bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Modifiers of the Drosophila Blue Cheese Gene Link Defects in Lysosomal Transport With Decreased Life Span and Altered Ubiquitinated-Protein Profiles
Authors: Simonsen Anne , Cumming Robert C , Lindmo Karine , Galaviz Vanessa , Cheng Susan , Rusten Tor Erik , Finley Kim D 
Published: April 2007

Abstract
Defects in lysosomal trafficking pathways lead to decreased cell viability and are associated with progressive disorders in humans. Previously we have found that loss-of-function (LOF) mutations in the Drosophila gene blue cheese (bchs) lead to reduced adult life span, increased neuronal death, and widespread CNS degeneration that is associated with the formation of ubiquitinated-protein aggregates. To identify potential genes that participate in the bchs functional pathway, we conducted a genetic modifier screen based on alterations of an eye phenotype that arises from high-level overexpression of Bchs. We found that mutations in select autophagic and endocytic trafficking genes, defects in cytoskeletal and motor proteins, as well as mutations in the SUMO and ubiquitin signaling pathways behave as modifiers of the Bchs gain-of-function (GOF) eye phenotype. Individual mutant alleles that produced viable adults were further examined for bchs-like phenotypes. Mutations in several lysosomal trafficking genes resulted in significantly decreased adult life spans and several mutants showed changes in ubiquitinated protein profiles as young adults. This work represents a novel approach to examine the role that lysosomal transport and function have on adult viability. The genes characterized in this study have direct human homologs, suggesting that similar defects in lysosomal transport may play a role in human health and age-related processes.
Gametogenesis in the Chlamydomonas reinhardtii minus Mating Type Is Controlled by Two Genes, MID and MTD1
Authors: Lin Huawen , Goodenough Ursula W 
Published: April 2007

Abstract
In the unicellular algae Chlamydomonas reinhardtii, the plus and minus mating types are controlled by a complex locus, MT, where the dominant MID gene in the MT− locus has been shown to be necessary for expression of minus-specific gamete-specific genes in response to nitrogen depletion. We report studies on MID expression patterns during gametogenesis and on a second gene unique to the MT− locus, MTD1. Vegetative cells express basal levels of MID. An early activation of MID transcription after nitrogen removal, and its sequence similarity to plant RWP-RK proteins involved in nitrogen-responsive processes, suggest that Mid conformation/activity may be nitrogen sensitive. A second stage of MID upregulation correlates with the acquisition of mating ability in minus gametes. Knockdown of MTD1 by RNAi in minus strains results in a failure to differentiate into gametes of either mating type after nitrogen deprivation. We propose that intermediate Mid levels are sufficient to activate MTD1 transcription and to repress plus gamete-specific genes and that MTD1 expression in turn allows the threshold-level MID expression needed to turn on minus gamete-specific genes. We further propose that an MTD1-equivalent system, utilizing at least one gene product encoded in the MT+ locus, is operant during plus gametogenesis.
Characterization of BEAF Mutations Isolated by Homologous Recombination in Drosophila
Authors: Roy Swarnava , Gilbert Matthew K , Hart Craig M 
Published: April 2007

Abstract
The Drosophila BEAF-32A and BEAF-32B proteins bind to the scs′ insulator and to hundreds of other sites on Drosophila chromosomes. These two proteins are encoded by the same gene. We used ends-in homologous recombination to generate the null BEAFAB-KO allele and also isolated the BEAFA-KO allele that eliminates production of only the BEAF-32A protein. We find that the BEAF proteins together are essential, but BEAF-32B alone is sufficient to obtain viable flies. Our results show that BEAF is important for both oogenesis and development. Maternal or zygotic BEAF is sufficient to obtain adults, although having only maternal BEAF impairs female fertility. In the absence of all BEAF, a few fertile but sickly males are obtained. Using both a chromosomal position-effect assay and an enhancer-blocking assay, we find that BEAF is necessary for scs′ insulator function. Lack of BEAF causes a disruption of male X polytene chromosome morphology. However, we did not find evidence that dosage compensation was affected. Position-effect variegation of the wm4h allele and different variegating y transgenes was enhanced by the knockout mutation. Combined with the effects on male X polytene chromosomes, we conclude that BEAF function affects chromatin structure or dynamics.
A Primary Assembly of a Bovine Haplotype Block Map Based on a 15,036-Single-Nucleotide Polymorphism Panel Genotyped in Holstein–Friesian Cattle
Authors: Khatkar Mehar S , Zenger Kyall R , Hobbs Matthew , Hawken Rachel J , Cavanagh Julie A L , Barris Wes , McClintock Alexander E , McClintock Sara , Thomson Peter C , Tier Bruce , Nicholas Frank W , Raadsma Herman W 
Published: April 2007

