bluuebunny/crossref_metadata_2025 huggingface dataset:
Fiber-Optic Sampling Combined with an Imaging Spectrograph for Routine Raman Spectroscopy
Authors: Newman Cathy D. , Bret Georges G. , McCreery Richard L.
Published: June 2005

A 250-mm imaging spectrograph was combined with a CCD detector, fiber-optic sampler, and diode laser (783 nm) to yield an efficient Raman spectrometer. A variety of sampling modes for liquids and solids were demonstrated, none of which required careful optical alignment. Of practical interest are spectra obtained from liquids inside glass containers, rapid (30 seconds each) spectral acquisition from successive solid and liquid samples, and spectra of normally fluorescent materials such as rhodamine 6G and common plastics.
Spectroscopic Properties of Polycyclic Aromatic Compounds: Examination of Nitromethane as a Selective Fluorescence Quenching Agent for Alternant Polycyclic Aromatic Nitrogen Hetero-Atom Derivatives
Authors: Tucker Sheryl A. , Acree William E. , Tanga Mary J. , Tokita Sumio , Hiruta Kimihiro , Langhals Heinz
Published: June 2005

Nitromethane is examined as a selective fluorescence quenching agent for alternant polycyclic aromatic nitrogen hetero-atoms (PANHs). Fluorescence emission behavior is reported for 1-azapyrene, 2-azapyrene, 4-azapyrene, 4-azachrysene, 12-azabenzo[a]pyrene, phenanthro[9, 10g]isoquinoline, phenanthro[2,3h]isoquinoline, phenanthro[3,2h]-isoquinoline, 2-azabenz[a]anthracene, 1-azabenz[a]anthracene, 9-azabenz[a]anthracene, dibenzo[c,i]phenanthro[1,10,9,8anmlk]phenanthridine, diphenanthro[9,10,1def;1',10',9'hij]phthalazine, and benz[de]isoquino[1,8gh]quinoline dissolved in acetonitrile or aqueous-acetonitrile solvent mixtures at various nitromethane concentrations. Results of these measurements show that nitromethane does quench fluorescence emission of ten of the solutes studied; however, phenanthro-[2,3h]isoquinoline, 9-azabenz[a]anthracene, benz[de]isoquino[1,8gh]-quinoline, and dibenzo[c,i]phenanthro[1,10,9,8anmlk]phenanthridine are notable exceptions.
Lifetime Analysis of Weak Emissions and Time-Resolved Spectral Measurements with a Subnanosecond Dye Laser and Gated Analog Detection
Authors: Hart Lucas P. , Daniels Malcolm
Published: June 2005

A relatively inexpensive UV fluorometer has been developed for the temporal and spectral characterization of weak emissions, with the use of a frequency-doubled nitrogen-pumped dye laser for excitation wavelengths down to 260 nm. Gated detection of the photomultiplier pulse provides 0.1-ns resolution of the 1.4-ns FWHM instrument response function. On-line statistical measurements characterize the waveforms, with NATA, tryptophan, and NADH as model compounds providing emission signals of the order of the water Raman scatter signal. Time-decay waveforms are analyzed with the use of nonlinear least-squares fitting, with scatter or p-terphenyl as the reference, and a time shift. Good agreement with the literature is found for the subnanosecond and nanosecond decay times, with resolution of multiple decays down to several percent fractional emission. With multichannel data acquisition, a set of time-windowed emission spectra can be obtained in the same period as is required for an additional time-decay waveform. Time-windowed spectra and the derived decay-associated spectra provide evidence concerning the decay model in addition to spectral characteristics. Practical limitations include the peak current linearity of the photomultiplier and the wavelength variation of the response function.
Resonance Raman Spectroscopic Detection System for Liquid Chromatography
Authors: Chong Chan Kong , Mann Charles K. , Vickers Thomas J.
Published: June 2005

A fiber-optic-based system for Raman detection in liquid chromatography is described. This system provides for on-the-fly acquisition of resonance Raman spectra with correction for sample absorption. Two azo dyes, eriochrome black T and eriochrome blue SE, are used to test the system. Detection limits are about 160 ng for these analytes. The ability to recover quantitative information for the case in which there is no chromatographic resolution of the components is demonstrated.
Dioxygen NIR FT-Emission (1Δg → 3Σ−g) and Raman Spectra of 1,4-Dimethylnaphthalene Endoperoxide: A Source of Singlet Molecular Oxygen
Authors: Di Mascio Paolo , Bechara Etelvino J. H. , Rubim Joel C.
Published: June 2005

Singlet molecular oxygen (1O2) monomol light emission (O2, 1Δ g → 3Σ− g) generated during the thermodissociation of 1,4-dimethylnaphthalene endoperoxide (1,4-DMNO2) has been directly detected with the use of an FT spectrophotometer equipped with a liquid nitrogen-cooled InGaAs detector. The 1O2 quenching by β-carotene has been observed. The bimol emission has also been detected by the use of an intensified diode array detector and characterized by enhancement with 1,4-diazabicyclo[2.2.2]octane (DABCO). With a multichannel detector it was possible to obtain the Raman spectrum of 1,4-DMNO2 and to follow its conversion into the parent hydrocarbon 1,4-dimethylnaphthalene (1,4-DMN) by the decrease of the Raman 715-cm−1 peak intensity attributed to the O-O stretching mode.
An Optimized Background Correction Algorithm in Automated Spectral Analysis Based on Convolution Signals
Authors: Janssens F. , François J.-P.
Published: June 2005

