se concluyó la existencia de una marcada biodiversidad en el material analizado, desde el punto de vista tanto agromorfológico como molecular. Por lo que resulta de gran importancia plantear la conservación de este patrimonio genético tanto ex situ, en bancos de germoplasma, como on farm, en las propias explotaciones de los agricultores del país, siempre que sea posible. ABSTRACT In the present work we have carried out a study of the biodiversity of the common bean (Phaseolus vulgaris L) in Honduras, which is the second of the basic grain crops in importance. This study was conducted through agro-morphological, molecular and ecogeographical characterization of a selection of 300 accessions conserved in the genebank located in the ‘Escuela Agrícola Panamericana (EAP) El Zamorano’ that were collected in 13 departments of the country during the 1990 to 1994 period. These accessions were collected four years before the occurrence of Mitch hurricane, which affected 96% of the total cultivable area at the time, which makes us to consider that the biodiversity of local landraces of common bean existing in situ were severely affected. The work aimed to analyze the biodiversity of local races of common bean in Honduras are scarce, and this work constitutes the first to include a large sample to be studied through a characterization on three complementary aspects (agromorphological, molecular and ecogeographical). Thirty two agromorphological characters, 12 quantitative and 20 qualitative, in various parts of the plant were evaluated. Correlations between agromorphological characters were established and a dendrogram with them was constructed, in which eight groups were formed, in part mainly related to the colors and sizes of the seeds. By principal component analysis the characters with more weight in each of the first three components were studied. Also, correlations between characters were studied, the highest of them being length and leaf width, days to maturity and harvest, and seed length and weight. Moreover, the map of agromorphological diversity showed the existence of three areas with more diversity: the west (departments of Santa Barbara, Copan and Lempira), the center-north (departments of Francisco Morazán, Yoro and Atlántida) and the south (department of El Paraiso and south of Francisco Morazán). For molecular characterization we started with 12 microsatellite markers, evaluated in 54 accessions, which were chosen because they formed groups that shared the same local name. Finally, four microsatellites (BM53, GATS91, BM211 and PV-AT007) were selected for the analysis of 300 accessions, since they were the most polymorphic and informative. They gave a total of 119 alleles (21 of them unique or private for the accession) and 256 different allelic patterns. To study the structure and genetic relationships in the 300 accessions, three controls or accessions of reference were included in the analysis: two of them belonging to the Andean gene pool and one to the Mesoamerican. In the dendrogram, 25 accession groups with identical allele combinations were obtained. Comparing this dendrogram to the obtained with agromorphological characters, several groups with marked similarity in both were observed. A total of 118 accessions were homozygous and homogeneous, while representing the group of 300 accessions, therefore they were analyzed in more detail. The analysis of the genetic structure defined the formation of two groups, supposedly related to the Andean (48) and the Mesoamerican (61) gene pools, and a small number of accessions (9) which may have a hybrid origin, due to the existence of some degree of introgression between both gene pools. Genetic differentiation between both groups was 13.3%. Also, 66 of the 82 detected alleles were private or unique for the group, 30 of the supposed Andean group and 36 of the Mesoamerican. With relation to the map of molecular diversity, it showed a quite similar distribution to the agromorphological, also detecting the areas of greatest genetic diversity in the west (departments of Lempira and Santa Bárbara), in the center-north (departments Atlántida and Yoro) and in the south (departments of El Paraíso and south of Francisco Morazán). For the ecogeographical characterization, bioclimatic (2), geophysical (2) and edaphic (8) variables were selected, and by the method of clustering partition around the medoids, the combination of the groups to each of the three types of variables defined a total of 32 ecogeographical categories in the country, having accessions in 16 of them. The distribution of accessions is likely related to the existence of more favorable conditions for the cultivation of beans. The map of ecogeographical diversity, again, several areas with high diversity both in the west and in the center-north and in the south of the country were observed. As a result of study, the existence of marked biodiversity in the analyzed material was concluded, both from the agromorphological and from the molecular point of view. Consequently it is very important to propose the conservation of this genetic heritage both ex situ, in genebanks, as on farm, in the holdings of the farmers of the country, whenever possible.

