bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Trait Loci Associated With Adventitious Shoot Formation in Tissue Culture and the Program of Shoot Development in Arabidopsis
Authors: Lall Sonia , Nettleton Dan , DeCook Rhonda , Che Ping , Howell Stephen H 
Published: September 2004

Abstract
Arabidopsis ecotypes, Columbia (Col) and Landsberg erecta (Ler), differ in their capacity to regenerate shoots in culture, as do many other cultivars and varieties of the same plant species. Recombinant inbred (RI) lines derived from a cross of Col × Ler were scored for shoot regeneration, and the Arabidopsis genome was scanned using composite interval mapping for loci associated with shoot regeneration. Three QTL were identified—a major one on chromosome 5 in which the Col parent contributed the superior allele and two minor QTL on chromosomes 1 and 4 in which the Ler parent contributed the superior alleles. The RI lines were binned into genotypic pools to isolate the effects of the major QTL on chromosome 5 while holding the minor QTL constant. To identify genes with expression levels that are associated with the allelic state of the major QTL on chromosome 5, oligonucleotide array expression patterns for genes in the LLC pool (Ler alleles at the minor QTL and a Col allele at the major QTL) were compared to those in the LLL pool (Ler alleles at all QTL). The genes that were significantly differentially expressed between the two pools included several encoding transcription factors and signaling or transposon-related proteins.
Heterogeneous Patterns of Variation Among Multiple Human X-Linked Loci
Authors: Hammer Michael F , Garrigan Daniel , Wood Elizabeth , Wilder Jason A , Mobasher Zahra , Bigham Abigail , Krenz James G , Nachman Michael W 
Published: September 2004

Abstract
Studies of human DNA sequence polymorphism reveal a range of diversity patterns throughout the genome. This variation among loci may be due to natural selection, demographic influences, and/or different sampling strategies. Here we build on a continuing study of noncoding regions on the X chromosome in a panel of 41 globally sampled humans representing African and non-African populations by examining patterns of DNA sequence variation at four loci (APXL, AMELX, TNFSF5, and RRM2P4) and comparing these patterns with those previously reported at six loci in the same panel of 41 individuals. We also include comparisons with patterns of noncoding variation seen at five additional X-linked loci that were sequenced in similar global panels. We find that, while almost all loci show a reduction in non-African diversity, the magnitude of the reduction varies substantially across loci. The large observed variance in non-African levels of diversity results in the rejection of a neutral model of molecular evolution with a multi-locus HKA test under both a constant size and a bottleneck model. In non-Africans, some loci harbor an excess of rare mutations over neutral equilibrium predictions, while other loci show no such deviation in the distribution of mutation frequencies. We also observe a positive relationship between recombination rate and frequency spectra in our non-African, but not in our African, sample. These results indicate that a simple out-of-Africa bottleneck model is not sufficient to explain the observed patterns of sequence variation and that diversity-reducing selection acting at a subset of loci and/or a more complex neutral model must be invoked.
A Potential Regulatory Polymorphism Upstream of hairy Is Not Associated With Bristle Number Variation in Wild-Caught DrosophilaSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY587211, AY587212, AY587213, AY587214, AY587215, AY587216, AY587217, AY587218, AY587219, AY587220, AY587221, AY587222, AY587223, AY587224, AY587225, AY587226.
Authors: Macdonald Stuart J , Long Anthony D 
Published: September 2004

Abstract
To extend results from laboratory genetic mapping experiments to natural populations it is necessary to estimate the phenotypic effects attributable to laboratory-identified genetic factors in nature. We retested a polymorphism found to be strongly associated with an increase of 0.35 sternopleural bristles in laboratory strains in two large samples of wild-caught Drosophila melanogaster. Despite &gt;90% power to detect effects as low as 0.27 bristles (&lt;1% of the total variation in bristle number) we did not replicate the association in nature. Potential explanations for this result are explored.
The Inheritance and Evolution of Leaf Pigmentation and Pubescence in Teosinte
Authors: Lauter Nick , Gustus Charles , Westerbergh Anna , Doebley John 
Published: September 2004

