bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetics of Barley Hooded Suppression
Authors: Roig Cristina , Pozzi Carlo , Santi Luca , Müller Judith , Wang Yamei , Stile Maria Rosaria , Rossini Laura , Stanca Michele , Salamini Francesco 
Published: August 2004

Abstract
The molecular basis of the barley dominant Hooded (K) mutant is a duplication of 305 bp in intron IV of the homeobox gene Bkn3. A chemical mutagenesis screen was carried out to identify genetical factors that participate in Bkn3 intron-mediated gene regulation. Plants from recurrently mutagenized KK seeds were examined for the suppression of the hooded awn phenotype induced by the K allele and, in total, 41 suK (suppressor of K) recessive mutants were identified. Complementation tests established the existence of five suK loci, and alleles suKB-4, suKC-33, suKD-25, suKE-74, and suKF-76 were studied in detail. All K-suppressed mutants showed a short-awn phenotype. The suK loci have been mapped by bulked segregant analysis nested in a standard mapping procedure based on AFLP markers. K suppressor loci suKB, B, E, and F all map in a short interval of chromosome 7H, while the locus suKD is assigned to chromosome 5H. A complementation test between the four suK mutants mapping on chromosome 7H and the short-awn mutant lks2, located nearby, excluded the allelism between suK loci and lks2. The last experiment made clear that the short-awn phenotype of suK mutants is due to a specific dominant function of the K allele, a function that is independent from the control on hood formation. The suK loci are discussed as candidate participants in the regulation of Bkn3 expression.
Comparative Mapping and Rapid Karyotypic Evolution in the Genus Helianthus
Authors: Burke John M , Lai Zhao , Salmaso Marzia , Nakazato Takuya , Tang Shunxue , Heesacker Adam , Knapp Steven J , Rieseberg Loren H 
Published: August 2004

AbstractComparative genetic linkage maps provide a powerful tool for the study of karyotypic evolution. We constructed a joint SSR/RAPD genetic linkage map of the Helianthus petiolaris genome and used it, along with an integrated SSR genetic linkage map derived from four independent H. annuus mapping populations, to examine the evolution of genome structure between these two annual sunflower species. The results of this work indicate the presence of 27 colinear segments resulting from a minimum of eight translocations and three inversions. These 11 rearrangements are more than previously suspected on the basis of either cytological or genetic map-based analyses. Taken together, these rearrangements required a minimum of 20 chromosomal breakages/fusions. On the basis of estimates of the time since divergence of these two species (750,000–1,000,000 years), this translates into an estimated rate of 5.5–7.3 chromosomal rearrangements per million years of evolution, the highest rate reported for any taxonomic group to date.
Genetic Variation at the Tomato Cf-4/Cf-9 Locus Induced by EMS Mutagenesis and Intralocus Recombination
Authors: Wulff Brande B H , Thomas Colwyn M , Parniske Martin , Jones Jonathan D G 
Published: August 2004

Abstract
The interaction between tomato (Lycopersicon esculentum) and the leaf mold pathogen Cladosporium fulvum is an excellent model for investigating disease resistance gene evolution. The interaction is controlled in a gene-for-gene manner by Cf genes that encode type I transmembrane extracellular leucinerich repeat glycoproteins that recognize their cognate fungal avirulence (Avr) proteins. Cf-4 from L. hirsutum and Cf-9 from L. pimpinellifolium are located at the same locus on the short arm of tomato chromosome 1 in an array of five paralogs. Molecular analysis has shown that one mechanism for generating sequence variation in Cf genes is intragenic sequence exchange through unequal crossing over or gene conversion. To investigate this we used a facile genetic selection to identify novel haplotypes in the progeny of Cf-4/Cf-9 trans-heterozygotes that lacked Cf-4 and Cf-9. This selection is based on the ability of Avr4 and Avr9 to induce Cf-4- or Cf-9-dependent seedling death. The crossovers were localized to the same intergenic region defining a recombination hotspot in this cross. As part of a structure-function analysis of Cf-9 and Cf-4, nine EMS-induced mutant alleles have been characterized. Most mutations result in single-amino-acid substitutions in their C terminus at residues that are conserved in other Cf proteins.
Comparative Population Genetics of the Panicoid Grasses: Sequence Polymorphism, Linkage Disequilibrium and Selection in a Diverse Sample of Sorghum bicolor
Authors: Hamblin Martha T , Mitchell Sharon E , White Gemma M , Gallego Javier , Kukatla Rakesh , Wing Rod A , Paterson Andrew H , Kresovich Stephen 
Published: August 2004

