bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and Gene Expression Analysis of Arabidopsis thaliana Mutants With Constitutive Expression of ATL2, an Early Elicitor-Response RING-H2 Zinc-Finger GeneThis article is dedicated to the memory of the late Gilberto Mosqueda Cano.
Authors: Serrano Mario , Guzmán Plinio
Published: August 2004

Genes with unstable transcripts often encode proteins that play important regulatory roles. ATL2 is a member of a multigene family coding highly related RING-H2 zinc-finger proteins that may function as E3 ubiquitin ligases. ATL2 mRNA accumulation occurs rapidly and transiently after incubation with elicitors of pathogen response. We screened 50,000 M2 families from a line that carries a fusion of pATL2 to the GUS reporter gene and isolated five mutants, which we named eca (expresión constitutiva de ATL2), that showed constitutive expression of the reporter gene. One mutant exhibits a drastic stunted phenotype while the other four grow similarly to wild type. Two early chitin-induced genes and known pathogenesis-related genes such as NPR1, PAL, and CHS are activated in all the mutants whereas members of the ATL family and PR-1 and PDF2.1, which are markers of the salicylic acid (SA) jasmonate (JA) defense-response pathways, display differential expression between the mutants. These observations indicate that the ECA gene products may function in the early steps of an elicitor-response pathway, although some of them may function at other stages on the SA or JA defense-response pathways. Likewise, the fact that ATL2 and other members of the ATL family are activated in eca mutants links the induction of this putative class of ubiquitin ligases to plant defense signaling pathways.
Defects Arising From Whole-Genome Duplications in Saccharomyces cerevisiae
Authors: Andalis Alex A , Storchova Zuzana , Styles Cora , Galitski Timothy , Pellman David , Fink Gerald R
Published: August 2004

Comparisons among closely related species have led to the proposal that the duplications found in many extant genomes are the remnants of an ancient polyploidization event, rather than a result of successive duplications of individual chromosomal segments. If this interpretation is correct, it would support Ohno's proposal that polyploidization drives evolution by generating the genetic material necessary for the creation of new genes. Paradoxically, analysis of contemporary polyploids suggests that increased ploidy is an inherently unstable state. To shed light on this apparent contradiction and to determine the effects of nascent duplications of the entire genome, we generated isogenic polyploid strains of the budding yeast Saccharomyces cerevisiae. Our data show that an increase in ploidy results in a marked decrease in a cell's ability to survive during stationary phase in growth medium. Tetraploid cells die rapidly, whereas isogenic haploids remain viable for weeks. Unlike haploid cells, which arrest growth as unbudded cells, tetraploid cells continue to bud and form mitotic spindles in stationary phase. The stationary-phase death of tetraploids can be prevented by mutations or conditions that result in growth arrest. These data show that whole-genome duplications are accompanied by defects that affect viability and subsequent survival of the new organism.
Does Random X-Inactivation in Mammals Reflect a Random Choice Between Two X Chromosomes?
Authors: Williams Benjamin R , Wu Chao-ting
Published: August 2004

Inactivation of the maternal or paternal X chromosome in a mammalian embryonic XX cell is believed to involve random choice between the two X's. We propose two alternative models. One suggests that choice is not random, while the other is consistent with random choice, but not one between two X's.
Introducing Student Inquiry in Large Introductory Genetics Classes
Authors: Pukkila Patricia J
Published: August 2004

An appreciation of genetic principles depends upon understanding the individual curiosity that sparked particular investigations, the creativity involved in imagining alternative outcomes and designing experiments to eliminate these outcomes, and the clarity of thought necessary to convince one's scientific peers of the validity of the conclusions. At large research universities, students usually begin their study of genetics in large lecture classes. It is widely assumed that the lecture format, coupled with the pressures to be certain that students become familiar with the principal conclusions of genetics investigations, constrains most if not all departures from the formats textbooks used to explain these conclusions. Here I present several examples of mechanisms to introduce meaningful student inquiry in an introductory genetics course and to evaluate student creative effort. Most of the examples involve altered student preparation prior to class and additional in-class activities, while a few depend upon a smaller recitation section, which accompanies the course from which the examples have been drawn. I conclude that large introductory classes are suitable venues to teach students how to identify scientific claims, determine the evidence that is essential to eliminate alternative conclusions, and convince their peers of the validity of their arguments.
The Podospora rmp1 Gene Implicated in Nucleus-Mitochondria Cross-Talk Encodes an Essential Protein Whose Subcellular Location Is Developmentally Regulated
Authors: Contamine Véronique , Zickler Denise , Picard Marguerite
Published: August 2004

It has been previously reported that, at the time of death, the Podospora anserina AS1-4 mutant strains accumulate specific deleted forms of the mitochondrial genome and that their life spans depend on two natural alleles (variants) of the rmp1 gene: AS1-4 rmp1-2 strains exhibit life spans strikingly longer than those of AS1-4 rmp1-1. Here, we show that rmp1 is an essential gene. In silico analyses of eight rmp1 natural alleles present in Podospora isolates and of the putative homologs of this orphan gene in other filamentous fungi suggest that rmp1 evolves rapidly. The RMP1 protein is localized in the mitochondrial and/or the cytosolic compartment, depending on cell type and developmental stage. Strains producing RMP1 without its mitochondrial targeting peptide are viable but exhibit vegetative and sexual defects.
sel-7, a Positive Regulator of lin-12 Activity, Encodes a Novel Nuclear Protein in Caenorhabditis elegans
Authors: Chen Jiabin , Li Xiajun , Greenwald Iva
Published: August 2004

