Gordon P. Moore

Evolution of Single-Copy DNA and the ADH Gene in Seven Drosophilids

SummarySingle-copy DNA was isolated fromDrosophila melanogaster and hybridized with total genomic DNA ofD. melanogaster, D. mauritiana, D. simulans, D. pseudoobscura, D. willistoni, D. hydei andD. virilis. The duplexes were thermally eluted from hydroxyapatite and the data used to assess the relatedness of each species toD. melanogaster. The general pattern of relatedness was similar to that predicted by morphological methods but with some notable exceptions. The rate of nucleotide substitution was estimated to be greater than 0.66% of bases per million years. An unexpected, rapidly evolving component ofD. melanogaster single-copy DNA was identified. The relatedness of these species was also studied with respect to the gene coding for alcohol dehydrogenase (ADH). The ADH gene, previously cloned fromD. melanogaster (Goldberg 1980), was hybridized with Southern blots of genomic digests of the seven species. The intensity and position of the hybridizing bands suggest the amount of divergence of the gene. Divergence was quantitated by reassociation of a fragment of the cloned ADH gene with total DNA of the seven drosophilids and thermal elution of the resultant duplexes from hydroxyapatite. The ADH gene was isolated from genomic clone libraries ofD. melanogaster, D. simulans andD. mauritiana and further studied by comparison of position of restriction sites. Species relationships deduced from comparison of total single-copy DNA and the ADH gene were consistent, demonstrating that a single gene can reflect divergence of the entire genome.

Nucleotide sequence comparison of the Adh gene in three drosophilids

SummaryThe alcohol dehydrogenase (Adh) gene has been isolated fromDrosophila simulans andD. mauritiana by screening λ clone libraries of each with a previously cloned Adh gene fromD. melanogaster. The isolated λ clones were subcloned and partially sequenced to determine the relatedness of these species and to examine details of evolutionary change in the structure of the Adh gene. We report the sequence of the first 704 nucleotides of each gene as well as 127 bases in the 5′ untranslated region. When these sequences are compared,D. melanogaster differs fromD. simulans andD. mauritiana by 2.8% and 3.1%, respectively.D. simulans andD. mauritiana differ by only 1.8%, implying that they are more closely related to each other than either is toD. melanogaster. This is consistent with phylogenetic relationships established by a variety of genetic, biochemical, and morphological means and illustrates that DNA sequencing of a single gene may be used to assess the evolutionary relationships of species.

Clinopyroxene-liquid thermometers and barometers specific to alkaline differentiated magmas

We present new thermometers and barometers based on clinopyroxene–liquid equilibria specific to alkaline differentiated magmas. The new models were calibrated through the regression analyses of experimental datasets obtained by merging phase equilibria experiments from the literature with new experiments performed by using trachytic and phonolitic starting compositions. The regression strategy was twofold: (1) we have tested previous thermometric and barometric equations and recalibrated these models using the new datasets; (2) we have calibrated a new thermometer and a new barometer including only regression parameters that closely describe the compositional variability of the datasets. The new models yield more precise estimates than previous thermometers and barometers when used to predict temperatures and pressures of alkaline differentiated magmas. We have tested the reliability of the new equations by using clinopyroxene–liquid pairs from trachytes and phonolites erupted during major explosive eruptions at the Phlegrean Fields and Mt. Vesuvius (central Italy). The test yielded crystallization conditions comparable to those determined by means of melt and fluid inclusion analyses and phase equilibria studies; this validates the use of the proposed models for precise estimates of crystallization temperatures and pressures in differentiated alkaline magmas. Because these magmas feed some of the most voluminous, explosive, and threatening volcanic eruptions in the world, a better understanding of the environmental conditions of their reservoirs is mandatory and this is now possible with the new models provided here.

Analysis of the mitochondrial and nuclear genomes of two basidiomycetes, Coprinus cinereus and Coprinus stercorarius

SummaryThe mitochondrial and nuclear genomes of Coprinus stercorarius and C. cinereus were compared to assess their evolutionary relatedness and to characterize at the molecular level changes that have occurred since they diverged from a common ancestor. The mitochondrial genome of C. stercorarius (91.1 kb) is approximately twice as large as that of C. cinereus (43.3 kb). The pattern of restriction enzyme recognition sites shows both genomes to be circular, but reveals no clear homologies; furthermore, the order of structural genes is different in each species. The C. stercorarius mitochondrial genome contains a region homologous to a probe derived from the yeast mitochondrial var1 gene, whereas its nuclear genome does not. By contrast, the C. cinereus nuclear, but not mitochondrial, genome contains a region homologous to the var1 probe. Only a small fraction of either the nuclear or mitochondrial genomes, perhaps corresponding to the coding sequences, is capable of forming duplexes in interspecies solution reassociations, as measured by binding to hydroxylapatite. Those sequences capable of reassociating were found to have approximately 15% divergence for the mitochondrial genomes and 7%–15% divergence for the nuclear genomes, depending on the conditions of reassociation.

Characterization of five members of the actin gene family in the sea urchin

Hybridization of an actin cDNA clone (pSA38) to restriction enzyme digests of Strongylocentrotus purpuratus DNA indicates that the sea urchin genome contains at least five different actin genes. A sea urchin genomic clone library was screened for recombinants which hydridize to pSA38 and four genomic clones were isolated. Restriction maps were generated which indicate that three of these recombinants contain different actin genes, and that the fourth may be an allele to one of these. The restriction maps suggest that one clone contains two linked actin genes. This fact, which was confirmed by heteroduplex analysis, indicates that the actin gene family may be clustered. The linked genes are oriented in the same direction and spaced about 8.0 kilobases apart. In heteroduplexes between genomic clones two intervening sequences were seen. Significant homology is confined to the actin coding region and does not include any flanking sequence. Southern blot analysis reveals that repetitive DNA sequences are found in the region of the actin genes.