Abstract
Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an outcrosser, has a high level of sequence variation and a limited extent of LD. Sorghum, a closely related but largely self-pollinating panicoid grass, is expected to have higher levels of LD. As a first step in estimation of population genetic parameters in sorghum, we surveyed 27 diverse S. bicolor accessions for sequence variation at a total of 29,186 bp in 95 short regions derived from genetically mapped RFLPs located throughout the genome. Consistent with its higher level of inbreeding, the extent of LD is at least severalfold greater in sorghum than in maize. Total sequence variation in sorghum is about fourfold lower than that in maize, while synonymous variation is fivefold lower, suggesting a smaller effective population size in sorghum. Because we surveyed a species-wide sample, the mating system, which primarily affects population-level diversity, may not be primarily responsible for this difference. Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome.
Frequency-Dependent Selection With Dominance: A Window Onto the Behavior of the Mean Fitness
Authors: Asmussen Marjorie A , Cartwright Reed A , Spencer Hamish G 
Published: August 2004

Abstract
Selection in which fitnesses vary with the changing genetic composition of the population may facilitate the maintenance of genetic diversity in a wide range of organisms. Here, a detailed theoretical investigation is made of a frequency-dependent selection model, in which fitnesses are based on pairwise interactions between the two phenotypes at a diploid, diallelic, autosomal locus with complete dominance. The allele frequency dynamics are fully delimited analytically, along with all possible shapes of the mean fitness function in terms of where it increases or decreases as a function of the current allele frequency in the population. These results in turn allow possibly the first complete characterization of the dynamical behavior by the mean fitness through time under frequency-dependent selection. Here the mean fitness (i) monotonically increases, (ii) monotonically decreases, (iii) initially increases and then decreases, or (iv) initially decreases and then increases as equilibrium is approached. We analytically derive the exact initial and fitness conditions that produce each dynamic and how often each arises. Computer simulations with random initial conditions and fitnesses reveal that the potential decline in mean fitness is not negligible; on average a net decrease occurs 20% of the time and reduces the mean fitness by &gt;17%.
In Vivo Analysis of Synaptonemal Complex Formation During Yeast Meiosis
Authors: White Eric J , Cowan Carrie , Cande W Zacheus , Kaback David B 
Published: August 2004

Abstract
During meiotic prophase a synaptonemal complex (SC) forms between each pair of homologous chromosomes and is believed to be involved in regulating recombination. Studies on SCs usually destroy nuclear architecture, making it impossible to examine the relationship of these structures to the rest of the nucleus. In Saccharomyces cerevisiae the meiosis-specific Zip1 protein is found throughout the entire length of each SC. To analyze the formation and structure of SCs in living cells, a functional ZIP1::GFP fusion was constructed and introduced into yeast. The ZIP1::GFP fusion produced fluorescent SCs and rescued the spore lethality phenotype of zip1 mutants. Optical sectioning and fluorescence deconvolution light microscopy revealed that, at zygotene, SC assembly was initiated at foci that appeared uniformly distributed throughout the nuclear volume. At early pachytene, the full-length SCs were more likely to be localized to the nuclear periphery while at later stages the SCs appeared to redistribute throughout the nuclear volume. These results suggest that SCs undergo dramatic rearrangements during meiotic prophase and that pachytene can be divided into two morphologically distinct substages: pachytene A, when SCs are perinuclear, and pachytene B, when SCs are uniformly distributed throughout the nucleus. ZIP1::GFP also facilitated the enrichment of fluorescent SC and the identification of meiosis-specific proteins by MALDI-TOF mass spectroscopy.
Mutators in Space: The Dynamics of High-Mutability Clones in a Two-Patch Model
Authors: Travis E R , Travis J M J 
Published: August 2004