Two methods for background calculation i.e., those of Taylor and Schutyser and of Van der Plas et al., both based on the use of a zero-area square wave filter, have been critically evaluated. Simulated data, consisting of Gaussian and Voigt profiles superimposed on known background distributions, were used to study the performance of these methods. Statistical noise was introduced on the spectral data with the use of a Gaussian pseudo-random generator. It was found that both methods tend to fail, especially for cases with lines that are interfered with and/or for curved backgrounds. Furthermore, both methods appear to be very sensitive to statistical noise. Therefore, another procedure, also based on the use of a digital filter, is proposed here. In general, it can be stated that this variant performs better than the former ones, especially for weak signals with important statistical fluctuations and for Voigt profiles with parameters a up to 1.0. The main differences between the new procedure and the other ones are: (1) no manual input of the peak position has to be done, which results in a fully automated procedure, and (2) the spectrum is divided into multiplets before reference channels for background calculation are looked up. In our procedure no allowance is given to look for reference channels within the multiplets. It has also been found that correct background corrections can be performed only if a sufficient number of reference channels are available.
Quantitative Infrared Emission Spectroscopy of Phosphosilicate Glass on Silicon Wafers Using Multivariate Calibration
Authors: Wangmaneerat B. , McGuire J. A. , Niemczyk T. M. , Haaland D. M. , Linn J. H.
Published: June 2005

Phosphosilicate glass (PSG) is widely used in the microelectronics industry as a dielectric thin film. Determination of phosphorus concentration in these films is important for quality control. Data are presented here indicating that infrared emission spectroscopy combined with multivariate calibration can produce concentration determinations with a precision comparable to that of the electron microprobe reference method. Partial least-squares multivariate calibration methods applied to infrared emission spectra of twelve calibration standards of PSG films on silicon wafers at 225°C yielded a cross-validated standard error of prediction of 0.11 wt % P. It was found that the precisions of the phosphorus determinations were comparable for the use of absorbance spectra, single-beam emission spectra, or single-beam emission spectra ratioed to a blackbody at the same temperature.
Tunable, Coherent Vacuum Ultraviolet Radiation for Photoionization Mass Spectrometry
Authors: Van Bramer S. E. , Johnston M. V.
Published: June 2005

Coherent vacuum ultraviolet radiation between 118 and 129 nm (10.5 and 9.6 eV) is generated by third-harmonic conversion of radiation between 355 and 390 nm. The conversion efficiency of a single negatively dispersive rare gas (xenon or krypton) is compared to the efficiency of a mixture of a negatively dispersive gas with a positively dispersive gas (argon). The rare-gas mixtures are found to give significantly higher third-harmonic conversion efficiencies. They also have much narrower wavelength tuning ranges than the single gases. Optimum gas pressures, mixing ratios, and conversion efficiencies are tabulated at selected wavelengths. The photoionization characteristics of compounds that exhibit little or no parent ion abundance with conventional 70-eV electron impact ionization are evaluated with tunable vacuum ultraviolet radiation. n-Alkanes, alkenes, aldehydes, amines, carboxylic acids, ethers, and ketones are ionized without significant fragmentation by using wavelengths close to the ionization thresholds. Alcohols and esters, however, fragment extensively, even at the ionization threshold.
Characterization of Boron-Modified Co/Al2O3 Catalysts by EXAFS Spectroscopy
Authors: Fay Martin J. , Proctor Andrew , Hoffmann Douglas P. , Houalla Marwan , Hercules David M.
Published: June 2005

EXAFS spectroscopy has been used to examine the effect of boron on the structure of Co/Al2O3 catalysts. The EXAFS results from unmodified Co/Al2O3 catalysts indicated that Co3O4 was formed at Co loadings of 1.5 wt % Co and higher. The lowest-loading (0.7 wt % Co) catalyst showed evidence of both tetrahedral and octahedral Co surface species. Modification of the Co/Al2O3 catalysts with 3 wt % B completely suppressed the formation of Co3O4 for Co loadings of 6 wt % Co and lower. In the absence of Co3O4, the Co species formed on the 3 wt % boron-modified catalysts were in a highly disordered state with large first shell Co-O coordinations and large Co-O nearest-neighbor distances. Results from a constant Co loading series (3 wt % Co) indicated that Co3O4 formation decreased as the boron loading increased. The distribution of supported Co species determined by EXAFS was compared with previous characterization by ESCA and gravimetric measurements; good agreement was found. A two-phase procedure was used to analyze the EXAFS data from the Co/B/Al2O3 catalysts. This two-phase analysis considered both the fraction of Co EXAFS from bulk Co oxide (Co3O4) and the remaining fraction from Co surface species. This allowed the amount of Co3O4 to be determined quantitatively and enabled structural information to be obtained from the Co surface phase.
Improvements in the Generation of Quasi-Continuous, Tunable Ultraviolet Excitation for Raman Spectroscopy: Applications to Drug/Nucleotide Interactions
Authors: Benson Ronda L. , Iwata Koichi , Weaver William L. , Gustafson Terry L.
Published: June 2005

