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PubMed2006

Al(III)-binding ability of an octapeptide and its phosphorylated derivative.

A synthetic octapeptide, H-GlyGluGlyGluGlySerGlyGly-OH, and its phosphorylated Ser derivative were synthetized and their solution speciation and binding modes in their complexes with Al(III) were measured. One goal of the work was find a lead compound for the design of a selective peptide-based Al(III) chelator. pH-potentiometry was used to characterize the stoichiometry and the stability of the species formed in the interactions of the metal ion and the peptides, while multinuclear NMR was applied to characterize the binding sites of the metal ion in the complexes. CD spectroscopy revealed a difference in the conformational behaviour of the phosphorylated peptide as compared with its non-phosphorylated parent derivative. The Al(III) is presumed to enhance aggregation through the -PO3H(-)-Al(3+)-PO3(2-)-Al(3+)- intermolecular bindings between the peptide chains. The results of molecular dynamics calculations supported the experimentally obtained secondary structures and the binding position of Al(III).

Aluminum↗
PubMed2006

Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.

Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.

Adaptation, Physiological↗
PubMed2005

Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome.

The application of a new gene-based strategy for sequencing the wheat mitochondrial genome shows its structure to be a 452 528 bp circular molecule, and provides nucleotide-level evidence of intra-molecular recombination. Single, reciprocal and double recombinant products, and the nucleotide sequences of the repeats that mediate their formation have been identified. The genome has 55 genes with exons, including 35 protein-coding, 3 rRNA and 17 tRNA genes. Nucleotide sequences of seven wheat genes have been determined here for the first time. Nine genes have an exon-intron structure. Gene amplification responsible for the production of multicopy mitochondrial genes, in general, is species-specific, suggesting the recent origin of these genes. About 16, 17, 15, 3.0 and 0.2% of wheat mitochondrial DNA (mtDNA) may be of genic (including introns), open reading frame, repetitive sequence, chloroplast and retro-element origin, respectively. The gene order of the wheat mitochondrial gene map shows little synteny to the rice and maize maps, indicative that thorough gene shuffling occurred during speciation. Almost all unique mtDNA sequences of wheat, as compared with rice and maize mtDNAs, are redundant DNA. Features of the gene-based strategy are discussed, and a mechanistic model of mitochondrial gene amplification is proposed.

Base Sequence↗
PubMed1996

Details of retropositional genome dynamics that provide a rationale for a generic division: the distinct branching of all the pacific salmon and trout (Oncorhynchus) from the Atlantic salmon and trout (Salmo).

Salmonid species contain numerous short interspersed repetitive elements (SINEs), known collectively as the HpaI family, in their genomes. Amplification and successive integration of individual SINEs into the genomes have occurred during the evolution of salmonids. We reported previously a strategy for determining the phylogenetic relationships among the Pacific salmonids in which these SINEs were used as temporal landmarks of evolution. Here, we provide evidence for extensive genomic rearrangements that involved retropositions and deletions in a common ancestor of all the Pacific salmon and trout. Our results provide genetic support for the recent phylogenetic reassignment of steelhead and related species from the genus Salmo to the genus Oncorhynchus. Several other informative loci identified by insertions of HpaI SINEs have been isolated, and previously proposed branching orders of the Oncorhynchus species have been confirmed. The authenticity of our phylogenetic tree is supported both by the isolation of more than two informative loci per branching point and by the congruence of all our data, which suggest that the period between successive speciations was sufficiently long for each SINE that had been amplified in the original species to become fixed in all individuals of that species.

Animals↗
PubMed2004

On the geographical differentiation of Gymnodactylus geckoides Spix, 1825 (Sauria, Gekkonidae): speciation in the Brazilian caatingas.