Molecular evidence for multiple origins of woodiness and a New World biogeographic connection of the Macaronesian Island endemic Pericallis (Asteraceae: Senecioneae)

The prevalence of woody species in oceanic islands has attracted the attention of evolutionary biologists for more than a century. We used a phylogeny based on sequences of the internal-transcribed spacer region of nuclear ribosomal DNA to trace the evolution of woodiness in Pericallis (Asteraceae: Senecioneae), a genus endemic to the Macaronesian archipelagos of the Azores, Madeira, and Canaries. Our results show that woodiness in Pericallis originated independently at least twice in these islands, further weakening some previous hypotheses concerning the value of this character for tracing the continental ancestry of island endemics. The same data suggest that the origin of woodiness is correlated with ecological shifts from open to species-rich habitats and that the ancestor of Pericallis was an herbaceous species adapted to marginal habitats of the laurel forest. Our results also support Pericallis as closely related to New World genera of the tribe Senecioneae.

The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus

Molecular differentiation between races or closely related species is often incongruent with the reproductive divergence of the taxa of interest. Shared ancient polymorphism and/or introgression during secondary contact may be responsible for the incongruence. At loci contributing to speciation, these two complications should be minimized (1, 2); hence, their variation may more faithfully reflect the history of the species' reproductive differentiation. In this study, we analyzed DNA polymorphism at the Odysseus (OdsH) locus of hybrid sterility between Drosophila mauritiana and Drosophila simulans and were able to verify such a prediction. Interestingly, DNA variation only a short distance away (1.8 kb) appears not to be influenced by the forces that shape the recent evolution of the OdsH coding region. This locus thus may represent a test case of inferring phylogeny of very closely related species.

Molecular phylogenetic analysis of evolutionary trends in stonefly wing structure and locomotor behavior

Insects in the order Plecoptera (stoneflies) use a form of two-dimensional aerodynamic locomotion called surface skimming to move across water surfaces. Because their weight is supported by water, skimmers can achieve effective aerodynamic locomotion even with small wings and weak flight muscles. These mechanical features stimulated the hypothesis that surface skimming may have been an intermediate stage in the evolution of insect flight, which has perhaps been retained in certain modern stoneflies. Here we present a phylogeny of Plecoptera based on nucleotide sequence data from the small subunit rRNA (18S) gene. By mapping locomotor behavior and wing structural data onto the phylogeny, we distinguish between the competing hypotheses that skimming is a retained ancestral trait or, alternatively, a relatively recent loss of flight. Our results show that basal stoneflies are surface skimmers, and that various forms of surface skimming are distributed widely across the plecopteran phylogeny. Stonefly wings show evolutionary trends in the number of cross veins and the thickness of the cuticle of the longitudinal veins that are consistent with elaboration and diversification of flight-related traits. These data support the hypothesis that the first stoneflies were surface skimmers, and that wing structures important for aerial flight have become elaborated and more diverse during the radiation of modern stoneflies.

Phylogeny of genes for secretion NTPases: Identification of the widespread tadA subfamily and development of a diagnostic key for gene classification

Macromolecular transport systems in bacteria currently are classified by function and sequence comparisons into five basic types. In this classification system, type II and type IV secretion systems both possess members of a superfamily of genes for putative NTP hydrolase (NTPase) proteins that are strikingly similar in structure, function, and sequence. These include VirB11, TrbB, TraG, GspE, PilB, PilT, and ComG1. The predicted protein product of tadA, a recently discovered gene required for tenacious adherence of Actinobacillus actinomycetemcomitans, also has significant sequence similarity to members of this superfamily and to several unclassified and uncharacterized gene products of both Archaea and Bacteria. To understand the relationship of tadA and tadA-like genes to those encoding the putative NTPases of type II/IV secretion, we used a phylogenetic approach to obtain a genealogy of 148 NTPase genes and reconstruct a scenario of gene superfamily evolution. In this phylogeny, clear distinctions can be made between type II and type IV families and their constituent subfamilies. In addition, the subgroup containing tadA constitutes a novel and extremely widespread subfamily of the family encompassing all putative NTPases of type IV secretion systems. We report diagnostic amino acid residue positions for each major monophyletic family and subfamily in the phylogenetic tree, and we propose an easy method for precisely classifying and naming putative NTPase genes based on phylogeny. This molecular key-based method can be applied to other gene superfamilies and represents a valuable tool for genome analysis.