Suppressor genetics in C. elegans has identified key components of the LIN-12/Notch signaling pathway. Here, we describe a genetic and molecular characterization of the suppressor gene sel-7. We show that reducing or eliminating sel-7 activity suppresses the effects of constitutive lin-12 activity, enhances the effects of partially reduced lin-12 activity, and causes a synthetic Lin-12(0) phenotype when combined with a null mutation in the sel-12 presenilin gene. These observations suggest that sel-7 is a positive regulator of lin-12 activity. We also show that SEL-7 encodes a novel nuclear protein. Through yeast two-hybrid screening, we identified an apparent interaction partner, K08E3.8, that also interacts with SEL-8, a known component of the nuclear complex that forms upon LIN-12 activation. Our data suggest potential roles for SEL-7 in the assembly or function of this nuclear complex.
eat-2 and eat-18 Are Required for Nicotinic Neurotransmission in the Caenorhabditis elegans Pharynx
Authors: McKay James P , Raizen David M , Gottschalk Alexander , Schafer William R , Avery Leon
Published: August 2004

Mutations in eat-2 and eat-18 cause the same defect in C. elegans feeding behavior: the pharynx is unable to pump rapidly in the presence of food. EAT-2 is a nicotinic acetylcholine receptor subunit that functions in the pharyngeal muscle. It is localized to the synapse between pharyngeal muscle and the main pharyngeal excitatory motor neuron MC, and it is required for MC stimulation of pharyngeal muscle. eat-18 encodes a small protein that has no homology to previously characterized proteins. It has a single transmembrane domain and a short extracellular region. Allele-specific genetic interactions between eat-2 and eat-18 suggest that EAT-18 interacts physically with the EAT-2 receptor. While eat-2 appears to be required specifically for MC neurotransmission, eat-18 also appears to be required for the function of other nicotinic receptors in the pharynx. In eat-18 mutants, the gross localization of EAT-2 at the MC synapse is normal, suggesting that it is not required for trafficking. These data indicate that eat-18 could be a novel component of the pharyngeal nicotinic receptor.
The sys-1 and sys-3 Genes Cooperate With Wnt Signaling to Establish the Proximal-Distal Axis of the Caenorhabditis elegans Gonad
Authors: Siegfried Kellee R , Kidd Ambrose R , Chesney Michael A , Kimble Judith
Published: August 2004

To form the proximal-distal axis of the C. elegans gonad, two somatic gonadal precursor cells, Z1 and Z4, divide asymmetrically to generate one daughter with a proximal fate and one with a distal fate. Genes governing this process include the lin-17 frizzled receptor, wrm-1/β-catenin, the pop-1/TCF transcription factor, lit-1/nemo-like kinase, and the sys-1 gene. Normally, all of these regulators promote the distal fate. Here we show that nuclear levels of a pop-1 GFP fusion protein are less abundant in the distal than in the proximal Z1/Z4 daughters. This POP-1 asymmetry is lost in mutants disrupting Wnt/MAPK regulation, but retained in sys-1 mutants. We find that sys-1 is haplo-insufficient for gonadogenesis defects and that sys-1 and pop-1 mutants display a strong genetic interaction in double heterozygotes. Therefore, sys-1 is a dose-sensitive locus and may function together with pop-1 to control Z1/Z4 asymmetry. To identify other regulatory genes in this process, we screened for mutants resembling sys-1. Four such genes were identified (gon-14, -15, -16, and sys-3) and shown to interact genetically with sys-1. However, only sys-3 promotes the distal fate at the expense of the proximal fate. We suggest that sys-3 is a new key gene in this pathway and that gon-14, gon-15, and gon-16 may cooperate with POP-1 and SYS-1 at multiple stages of gonad development.
A Mosaic Genetic Screen Reveals Distinct Roles for trithorax and Polycomb Group Genes in Drosophila Eye Development
Authors: Janody Florence , Lee Jeffrey D , Jahren Neal , Hazelett Dennis J , Benlali Aude , Miura Grant I , Draskovic Irena , Treisman Jessica E
Published: August 2004

The wave of differentiation that traverses the Drosophila eye disc requires rapid transitions in gene expression that are controlled by a number of signaling molecules also required in other developmental processes. We have used a mosaic genetic screen to systematically identify autosomal genes required for the normal pattern of photoreceptor differentiation, independent of their requirements for viability. In addition to genes known to be important for eye development and to known and novel components of the Hedgehog, Decapentaplegic, Wingless, Epidermal growth factor receptor, and Notch signaling pathways, we identified several members of the Polycomb and trithorax classes of genes encoding general transcriptional regulators. Mutations in these genes disrupt the transitions between zones along the anterior-posterior axis of the eye disc that express different combinations of transcription factors. Different trithorax group genes have very different mutant phenotypes, indicating that target genes differ in their requirements for chromatin remodeling, histone modification, and coactivation factors.
Knockouts of Kekkon1 Define Sequence Elements Essential for Drosophila Epidermal Growth Factor Receptor Inhibition
Authors: Alvarado Diego , Rice Amy H , Duffy Joseph B
Published: August 2004