AbstractTo investigate the genetic mechanisms that underlie morphological evolution in natural populations, we employed QTL mapping to dissect the inheritance of leaf sheath characters that distinguish Chalco from Balsas teosinte. Abundant macrohairs (trichomes) and intense anthocyanin accumulation are found in Chalco teosinte sheaths whereas Balsas teosinte leaf sheaths are green and glabrous. These character states may represent adaptations to the cooler highland (Chalco) vs. warmer middle-elevation (Balsas) climates. QTL mapping in multiple populations revealed a mix of major- and minor-effect QTL affecting both sheath color (anthocyanin) and macrohair abundance. The major QTL for macrohairs accounts for 52% of the parental difference. Epistatic interactions were detected between the major-effect QTL and multiple other QTL for both traits, accounting for substantial portions of phenotypic variance. Developmental analyses suggest that regulatory program changes underlie the phenotypic differences. Sheath anthocyanin QTL are clearly associated with b1 and a3, both of which are regulators of anthocyanin biosynthesis. Our findings suggest that changes in a small number of QTL can lead to morphological evolution by modulating existing developmental programs.
Dikaryons of the Basidiomycete Fungus Schizophyllum commune
Authors: Clark Travis A , Anderson James B 
Published: September 2004

Abstract
The impact of ploidy on adaptation is a central issue in evolutionary biology. While many eukaryotic organisms exist as diploids, with two sets of gametic genomes residing in the same nucleus, most basidiomycete fungi exist as dikaryons in which the two genomes exist in separate nuclei that are physically paired and that divide in a coordinated manner during hyphal extension. To determine if haploid monokaryotic and dikaryotic mycelia adapt to novel environments under natural selection, we serially transferred replicate populations of each ploidy state on minimal medium for 18 months (∼13,000 generations). Dikaryotic mycelia responded to selection with increases in growth rate, while haploid monokaryotic mycelia did not. To determine if the haploid components of the dikaryon adapt reciprocally to one another's presence over time, we recovered the intact haploid components of dikaryotic mycelia at different time points (without meiosis) and mated them with nuclei of different evolutionary histories. We found evidence for coadaptation between nuclei in one dikaryotic line, in which a dominant deleterious mutation in one nucleus was followed by a compensatory mutation in the other nucleus; the mutant nuclei that evolved together had the best overall fitness. In other lines, nuclei had equal or higher fitness when paired with nuclei of other histories, indicating a heterozygote advantage. To determine if genetic exchange occurs between the two nuclei of a dikaryon, we developed a 24-locus genotyping system based on single nucleotide polymorphisms to monitor somatic exchange. We observed genetic exchange and recombination between the nuclei of several different dikaryons, resulting in genotypic variation in these mitotic cell lineages.
Genome Image Programs
Authors: Zimmer Daniel P , Paliy Oleg , Thomas Brian , Gyaneshwar Prasad , Kustu Sydney 
Published: September 2004

Abstract
We have developed programs to facilitate analysis of microarray data in Escherichia coli. They fall into two categories: manipulation of microarray images and identification of known biological relationships among lists of genes. A program in the first category arranges spots from glass-slide DNA microarrays according to their position in the E. coli genome and displays them compactly in genome order. The resulting genome image is presented in a web browser with an image map that allows the user to identify genes in the reordered image. Another program in the first category aligns genome images from two or more experiments. These images assist in visualizing regions of the genome with common transcriptional control. Such regions include multigene operons and clusters of operons, which are easily identified as strings of adjacent, similarly colored spots. The images are also useful for assessing the overall quality of experiments. The second category of programs includes a database and a number of tools for displaying biological information about many E. coli genes simultaneously rather than one gene at a time, which facilitates identifying relationships among them. These programs have accelerated and enhanced our interpretation of results from E. coli DNA microarray experiments. Examples are given.
Stochastic and Epigenetic Changes of Gene Expression in Arabidopsis Polyploids
Authors: Wang Jianlin , Tian Lu , Madlung Andreas , Lee Hyeon-Se , Chen Meng , Lee Jinsuk J , Watson Brian , Kagochi Trevor , Comai Luca , Chen Z Jeffrey 
Published: September 2004