We demonstrate the generation of quasi-continuous ultraviolet excitation at wavelengths shorter than 240 nm using the frequency-doubled output of a synchronously pumped picosecond dye laser operating in the region of 420 nm. Owing to the relatively low peak power but high average power of the system, we obtain high-quality resonance Raman spectra at wavelengths as short as 209 nm. We apply the source to the study of the binding of anticancer drugs to DNA. In particular, we compare the binding of cis-diamminedichloroplatinum (II) (cisplatin) and cis-diammine-1, 1-cyclobutane dicarboxylate platinum (II) (carboplatin) to certain mononucleotides.
Quantitative Characterization of Fe/Al2O3 Catalysts. Part I: Oxidic Precursors
Authors: Hoffmann Douglas P. , Houalla Marwan , Proctor Andrew , Fay Martin J. , Hercules David M.
Published: June 2005

The structure of a series of Fe/Al2O3 catalysts containing from 1 to 24 weight percent iron has been examined by XRD, EXAFS, Mössbauer, ESCA, and gravimetric analysis. Two iron phases, Fe2O3 and Fe+3 in solid solution in the alumina support, are characterized as a function of iron loading. The combination of ESCA H2 titration and gravimetric analysis allows both quantitative and qualitative measurement of the two species. The amount of Fe2O3 phase increases with increasing iron loading for Fe1 to Fe24, whereas the amount of Fe+3 solid-solution phase increases with increasing iron loading for Fe1 to Fe6 and then levels off to approximately 2.2 wt % Fe for Fe8 to Fe24. The particle size of the Fe2O3 phase, determined from ESCA measurements, increases with increasing iron loading.
Infrared Study of 4-Substituted Benzaldehydes in Dilute Solution in Various Solvents: The Carbonyl Stretching Mode
Authors: Nyquist Richard A.
Published: June 2005

The carbonyl stretching mode in some of the 4- x-benzaldehydes is in Fermi resonance with an overtone of a fundamental which occurs at lower frequency. In general, the unperturbed vC=O frequencies for 4- x-benzaldehydes do appear to correlate with the σp values of the 4- x atom or group. The AN values of the solvents show a pseudo-correlation with the carbonyl and vasym. NO2 stretch vibrations of 4- x-benzaldehyde. However, neither σp nor AN values appear to take into account solute/solvent interactions such as intermolecular hydrogen bonding with the C=O group and with other sites in the molecule such as the phenyl group π system and with the electronic system of other functional groups, since the points in each plot do not correlate in the exact manner in each case.
Microheterogeneity of Sodium Dodecylsulfate Micelles Probed by Frequency-Domain Fluorometry
Authors: Huang Jingfan , Bright Frank V.
Published: June 2005

The microenvironment of sodium dodecylsulfate (SDS) micelles has been examined with the use of two fluorescent probes, 2-anilinonaphthalene-6-sulfonic acid (2,6-ANS) and N-phenyl-naphthylamine (1-AN). The fluorescence lifetimes are recovered from multifrequency phase and modulation data with the use of a global analysis protocol. The fluorescence decay kinetics of 2,6-ANS, which probes the outer-core region (i.e., the palisade layer) of SDS micelles, is characterized by a Lorentzian distribution. In contrast, a single discrete excited-state lifetime is observed for 1-AN, which is expected to position itself in the inner-core region of the micelle. Fluorescence lifetimes of these probes are investigated also as functions of temperature, concentration of counter ions (Na+ and Mg2+) and linear alcohols ( n-BuOH, n-PeOH, n-HeOH, and n-HepOH). The collective results confirm that the outer-core region of SDS micelles is microheterogeneous and the inner core is essentially homogeneous. In addition, the lifetimes and the partitioning of the outer-core probe, 2,6-ANS, appear to be more sensitive to variations in temperature and counter ions in comparison to those of the inner-core probe, 1-AN. The microenvironment of 2,6-ANS is found to be more heterogeneous at high temperature and low salt concentrations. This observation, we propose, is a result of different degrees of water penetration in the outer-core region. In the SDS system, the effects of micelle polydispersity and compositional diversity, on the environmental microheterogeneity of the fluorescent probe, seem to be minimal in comparison to water gradient effects.
Probing the Concentration Profiles of Additives in Polymers by IR Microspectroscopy: The Diffusion of Cyasorb UV531 in Polypropylene
Authors: Hsu S. C. , Lin-Vien D. , French R. N.
Published: June 2005

The recent advancement in FT-IR microspectrometry has provided a convenient way to probe the concentration profiles of additives in polymers. This technique opens up intriguing prospects for investigating additive/polymer or polymer/polymer interaction. In this work, the diffusion of a UV stabilizer, UV531, in polypropylene was selected to illustrate the applications of an IR microscope to monitor the concentration profiles of additives in polymers. In addition, a nonlinear least-squares fitting program was written to obtain diffusion coefficients from concentration profiles based on a theoretical model of the diffusion process. Because IR spectroscopy is functional-group specific, this technique is relatively insensitive to the presence of impurities or other additives in studying additive diffusion in polymers. The sensitivity, the aperturing capability, and the high spatial resolution of FT-IR microprobes make it possible to characterize a wider range of diffusion experiments in a shorter period of time than can be done using traditional techniques.
Memory and mediation in Los rubios: a contemporary perspective on the Argentine dictatorship
Authors: Page Joanna
Published: June 2005