Throughout development, cells utilize feedback inhibition of receptor tyrosine kinase (RTK) signaling as an important means to direct cellular fates. In Drosophila, epidermal growth factor receptor (EGFR) activity is tightly regulated by a complex array of autoregulatory loops, involving an assortment of inhibitory proteins. One inhibitor, the transmembrane protein Kekkon1 (Kek1) functions during oogenesis in a negative feedback loop to directly attenuate EGFR activity. Kek1 contains both leucine-rich repeats (LRRs) and an immunoglobulin (Ig) domain, two of the most prevalent motifs found within metazoan genomes. Here we demonstrate that Kek1 inhibits EGFR activity during eye development and use this role to identify kek1 loss-of-function mutations that implicate the LRRs in directing receptor inhibition. Using a GMR-GAL4, UAS kek1-GFP misexpression phenotype we isolated missense mutations in the kek1 transgene affecting its ability to inhibit EGFR signaling. Genetic, molecular, and biochemical characterization of these alleles indicated that they represent two functionally distinct classes. Class I alleles directly diminish Kek1's affinity for EGFR, while class II alleles disrupt Kek1's subcellular localization, thereby indirectly affecting its ability to associate with and inhibit the receptor. All class I alleles map to the first and second LRRs of Kek1, suggesting a primary role for these two repeats in specifying association with and inhibition of EGFR. Last, our analysis implicates glycine 160 of the second LRR in regulating EGFR binding.
The P Cytotype in Drosophila melanogaster: A Maternally Transmitted Regulatory State of the Germ Line Associated With Telomeric P Elements
Authors: Simmons Michael J , Raymond John D , Niemi Jarad B , Stuart Jeremy R , Merriman Peter J
Published: August 2004

The incomplete P elements TP5 and TP6 are inserted in the TAS repeats near the left telomere of the Drosophila melanogaster X chromosome. These telomeric P elements repress P-induced gonadal dysgenesis and germ-line hypermutability in both sexes. However, their capacity to repress hypermutability is lost when they are transmitted patroclinously in a cross. TP5 and TP6 do not repress P-element activity in somatic cells, nor do they alter the somatic or germ-line phenotypes of P-insertion alleles. In the germ line, these elements suppress the phenotype of a P-insertion allele of the singed gene that is evoked by other P elements, presumably because these other elements encode repressor polypeptides. This suppression is more effective when the telomeric P elements are inherited maternally. Regulation by telomeric P elements parallels that of the P cytotype, a state that represses P-element activity in some strains of Drosophila. This state exists only in the germ line and is maternally transmitted along with the P elements themselves. Regulation by known repressor P polypeptides is not restricted to the germ line and does not require maternal transmission of the relevant P elements. Regulation by telomeric P elements appears to be epistatic to regulation by repressor P polypeptides.
Strong Positive Selection and Recombination Drive the Antigenic Variation of the PilE Protein of the Human Pathogen Neisseria meningitidis
Authors: Andrews T Daniel , Gojobori Takashi
Published: August 2004

The PilE protein is the major component of the Neisseria meningitidis pilus, which is encoded by the pilE/pilS locus that includes an expressed gene and eight homologous silent fragments. The silent gene fragments have been shown to recombine through gene conversion with the expressed gene and thereby provide a means by which novel antigenic variants of the PilE protein can be generated. We have analyzed the evolutionary rate of the pilE gene using the nucleotide sequence of two complete pilE/pilS loci. The very high rate of evolution displayed by the PilE protein appears driven by both recombination and positive selection. Within the semivariable region of the pilE and pilS genes, recombination appears to occur within multiple small sequence blocks that lie between conserved sequence elements. Within the hypervariable region, positive selection was identified from comparison of the silent and expressed genes. The unusual gene conversion mechanism that operates at the pilE/pilS locus is a strategy employed by N. meningitidis to enhance mutation of certain regions of the PilE protein. The silent copies of the gene effectively allow “parallelized” evolution of pilE, thus enabling the encoded protein to rapidly explore a large area of sequence space in an effort to find novel antigenic variants.
Establishment and Maintenance of the P Cytotype Associated With Telomeric P Elements in Drosophila melanogaster
Authors: Niemi Jarad B , Raymond John D , Patrek Ryan , Simmons Michael J
Published: August 2004