The specific concept of G. geckoides was initially ascertained based on a topotypical sample from Salvador, Bahia. Geographic differentiation was studied through the analysis of two meristic characters (tubercles in a paramedian row and fourth toe lamellae) and color pattern of 327 specimens from 23 localities. It is shown that the population from the southernmost locality, Mucugê, is markedly divergent in all characters studied. A Holocene refuge model is proposed to explain the pattern. A decision about the rank to be attributed to the Mucugê population is deferred until more detailed sampling is effected and molecular methods are applied.

Animals↗
PubMed1995

Chromium speciation by anion-exchange high-performance liquid chromatography with both inductively coupled plasma atomic emission spectroscopic and inductively coupled plasma mass spectrometric detection.

Development of a new method for the determination of Cr(III) and Cr(VI) is described. Anion-exchange high-performance liquid chromatography (HPLC) was used to separate Cr(III) and Cr(VI) with on-line detection by inductively coupled plasma atomic emission spectroscopy (ICP-AES) at 2766 A in preliminary studies, and inductively coupled plasma mass spectrometry (ICP-MS) with single-ion monitoring at m/z 52 and m/z 53 for final work. A mobile phase consisting of ammonium sulfate and ammonium hydroxide was used, and a simple chelation procedure with EDTA was followed to stabilize the Cr(III) species in standard solutions. ICP-MS results indicated the feasibility of using chromium isotope m/z 53 instead of the more abundant m/z 52 isotope due to a high mobile-phase background most significantly from the SO+ polyatomic interference. The absolute detection limits based on peak-height calculations were 40 pg for Cr(III) and 100 pg for Cr(VI) in aqueous media by HPLC-ICP-MS. The linear dynamic range extended from 5 ppb (ng/ml) to 1 ppm (micrograms/ml) for both species. By HPLC-ICP-AES, detection limits were 100 ng for Cr(III) and 200 ng for Cr(VI). Cr(III) was detected in NIST-SRM 1643c (National Institute of Standards and Technology-Standard Reference Material, Trace Elements in Water) by HPLC-ICP-MS at the 20 ppb level.

Chromatography, High Pressure Liquid↗
PubMed1997

Binding of arsenicals to proteins in an in vitro methylation system.

The dynamics of interactions between rat liver cytosolic proteins and arsenicals were examined in an in vitro methylation system that contained cytosol, glutathione, S-adenosylmethionine, and 1 microM -73As-arsenite. After incubation at 37 degrees C for up to 90 min, low-molecular-weight components of the assay system (<10 kDa) were removed by ultrafiltration and cytosolic proteins were separated by size-exclusion chromatography on Sephacryl S-300 gel. Five 73As-labeled protein peaks were found in chromatographic profiles. The estimated molecular masses of 73As-labeled proteins eluting in the three earliest peaks were as follows: Vo, >/=1000 kDa; A, 135 kDa; and B, 38 kDa. Peak C eluted immediately before the total volume (VT) of the chromatographic column; peak D eluted after the VT. 73As bound to proteins was released by CuCl treatment and speciated by thin-layer chromatography. Amounts and ratios of inorganic As, methyl As, and dimethyl As associated with cytosolic proteins depended upon the incubation interval. Inorganic As was present in all protein peaks. Methyl As was primarily associated with peaks A and C; dimethyl As was associated with peaks B and C. To examine the effect of valence on the binding of methylarsenicals to cytosolic proteins, trivalent or pentavalent 14C-labeled methyl As or dimethyl As was incubated in an in vitro system designed to minimize the enzymatically catalyzed production of methylated arsenicals. Proteins in peaks A, B, and C bound preferentially trivalent methyl and dimethyl As. Peak D bound either trivalent or pentavalent methyl and dimethyl As. Protein-bound inorganic and methyl As were substrates for the production of dimethyl As in an in vitro methylation system, suggesting a role for protein-bound arsenicals in the biomethylation of this metalloid.

Animals↗
PubMed2002

Divergence of mitochondrial dna is not corroborated by nuclear dna, morphology, or behavior in Drosophila simulans.