Abstract
Analysis of data on 1000 Holstein–Friesian bulls genotyped for 15,036 single-nucleotide polymorphisms (SNPs) has enabled genomewide identification of haplotype blocks and tag SNPs. A final subset of 9195 SNPs in Hardy–Weinberg equilibrium and mapped on autosomes on the bovine sequence assembly (release Btau 3.1) was used in this study. The average intermarker spacing was 251.8 kb. The average minor allele frequency (MAF) was 0.29 (0.05–0.5). Following recent precedents in human HapMap studies, a haplotype block was defined where 95% of combinations of SNPs within a region are in very high linkage disequilibrium. A total of 727 haplotype blocks consisting of ≥3 SNPs were identified. The average block length was 69.7 ± 7.7 kb, which is ∼5–10 times larger than in humans. These blocks comprised a total of 2964 SNPs and covered 50,638 kb of the sequence map, which constitutes 2.18% of the length of all autosomes. A set of tag SNPs, which will be useful for further fine-mapping studies, has been identified. Overall, the results suggest that as many as 75,000–100,000 tag SNPs would be needed to track all important haplotype blocks in the bovine genome. This would require ∼250,000 SNPs in the discovery phase.
Mitochondrial Genome Haplotype Hypervariation Within the Isopod Parasitic Nematode Thaumamermis cosgrovei
Authors: Tang Sha , Hyman Bradley C 
Published: April 2007

Abstract
Characterization of mitochondrial genomes from individual Thaumamermis cosgrovei nematodes, obligate parasites of the isopod Armadillidium vulgare, revealed that numerous mtDNA haplotypes, ranging in size from 19 to 34 kb, are maintained in several spatially separated isopod populations. The magnitude and frequency of conspecific mtDNA size variation is unprecedented among all studied size-polymorphic metazoan mitochondrial genomes. To understand the molecular basis of this hypervariation, complete nucleotide sequences of two T. cosgrovei mtDNA haplotypes were determined. A hypervariable segment, residing between the atp6 and rrnL genes, contributes exclusively to T. cosgrovei mtDNA size variation. Within this region, mtDNA coding genes and putative nonfunctional sequences have accumulated substitutions and are duplicated and rearranged to varying extents. Hypervariation at this level has enabled a first insight into the life history of T. cosgrovei. In five A. vulgare hosts infected with multiple nematodes, four carried nematodes with identical mtDNA haplotypes, suggesting that hosts may become infected by ingesting a recently hatched egg clutch or become parasitized by individuals from the same brood prior to dispersal of siblings within the soil.
Joint Estimates of Quantitative Trait Locus Effect and Frequency Using Synthetic Recombinant Populations ofDrosophila melanogaster
Authors: Macdonald Stuart J , Long Anthony D 
Published: April 2007

AbstractWe develop and implement a strategy to map QTL in two synthetic populations of Drosophila melanogaster each initiated with eight inbred founder strains. These recombinant populations allow simultaneous estimates of QTL location, effect, and frequency. Five X-linked QTL influencing bristle number were resolved to intervals of ∼1.3 cM. We confirm previous observations of bristle number QTL distal to 4A at the tip of the chromosome and identify two novel QTL in 7F–8C, an interval that does not include any classic bristle number candidate genes. If QTL at the tip of the X are biallelic they appear to be intermediate in frequency, although there is evidence that these QTL may reside in multiallelic haplotypes. Conversely, the two QTL mapping to the middle of the X chromosome are likely rare: in each case the minor allele is observed in only 1 of the 16 founders. Assuming additivity and biallelism we estimate that identified QTL contribute 1.0 and 8.7%, respectively, to total phenotypic variation in male abdominal and sternopleural bristle number in nature. Models that seek to explain the maintenance of genetic variation make different predictions about the population frequency of QTL alleles. Thus, mapping QTL in eight-way recombinant populations can distinguish between these models.
The Bursicon Gene in Mosquitoes: An Unusual Example of mRNA Trans-splicing
Authors: Robertson Hugh M , Navik Julia A , Walden Kimberly K O , Honegger Hans-Willi 
Published: April 2007