Change in expression of the actin gene family during early sea urchin development

Abstract Expression of the actin gene family was studied during early sea urchin development using in vitro translation and nucleic acid hybridization techniques. Poly(A) + RNA from four-cell and gastrula-stage S. purpuratus embryos was translated in vitro and the translation products were monitored for the presence of actin. In addition, poly(A) + and total RNA were prepared from various stages of development, electrophoresed on agarose gels, transferred to diazobenzyloxymethyl paper, and then hybridized with a cloned actin cDNA probe. Results of these experiments indicate that there is a sharp increase in the level of RNA coding for actin during early development, and that there are two forms of actin specific RNA exhibiting different patterns of control.

Evolution of two actin genes in the sea urchin Strongylocentrotus franciscanus

SummaryThe complete nucleotide sequences of two chromosomally linked actin genes from the sea urchinStrongylocentrotus franciscanus are presented. The genes are separated by 5.7 kilobases, occur in the same transcriptional orientation, and contain introns in identical positions. The structures and nucleotide sequences of the two genes are extremely similar, suggesting that they arose through a recent duplication. Comparison of the nucleotide sequences of the genes allows inferences to be made about mutational mechanisms active since the duplication event. Whereas point mutations predominate in the coding regions, the introns and flanking DNA are more heavily influenced by a variety of events that cause simultaneous changes in short regions of DNA.

Organization and evolution of the actin gene family in sea urchins

Genomic libraries of the sea urchins Strongylocentrotus franciscanus and Lytechinus pictus were screened with an actin cDNA clone from Strongylocentrotus purpuratus. Four nonoverlapping clones were isolated and characterized from the S. franciscanus library; three were isolated and characterized from the L. pictus library. Linked genes having the same transcriptional orientation were found on all S. franciscanus clones. Three clones contained two actin genes each; the other clone contained three. In contrast, the L. pictus clones contained only one actin gene. Comparison of actin genomic clones from these three species indicated a difference in the genomic organization of sea urchin actin genes in that the genes appear to be more highly clustered in S. franciscanus than in S. purpuratus and L. pictus. Genomic dot blots and reassociation kinetics demonstrated that the copy number of actin genes in all three species is 15 to 20. Nucleotide sequence homology of actin genes within and among the species was measured by thermal elution. These experiments indicated that there is a high degree of interspecies actin gene sequence homology but that, within each species, actin gene sequences may differ by as much as 30%. Sequencing of two S. franciscanus actin genes revealed introns at the same amino acid positions, 121 and 204, reported for S. purpuratus actin genes. These data demonstrated that the genomic copy number, the transcriptional orientation of linked genes, and, to the extent studied, the intron position of actin genes have evolved similarly in these three species. In contrast, significant change has occurred in the chromosomal arrangement of sea urchin actin genes.

Calibration of Fe XANES for high-precision determination of Fe oxidation state in glasses: Comparison of new and existing results obtained at different synchrotron radiation sources

Abstract Micro-X-ray absorption near-edge structure (m-XANES) spectroscopy has been used by several recent studies to determine the oxidation state and coordination of iron in silicate glasses. Here, we present new results from Fe m-XANES analyses on a set of 19 Fe-bearing felsic glasses and 9 basaltic glasses with known, independently determined, iron oxidation state. Some of these glasses were measured previously via Fe XANES (7 rhyolitic, 9 basaltic glasses; Cottrell et al. 2009), while most felsic reference glasses (12) were analyzed for the first time. The main purpose of this study was to understand how small changes in glass composition, especially at the evolved end of silicate melt compositions occurring in nature, may affect a calibration of the Fe m-XANES method. We performed Fe m-XANES analyses at different synchrotron radiation sources [Advanced Photon Source (APS), Argonne, U.S.A., and Angströmquelle Karlsruhe (ANKA), Germany] and compared our results to existing calibrations obtained at other synchrotron radiation sources worldwide. The compiled results revealed that changes in instrumentation have a negligible effect on the correlation between the centroid energy of the Fe pre-edge peak and the Fe oxidation state in the glasses. Oxidation of the glasses during extended exposure (up to 50 min) to the X-ray beam was not observed. Based on the new results and literature data we determined a set of equations for different glass compositions, which can be applied for the calculation of the iron valence ratio (Fe3+/ΣFe) in glasses by using XANES spectra collected at different synchrotron beamlines. For instance, the compiled felsic reference material data demonstrated that the correlation between the centroid energy of the Fe pre-edge peak CFe (eV) and the Fe3+/ΣFe ratio of felsic glasses containing 60.9 to 77.5 wt% SiO2 and 1.3 to 5.7 wt% FeOtot can be accurately described by a single linear trend, if the spectra were collected at 13-ID-E beamline at APS and for 0.3 ≤ Fe3+/ΣFe ≤ 0.85: CFe [eV] = 0.012395 (±0.00026217) × Fe3+/ΣFe + 7112.1 (±0.014525); R2 = 0.987. Based on this equation, the Fe oxidation state of felsic glasses can be estimated at an absolute uncertainty of ±2.4% Fe3+/ΣFe. In general, the differences between the calibrations for felsic and mafic glasses were small and the compiled data set (i.e., results collected at four different beamlines on 79 reference glass materials) is well described by a single second-order polynomial equation.

A comparison of olivine-melt thermometers based on DMg and DNi: The effects of melt composition, temperature, and pressure with applications to MORBs and hydrous arc basalts

Abstract A new olivine-melt thermometer based on the partitioning of Ni ( DNiOl/liq