We ask whether the observed mitochondrial DNA (mtDNA) population subdivision of Drosophila simulans is indicative of organismal structure or of specific processes acting on the mitochondrial genome. Factors either intrinsic or extrinsic to the host genome may influence the evolutionary dynamics of mtDNA. Potential intrinsic factors include adaptation of the mitochondrial genome and of nucleomitochondrial gene complexes specific to the local environment. An extrinsic force that has been shown to influence mtDNA evolution in invertebrates is the bacterial endosymbiont Wolbachia. Evidence presented in this study suggests that mtDNA is not a good indicator of organismal subdivision in D. simulans. Furthermore, there is no evidence to suggest that Wolbachia causes any reduction in nuclear gene flow in this species. The observed differentiation in mtDNA is not corroborated by data from NADH: ubiquinone reductase 75kD subunit precursor or the Alcohol dehydrogenase-related loci, from the shape or size of the male genital arch, or from assortative premating behavior. We discuss these results in relation to a mitochondrial genetic species concept and the potential for Wolbachia-induced incompatibility to be a mechanism of speciation in insects. We conclude with an iterated appeal to include phylogenetic and statistical tests of neutrality as a supplement to phylogenetic and population genetic analyses when using mtDNA as an evolutionary marker.

Animals↗
PubMed2003

Phylogenetics of the grass genus Ehrharta: evidence for radiation in the summer-arid zone of the South African Cape.

Climatic and geological change may play a key role in stimulating biological radiations. Here, we use phylogenetic data to test whether the comparatively high diversity of ehrharteoid grasses in the Cape region of South Africa is the result of rapid radiation associated with the onset of a seasonally arid climate during the late Miocene. A phylogenetic hypothesis based on morphological and nucleotide sequence (nuclear ITS1 and plastid trnL-F) data confirms the monophyly of the African Ehrharta species and shows that the diversification of this lineage was centered in the Cape region. Sequence divergence data (ITS1 + trnL-F) indicate a pulse of rapid speciation, which may explain poor phylogenetic resolution within the African Ehrharta clade. Alternative calibrations yield a broad range of time estimates for the start and end of this radiation, most of which indicate a radiation inside the last 11 million years. A calibration based on the age of Ehrhartoideae suggests that radiation started 9.82 +/- 0.20 million years ago and ended 8.74 +/- 0.21 million years ago. Under alternative calibrations, estimated speciation rates during the period of radiation range between 0.87 and 4.18 species per million years. Parsimony optimization of habitat parameters reveals that radiation was correlated with the occupation of seasonally arid succulent karoo environments, wet heathy (fynbos) environments being ancestral. These data support earlier suggestions that late Miocene climatic change stimulated floristic radiation at the Cape, and highlight the potential importance of environmental change in powering diversification in continental floras.

Base Sequence↗
PubMed2003

Speciation on a conveyor belt: sequential colonization of the hawaiian islands by Orsonwelles spiders (Araneae, Linyphiidae).

Spiders of the recently described linyphiid genus Orsonwelles (Araneae, Linyphiidae) are one of the most conspicuous groups of terrestrial arthropods of Hawaiian native forests. There are 13 known Orsonwelles species, and all are single- island endemics. This radiation provides an excellent example of insular gigantism. We reconstructed the cladistic relationships of Orsonwelles species using a combination of morphological and molecular characters (both mitochondrial and nuclear sequences) within a parsimony framework. We explored and quantified the contribution of different character partitions and their sensitivity to changes in the traditional parameters (gap, transition, and transversion costs). The character data show a strong phylogenetic signal, robust to parameter changes. The monophyly of the genus Orsonwelles is strongly supported. The parsimony analysis of all character evidence combined recovered a clade with of all the non-Kauai Orsonwelles species; the species from Kauai form a paraphyletic assemblage with respect to the latter former clade. The biogeographic pattern of the Hawaiian Orsonwelles species is consistent with colonization by island progression, but alternative explanations for our data exist. Although the geographic origin of the radiation remains unknown, it appears that the ancestral colonizing species arrived first on Kauai (or an older island). The ambiguity in the area cladogram (i.e., post-Oahu colonization) is not derived from conflicting or unresolved phylogenetic signal among Orsonwelles species but rather from the number of taxa on the youngest islands. Speciation in Orsonwelles occurred more often within islands (8 of the 12 cladogenic events) than between islands. A molecular clock was rejected for the sequence data. Divergence times were estimated by using the nonparametric rate smoothing method of Sanderson (1997, Mol. Biol. Evol. 14:1218-1231) and the available geological data for calibration. The results suggest that the oldest divergences of Orsonwelles spiders (on Kauai) go back about 4 million years.