Does behavior reflect phylogeny in swiftlets (Aves: Apodidae)? A test using cytochrome b mitochondrial DNA sequences.

Swiftlets are small insectivorous birds, many of which nest in caves and are known to echolocate. Due to a lack of distinguishing morphological characters, the taxonomy of swiftlets is primarily based on the presence or absence of echolocating ability, together with nest characters. To test the reliability of these behavioral characters, we constructed an independent phylogeny using cytochrome b mitochondrial DNA sequences from swiftlets and their relatives. This phylogeny is broadly consistent with the higher classification of swifts but does not support the monophyly of swiftlets. Echolocating swiftlets (Aerodramus) and the nonecholocating "giant swiftlet" (Hydrochous gigas) group together, but the remaining nonecholocating swiftlets belonging to Collocalia are not sister taxa to these swiftlets. While echolocation may be a synapomorphy of Aerodramus (perhaps secondarily lost in Hydrochous), no character of Aerodramus nests showed a statistically significant fit to the molecular phylogeny, indicating that nest characters are not phylogenetically reliable in this group.

Molecular cloning of the first metazoan beta-1,3 glucanase from eggs of the sea urchin Strongylocentrotus purpuratus.

We report the molecular cloning of the first beta-1,3 glucanase from animal tissue. Three peptide sequences were obtained from beta-1,3 glucanase that had been purified from eggs of the sea urchin Strongylocentrotus purpuratus and the gene was cloned by PCR using oligonucleotides deduced from the peptide sequences. The full-length cDNA shows a predicted enzyme structure of 499 aa with a hydrophobic signal sequence. A 3.2-kb message is present in eggs, during early embryogenesis, and in adult gut tissue. A polyclonal antibody to the native 68-kDa enzyme recognizes a single band during early embryogenesis that reappears in the adult gut, and recognizes a 57-kDa fusion protein made from a full-length cDNA clone for beta-1,3 glucanase. The identity of this molecule as beta-1,3 glucanase is confirmed by sequence homology, by the presence of all three peptide sequences in the deduced amino acid sequence, and by the recognition of the bacterial fusion protein by the antibody directed against the native enzyme. Data base searches show significant homology at the amino acid level to beta-1,3 glucanases from two species of bacteria and a clotting factor from the horseshoe crab. The homology with the bacteria is centered in a 304-aa region in which there are seven scattered regions of high homology between the four divergent species. These four species were also found to have two homologous regions in common with more distantly related plant, fungal, and bacterial proteins. A global phylogeny based on these regions strongly suggests that the glucanases are a very ancient family of genes. In particular, there is an especially deep split within genes taken from the bacterial genus Bacillus.

A new high molecular weight immunoglobulin class from the carcharhine shark: implications for the properties of the primordial immunoglobulin.

All immunoglobulins and T-cell receptors throughout phylogeny share regions of highly conserved amino acid sequence. To identify possible primitive immunoglobulins and immunoglobulin-like molecules, we utilized 3' RACE (rapid amplification of cDNA ends) and a highly conserved constant region consensus amino acid sequence to isolate a new immunoglobulin class from the sandbar shark Carcharhinus plumbeus. The immunoglobulin, termed IgW, in its secreted form consists of 782 amino acids and is expressed in both the thymus and the spleen. The molecule overall most closely resembles mu chains of the skate and human and a new putative antigen binding molecule isolated from the nurse shark (NAR). The full-length IgW chain has a variable region resembling human and shark heavy-chain (VH) sequences and a novel joining segment containing the WGXGT motif characteristic of H chains. However, unlike any other H-chain-type molecule, it contains six constant (C) domains. The first C domain contains the cysteine residue characteristic of C mu1 that would allow dimerization with a light (L) chain. The fourth and sixth domains also contain comparable cysteines that would enable dimerization with other H chains or homodimerization. Comparison of the sequences of IgW V and C domains shows homology greater than that found in comparisons among VH and C mu or VL, or CL thereby suggesting that IgW may retain features of the primordial immunoglobulin in evolution.