Abstract
The bursicon gene in Anopheles gambiae is encoded by two loci. Burs124 on chromosome arm 2L contains exons 1, 2, and 4, while burs3 on arm 2R contains exon 3. Exon 3 is efficiently spliced into position in the mature transcript. This unusual gene arrangement is ancient within mosquitoes, being shared by Aedes aegypti and Culex pipiens.
Sex-Specific Viability, Sex Linkage and Dominance in Genomic Imprinting
Authors: Van Cleve Jeremy , Feldman Marcus W 
Published: April 2007

AbstractGenomic imprinting is a phenomenon by which the expression of an allele at a locus depends on the parent of origin. Two different two-locus evolutionary models are presented in which a second locus modifies the imprinting status of the primary locus, which is under differential selection in males and females. In the first model, a modifier allele that imprints the primary locus invades the population when the average dominance coefficient among females and males is $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({&gt;}\frac{1}{2}\) \end{document}$ and selection is weak. The condition for invasion is always heavily contingent upon the extent of dominance. Imprinting is more likely in the sex experiencing weaker selection only under some parameter regimes, whereas imprinting by either sex is equally likely under other regimes. The second model shows that a modifier allele that induces imprinting will increase when imprinting has a direct selective advantage. The results are not qualitatively dependent on whether the modifier locus is autosomal or X linked.
Fatty Acid Desaturation and the Regulation of Adiposity in Caenorhabditis elegans
Authors: Brock Trisha J , Browse John , Watts Jennifer L 
Published: April 2007

Abstract
Monounsaturated fatty acids are essential components of membrane and storage lipids. Their synthesis depends on the conversion of saturated fatty acids to unsaturated fatty acids by Δ9 desaturases. Caenorhabditis elegans has three Δ9 desaturases encoded by the genes fat-5, fat-6, and fat-7. We generated nematodes that display a range of altered fatty acid compositions by constructing double-mutant strains that combine mutations in fat-5, fat-6, and fat-7. All three double-mutant combinations have reduced survival at low temperatures. The fat-5;fat-6 double mutants display relatively subtle fatty acid composition alterations under standard conditions, but extreme fatty acid composition changes and reduced survival in the absence of food. The strain with the most severe defect in the production of unsaturated fatty acids, fat-6;fat-7, exhibits slow growth and reduced fertility. Strikingly, the fat-6;fat-7 double-mutant animals have decreased fat stores and increased expression of genes involved in fatty acid oxidation. We conclude that the Δ9 desaturases, in addition to synthesizing unsaturated fatty acids for properly functioning membranes, play key roles in lipid partitioning and in the regulation of fat storage.
Involvement of the Mitochondrial Protein Translocator Component Tim50 in Growth, Cell Proliferation and the Modulation of Respiration in Drosophila
Authors: Sugiyama Shin , Moritoh Satoru , Furukawa Yoshimi , Mizuno Tomohiko , Lim Young-Mi , Tsuda Leo , Nishida Yasuyoshi 
Published: April 2007

Abstract
Allelic mutants exhibiting growth defects in Drosophila were isolated. Molecular cloning identified the responsible gene as a budding yeast Tim50 ortholog, and thus it was named tiny tim 50 (ttm50). The weak allele (ttm50Gp99) produced small flies due to reduced cell size and number, and growth terminated at the larval stage in the strong alleles (ttm50IE1 and ttm50IE2). Twin-spot analysis showed fewer cells in ttm50Gp99 clones, whereas ttm50IE1 clones did not proliferate, suggesting that the gene has an essential cellular function. Tim50 is known to maintain mitochondrial membrane potential (MMP) while facilitating inner-membrane protein transport. We found that tagged Ttm50 also localized to mitochondria and that mitochondrial morphology and MMP were affected in mutants, indicating that mitochondrial dysfunction causes the developmental phenotype. Conversely, ttm50 overexpression increased MMP and apoptosis. Co-expression of p35 suppressed this apoptosis, resulting in cell overproliferation. Interestingly, ttm50 transcription was tissue specific, corresponding to elevated MMP in the larval midgut, which was decreased in the mutant. The correlation of ttm50 expression levels with differences in MMP match its proposed role in mitochondrial permeability barrier maintenance. Thus a mitochondrial protein translocase component can play active roles in regulating metabolic levels, possibly for modulation of physiological function or growth in development.
A Polygenic Hypothesis for Sex Determination in the European Sea Bass Dicentrarchus labrax
Authors: Vandeputte Marc , Dupont-Nivet Mathilde , Chavanne Hervé , Chatain Béatrice 
Published: April 2007