Animals↗
PubMed2002

Phylogenetic relationships of the Asian box turtles of the genus Cuora sensu lato (Reptilia: Bataguridae) inferred from mitochondrial DNA sequences.

Phylogenetic relationships of the genus Cuora sensu lato (Cuora sensu stricto and Cistoclemmys) and other testudinoid genera were inferred from variations in 882 base positions of mitochondrial 12S and 16S rRNA genes. Results yielded a robust support to the monophyly of a group (Cuora group) consisting of Cuora sensu lato and the monotypic Pyxidea. Within the Cuora group, the continental Cuora (sensu stricto) and the two subspecies of Ci. flavomarginata constituted two well-supported monophyletic groups. Distinctly small interspecific genetic distances in the former groups suggested that in the continent speciations in Cuora took place much later than the primary divergences in the Cuora group, or speciations in other related genera, such as Mauremys. Our analyses failed to provide a substantial support to the monophyly of any other combinations of taxa within the Cuora group, including Cuora in broad and strict senses, and Cistoclemmys as consisting of Ci. galbinifrons and Ci. flavomarginata. Besides these, our results also suggested the non-monophyly for the Batagurinae and the Geoemydinae, and sister relationships of the Bataguridae with Testudinidae rather than with the Emydidae.

Animals↗
PubMed2000

Gas sampling glow discharge: a versatile ionization source for gas chromatography time-of-flight mass spectrometry

A gas chromatograph has been coupled to a direct-current gas sampling glow discharge (GSGD) ionization source for the mass spectrometric analysis of halogenated hydrocarbons. The continuous discharge is contained within the first vacuum stage of the differentially pumped spectrometer interface. The discharge can be operated statically or rapidly switched between atomic and molecular ionization modes; both atomic and molecular spectra could be generated in the helium-supported plasma. In the switched configuration, the duty cycle is 50% for each mode. The ionization mode is selected by application of either a positive (molecular) or negative (atomic) potential to the sample introduction electrode, and the two kinds of spectra can be sequentially collected by changing the voltage and current between two preset values. Similar ion-optical voltage settings could be employed for both modes of operation, with the exception of the steering-plate potential, which had to be modulated between two different values (at the plasma switching frequency) to obtain the greatest atomic and molecular signal levels. The source is capable of generating mass spectra resembling those from an electron-impact source while operated in the molecular ionization mode (both static and dynamic). The best atomic detection limits (1-25 fg of analyte/ second) were obtained when the plasma was operated in the static mode with single-channel gated ion counting. Atomic detection limits obtained with boxcar averager data collection were comparable for static and switched operation of the source (1-30 pg/s). Likewise, the molecular detection limits were similar for the static and switched modes and span the range of 7-140 pg/s (boxcar averagers). Precision was better than 7% RSD under all conditions. The atomic and molecular chromatographic peak heights were nearly unchanged over a range of modulation rates from 5 to 100 Hz. The elemental ratio (35Cl+/12C+) for chloroform was also measured over a range of plasma modulation rates (5-90 Hz) and found to be randomly distributed about the sample mean. Several chlorinated hydrocarbons were introduced into the discharge and could be successfully differentiated (or speciated) on the basis of their 35Cl+/12C+ ratios.