AbstractClones of bacteria possessing high-mutability rates (or mutators) are being observed in an increasing number of species. In a constant environment most mutations are deleterious, and hence the spontaneous mutation rate is generally low. However, mutators may play an important role in the adaptation of organisms to changing environments. To date, theoretical work has focused on temporal variability in the environment, implicitly assuming that environmental conditions are constant through space. Here, we develop a two-patch model to investigate how spatiotemporal environmental variability and dispersal might influence mutator dynamics. Environmental conditions in each patch fluctuate between two states; the rate of fluctuation varies in each patch at differing phase angles. We find that at low and intermediate rates of fluctuation, an increase in dispersal results in a decrease in the density of mutators. However, at high rates of environmental change, dispersal causes an increase in mutator density. For all frequencies of environmental fluctuation these trends are enhanced as the phase angle approaches 180°. We argue that future work, both empirical and theoretical, is needed to improve our understanding of how spatiotemporal variability impacts on mutator densities and dynamics.
Stochastic Gene Expression in Fluctuating Environments
Authors: Thattai Mukund , van Oudenaarden Alexander 
Published: August 2004

Abstract
Stochastic mechanisms can cause a group of isogenic bacteria, each subject to identical environmental conditions, to nevertheless exhibit diverse patterns of gene expression. The resulting phenotypic subpopulations will typically have distinct growth rates. This behavior has been observed in several contexts, including sugar metabolism and pili phase variation. Under fixed environmental conditions, the net growth rate of the population is maximized when all cells are of the fastest growing phenotype, so it is unclear what fitness advantage is conferred by population heterogeneity. However, unlike ideal laboratory conditions, natural environments tend to fluctuate, either periodically or randomly. Here we use a stochastic population model to show that, during growth in such fluctuating environments, a dynamically heterogenous bacterial population can sometimes achieve a higher net growth rate than a homogenous one. By using stochastic mechanisms to sample several distinct phenotypes, the bacteria are able to anticipate and take advantage of sudden changes in their environment. However, this heterogeneity is beneficial only if the bacterial response rate is sufficiently low. Our results could be useful in the design of artificial evolution experiments and in the optimization of fermentation processes.
Natural Selection Affects Frequencies of AG and GT Dinucleotides at the 5′ and 3′ Ends of Exons
Authors: Eskesen S T , Eskesen F N , Ruvinsky A 
Published: August 2004

Abstract
GT and AG, located at the 5′ and 3′ ends of introns, are important for correct splicing. It is anticipated that natural selection decreases frequency of AG and GT near the 5′ and 3′ ends of exons, preventing appearance of cryptic splicing sites. The data presented in this article support the expectation.
MrpL36p, a Highly Diverged L31 Ribosomal Protein Homolog With Additional Functional Domains in Saccharomyces cerevisiae Mitochondria
Authors: Williams Elizabeth H , Perez-Martinez Xochitl , Fox Thomas D 
Published: August 2004

Abstract
Translation in mitochondria utilizes a large complement of ribosomal proteins. Many mitochondrial ribosomal components are clearly homologous to eubacterial ribosomal proteins, but others appear unique to the mitochondrial system. A handful of mitochondrial ribosomal proteins appear to be eubacterial in origin but to have evolved additional functional domains. MrpL36p is an essential mitochondrial ribosomal large-subunit component in Saccharomyces cerevisiae. Increased dosage of MRPL36 also has been shown to suppress certain types of translation defects encoded within the mitochondrial COX2 mRNA. A central domain of MrpL36p that is similar to eubacterial ribosomal large-subunit protein L31 is sufficient for general mitochondrial translation but not suppression, and proteins bearing this domain sediment with the ribosomal large subunit in sucrose gradients. In contrast, proteins lacking the L31 domain, but retaining a novel N-terminal sequence and a C-terminal sequence with weak similarity to the Escherichia coli signal recognition particle component Ffh, are sufficient for dosage suppression and do not sediment with the large subunit of the ribosome. Interestingly, the activity of MrpL36p as a dosage suppressor exhibits gene and allele specificity. We propose that MrpL36p represents a highly diverged L31 homolog with derived domains functioning in mRNA selection in yeast mitochondria.
Phenotypic Plasticity in Bacterial Plasmids
Authors: Turner Paul E 
Published: August 2004