Abstract
Polygenic sex determination, although suspected in several species, is thought to be evolutionarily unstable and has been proven in very few cases. In the European sea bass, temperature is known to influence the sex ratio. We set up a factorial mating, producing 5.893 individuals from 253 full-sib families, all reared in a single batch to avoid any between-families environmental effects. The proportion of females in the offspring was 18.3%, with a large variation between families. Interpreting sex as a threshold trait, the heritability estimate was 0.62 ± 0.12. The observed distribution of family sex ratios was in accordance with a polygenic model or with a four-sex-factors system with environmental variance and could not be explained by any genetic model without environmental variance. We showed that there was a positive genetic correlation between weight and sex (rA = 0.50 ± 0.09), apart from the phenotypic sex dimorphism in favor of females. This supports the hypothesis that a minimum size is required for sea bass juveniles to differentiate as females. An evolution of sex ratio by frequency-dependent selection is expected during the domestication process of Dicentrarchus labrax populations, raising concern about the release of such fish in the wild.
Multiple Trans-Sensing Interactions Affect Meiotically Heritable Epigenetic States at the Maize pl1 Locus
Authors: Gross Stephen M , Hollick Jay B 
Published: April 2007

Abstract
Interactions between specific maize purple plant1 (pl1) alleles result in heritable changes of gene regulation that are manifested as differences in anthocyanin pigmentation. Transcriptionally repressed states of Pl1-Rhoades alleles (termed Pl′) are remarkably stable and invariably facilitate heritable changes of highly expressed states (termed Pl-Rh) in Pl′/Pl-Rh plants. However, Pl′ can revert to Pl-Rh when hemizygous, when heterozygous with pl1 alleles other than Pl1-Rhoades, or in the absence of trans-acting factors required to maintain repressed states. Cis-linked features of Pl1-Rhoades responsible for these trans-sensing behaviors remain unknown. Here, genetic tests of a pl1 allelic series identify two potentially separate cis-linked features: one facilitating repression of Pl-Rh and another stabilizing Pl′ in trans. Neither function is affected in ethyl-methanesulfonate-induced Pl1-Rhoades derivatives that produce truncated PL1 peptides, indicating that PL1 is unlikely to mediate trans interactions. Both functions, however, are impaired in a spontaneous Pl1-Rhoades derivative that fails to produce detectable pl1 RNA. Pl′-like states can also repress expression of a pl1-W22 allele, but this repression is not meiotically heritable. As the Pl′ state is not associated with unique small RNA species representing the pl1-coding region, the available data suggest that interactions between elements required for transcription underlie Pl1-Rhoades epigenetic behaviors.
Adaptive Walks Toward a Moving Optimum
Authors: Collins Sinéad , de Meaux Juliette , Acquisti Claudia 
Published: April 2007

Abstract
We investigate how the dynamics and outcomes of adaptation by natural selection are affected by environmental stability by simulating adaptive walks in response to an environmental change of fixed magnitude but variable speed. Here we consider monomorphic lineages that adapt by the sequential fixation of beneficial mutations. This is modeled by selecting short RNA sequences for folding stability and secondary structure conservation at increasing temperatures. Using short RNA sequences allows us to describe adaptive outcomes in terms of genotype (sequence) and phenotype (secondary structure) and to follow the dynamics of fitness increase. We find that slower rates of environmental change affect the dynamics of adaptive walks by reducing the fitness effect of fixed beneficial mutations, as well as by increasing the range of time in which the substitutions of largest effect are likely to occur. In addition, adaptation to slower rates of environmental change results in fitter endpoints with fewer possible end phenotypes relative to lineages that adapt to a sudden change. This suggests that care should be taken when experiments using sudden environmental changes are used to make predictions about adaptive responses to gradual change.
Loss-of-Function Alleles of the JIL-1 Histone H3S10 Kinase Enhance Position-Effect Variegation at Pericentric Sites in Drosophila Heterochromatin
Authors: Bao Xiaomin , Deng Huai , Johansen Jørgen , Girton Jack , Johansen Kristen M 
Published: April 2007