P elements inserted near the left telomere of the X chromosome are associated with the P cytotype, a maternally transmitted condition that strongly regulates the activity of the P transposon family in some strains of Drosophila. The regulatory abilities of two such elements, TP5 and TP6, are stable in homozygous stocks over many generations. However, these regulatory abilities are attenuated when the telomeric P elements are transmitted through heterozygous females, and they are utterly lost when the elements are transmitted through males. Paternally transmitted telomeric P elements reacquire regulatory ability when they pass through a female germ line. This reacquisition is enhanced if the females in which it occurs came from mothers who carried a telomeric P element. The enhancement has two components: (1) a strictly maternal effect that is transmitted to the females independently of the mother's telomeric P element (“presetting” or the “pre-P cytotype”) and (2) a zygotic effect associated with inheritance of the mother's telomeric P element. One telomeric P element can enhance the reacquisition of another's regulatory ability. When X chromosomes that carry telomeric P elements are extracted through males and made homozygous by using a balancer chromosome, most of the resulting stocks develop strong regulatory abilities in a few generations. However, some of the stocks do not attain the regulatory ability of the original population.
No Evidence for an Association Between Common Nonsynonymous Polymorphisms in Delta and Bristle Number Variation in Natural and Laboratory Populations of Drosophila melanogaster
Authors: Genissel Anne , Pastinen Tomi , Dowell Andrea , Mackay Trudy F C , Long Anthony D
Published: August 2004

We test the hypothesis that naturally occurring nonsynonymous variants in the Delta ligand of the Notch signaling pathway contribute to standing variation in sternopleural and/or abdominal bristle number in Drosophila melanogaster, for both a large cohort of wild-caught flies and previously described laboratory lines. We sequenced the transcribed region of Delta for 16 naturally occurring chromosomes and 65 SNPs, including 7 nonsynonymous SNPs (nsSNPs), were observed. Identified nsSNPs and 6 additional common SNPs, all located in exon 6 and the 3′ UTR, were genotyped in 2060 wild-caught flies using an OLA-based methodology and genotyped in 38 additional natural chromosomes via DNA sequencing. None of the genotyped nsSNPs were significantly associated with natural variation in bristle number as assessed by a permutation test. A 95% upper bound on the additive genetic variance attributable to each genotyped SNP in the large natural cohort is <2% of the total phenotypic variation. Results suggest that two previously detected genotype/phenotype associations between bristle number and variants in the introns of Delta cannot be explained by linkage disequilibrium between these variants and nearby nonsynonymous variants. Unidentified regulatory variants more parsimoniously explain previous observations.
First-Generation Linkage Map of the Gray, Short-Tailed Opossum,Monodelphis domestica, Reveals Genome-Wide Reduction in Female Recombination Rates
Authors: Samollow Paul B , Kammerer Candace M , Mahaney Susan M , Schneider Jennifer L , Westenberger Scott J , VandeBerg John L , Robinson Edward S
Published: August 2004

The gray, short-tailed opossum, Monodelphis domestica, is the most extensively used, laboratory-bred marsupial resource for basic biologic and biomedical research worldwide. To enhance the research utility of this species, we are building a linkage map, using both anonymous markers and functional gene loci, that will enable the localization of quantitative trait loci (QTL) and provide comparative information regarding the evolution of mammalian and other vertebrate genomes. The current map is composed of 83 loci distributed among eight autosomal linkage groups and the X chromosome. The autosomal linkage groups appear to encompass a very large portion of the genome, yet span a sex-average distance of only 633.0 cM, making this the most compact linkage map known among vertebrates. Most surprising, the male map is much larger than the female map (884.6 cM vs. 443.1 cM), a pattern contrary to that in eutherian mammals and other vertebrates. The finding of genome-wide reduction in female recombination in M. domestica, coupled with recombination data from two other, distantly related marsupial species, suggests that reduced female recombination might be a widespread metatherian attribute. We discuss possible explanations for reduced female recombination in marsupials as a consequence of the metatherian characteristic of determinate paternal X chromosome inactivation.
Optimal Designs for Linkage Disequilibrium Mapping and Candidate Gene Association Tests in Livestock Populations
Authors: Stella Alessandra , Boettcher Paul J
Published: August 2004

Simulation was used to evaluate the performance of different selective genotyping strategies when using linkage disequilibrium across large half-sib families to position a QTL within a previously defined genomic region. Strategies examined included standard selective genotyping and different approaches of discordant and concordant sib selection applied to arbitrary or selected families. Strategies were compared as a function of effect and frequency of QTL alleles, heritability, and phenotypic expression of the trait. Large half-sib families were simulated for 100 generations and 2% of the population was genotyped in the final generation. Simple ANOVA was applied and the marker with the greatest F-value was considered the most likely QTL position. For traits with continuous phenotypes, genotyping the most divergent pairs of half-sibs from all families was the best strategy in general, but standard selective genotyping was somewhat more precise when heritability was low. When the phenotype was distributed in ordered categories, discordant sib selection was the optimal approach for positioning QTL for traits with high heritability and concordant sib selection was the best approach when genetic effects were small. Genotyping of a few selected sibs from many families was generally more efficient than genotyping many individuals from a few highly selected sires.
The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations
Authors: Marth Gabor T , Czabarka Eva , Murvai Janos , Sherry Stephen T
Published: August 2004