Population dynamics of flaviviruses revealed by molecular phylogenies.

The phylogeny of 123 complete envelope gene sequences was reconstructed in order to understand the evolution of tick- and mosquito-borne flaviviruses. An analysis of phylogenetic tree structure reveals a continual and asymmetric branching process in the tick-borne flaviviruses, compared with an explosive radiation in the last 200 years in viruses transmitted by mosquitoes. The distinction between these two viral groups probably reflects differences in modes of dispersal, propagation, and changes in the size of host populations. The most serious implication of this work is that growing human populations are being exposed to an expanding range of increasingly diverse viral strains.

Molecular and biochemical characterization of dNOS: a Drosophila Ca2+/calmodulin-dependent nitric oxide synthase.

Nitric oxide (NO) is an intercellular messenger involved with various aspects of mammalian physiology ranging from vasodilation and macrophage cytotoxicity to neuronal transmission. NO is synthesized from L-arginine by NO synthase (NOS). Here, we report the cloning of a Drosophila NOS gene, dNOS, located at cytological position 32B. The dNOS cDNA encodes a protein of 152 kDa, with 43% amino acid sequence identity to rat neuronal NOS. Like mammalian NOSs, DNOS protein contains putative binding sites for calmodulin, FMN, FAD, and NADPH. DNOS activity is Ca2+/calmodulin dependent when expressed in cell culture. An alternative RNA splicing pattern also exists for dNOS, which is identical to that for vertebrate neuronal NOS. These structural and functional observations demonstrate remarkable conservation of NOS between vertebrates and invertebrates.

A mitochondrial phylogeny of the rainforest skink genus Saproscincus, Wells and Wellington (1984)

The phylogenetic relationships and historical biogeography of 10 currently described rainforest skinks in the genus Saproscincus were investigated using mitochondrial protein-coding ND4 and ribosomal RNA 16S genes. A robust phylogeny is inferred using both maximum likelihood and Bayesian analysis, with all inter-specific nodes strongly supported when datasets are combined. The phylogeny supports the recognition of two major lineages (northern and southern), each of which comprises two divergent clades. Both northern and southern lineages have comparably divergent representatives in mid-east Queensland (MEQ), providing further molecular evidence for the importance of two major biogeographic breaks, the St. Lawrence gap and Burdekin gap separating MEQ from southern and northern counterparts respectively. Vicariance associated with the fragmentation and contraction of temperate rainforest during the mid-late Miocene epoch underpins the deep divergence between morphologically conservative lineages in at least three instances. In contrast, one species, Saproseincus oriarus, shows very low sequence divergence but distinct morphological and ecological differentiation from its allopatric sister clade within Saproseincus mustelinus. These results suggest that while vicariance has played a prominent role in diversification and historical biogeography of Saproscincus, divergent selection may also be important. (C) 2004 Elsevier Inc. All rights reserved.

Australian microhylid frogs (Cophixalus and Austrochaperina): phylogeny, taxonomy, calls, distributions and breeding biology