AbstractPlasmid pB15 was previously shown to evolve increased horizontal (infectious) transfer at the expense of reduced vertical (intergenerational) transfer and vice versa, a key trade-off assumed in theories of parasite virulence. Whereas the models predict that susceptible host abundance should determine which mode of transfer is selectively favored, host density failed to mediate the trade-off in pB15. One possibility is that the plasmid's transfer deviates from the assumption that horizontal spread (conjugation) occurs in direct proportion to cell density. I tested this hypothesis using Escherichia coli/pB15 associations in laboratory serial culture. Contrary to most models of plasmid transfer kinetics, my data show that pB15 invades static (nonshaking) bacterial cultures only at intermediate densities. The results can be explained by phenotypic plasticity in traits governing plasmid transfer. As cells become more numerous, the plasmid's conjugative transfer unexpectedly declines, while the trade-off between transmission routes causes vertical transfer to increase. Thus, at intermediate densities the plasmid's horizontal transfer can offset selection against plasmid-bearing cells, but at high densities pB15 conjugates so poorly that it cannot invade. I discuss adaptive vs. nonadaptive causes for the phenotypic plasticity, as well as potential mechanisms that may lead to complex transfer dynamics of plasmids in liquid environments.
Genetic Interactions With C-Terminal Domain (CTD) Kinases and the CTD of RNA Pol II Suggest a Role for ESS1 in Transcription Initiation and Elongation in Saccharomyces cerevisiae
Authors: Wilcox Cathy B , Rossettini Anne , Hanes Steven D 
Published: August 2004

Abstract
Ess1 is an essential prolyl isomerase that binds the C-terminal domain (CTD) of Rpb1, the large subunit of RNA polymerase II. Ess1 is proposed to control transcription by isomerizing phospho-Ser-Pro peptide bonds within the CTD repeat. To determine which step(s) in the transcription cycle might require Ess1, we examined genetic interactions between ESS1 and genes encoding the known CTD kinases (KIN28, CTK1, BUR1, and SRB10). Although genetic interactions were identified between ESS1 and all four kinases, the clearest interactions were with CTK1 and SRB10. Reduced dosage of CTK1 rescued the growth defect of ess1ts mutants, while overexpression of CTK1 enhanced the growth defects of ess1ts mutants. Deletion of SRB10 suppressed ess1ts and ess1Δ mutants. The interactions suggest that Ess1 opposes the functions of these kinases, which are thought to function in preinitiation and elongation. Using a series of CTD substitution alleles, we also identified Ser5-Pro6 as a potential target for Ess1 isomerization within the first “half” of the CTD repeats. On the basis of the results, we suggest a model in which Ess1-directed conformational changes promote dephosphorylation of Ser5 to stimulate preinitiation complex formation and, later, to inhibit elongation.
Ceramic Membranes for Filtration Applications — Preparation and Characterization
Authors: Benfer S. , Árki P. , Tomandl G. 
Published: August 2004

AbstractThis article gives an overview about the preparation and characterization of asymmetric ceramic membranes that have been developed at our institute within the last years. Depending on the required pore size of the filter active layer for filtration applications ranging from microfiltration (MF) up to nanofiltration (NF) different preparation routes have to be applied.
Basic Mechanisms and Models of Multi‐Wire Sawing
Authors: Möller H.J. 
Published: August 2004

AbstractMore than 80 % of the current solar cell production requires the cutting of large silicon crystals. While in the last years the cost of solar cell processing and module fabrication could be reduced considerably, the sawing costs remain high, about 30 % of the wafer production. At present the large crystals are cut using the multi‐wire slicing technology[2]which has the advantage of a high throughput (several hundred wafers per day and machine), a small kerf loss of about 200 μm and almost no restrictions on the size of the ingots. Basic knowledge about the microscopic details of the sawing process is required in order to slice crystals in a controlled way. In the following the principles of the sawing process will be described in this review article as far as they are understood today.
Empirical and Data Based Modelling of Steel Technology Processes for Industrial Application
Authors: Scheller P.R. , Peisker D. 
Published: August 2004