This article analyses the particular contribution made to post-dictatorship memory by one of the most innovative films to have emerged in Argentina in recent years, Los rubios (Albertina Carri, 2003). It examines ways in which the film’s reflexivity and its subversion of
cinematic conventions become essential to its reworking of the themes of memory, absence and identity. The film comments explicitly on the difficulty of its own production, and indeed the debates surrounding the funding and distribution of Los rubios reveal with unusual clarity the complexity
of relationships between aesthetic, political and economic interests in contemporary Argentine film-making.
Personal States: Making Connections between People and Bureaucracy in Turkey
Authors: Bryant Rebecca
Published: June 2005

Personal States: Making Connections between People and Bureaucracy in Turkey Catherine Alexander (New York: Oxford University Press, 2002)
Droit et Cultures, special issue 2004, “Images and Uses of Law among Ordinary People”
Authors: Pottage Alain
Published: June 2005

Droit et Cultures, special issue 2004, “Images and Uses of Law among Ordinary People”Edited by Chantal Kourilsky‐Augeven (Paris: Société de Législation Comparée)
The Consumption of Justice: Emotions, Publicity, and Legal Culture in Marseille, 1264–1423
Authors: Ratel Guillaume
Published: June 2005

The Consumption of Justice: Emotions, Publicity, and Legal Culture in Marseille, 1264–1423 Daniel Lord Smail (Ithaca and London: Cornell University Press, 2003)
Anthropology and Law
Authors: Riley Mary
Published: June 2005

Anthropology and Law James M. Donovan and H. Edwin Anderson, III (New York: Berghahn Books, 2003)
The Dark Sides of Virtue: Reassessing International Humanitarianism
Authors: Session Noni
Published: June 2005

The Dark Sides of Virtue: Reassessing International Humanitarianism David Kennedy (Princeton: Princeton University Press, 2004)
Polygenic Mutation in Drosophila melanogaster
Authors: Mackay Trudy F C , Lyman Richard F , Lawrence Faye
Published: June 2005

Our ability to predict long-term responses to artificial and natural selection, and understand the mechanisms by which naturally occurring variation for quantitative traits is maintained, depends on detailed knowledge of the properties of spontaneous polygenic mutations, including the quantitative trait loci (QTL) at which mutations occur, mutation rates, and mutational effects. These parameters can be estimated by mapping QTL that cause divergence between mutation-accumulation lines that have been established from an inbred base population and selected for high and low trait values. Here, we have utilized quantitative complementation to deficiencies to map QTL at which spontaneous mutations affecting Drosophila abdominal and sternopleural bristle number have occurred in 11 replicate lines during 206 generations of divergent selection. Estimates of the numbers of mutations were consistent with diploid per-character mutation rates for bristle traits of 0.03. The ratio of the per-character mutation rate to total mutation rate (0.023) implies that >2% of the genome could affect just one bristle trait and that there must be extensive pleiotropy for quantitative phenotypes. The estimated mutational effects were not, however, additive and exhibited dependency on genetic background consistent with diminishing epistasis. However, these inferences must be tempered by the potential for epistatic interactions between spontaneous mutations and QTL affecting bristle number on the deficiency-bearing chromosomes, which could lead to overestimates in numbers of QTL and inaccurate inference of gene action.
Neutral Evolution of the Nonbinding Region of the Anthocyanin Regulatory Gene Ipmyb1 in IpomoeaSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY986823, AY986824, AY986825, AY986826, AY986827, AY986828, AY986829, AY986830, AY986831, AY986832, AY986833, AY986834, AY986835, AY986836, AY986837, AY986838, AY986839, AY986840, AY986841, AY986842, AY986843, AY986844, AY986845, AY986846, AY986847, AY986848, AY986849, AY986850, AY986851, AY986852, AY986853, AY986854, AY986855, AY986856, AY986857, AY986858, AY986859, AY986860, AY986861, AY986862, AY986863, AY986864, AY986865, AY986866, AY986867, AY986868, AY986869, AY986870, AY986871, AY986872, AY986873, AY986874, AY986875, AY986876, AY986877, AY986878, AY986879, AY986880, AY986881, AY986882, AY986883, AY986884, AY986885, AY986886, AY986887, AY986888, AY986889, AY986890, AY986891, AY986892, AY986893, AY986894, AY986895, AY986896, AY986897, AY986898.
Authors: Chang Shu-Mei , Lu Yingqing , Rausher Mark D
Published: June 2005

Plant transcription factors often contain domains that evolve very rapidly. Although it has been suggested that this rapid evolution may contribute substantially to phenotypic differentiation among species, this suggestion has seldom been tested explicitly. We tested the validity of this hypothesis by examining the rapidly evolving non-DNA-binding region of an R2R3-myb transcription factor that regulates anthocyanin expression in flowers of the genus Ipomoea. We first provide evidence that the W locus in Ipomoea purpurea, which determines whether flowers will be pigmented or white, corresponds to a myb gene segregating in southeastern U.S. populations for one functional allele and one nonfunctional allele. While the binding domain exhibits substantial selective constraint, the nonbinding region evolves at an average Ka/Ks ratio of 0.74. This elevated rate of evolution is due to relaxed constraint rather than to increased levels of positive selection. Despite this relaxed constraint, however, ∼20–25% of the codons, randomly distributed throughout the nonbinding region, are highly constrained, with the remainder evolving neutrally, indicating that the entire region performs important function(s). Our results provide little indication that rapid evolution in this regulatory gene is driven by natural selection or that it is responsible for floral-color differences among Ipomoea species.
Balancing Selection in the Wild: Testing Population Genetics Theory of Self-Incompatibility in the Rare SpeciesBrassica insularis
Authors: Glémin Sylvain , Gaude Thierry , Guillemin Marie-Laure , Lourmas Mathieu , Olivieri Isabelle , Mignot Agnès
Published: June 2005