Journal Article↗
PubMed2001

Intraspecific competition favours niche width expansion in Drosophila melanogaster.

Ecologists have proposed that when interspecific competition is reduced, competition within a species becomes a potent evolutionary force leading to rapid diversification. This view reflects the observation that populations invading species-poor communities frequently evolve broader niches. Niche expansion can be associated with an increase in phenotypic variance (known as character release), with the evolution of polymorphisms, or with divergence into many species using distinct resources (adaptive radiation). The relationship between intraspecific competition and diversification is known from theory, and has been used as the foundation for some models of speciation. However, there has been little empirical proof that niches evolve in response to intraspecific competition. To test this hypothesis, I introduced cadmium-intolerant Drosophila melanogaster populations to environments containing both cadmium-free and cadmium-laced resources. Here I show that populations experiencing high competition adapted to cadmium more rapidly than low competition populations. This provides experimental confirmation that competition in a population can drive niche expansion onto new resources for which competition is less severe.

Adaptation, Physiological↗
PubMed2004

Do species populations really start small? New perspectives from the Late Neogene fossil record of African mammals.

This analysis of all known African larger mammals of the past 10 Myr offers new perspectives on the geographical circumstances of speciation. Our central question is: does the fossil evidence support the idea that most new species start as small populations and, if true, how long is the average growth interval until species are established at their mean later size? This simple question is important to unravelling the competing claims of rival models of speciation. We approached it by direct use of fossil data, which, to our knowledge, has not been done previously. We compared the numbers of fossil site records, as a proxy for magnitude of geographical spread, between survivorship intervals across all species. The results show that the average mammal species has indeed started its life in a relatively small population, and thereafter increased rapidly in geographical spread to reach its long-term equilibrium abundance by about 1 million years after origin. Some theoretical implications of these results are discussed.

Africa↗
PubMed2002

Evolution of mutualism between globeflowers and their pollinating flies.

Plant/seed-eater pollinators mutualisms involve a plant pollinated by an insect whose larvae develop by eating a fraction of host-plant seeds. The outcome of the interaction therefore depends on the number of ovules fertilized by adult visits and the number of seeds destroyed by larvae. Among the very few cases of such mutualisms reported so far is the globeflower-globeflower flies mutualism, which is unique in that it involves several congeneric fly species (Chiastocheta genus) coexisting within a single host-plant species, Trollius europaeus. These species exhibit contrasted oviposition behaviors resulting in a more or less beneficial outcome for the plant. We designed an adaptive dynamics model to investigate how morphological traits of globeflower could affect the evolution of oviposition in its pollinating flies. Three fly traits (flower age at oviposition, clutch size and the level of avoidance of already parasitized flowers) and one plant trait (closed or open corolla) were examined. Whatever the shape of the flower, evolutionary branching occurs between early and late ovipositing flies, driven by strong competition among larvae within a fruit. Once this branching occurred, the closed shape of the corolla is likely to offer a better protection to eggs of early but not of late ovipositing flies. The difference in egg survival results in higher competition among early larvae and thus selects for decreased clutch size in early flies. This can be seen as a first step in the evolution of a mutualistic behavior. The prediction of our model fits field observations of fly behavior, giving theoretical support to the hypothesis of fly sympatric speciation within its host plant. Moreover, flower closed globe shape can be positively selected in globeflowers as it results in a reduction of parasitism strength. This last evolution therefore leads to a stable mutualism between globeflowers and globeflower flies.

Animals↗
PubMed1999

Oxidation of arsenic bearing fly ash as pretreatment before solidification.