Abstract
Polyploidization is an abrupt speciation mechanism for eukaryotes and is especially common in plants. However, little is known about patterns and mechanisms of gene regulation during early stages of polyploid formation. Here we analyzed differential expression patterns of the progenitors' genes among successive selfing generations and independent lineages. The synthetic Arabidopsis allotetraploid lines were produced by a genetic cross between A. thaliana and A. arenosa autotetraploids. We found that some progenitors' genes are differentially expressed in early generations, whereas other genes are silenced in late generations or among different siblings within a selfing generation, suggesting that the silencing of progenitors' genes is rapidly and/or stochastically established. Moreover, a subset of genes is affected in autotetraploid and multiple independent allotetraploid lines and in A. suecica, a natural allotetraploid derived from A. thaliana and A. arenosa, indicating locus-specific susceptibility to ploidy-dependent gene regulation. The role of DNA methylation in silencing progenitors' genes is tested in DNA-hypomethylation transgenic lines of A. suecica using RNA interference (RNAi). Two silenced genes are reactivated in both ddm1- and met1-RNAi lines, consistent with the demethylation of centromeric repeats and gene-specific regions in the genome. A rapid and stochastic process of differential gene expression is reinforced by epigenetic regulation during polyploid formation and evolution.
Expansion and Contraction of the DUP240 Multigene Family in Saccharomyces cerevisiae PopulationsSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AJ585103, AJ585104, AJ585105, AJ585106, AJ585107, AJ585108, AJ585190, AJ585524, AJ585525, AJ586490, AJ586491, AJ586492, AJ586493, AJ586494, AJ586495, AJ586496, AJ586497, AJ586498, AJ586499, AJ586500, AJ586501, AJ586502, AJ586503, AJ586504, AJ586505, AJ586506, AJ586507, AJ586508, and AJ586612.
Authors: Leh-Louis Véronique , Wirth Bénédicte , Potier Serge , Souciet Jean-Luc , Despons Laurence 
Published: September 2004

Abstract
The influence of duplicated sequences on chromosomal stability is poorly understood. To characterize chromosomal rearrangements involving duplicated sequences, we compared the organization of tandem repeats of the DUP240 gene family in 15 Saccharomyces cerevisiae strains of various origins. The DUP240 gene family consists of 10 members of unknown function in the reference strain S288C. Five DUP240 paralogs on chromosome I and two on chromosome VII are arranged as tandem repeats that are highly polymorphic in copy number and sequence. We characterized DNA sequences that are likely involved in homologous or nonhomologous recombination events and are responsible for intra- and interchromosomal rearrangements that cause the creation and disappearance of DUP240 paralogs. The tandemly repeated DUP240 genes seem to be privileged sites of gene birth and death.
Conditional Expression in the Malaria Mosquito Anopheles stephensi With Tet-On and Tet-Off Systems
Authors: Lycett Gareth J , Kafatos Fotis C , Loukeris Thanasis G 
Published: September 2004

Abstract
We report successful conditional gene expression in the malaria vector, Anopheles stephensi, on the basis of binary systems consisting of gene driver and responder transgenic lines generated by Minos-mediated germline transformation. An A. gambiae tissue-specific enhancer derived from a serpin (SRPN10) gene was utilized to control the temporal and spatial expression of doxycycline (dox)-sensitive transcriptional regulators in the driver lines. The “Tet-Off” driver utilized the tetracycline-controlled transcriptional activator (tTA) that is unable to bind and activate transcription from tetracycline operators (TetO) in the presence of dox; the “Tet-on” driver utilized the reverse tTA (rtTA) that, conversely, binds and activates TetO operators in the presence of dox. The responder lines carried insertions encompassing a LacZ reporter gene, cis-regulated by a TetO-P-element hybrid promoter. The progeny of crosses between driver and responder lines expressed β-galactosidase under dual, tissue-specific and dox-mediated regulation. In adult rtTA/TetOPlacZ progeny, dox treatment rapidly induced β-galactosidase activity throughout the midgut epithelium and especially in malaria parasite-invaded epithelial cells. Transactivator-dependent, dox-mediated regulation was observed in hemocytes and pericardial cells using both systems. Conditional tissue-specific regulation is a powerful tool for analyzing gene function in mosquitoes and potentially for development of strategies to control disease transmission.
A Genetic Mechanism Implicates Chromosome 11 in Schizophrenia and Bipolar Diseases
Authors: Klar Amar J S 
Published: September 2004