Self-incompatibility (SI) systems are widespread mechanisms that prevent self-fertilization in angiosperms. They are generally encoded by one genome region containing several multiallelic genes, usually called the S-locus. They involve a recognition step between the pollen and the pistil component and pollen is rejected when it shares alleles with the pistil. The direct consequence is that rare alleles are favored, such that the S-alleles are subject to negative frequency-dependent selection. Several theoretical articles have predicted the specific patterns of polymorphism, compared to neutral loci, expected for such genes under balancing selection. For instance, many more alleles should be maintained and populations should be less differentiated than for neutral loci. However, empirical tests of these predictions in natural populations have remained scarce. Here, we compare the genetic structure at the S-locus and microsatellite markers for five natural populations of the rare species Brassica insularis. As in other Brassica species, B. insularis has a sporophytic SI system for which molecular markers are available. Our results match well the theoretical predictions and constitute the first general comparison of S-allele and neutral polymorphism.
Drosophila ERCC1 Is Required for a Subset of MEI-9-Dependent Meiotic Crossovers
Authors: Radford Sarah J , Goley Elizabeth , Baxter Kimberly , McMahan Susan , Sekelsky Jeff
Published: June 2005

Drosophila MEI-9 is the catalytic subunit of a DNA structure-specific endonuclease required for nucleotide excision repair (NER). The enzymatic activity of this endonuclease during NER requires the presence of a second, noncatalytic subunit called ERCC1. In addition to its role in NER, MEI-9 is required for the generation of most meiotic crossovers. To better understand the role of MEI-9 in crossover formation, we report here the characterization of the Drosophila Ercc1 gene. We created an Ercc1 mutant through homologous gene targeting. We find that Ercc1 mutants are identical to mei-9 mutants in sensitivity to DNA-damaging agents, but have a less severe reduction in the number of meiotic crossovers. MEI-9 protein levels are reduced in Ercc1 mutants; however, overexpression of MEI-9 is not sufficient to restore meiotic crossing over in Ercc1 mutants. We conclude that MEI-9 can generate some meiotic crossovers in an ERCC1-independent manner.
Aneuploidy and Genetic Variation in the Arabidopsis thaliana Triploid Response
Authors: Henry Isabelle M , Dilkes Brian P , Young Kim , Watson Brian , Wu Helen , Comai Luca
Published: June 2005

Polyploidy, the inheritance of more than two genome copies per cell, has played a major role in the evolution of higher plants. Little is known about the transition from diploidy to polyploidy but in some species, triploids are thought to function as intermediates in this transition. In contrast, in other species triploidy is viewed as a block. We investigated the responses of Arabidopsis thaliana to triploidy. The role of genetic variability was tested by comparing triploids generated from crosses between Col-0, a diploid, and either a natural autotetraploid (Wa-1) or an induced tetraploid of Col-0. In this study, we demonstrate that triploids of A. thaliana are fertile, producing a swarm of different aneuploids. Propagation of the progeny of a triploid for a few generations resulted in diploid and tetraploid cohorts. This demonstrated that, in A. thaliana, triploids can readily form tetraploids and function as bridges between euploid types. Genetic analysis of recombinant inbred lines produced from a triploid identified a locus on chromosome I exhibiting allelic bias in the tetraploid lines but not in the diploid lines. Thus, genetic variation was subject to selection contingent on the final ploidy and possibly acting during the protracted aneuploid phase.
The Exchangeability of Amino Acids in Proteins
Authors: Yampolsky Lev Y , Stoltzfus Arlin
Published: June 2005

The comparative analysis of protein sequences depends crucially on measures of amino acid similarity or distance. Many such measures exist, yet it is not known how well these measures reflect the operational exchangeability of amino acids in proteins, since most are derived by methods that confound a variety of effects, including effects of mutation. In pursuit of a pure measure of exchangeability, we present (1) a compilation of data on the effects of 9671 amino acid exchanges engineered and assayed in a set of 12 proteins; (2) a statistical procedure to combine results from diverse assays of exchange effects; (3) a matrix of “experimental exchangeability” values EXij derived from applying this procedure to the compiled data; and (4) a set of three tests designed to evaluate the power of an exchangeability measure to (i) predict the effects of amino acid exchanges in the laboratory, (ii) account for the disease-causing potential of missense mutations in the human population, and (iii) model the probability of fixation of missense mutations in evolution. EX not only captures useful information on exchangeability while remaining free of other effects, but also outperforms all measures tested except for the best-performing alignment scoring matrix, which is comparable in performance.
Distributions of Beneficial Fitness Effects in RNA
Authors: Cowperthwaite Matthew C , Bull J J , Meyers Lauren Ancel
Published: June 2005