AbstractProcess models and modelling of the fundamental relationships between the process parameters and the material properties are significant for process automation. Examples taken from the liquid steel treatment, the casting and solidification process and also from the microstructure formation and thermal influence of its properties show the practice oriented modelling of individual processing steps in the manufacturing of steel. Modelling is based both on physical and chemical fundamental principles and on data‐based methods. The used data are based on own empirical investigations as well as on selected published data which are collected in the own data base.
Fatigue Behaviour of Al‐Matrix Composites
Authors: Hartmann O. , Herrmann K. , Biermann H. 
Published: August 2004

AbstractThe cyclic deformation behaviour and fatigue lives of different Al‐matrix composites reinforced by alumina reinforcements were investigated under total strain control mode at room temperature. The composites differ in either matrix strength (peak aged vs. overaged AA6061 alloy and soft Al99.85, respectively) and/or type of reinforcement (particles, Saffil short fibres and Almax continuous fibres). The damage evolution was characterized by compliance experiments within individual stress‐strain hysteresis loops. The differences of the material behaviour are discussed with respect to matrix strength and reinforcement geometry.
Brachydactyly and short stature in a kindred with early‐onset parkinsonism
Authors: Dekker Marieke C.J. , Galjaard R.J.H. , Snijders P.J.L.M. , Heutink P. , Oostra B.A. , van Duijn C.M. 
Published: August 2004

AbstractIn a Dutch kindred we have identified a deletion of the DJ‐1 gene, leading to autosomal‐recessive parkinsonism. The parkinsonism patients also had short stature and brachydactyly. In the family and a control group from the same community, we used the DJ‐1 deletion as a marker for the originally linked PARK7 region and found a significant association with body height (P = 0.005), which suggests a gene in linkage disequilibrium with DJ‐1 to be implicated in short stature. Analysis of hand‐bone length showed incomplete segregation of the PARK7 region with brachydactyly, such that a gene in PARK7 is unlikely to fully explain the brachydactyly. Since the bone length reduction was more pronounced in the homozygous parkinsonism patients than in their heterozygous relatives, however, the PARK7 region may contain a modifier gene for growth. © 2004 Wiley‐Liss, Inc.
Activation of 5‐HT1B/1D receptor in the periaqueductal gray inhibits nociception
Authors: Bartsch T. , Knight Y. E. , Goadsby P. J. 
Published: August 2004

AbstractIt is considered that the site of action of the abortive antimigraine compounds acting at serotonin, 5‐HT1B/1D, receptors (triptans) is the trigeminovascular system. We tested whether there is a non‐trigeminal site of action. The 5‐HT1B/1D agonist, naratriptan, was microinjected into the ventrolateral periaqueductal gray (vlPAG), and activity in the trigeminal nucleus caudalis (TNC) was monitored. Recordings were made from 20 nociceptive neurons in the dorsal horn of the TNC that received convergent input from the dura mater and face. Responses of neurons to dural, facial cutaneous and corneal stimulation were studied before and after injection of naratriptan. Naratriptan decreased the excitability to electrical stimulation of the dura mater as the A‐fiber response decreased by 24 ± 4.1% (p < 0.001) and the C‐fiber response decreased by 42 ± 8.2% (p < 0.001). Spontaneous activity was decreased by 38 ± 7.5% (p < 0.001). After injection, the mechanical thresholds of the dura mater increased from (n = 14, p < 0.01). Responses to stimulation of the face and cornea were not altered by injection of naratriptan. These results suggest that 5‐HT1B/1D receptor activation in the vlPAG activates descending pain‐modulating pathways that inhibit dural, but not facial and corneal nociceptive input. These findings have implications for the understanding of the action of triptans in migraine and cluster headache, suggesting that brain loci other than the trigeminal nucleus may play a role in the clinical action of triptans. Ann Neurol 2004