We have studied a genome-wide set of single-nucleotide polymorphism (SNP) allele frequency measures for African-American, East Asian, and European-American samples. For this analysis we derived a simple, closed mathematical formulation for the spectrum of expected allele frequencies when the sampled populations have experienced nonstationary demographic histories. The direct calculation generates the spectrum orders of magnitude faster than coalescent simulations do and allows us to generate spectra for a large number of alternative histories on a multidimensional parameter grid. Model-fitting experiments using this grid reveal significant population-specific differences among the demographic histories that best describe the observed allele frequency spectra. European and Asian spectra show a bottleneck-shaped history: a reduction of effective population size in the past followed by a recent phase of size recovery. In contrast, the African-American spectrum shows a history of moderate but uninterrupted population expansion. These differences are expected to have profound consequences for the design of medical association studies. The analytical methods developed for this study, i.e., a closed mathematical formulation for the allele frequency spectrum, correcting the ascertainment bias introduced by shallow SNP sampling, and dealing with variable sample sizes provide a general framework for the analysis of public variation data.
A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium)
Authors: Rong Junkang , Abbey Colette , Bowers John E , Brubaker Curt L , Chang Charlene , Chee Peng W , Delmonte Terrye A , Ding Xiaoling , Garza Juan J , Marler Barry S , Park Chan-hwa , Pierce Gary J , Rainey Katy M , Rastogi Vipin K , Schulze Stefan R , Trolinder Norma L , Wendel Jonathan F , Wilkins Thea A , Williams-Coplin T Dawn , Wing Rod A , Wright Robert J , Zhao Xinping , Zhu Linghua , Paterson Andrew H
Published: August 2004

We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps include, respectively, 2584 loci at 1.72-cM (∼600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM (∼500 kb) intervals detected by 662 probes (D). Both diploid and tetraploid cottons exhibit negative crossover interference; i.e., double recombinants are unexpectedly abundant. We found no major structural changes between Dt and D chromosomes, but confirmed two reciprocal translocations between At chromosomes and several inversions. Concentrations of probes in corresponding regions of the various genomes may represent centromeres, while genome-specific concentrations may represent heterochromatin. Locus duplication patterns reveal all 13 expected homeologous chromosome sets and lend new support to the possibility that a more ancient polyploidization event may have predated the A-D divergence of 6–11 million years ago. Identification of SSRs within 312 RFLP sequences plus direct mapping of 124 SSRs and exploration for CAPS and SNPs illustrate the “portability” of these STS loci across populations and detection systems useful for marker-assisted improvement of the world's leading fiber crop. These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome.
High-Density Linkage Mapping Revealed Suppression of Recombination at the Sex Determination Locus in Papaya
Authors: Ma Hao , Moore Paul H , Liu Zhiyong , Kim Minna S , Yu Qingyi , Fitch Maureen M M , Sekioka Terry , Paterson Andrew H , Ming Ray
Published: August 2004

A high-density genetic map of papaya (Carica papaya L.) was constructed using 54 F2 plants derived from cultivars Kapoho and SunUp with 1501 markers, including 1498 amplified fragment length polymorphism (AFLP) markers, the papaya ringspot virus coat protein marker, morphological sex type, and fruit flesh color. These markers were mapped into 12 linkage groups at a LOD score of 5.0 and recombination frequency of 0.25. The 12 major linkage groups covered a total length of 3294.2 cM, with an average distance of 2.2 cM between adjacent markers. This map revealed severe suppression of recombination around the sex determination locus with a total of 225 markers cosegregating with sex types. The cytosine bases were highly methylated in this region on the basis of the distribution of methylation-sensitive and -insensitive markers. This high-density genetic map is essential for cloning of specific genes of interest such as the sex determination gene and for the integration of genetic and physical maps of papaya.
An Internal Rearrangement in an Arabidopsis Inverted Repeat Locus Impairs DNA Methylation Triggered by the Locus
Authors: Melquist Stacey , Bender Judith
Published: August 2004

In plants, transcribed inverted repeats trigger RNA interference (RNAi) and DNA methylation of identical sequences. RNAi is caused by processing of the double-stranded RNA (dsRNA) transcript into small RNAs that promote degradation of complementary RNA sequences. However, the signals for DNA methylation remain to be fully elucidated. The Arabidopsis tryptophan biosynthetic PAI genes provide an endogenous inverted repeat that triggers DNA methylation of PAI-identical sequences. In the Wassilewskija strain, two PAI genes are arranged as a tail-to-tail inverted repeat and transcribed from an unmethylated upstream promoter. This locus directs its own methylation, as well as methylation of two unlinked singlet PAI genes. Previously, we showed that the locus is likely to make an RNA signal for methylation because suppressed transcription of the inverted repeat leads to reduced PAI methylation. Here we characterize a central rearrangement in the inverted repeat that also confers reduced PAI methylation. The rearrangement creates a premature polyadenylation signal and suppresses readthrough transcription into palindromic PAI sequences. Thus, a likely explanation for the methylation defect of the mutant locus is a failure to produce readthrough dsRNA methylation triggers.
Formation of Unreduced Megaspores (Diplospory) in Apomictic Dandelions (Taraxacum officinale, s.l.) Is Controlled by a Sex-Specific Dominant Locus
Authors: van Dijk Peter J , Bakx-Schotman J M Tanja
Published: August 2004