Beneficial mutations are the driving force of evolution by natural selection. Yet, relatively little is known about the distribution of the fitness effects of beneficial mutations in populations. Recent work of Gillespie and Orr suggested some of the first generalizations for the distributions of beneficial fitness effects and, surprisingly, they depend only weakly on biological details. In particular, the theory suggests that beneficial mutations obey an exponential distribution of fitness effects, with the same exponential parameter across different regions of genotype space, provided only that few possible beneficial mutations are available to that genotype. Here we tested this hypothesis with a quasi-empirical model of RNA evolution in which fitness is based on the secondary structures of molecules and their thermodynamic stabilities. The fitnesses of randomly selected genotypes appeared to follow a Gumbel-type distribution and thus conform to a basic assumption of adaptation theory. However, the observed distributions of beneficial fitness effects conflict with specific predictions of the theory. In particular, the distributions of beneficial fitness effects appeared exponential only when the vast majority of small-effect beneficial mutations were ignored. Additionally, the distribution of beneficial fitness effects varied with the fitness of the parent genotype. We believe that correlation of the fitness values among similar genotypes is likely the cause of the departure from the predictions of recent adaptation theory. Although in conflict with the current theory, these results suggest that more complex statistical generalizations about beneficial mutations may be possible.
Natural Variation in the Pto Pathogen Resistance Gene Within Species of Wild Tomato (Lycopersicon). I. Functional Analysis of Pto Alleles
Authors: Rose Laura E , Langley Charles H , Bernal Adriana J , Michelmore Richard W
Published: June 2005

Disease resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) in the cultivated tomato, Lycopersicon esculentum, and the closely related L. pimpinellifolium is triggered by the physical interaction between plant disease resistance protein, Pto, and the pathogen avirulence protein, AvrPto. To investigate the extent to which variation in the Pto gene is responsible for naturally occurring variation in resistance to Pst, we determined the resistance phenotype of 51 accessions from seven species of Lycopersicon to isogenic strains of Pst differing in the presence of avrPto. One-third of the plants displayed resistance specifically when the pathogen expressed AvrPto, consistent with a gene-for-gene interaction. To test whether this resistance in these species was conferred specifically by the Pto gene, alleles of Pto were amplified and sequenced from 49 individuals and a subset (16) of these alleles was tested in planta using Agrobacterium-mediated transient assays. Eleven alleles conferred a hypersensitive resistance response (HR) in the presence of AvrPto, while 5 did not. Ten amino acid substitutions associated with the absence of AvrPto recognition and HR were identified, none of which had been identified in previous structure-function studies. Additionally, 3 alleles encoding putative pseudogenes of Pto were isolated from two species of Lycopersicon. Therefore, a large proportion, but not all, of the natural variation in the reaction to strains of Pst expressing AvrPto can be attributed to sequence variation in the Pto gene.
Genome-Wide Analysis on Inbreeding Effects on Gene Expression in Drosophila melanogaster
Authors: Kristensen Torsten Nygaard , Sørensen Peter , Kruhøffer Mogens , Pedersen Kamilla Sofie , Loeschcke Volker
Published: June 2005

The deleterious consequences of inbreeding, especially in the form of inbreeding depression, are well known. However, little is known about how inbreeding affects genome-wide gene expression. Here, we show that inbreeding changes transcription levels for a number of genes. Gene expression profiles of Drosophila melanogaster lines inbred to F ≈ 0.67 at different rates changed relative to those of noninbred lines, but the rate of inbreeding did not significantly affect gene expression patterns. Genes being differentially expressed with inbreeding are disproportionately involved in metabolism and stress responses, suggesting that inbreeding acts like an environmental stress factor.
Selection for Recombination in Structured Populations
Authors: Martin Guillaume , Otto Sarah P , Lenormand Thomas
Published: June 2005

In finite populations, linkage disequilibria generated by the interaction of drift and directional selection (Hill-Robertson effect) can select for sex and recombination, even in the absence of epistasis. Previous models of this process predict very little advantage to recombination in large panmictic populations. In this article we demonstrate that substantial levels of linkage disequilibria can accumulate by drift in the presence of selection in populations of any size, provided that the population is subdivided. We quantify (i) the linkage disequilibrium produced by the interaction of drift and selection during the selective sweep of beneficial alleles at two loci in a subdivided population and (ii) the selection for recombination generated by these disequilibria. We show that, in a population subdivided into n demes of large size N, both the disequilibrium and the selection for recombination are equivalent to that expected in a single population of a size intermediate between the size of each deme (N) and the total size (nN), depending on the rate of migration among demes, m. We also show by simulations that, with small demes, the selection for recombination is stronger than both that expected in an unstructured population (m = 1 − 1/n) and that expected in a set of isolated demes (m = 0). Indeed, migration maintains polymorphisms that would otherwise be lost rapidly from small demes, while population structure maintains enough local stochasticity to generate linkage disequilibria. These effects are also strong enough to overcome the twofold cost of sex under strong selection when sex is initially rare. Overall, our results show that the stochastic theories of the evolution of sex apply to a much broader range of conditions than previously expected.
A 1927 Study Supports a Current Genetic Model for Inheritance of Human Scalp Hair-Whorl Orientation and Hand-Use Preference Traits
Authors: Klar Amar J S
Published: June 2005

The basis of right- vs. left-hand-use preference in humans has been debated for a long time. Culturally learned, birth stress, and biologically specified causes are the prominent etiologies under consideration. A 2003 (Klar 2003) study reported a correlation between a person's preferred hand and the scalp hair-whorl orientation developed on the head. By reinterpreting results of a 1927 (Schwarzburg 1927) study on the genetics of the hair-whorl trait, support for a recent single gene, two-allele “random-recessive model” for both hair-whorl orientation and handedness trait inheritance is demonstrated.
Imprinting Capacity of Gamete Lineages in Caenorhabditis elegans
Authors: Sha Ky , Fire Andrew
Published: June 2005