AbstractIn this study we show that loss-of-function alleles of the JIL-1 histone H3S10 kinase act as enhancers of position-effect variegation at pericentric sites whereas the gain-of-function JIL-1Su(var)3-1[3] allele acts as a suppressor strongly supporting a functional role for JIL-1 in maintaining euchromatic chromatin and counteracting heterochromatic spreading and gene silencing.
Year-Class Formation of Upper St. Lawrence River Northern Pike
Authors: Smith Brian M. , Farrell John M. , Underwood H. Brian , Smith Stephen J. 
Published: April 2007

Abstract
Variables associated with year-class formation in upper St. Lawrence River northern pike Esox lucius were examined to explore population trends. A partial least-squares (PLS) regression model (PLS 1) was used to relate a year-class strength index (YCSI; 1974–1997) to explanatory variables associated with spawning and nursery areas (seasonal water level and temperature and their variability, number of ice days, and last day of ice presence). A second model (PLS 2) incorporated four additional ecological variables: potential predators (abundance of double-crested cormorants Phalacrocorax auritus and yellow perch Perca flavescens), female northern pike biomass (as a measure of stock–recruitment effects), and total phosphorus (productivity). Trends in adult northern pike catch revealed a decline (1981–2005), and year-class strength was positively related to catch per unit effort (CPUE; R2 = 0.58). The YCSI exceeded the 23-year mean in only 2 of the last 10 years. Cyclic patterns in the YCSI time series (along with strong year-classes every 4–6 years) were apparent, as was a dampening effect of amplitude beginning around 1990. The PLS 1 model explained over 50% of variation in both explanatory variables and the dependent variable, YCSI first-order moving-average residuals. Variables retained (N = 10; Wold's statistic ≥ 0.8) included negative YCSI associations with high summer water levels, high variability in spring and fall water levels, and variability in fall water temperature. The YCSI exhibited positive associations with high spring, summer, and fall water temperature, variability in spring temperature, and high winter and spring water level. The PLS 2 model led to positive YCSI associations with phosphorus and yellow perch CPUE and a negative correlation with double-crested cormorant abundance. Environmental variables (water level and temperature) are hypothesized to regulate northern pike YCSI cycles, and dampening in YCSI magnitude may be related to a combination of factors, including wetland habitat changes, reduced nutrient loading, and increased predation by double-crested cormorants.
Fish Distribution, Abundance, and Behavior along City Shoreline Types in Puget Sound
Authors: Toft Jason D. , Cordell Jeffery R. , Simenstad Charles A. , Stamatiou Lia A. 
Published: April 2007

Abstract
Shoreline modifications, such as bulkheads, riprap, and overwater structures, have altered many of the natural habitats in nearshore urbanized areas surrounding coastal cities, including those in Puget Sound, Washington. The effects of such structures on ecological processes are poorly known, especially those impacting juvenile salmonids Oncorhynchus spp. The goal of our study was to compare the relative abundance and behavior of juvenile salmonids and other fishes along various modified and undeveloped shoreline types. We used enclosure nets and snorkel surveys to sample fishes during high tides in areas adjacent to shore at five main habitat types: cobble beach, sand beach, riprap extending into the upper intertidal zone, deep riprap extending into the subtidal zone, and the edge of overwater structures. Bottom-dwelling fishes exhibited the only significant differences in density among cobble beach, sand beach, and riprap that extended into the upper intertidal zone. This suggests that substrate type and slope are important influences on fish densities when shoreline modifications only extend into the upper intertidal zone. Differences in pelagic fish density and behavior were more evident when shoreline modifications extended into shallow subtidal waters, truncating the shallow-water zone and creating deep water at the shoreline. We typically found higher fish densities, larger schools of salmon, and fewer terrestrial riparian insects in salmon diets at these sites. Juvenile salmonids avoided swimming beneath overwater structures, whereas surfperch (family Embiotocidae), crabs (infraorder Brachyura), and sculpins (family Cottidae) were observed beneath or adjacent to pilings. Overall, our results indicate that shoreline modifications have the greatest effect on nearshore fish assemblages when the alterations extend from the supratidal zone into the subtidal zone. Our data suggest that the differences in fish behavior and usage between modified and unmodified shorelines were caused by physical and biological effects of the modifications, such as changes in water depth, slope, substrate, and shoreline vegetation.