In apomictic dandelions, Taraxacum officinale, unreduced megaspores are formed via a modified meiotic division (diplospory). The genetic basis of diplospory was investigated in a triploid (3x = 24) mapping population of 61 individuals that segregated ∼1:1 for diplospory and meiotic reduction. This population was created by crossing a sexual diploid (2x = 16) with a tetraploid diplosporous pollen donor (4x = 32) that was derived from a triploid apomict. Six different inheritance models for diplospory were tested. The segregation ratio and the tight association with specific alleles at the microsatellite loci MSTA53 and MSTA78 strongly suggest that diplospory is controlled by a dominant allele D on a locus, which we have named DIPLOSPOROUS (DIP). Diplosporous plants have a simplex genotype, Ddd or Dddd. MSTA53 and MSTA78 were weakly linked to the 18S-25S rDNA locus. The D-linked allele of MSTA78 was absent in a hypotriploid (2n = 3x – 1) that also lacked one of the satellite chromosomes. Together these results suggest that DIP is located on the satellite chromosome. DIP is female specific, as unreduced gametes are not formed during male meiosis. Furthermore, DIP does not affect parthenogenesis, implying that several independently segregating genes control apomixis in dandelions.
Recombination Within a Nucleotide-Binding-Site/Leucine-Rich-Repeat Gene Cluster Produces New Variants Conditioning Resistance to Soybean Mosaic Virus in Soybeans
Authors: Hayes A J , Jeong S C , Gore M A , Yu Y G , Buss G R , Tolin S A , Maroof M A Saghai
Published: August 2004

The soybean Rsv1 gene for resistance to soybean mosaic virus (SMV; Potyvirus) has previously been described as a single-locus multi-allelic gene mapping to molecular linkage group (MLG) F. Various Rsv1 alleles condition different responses to the seven (G1–G7) described strains of SMV, including extreme resistance, localized and systemic necrosis, and mosaic symptoms. We describe the cloning of a cluster of NBS-LRR resistance gene candidates from MLG F of the virus-resistant soybean line PI96983 and demonstrate that multiple genes within this cluster interact to condition unique responses to SMV strains. In addition to cloning 3gG2, a strong candidate for the major Rsv1 resistance gene from PI96983, we describe various unique resistant and necrotic reactions coincident with the presence or absence of other members of this gene cluster. Responses of recombinant lines from a high-resolution mapping population of PI96983 (resistant) × Lee 68 (susceptible) demonstrate that more than one gene in this region of the PI96983 chromosome conditions resistance and/or necrosis to SMV. In addition, the soybean cultivars Marshall and Ogden, which carry other previously described Rsv1 alleles, are shown to possess the 3gG2 gene in a NBS-LRR gene cluster background distinct from PI96983. These observations suggest that two or more related non-TIR-NBS-LRR gene products are likely involved in the allelic response of several Rsv1-containing lines to SMV.
Inference on Recombination and Block Structure Using Unphased Data
Authors: Wiuf Carsten
Published: August 2004

In this study compatibility with a tree for unphased genotype data is discussed. If the data are compatible with a tree, the data are consistent with an assumption of no recombination in its evolutionary history. Further, it is said that there is a solution to the perfect phylogeny problem; i.e., for each individual a pair of haplotypes can be defined and the set of all haplotypes can be explained without invoking recombination. A new algorithm to decide whether or not a sample is compatible with a tree is derived. The new algorithm relies on an equivalence relation between sites that mutually determine the phase of each other. (The previous algorithm was based on advanced graph theoretical tools.) The equivalence relation is used to derive the number of solutions to the perfect phylogeny problem. Further, a series of statistics, RjM, j ≥ 2, are defined. These can be used to detect recombination events in the sample's history and to divide the sample into regions that are compatible with a tree. The new statistics are applied to real data from human genes. The results from this application are discussed with reference to recent suggestions that recombination in the human genome is highly heterogeneous.
In Silico Study of Transcriptome Genetic Variation in Outbred Populations
Authors: Pérez-Enciso Miguel
Published: August 2004

Dissecting the genetic architecture of regulatory elements on a genome-wide basis is now technically feasible. The potential medical and genetical implications of this kind of experiment being very large, it is paramount to assess the reliability and repeatability of the results. This is especially relevant in outbred populations, such as humans, where the genetic architecture is necessarily more complex than in crosses between inbred lines. Here we simulated a chromosome-wide SNP association study using real human microarray data. Our model predicted, as observed, a highly significant clustering of quantitative trait loci (QTL) for gene expression. Importantly, the estimates of QTL positions were often unstable, and a decrease in the number of individuals of 16% resulted in a loss of power of ∼30% and a large shift in the position estimate in ∼30–40% of the remaining significant QTL. We also found that the analysis of two repeated measures of the same mRNA can also result in two QTL that are located far apart. The intrinsic difficulties of analyzing outbred populations should not be underestimated. We anticipate that (many) conflicting results may be collected in the future if whole-genome association studies for mRNA levels are carried out in outbred populations.
The Effect of Genetic Conflict on Genomic Imprinting and Modification of Expression at a Sex-Linked Locus
Authors: Spencer Hamish G , Feldman Marcus W , Clark Andrew G , Weisstein Anton E
Published: August 2004