We have observed a gamete-of-origin imprinting effect in C. elegans using a set of GFP reporter transgenes. From a single progenitor line carrying an extrachromosomal unc-54::gfp transgene array, we generated three independent autosomal integrations of the unc-54::gfp transgene. The progenitor line, two of its three integrated derivatives, and a nonrelated unc-119:gfp transgene exhibit an imprinting effect: single-generation transmission of these transgenes through the male germline results in ∼1.5- to 2.0-fold greater expression than transmission through the female germline. There is a detectable resetting of the imprint after passage through the opposite germline for a single generation, indicating that the imprinted status of the transgenes is reversible. In cases where the transgene is maintained in either the oocyte lineage or sperm lineage for multiple, consecutive generations, a full reset requires passage through the opposite germline for several generations. Taken together, our results indicate that C. elegans has the ability to imprint chromosomes and that differences in the cell and/or molecular biology of oogenesis and spermatogenesis are manifest in an imprint that can persist in both somatic and germline gene expression for multiple generations.
Genomic Mapping of Direct and Correlated Responses to Long-Term Selection for Rapid Growth Rate in Mice
Authors: Allan Mark F , Eisen Eugene J , Pomp Daniel
Published: June 2005

Understanding the genetic architecture of traits such as growth, body composition, and energy balance has become a primary focus for biomedical and agricultural research. The objective of this study was to map QTL in a large F2 (n = 1181) population resulting from an intercross between the M16 and ICR lines of mice. The M16 line, developed by long-term selection for 3- to 6-week weight gain, is larger, heavier, fatter, hyperphagic, and diabetic relative to its randomly selected control line of ICR origin. The F2 population was phenotyped for growth and energy intake at weekly intervals from 4 to 8 weeks of age and for body composition and plasma levels of insulin, leptin, TNFα, IL6, and glucose at 8 weeks and was genotyped for 80 microsatellite markers. Since the F2 was a cross between a selection line and its unselected control, the QTL identified likely represent genes that contributed to direct and correlated responses to long-term selection for rapid growth rate. Across all traits measured, 95 QTL were identified, likely representing 19 unique regions on 13 chromosomes. Four chromosomes (2, 6, 11, and 17) harbored loci contributing disproportionately to selection response. Several QTL demonstrating differential regulation of regional adipose deposition and age-dependent regulation of growth and energy consumption were identified.
Genetic Screens for Enhancers of brahma Reveal Functional Interactions Between the BRM Chromatin-Remodeling Complex and the Delta-Notch Signal Transduction Pathway in Drosophila
Authors: Armstrong Jennifer A , Sperling Adam S , Deuring Renate , Manning Laurina , Moseley Sarah L , Papoulas Ophelia , Piatek Caroline I , Doe Chris Q , Tamkun John W
Published: June 2005

The Drosophila trithorax group gene brahma (brm) encodes the ATPase subunit of a 2-MDa chromatin-remodeling complex. brm was identified in a screen for transcriptional activators of homeotic genes and subsequently shown to play a global role in transcription by RNA polymerase II. To gain insight into the targeting, function, and regulation of the BRM complex, we screened for mutations that genetically interact with a dominant-negative allele of brm (brmK804R). We first screened for dominant mutations that are lethal in combination with a brmK804R transgene under control of the brm promoter. In a distinct but related screen, we identified dominant mutations that modify eye defects resulting from expression of brmK804R in the eye-antennal imaginal disc. Mutations in three classes of genes were identified in our screens: genes encoding subunits of the BRM complex (brm, moira, and osa), other proteins directly involved in transcription (zerknullt and RpII140), and signaling molecules (Delta and vein). Expression of brmK804R in the adult sense organ precursor lineage causes phenotypes similar to those resulting from impaired Delta-Notch signaling. Our results suggest that signaling pathways may regulate the transcription of target genes by regulating the activity of the BRM complex.
Transvection at the vestigial Locus of Drosophila melanogaster
Authors: Coulthard Alistair B , Nolan Nadia , Bell John B , Hilliker Arthur J
Published: June 2005

Transvection is a phenomenon wherein gene expression is effected by the interaction of alleles in trans and often results in partial complementation between mutant alleles. Transvection is dependent upon somatic pairing between homologous chromosome regions and is a form of interallelic complementation that does not occur at the polypeptide level. In this study we demonstrated that transvection could occur at the vestigial (vg) locus by revealing that partial complementation between two vg mutant alleles could be disrupted by changing the genomic location of the alleles through chromosome rearrangement. If chromosome rearrangements affect transvection by disrupting somatic pairing, then combining chromosome rearrangements that restore somatic pairing should restore transvection. We were able to restore partial complementation in numerous rearrangement trans-heterozygotes, thus providing substantial evidence that the observed complementation at vg results from a transvection effect. Cytological analyses revealed this transvection effect to have a large proximal critical region, a feature common to other transvection effects. In the Drosophila interphase nucleus, paired chromosome arms are separated into distinct, nonoverlapping domains. We propose that if the relative position of each arm in the nucleus is determined by the centromere as a relic of chromosome positions after the last mitotic division, then a locus will be displaced to a different territory of the interphase nucleus relative to its nonrearranged homolog by any rearrangement that links that locus to a different centromere. This physical displacement in the nucleus hinders transvection by disrupting the somatic pairing of homologous chromosomes and gives rise to proximal critical regions.
End3p-Mediated Endocytosis Is Required for Spore Wall Formation in Saccharomyces cerevisiae
Authors: Morishita Masayo , Engebrecht JoAnne
Published: June 2005