Despite a considerable surge in herpetological research in Australia over the last couple of decades the Australian microhylid frogs (Cophixalus and Austrochaperina) remain relatively poorly known. Herein I present the results of extensive fieldwork and molecular, morphological and call analysis with the aim of resolving taxonomy, call variation and distributions, and increasing our understanding of breeding biology. Analysis of 943 base pairs of mitochondrial 16S rRNA and 12S rRNA provides a well supported phylogeny that is largely consistent with current taxonomy. Levels of divergence between species are substantial and significant phylogeographic structuring is evident in C. ornatus, C. neglectus and C. aenigma, sp. nov. The description of C. concinnus was based on a mixed collection of two species from Thornton Peak and a new species is described to resolve this. C. aenigma, sp. nov., is described from high-elevation (>750 m) rainforest across the Carbine, Thornton, Finnigan and Bakers Blue Mountain uplands, north-east Queensland. C. concinnus is redescribed as a highly distinct species restricted to rainforest and boulder fields at the summit of Thornton Peak (>1100 m). Despite protection in Daintree National Park in the Wet Tropics World Heritage Area, predictions of the impact of global warming suggest C. concinnus to be of very high conservation concern ( Critically Endangered, IUCN criteria). The mating call of two species ( C. mcdonaldi and C. exiguus) is described for the first time and high levels of call variation within C. ornatus, C. neglectus, C. hosmeri, C. aenigma and Austrochaperina fryi are presented. Such variation is often attributable to genetically divergent lineages, altitudinal variation and courtship; however, in some instances ( particularly within C. hosmeri) the source or function of highly distinct calls at a site remains obscure. Molecular, morphological and call analyses allow the clarification of species distributions, especially in the northern mountains of the Wet Tropics. Notes are presented on the breeding biology of C. aenigma, C. bombiens, C. concinnus, C. exiguus, C. infacetus, C. mcdonaldi, C. monticola, C. neglectus, C. ornatus and C. saxatilis, which are largely consistent with previous accounts: small terrestrial clutches usually attended by a male. Courtship behaviour in C. ornatus is described and the first records of multiple clutching in Australian microhylids are presented (for C. ornatus and C. infacetus).

Cytochrome c(551) from Starkeya novella - Characterization, spectroscopic properties, and phylogeny of a diheme protein of the SoxAX family

Cytochromes from the SoxAX family have a major role in thiosulfate oxidation via the thiosulfate-oxidizing multi-enzyme system (TOMES). Previously characterized SoxAX proteins from Rhodovulum sulficlophilum and Paracoccus pantotrophus contain three heme c groups, two of which are located on the SoxA subunit. In contrast, the SoxAX protein purified from Starkeya novella was found to contain only two heme groups. Mass spectrometry showed that a disulfide bond replaced the second heme group found in the diheme SoxA subunits. Apparent molecular masses of 27,229 +/- 10.3 Da and 20,258.6 +/- 1 Da were determined for SoxA and SoxX with an overall mass of 49.7 kDa, indicating a heterodimeric structure. Optical redox potentiometry found that the two heme cofactors are reduced at similar potentials (versus NHE) that are as follows: + 133 mV (pH 6.0); + 104 mV (pH 7.0); +49 (pH 7.9) and +10 mV (pH 8.7). EPR spectroscopy revealed that both ferric heme groups are in the low spin state, and the spectra were consistent with one heme having a His/Cys axial ligation and the other having a His/Met axial ligation. The His/Cys ligated heme is present in different conformational states and gives rise to three distinct signals. Amino acid sequencing was used to unambiguously assign the protein to the encoding genes, soxAX, which are part of a complete sox gene cluster found in S. novella. Phylogenetic analysis of soxA- and soxX-related gene sequences indicates a parallel development of SoxA and SoxY, with the diheme and monoheme SoxA sequences located on clearly separated branches of a phylogenetic tree.

Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda : Parastacidae) based on nuclear and mitochondrial DNA

Euastacus crayfish are endemic to freshwater ecosystems of the eastern coast of Australia. While recent evolutionary studies have focused on a few of these species, here we provide a comprehensive phylogenetic estimate of relationships among the species within the genus. We sequenced three mitochondrial gene regions (COI, 16S, and 12S) and one nuclear region (28S) from 40 species of the genus Euastacus, as well as one undescribed species. Using these data, we estimated the phylogenetic relationships within the genus using maximum-likelihood, parsimony, and Bayesian Markov Chain Monte Carlo analyses. Using Bayes factors to test different model hypotheses, we found that the best phylogeny supports monophyletic groupings of all but two recognized species and suggests a widespread ancestor that diverged by vicariance. We also show that Eitastacus and Astacopsis are most likely monophyletic sister genera. We use the resulting phylogeny as a framework to test biogeographic hypotheses relating to the diversification of the genus. (c) 2005 Elsevier Inc. All rights reserved.