We examine how genomic imprinting may have evolved at an X-linked locus, using six diallelic models of selection in which one allele is imprintable and the other is not. Selection pressures are generated by genetic conflict between mothers and their offspring. The various models describe cases of maternal and paternal inactivation, in which females may be monogamous or bigamous. When inactivation is maternal, we examine the situations in which only female offspring exhibit imprinting as well as when both sexes do. We compare our results to those previously obtained for an autosomal locus and to four models in which a dominant modifier of biallelic expression is subjected to the same selection pressures. We find that, in accord with verbal predictions, maternal inactivation of growth enhancers and paternal inactivation of growth inhibitors are more likely than imprinting in the respective opposite directions, although these latter outcomes are possible for certain parameter combinations. The expected outcomes are easier to evolve than the same outcomes for autosomal loci, contradicting the available evidence concerning the direction of imprinting on mammalian sex chromosomes. In most of our models stable polymorphism of imprinting status is possible, a behavior not predicted by verbal accounts.
Controlling the Proportion of False Positives in Multiple Dependent Tests
Authors: Fernando R L , Nettleton D , Southey B R , Dekkers J C M , Rothschild M F , Soller M
Published: August 2004

Genome scan mapping experiments involve multiple tests of significance. Thus, controlling the error rate in such experiments is important. Simple extension of classical concepts results in attempts to control the genomewise error rate (GWER), i.e., the probability of even a single false positive among all tests. This results in very stringent comparisonwise error rates (CWER) and, consequently, low experimental power. We here present an approach based on controlling the proportion of false positives (PFP) among all positive test results. The CWER needed to attain a desired PFP level does not depend on the correlation among the tests or on the number of tests as in other approaches. To estimate the PFP it is necessary to estimate the proportion of true null hypotheses. Here we show how this can be estimated directly from experimental results. The PFP approach is similar to the false discovery rate (FDR) and positive false discovery rate (pFDR) approaches. For a fixed CWER, we have estimated PFP, FDR, pFDR, and GWER through simulation under a variety of models to illustrate practical and philosophical similarities and differences among the methods.
One-Hybrid Screens at the Saccharomyces cerevisiae HMR Locus Identify Novel Transcriptional Silencing Factors
Authors: Andrulis Erik D , Zappulla David C , Alexieva-Botcheva Krassimira , Evangelista Carlos , Sternglanz Rolf
Published: August 2004

In Saccharomyces cerevisiae, genes located at the telomeres and the HM loci are subject to transcriptional silencing. Here, we report results of screening a Gal4 DNA-binding domain hybrid library for proteins that cause silencing when targeted to a silencer-defective HMR locus.
Compensatory Evolution in the Human Malaria Parasite Plasmodium ovale
Authors: McCutchan Thomas F , Rathore Dharmendar , Li Jun
Published: August 2004

The fixation of neutral compensatory mutations in a population depends on the effective population size of the species, which can fluctuate dramatically within a few generations, the mutation rate, and the selection intensity associated with the individual mutations. We observe compensatory mutations and intermediate states in populations of the malaria parasite Plasmodium ovale. The appearance of compensatory mutations and intermediate states in P. ovale raises interesting questions about population structure that could have considerable impact on the control of the associated disease.
Fus1p Interacts With Components of the Hog1p Mitogen-Activated Protein Kinase and Cdc42p Morphogenesis Signaling Pathways to Control Cell Fusion During Yeast Mating
Authors: Nelson Bryce , Parsons Ainslie B , Evangelista Marie , Schaefer Karen , Kennedy Kathy , Ritchie Steven , Petryshen Tracey L , Boone Charles
Published: August 2004

Cell fusion in the budding yeast Saccharomyces cerevisiae is a temporally and spatially regulated process that involves degradation of the septum, which is composed of cell wall material, and occurs between conjugating cells within a prezygote, followed by plasma membrane fusion. The plasma membrane protein Fus1p is known to be required for septum degradation during cell fusion, yet its role at the molecular level is not understood. We identified Sho1p, an osmosensor for the HOG MAPK pathway, as a binding partner for Fus1 in a two-hybrid screen. The Sho1p-Fus1p interaction occurs directly and is mediated through the Sho1p-SH3 domain and a proline-rich peptide ligand on the Fus1p COOH-terminal cytoplasmic region. The cell fusion defect associated with fus1Δ mutants is suppressed by a sho1Δ deletion allele, suggesting that Fus1p negatively regulates Sho1p signaling to ensure efficient cell fusion. A two-hybrid matrix containing fusion proteins and pheromone response pathway signaling molecules reveals that Fus1p may participate in a complex network of interactions. In particular, the Fus1p cytoplasmic domain interacts with Chs5p, a protein required for secretion of specialized Chs3p-containing vesicles during bud development, and chs5Δ mutants were defective in cell surface localization of Fus1p. The Fus1p cytoplasmic domain also interacts with the activated GTP-bound form of Cdc42p and the Fus1p-SH3 domain interacts with Bni1p, a yeast formin that participates in cell fusion and controls the assembly of actin cables to polarize secretion in response to Cdc42p signaling. Taken together, our results suggest that Fus1p acts as a scaffold for the assembly of a cell surface complex involved in polarized secretion of septum-degrading enzymes and inhibition of HOG pathway signaling to promote cell fusion.
REP3-Mediated Silencing in Saccharomyces cerevisiae
Authors: Papacs Laurie Ann , Sun Yu , Anderson Erica L , Sun Jianjun , Holmes Scott G
Published: August 2004