During sporulation in Saccharomyces cerevisiae, vesicles transported to the vicinity of spindle pole bodies are fused to each other to generate bilayered prospore membranes (PSMs). PSMs encapsulate the haploid nuclei that arise from the meiotic divisions and serve as platforms for spore wall deposition. Membrane trafficking plays an important role in supplying vesicles for these processes. The endocytosis-deficient mutant, end3Δ, sporulated poorly and the spores produced lost resistance to ether vapor, suggesting that END3-mediated endocytosis is important for sporulation. End3p-GFP localized to cell and spore peripheries in vegetative and sporulating cells and colocalized with actin structures. Correspondingly, the actin cytoskeleton appeared aberrant during sporulation in end3Δ. Analysis of meiosis in end3Δ mutants revealed that the meiotic divisions occurred with wild-type kinetics. Furthermore, PSMs were assembled normally. However, the levels of proteins required for spore wall synthesis and components of the spore wall layers at spores were reduced, indicating that end3Δ mutants are defective in spore wall synthesis. Thus, END3-mediated endocytosis is important for spore wall formation. Additionally, cytological analyses suggest that trafficking between the plasma membrane and PSMs is important earlier during sporulation.
Epistasis in Monkeyflowers
Authors: Kelly John K
Published: June 2005

Epistasis contributes significantly to intrapopulation variation in floral morphology, development time, and male fitness components of Mimulus guttatus. This is demonstrated with a replicated line-cross experiment involving slightly over 7000 plants. The line-cross methodology is based on estimates for means. It thus has greater power than the variance partitioning approaches historically used to estimate epistasis within populations. The replication of the breeding design across many pairs of randomly extracted, inbred lines is necessary given the diversity of multilocus genotypes residing within an outbred deme. Male fitness is shown to exhibit synergistic epistasis, an accelerating decline in fitness with inbreeding. Synergism is a necessary, but not sufficient, condition for a mutational deterministic hypothesis for the evolutionary maintenance of sexual reproduction. Unlike male fitness measures, flower morphology and development time yield positive evidence of epistasis but not of synergism. The results for these traits suggest that epistatic effects are variable across genetic backgrounds or sets of interacting loci.
A Duplication in the Canine β-Galactosidase Gene GLB1 Causes Exon Skipping and GM1-Gangliosidosis in Alaskan Huskies
Authors: Kreutzer Robert , Leeb Tosso , Müller Gundi , Moritz Andreas , Baumgärtner Wolfgang
Published: June 2005

GM1-gangliosidosis is a lysosomal storage disease that is inherited as an autosomal recessive disorder, predominantly caused by structural defects in the β-galactosidase gene (GLB1). The molecular cause of GM1-gangliosidosis in Alaskan huskies was investigated and a novel 19-bp duplication in exon 15 of the GLB1 gene was identified. The duplication comprised positions +1688–+1706 of the GLB1 cDNA. It partially disrupted a potential exon splicing enhancer (ESE), leading to exon skipping in a fraction of the transcripts. Thus, the mutation caused the expression of two different mRNAs from the mutant allele. One transcript contained the complete exon 15 with the 19-bp duplication, while the other transcript lacked exon 15. In the transcript containing exon 15 with the 19-bp duplication a premature termination codon (PTC) appeared, but due to its localization in the last exon of canine GLB1, nonsense-mediated RNA decay (NMD) did not occur. As a consequence of these molecular events two different truncated GLB1 proteins are predicted to be expressed from the mutant GLB1 allele. In heterozygous carrier animals the wild-type allele produces sufficient amounts of the active enzyme to prevent clinical signs of disease. In affected homozygous dogs no functional GLB1 is synthesized and GM1-gangliosidosis occurs.
Multiple Roles of a Heterotrimeric G-Protein γ-Subunit in Governing Growth and Development of Aspergillus nidulans
Authors: Seo Jeong-Ah , Han Kap-Hoon , Yu Jae-Hyuk
Published: June 2005

Vegetative growth signaling in the filamentous fungus Aspergillus nidulans is primarily mediated by the heterotrimeric G-protein composed of FadA (Gα), SfaD (Gβ), and a presumed Gγ. Analysis of the A. nidulans genome identified a single gene named gpgA encoding a putative Gγ-subunit. The predicted GpgA protein consists of 90 amino acids showing 72% similarity with yeast Ste18p. Deletion (Δ) of gpgA resulted in restricted vegetative growth and lowered asexual sporulation. Moreover, similar to the ΔsfaD mutant, the ΔgpgA mutant was unable to produce sexual fruiting bodies (cleistothecia) in self-fertilization and was severely impaired with cleistothecial development in outcross, indicating that both SfaD and GpgA are required for fruiting body formation. Developmental and morphological defects caused by deletion of flbA encoding an RGS protein negatively controlling FadA-mediated vegetative growth signaling were suppressed by ΔgpgA, indicating that GpgA functions in FadA-SfaD-mediated vegetative growth signaling. However, deletion of gpgA could not bypass the need for the early developmental activator FluG in asexual sporulation, suggesting that GpgA functions in a separate signaling pathway. We propose that GpgA is the only A. nidulans Gγ-subunit and is required for normal vegetative growth as well as proper asexual and sexual developmental progression.