When a waste fly ash, containing large amounts of As(2)O(3), is solidified using cement and lime, the arsenic concentration in the leachate (extraction test DIN 38 414 S4) is determined by the solubility of CaHAsO(3) and can be lowered to a value of ca. 5 mg/l, in a saturated solution of Ca(OH)(2). One of the criteria for landfilling of hazardous waste is, however, that the arsenic concentration in the leachate must be lower than 1 mg/l. In this paper, it is shown that oxidation of the waste before solidification, whereby As(III) is oxidised to As(V) using H(2)O(2), lowers the leaching of arsenic, and other contaminants, from the solidified product. With the speciation program MINTEQA2, it is calculated that the solubility of As(V) in the presence of a pure Ca(3)(AsO(4))(2) precipitate is lower than the solubility of As(III) in the presence of a pure CaHAsO(3) precipitate. The arsenic concentration in the presence of both a Ca(OH)(2) and a Ca(3)(AsO(4))(2) precipitate can even be lowered to 0.47 mg/l (pH 12.5). The As concentration in the leachate of the extraction test on an oxidised S/S sample was indeed lowered to ca. 0.5 mg/l, which is a reduction by a factor of 10 compared to the concentration of ca. 5 mg/l, obtained in the leachate of the extraction test on a non-oxidised S/S sample. This is in very good agreement with the calculated value of 0.47 mg/l. Also, the pretreatment decreased the cumulative fraction of arsenic released over the entire test period of a semi-dynamic leach test by a factor of 7. At all times during the test, the As concentration did not exceed the norm of 1 mg/l.

Algorithms↗
PubMed2006

The measurement of fine particulate semivolatile material in urban aerosols.

Ammonium nitrate and semivolatile organic material (SVOM) are significant components of fine particles in urban atmospheres. These components, however, are not properly determined with methods such as the fine particulate matter (PM2.5) Federal Reference Method (FRM) or other single filter samplers because of significant losses of semivolatile material (SVM) from particles collected on the filter during sampling. The R&P tapered element oscillating microbalance (TEOM) monitor also does not measure SVM, because this method heats the sample to remove particle bound water, which also results in evaporation of SVM. Recent advances in monitoring techniques have resulted in samplers for both integrated and continuous measurement of total PM2.5, including the particle concentrator-Brigham Young University organic sampling system (PC-BOSS), the real-time total ambient mass sampler (RAMS), and the R&P filter dynamics measurement system (FDMS) TEOM monitor. Results obtained using these samplers have been compared with those obtained with either a PM2.5 FRM sampler or a TEOM monitor in studies conducted during the past five years. These studies have shown the following: (1) the PC-BOSS, RAMS, and FDMS TEOM are all comparable. Each instrument measures both the nonvolatile material and the SVM. (2) The SVM is not retained on the heated filter of a regular TEOM monitor and is not measured by this sampling technique. (3) Much of the SVM is also lost during sampling from single filter samplers such as the PM2.5 FRM sampler. (4) The amount of SVM lost from single filter samplers can vary from less than one-third of that lost from heated TEOM filters during cold winter conditions to essentially all during warm summer conditions. (5) SVOM can only be reliably collected using an appropriate denuder sampler. (6) A PM2.5 speciation sampler can be easily modified to a denuder sampler with filters that can be analyzed for semivolatile organic carbon (OC), nonvolatile OC, and elemental carbon using existing OC/elemental carbon analytical techniques. The research upon which these statements are based for various urban studies are summarized in this paper.

Air Pollutants, Occupational↗
PubMed2003

Temporal variability of dissolved P speciation in a eutrophic reservoir--implications for predicating algal growth.

Weak-anion exchange chromatography was used to explore the temporal variability in the speciation of dissolved P in the surface layer of a eutrophic reservoir. Authentic free ortho-P ion was the most common form of P on three of the five sampling occasions-including during a bloom of the green algae Botryococcus braunii indicating that the bloom was not P limited. Conversely, the absence of authentic ortho-P during a bloom of the dinoflagellate Ceratium hirundinella suggested the bloom was either P limited or co-limited. These observations were confirmed by algal-growth bioassay experiments.

Chlorophyta↗