In yeast the Sir proteins and Rap1p are key regulators of transcriptional silencing at telomeres and the silent mating-type loci. Rap1 and Sir4 also possess anchoring activity; the rotation of plasmids bound by Sir4 or Rap1 is constrained in vivo, and Rap1 or Sir4 binding can also correct the segregation bias of plasmids lacking centromeres. To investigate the mechanistic link between DNA anchoring and regulation of transcription, we examined the ability of a third defined anchor in yeast, the 2μ circle REP3 segregation element, to mediate transcriptional silencing. We find that placement of the REP3 sequence adjacent to the HML locus in a strain deleted for natural silencer sequences confers transcriptional repression on HML. This repression requires the Sir proteins and is decreased in strains lacking the REP3-binding factors Rep1 and Rep2. The yeast cohesin complex associates with REP3; we show that REP3 silencing is also decreased in strains bearing a mutated allele of the MCD1/SCC1 cohesin gene. Conventional silencing is increased in some strains lacking the 2μ circle and decreased in strains overexpressing the Rep1 and Rep2 proteins, suggesting that the Rep proteins antagonize conventional silencing.
Genetic Evidence of a Role for Membrane Lipid Composition in the Regulation of Soluble NEM-Sensitive Factor Receptor Function in Saccharomyces cerevisiae
Authors: Coluccio Alison , Malzone Maria , Neiman Aaron M
Published: August 2004

SEC9 and SPO20 encode SNARE proteins related to the mammalian SNAP-25 family. Sec9p associates with the SNAREs Sso1/2p and Snc1/2p to promote the fusion of vesicles with the plasma membrane. Spo20p functions with the same two partner SNAREs to mediate the fusion of vesicles with the prospore membrane during sporogenesis. A chimeric molecule, in which the helices of Sec9p that bind to Sso1/2p and Snc1/2p are replaced with the homologous regions of Spo20p, will not support vesicle fusion in vegetative cells. The phosphatidylinositol-4-phosphate-5-kinase MSS4 was isolated as a high-copy suppressor that permits this chimera to rescue the temperature-sensitive growth of a sec9-4 mutant. Suppression by MSS4 is specific to molecules that contain the Spo20p helical domains. This suppression requires an intact copy of SPO14, encoding phospholipase D. Overexpression of MSS4 leads to a recruitment of the Spo14 protein to the plasma membrane and this may be the basis for MSS4 action. Consistent with this, deletion of KES1, a gene that behaves as a negative regulator of SPO14, also promotes the function of SPO20 in vegetative cells. These results indicate that elevated levels of phosphatidic acid in the membrane may be required specifically for the function of SNARE complexes containing Spo20p.
Neurological Proteins Are Not Enriched For Repetitive Sequences
Authors: Huntley Melanie A , Golding G Brian
Published: August 2004

Proteins associated with disease and development of the nervous system are thought to contain repetitive, simple sequences. However, genome-wide surveys for simple sequences within proteins have revealed that repetitive peptide sequences are the most frequent shared peptide segments among eukaryotic proteins, including those of Saccharomyces cerevisiae, which has few to no specialized developmental and neurological proteins. It is therefore of interest to determine if these specialized proteins have an excess of simple sequences when compared to other sets of compositionally similar proteins. We have determined the relative abundance of simple sequences within neurological proteins and find no excess of repetitive simple sequence within this class. In fact, polyglutamine repeats that are associated with many neurodegenerative diseases are no more abundant within neurological specialized proteins than within nonneurological collections of proteins. We also examined the codon composition of serine homopolymers to determine what forces may play a role in the evolution of extended homopolymers. Codon type homogeneity tends to be favored, suggesting replicative slippage instead of selection as the main force responsible for producing these homopolymers.
Influence of Random Genetic Drift on Human Immunodeficiency Virus Type 1envEvolution During Chronic Infection
Authors: Shriner Daniel , Shankarappa Raj , Jensen Mark A , Nickle David C , Mittler John E , Margolick Joseph B , Mullins James I
Published: August 2004

Human immunodeficiency virus type 1 (HIV-1) has high replication and mutation rates that generate large census populations and high levels of genetic variation. We examined the roles of natural selection, population growth, random genetic drift, and recombination in shaping the variation in 1509 C2-V5 env sequences derived from nine men with chronic HIV-1 infection. These sequences were obtained from clinical visits that reflect the first 6-13.7 years of infection. Pairwise comparisons of nonsynonymous and synonymous distances, Tajima's D test, Fu and Li's D* test, and a test of recurrent mutation revealed evidence for episodes of nonneutral evolution in a total of 22 out of 145 blood samples, representing six of the nine individuals. Using three coalescent-based maximum-likelihood estimators, we found viral effective population sizes in all nine individuals to be ∼103. We also show that a previous estimate of the effective population size of ∼105 based on rare haplotype frequencies decreases to ∼103 upon correcting a biased sampling procedure. We conclude that the genetic variation in these data sets can be explained by a predominance of random genetic drift of neutral mutations with brief episodes of natural selection that were frequently masked by recombination.