Abstract
The causes of schizophrenia and bipolar human psychiatric disorders are unknown. A novel somatic cell genetic model postulated nonrandom segregation of “Watson” vs. “Crick” DNA chains of both copies of a chromosome to specific daughter cells. Such an oriented asymmetric cell division causes development of healthy, functionally nonequivalent brain hemispheres. Genetic translocations of the chromosome may cause disease by disrupting the biased strand-segregation process. Only one-half of chromosome 1 and 11 translocation carriers developing disease were recently explained as a result consistent with the model (Klar 2002). Is chromosome 1 or 11 involved? Does the translocation breakpoint cause disease? Remarkably, two other unrelated chromosome 11 translocations discovered from the literature likewise caused disease in ∼50% of carriers. Together, their breakpoints lie at three distinct regions spanning ∼40% of chromosome 11. Thus, chromosome 11 is implicated but the breakpoints themselves are unlikely to cause the disease. The results suggest that the genetically caused disease develops without a Mendelian gene mutation.
Detecting the Footprint of Positive Selection in a European Population of Drosophila melanogasterSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AJ781836, AJ783306.
Authors: Orengo Dorcas J , Aguadé Montserrat 
Published: September 2004

Abstract
The effects on nucleotide variation of adaptations to temperate habitats and of the possible bottleneck associated with the origin of European populations of Drosophila melanogaster should be detectable in DNA sequences given the short time elapsed relative to the species population size. We surveyed nucleotide variation in 109 fragments distributed across the X chromosome in a European population of D. melanogaster to detect the footprint of positive selection. Fragments were located primarily in large noncoding regions. Multilocus tests based on Tajima's D statistic revealed a significant departure from neutral expectations in a stationary panmictic population, with an important contribution from both positive and negative D values. A positive relationship between Tajima's D values and distance to coding region was detected, with a comparative excess of significantly negative D values in the subset of fragments closer to coding regions. Also, there was a significant heterogeneity in the polymorphism to divergence ratio, with 12 fragments contributing 42% to the test statistic. Moreover, these fragments were comparatively closer to coding regions. These findings would imply positive selection events, and thus selective sweeps, during the species expansion to Europe.
Identification of Residues of the Caenorhabditis elegans LIN-1 ETS Domain That Are Necessary for DNA Binding and Regulation of Vulval Cell Fates
Authors: Miley Ginger R , Fantz Douglas , Glossip Danielle , Lu Xiaowei , Saito R Mako , Palmer Robert E , Inoue Takao , van den Heuvel Sander , Sternberg Paul W , Kornfeld Kerry 
Published: September 2004

Abstract
LIN-1 is an ETS domain protein. A receptor tyrosine kinase/Ras/mitogen-activated protein kinase signaling pathway regulates LIN-1 in the P6.p cell to induce the primary vulval cell fate during Caenorhabditis elegans development. We identified 23 lin-1 loss-of-function mutations by conducting several genetic screens. We characterized the molecular lesions in these lin-1 alleles and in several previously identified lin-1 alleles. Nine missense mutations and 10 nonsense mutations were identified. All of these lin-1 missense mutations affect highly conserved residues in the ETS domain. These missense mutations can be arranged in an allelic series; the strongest mutations eliminate most or all lin-1 functions, and the weakest mutation partially reduces lin-1 function. An electrophoretic mobility shift assay was used to demonstrate that purified LIN-1 protein has sequence-specific DNA-binding activity that required the core sequence GGAA. LIN-1 mutant proteins containing the missense substitutions had dramatically reduced DNA binding. These experiments identify eight highly conserved residues of the ETS domain that are necessary for DNA binding. The identification of multiple mutations that reduce the function of lin-1 as an inhibitor of the primary vulval cell fate and also reduce DNA binding suggest that DNA binding is essential for LIN-1 function in an animal.
Allelic and Haplotypic Diversity at the Rp1 Rust Resistance Locus of MaizeSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY309779, AY309780, AY309781, AY309782, AY309783sc and scAY581258sc.
Authors: Smith Shavannor M , Pryor Anthony J , Hulbert Scot H 
Published: September 2004

Abstract
The maize Rp1 rust resistance locus is a complex consisting of a family of closely related resistance genes. The number of Rp1 paralogs in different maize lines (haplotypes) varied from a single gene in some stocks of the inbred A188 to &gt;50 genes in haplotypes carrying the Rp1-A and Rp1-H specificities. The sequences of paralogs in unrelated haplotypes differ, indicating that the genetic diversity of Rp1-related genes is extremely broad in maize. Two unrelated haplotypes with five or nine paralogs had identical resistance phenotypes (Rp1-D) encoded in genes that differed by three nucleotides resulting in a single amino acid substitution. Genes in some haplotypes are more similar to each other than to any of the genes in other haplotypes indicating that they are evolving in a concerted fashion.
High-Density Genetic Linkage Maps of Phytophthora infestans Reveal Trisomic Progeny and Chromosomal Rearrangements
Authors: van der Lee Theo , Testa Antonino , Robold Andrea , van ‘t Klooster John , Govers Francine 
Published: September 2004

Abstract
Detailed analysis of the inheritance of molecular markers was performed in the oomycete plant pathogen Phytophthora infestans. Linkage analysis in the sexual progeny of two Dutch field isolates (cross 71) resulted in a high-density map containing 508 markers on 13 major and 10 minor linkage groups. The map showed strong clustering of markers, particularly of markers originating from one parent, and dissimilarity between the parental isolates on linkage group III in the vicinity of the mating-type locus, indicating a chromosomal translocation. A second genetic map, constructed by linkage analysis in sexual progeny of two Mexican isolates (cross 68), contained 363 markers and is thus less dense than the cross 71 map. For some linkage groups the two independent linkage maps could be aligned, but sometimes markers appeared to be in a different order, or not linked at all, indicating chromosomal rearrangements between genotypes. Graphical genotyping showed that some progeny contained three copies of a homologous linkage group. This trisomy was found for several linkage groups in both crosses. Together, these analyses suggest a genome with a high degree of flexibility, which may have implications for evolution of new races and resistance development to crop protection agents.
Analysis of Transposon Insertion Mutants Highlights the Diversity of Mechanisms Underlying Male Progamic Development in Arabidopsis
Authors: Lalanne Eric , Michaelidis Christos , Moore James M , Gagliano Wendy , Johnson Andrew , Patel Ramesh , Howden Ross , Vielle-Calzada Jean-Phillippe , Grossniklaus Ueli , Twell David 
Published: September 2004

Abstract
To identify genes with essential roles in male gametophytic development, including postpollination (progamic) events, we have undertaken a genetic screen based on segregation ratio distortion of a transposon-borne kanamycin-resistance marker. In a population of 3359 Arabidopsis Ds transposon insertion lines, we identified 20 mutants with stably reduced segregation ratios arising from reduced gametophytic transmission. All 20 mutants showed strict cosegregation of Ds and the reduced gametophytic transmission phenotype. Among these, 10 mutants affected both male and female transmission and 10 mutants showed male-specific transmission defects. Four male and female (ungud) mutants and 1 male-specific mutant showed cellular defects in microspores and/or in developing pollen. The 6 remaining ungud mutants and 9 male-specific (seth) mutants affected pollen functions during progamic development. In vitro and in vivo analyses are reported for 5 seth mutants. seth6 completely blocked pollen germination, while seth7 strongly reduced pollen germination efficiency and tube growth. In contrast, seth8, seth9, or seth10 pollen showed reduced competitive ability that was linked to slower rates of pollen tube growth. Gene sequences disrupted in seth insertions suggest essential functions for putative SETH proteins in diverse processes including protein anchoring, cell wall biosynthesis, signaling, and metabolism.