bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Analysis of Contributions of Dorsal Group and JAK-Stat92E Pathway Genes to Larval Hemocyte Concentration and the Egg Encapsulation Response in Drosophila
Authors: Sorrentino Richard Paul , Melk Jonathan P , Govind Shubha 
Published: August 2004

Abstract
Drosophila larvae defend themselves against parasitoid wasps by completely surrounding the egg with layers of specialized hemocytes called lamellocytes. Similar capsules of lamellocytes, called melanotic capsules, are also formed around “self” tissues in larvae carrying gain-of-function mutations in Toll and hopscotch. Constitutive differentiation of lamellocytes in larvae carrying these mutations is accompanied by high concentrations of plasmatocytes, the major hemocyte class in uninfected control larvae. The relative contributions of hemocyte concentration vs. lamellocyte differentiation to wasp egg encapsulation are not known. To address this question, we used Leptopilina boulardi to infect more than a dozen strains of host larvae harboring a wide range of hemocyte densities. We report a significant correlation between hemocyte concentration and encapsulation capacity among wild-type larvae and larvae heterozygous for mutations in the Hopscotch-Stat92E and Toll-Dorsal pathways. Larvae carrying loss-of-function mutations in Hopscotch, Stat92E, or dorsal group genes exhibit significant reduction in encapsulation capacity. Larvae carrying loss-of-function mutations in dorsal group genes (including Toll and tube) have reduced hemocyte concentrations, whereas larvae deficient in Hopscotch-Stat92E signaling do not. Surprisingly, unlike hopscotch mutants, Toll and tube mutants are not compromised in their ability to generate lamellocytes. Our results suggest that circulating hemocyte concentration and lamellocyte differentiation constitute two distinct physiological requirements of wasp egg encapsulation and Toll and Hopscotch proteins serve distinct roles in this process.
Signature of Selective Sweep Associated With the Evolution of sex-ratio Drive in Drosophila simulans
Authors: Derome Nicolas , Métayer Karine , Montchamp-Moreau Catherine , Veuille Michel 
Published: August 2004

Abstract
In several Drosophila species, the XY Mendelian ratio is disturbed by X-linked segregation distorters (sexratio drive). We used a collection of recombinants between a nondistorting chromosome and a distorting X chromosome originating from the Seychelles to map a candidate sex-ratio region in Drosophila simulans using molecular biallelic markers. Our data were compatible with the presence of a sex-ratio locus in the 7F cytological region. Using sequence polymorphism at the Nrg locus, we showed that sex-ratio has induced a strong selective sweep in populations from Madagascar and Réunion, where distorting chromosomes are close to a 50% frequency. The complete association between the marker and the sex-ratio phenotype and the near absence of mutations and recombination in the studied fragment after the sweep event indicate that this event is recent. Examples of selective sweeps are increasingly reported in a number of genomes. This case identifies the causal selective force. It illustrates that all selective sweeps are not necessarily indicative of an increase in the average fitness of populations.
Molecular Cytogenetic Definition of the Chicken Genome: The First Complete Avian Karyotype
Authors: Masabanda Julio S , Burt Dave W , O'Brien Patricia C M , Vignal Alain , Fillon Valerie , Walsh Philippa S , Cox Helen , Tempest Helen G , Smith Jacqueline , Habermann Felix , Schmid Michael , Matsuda Yoichi , Ferguson-Smith Malcolm A , Crooijmans Richard P M A , Groenen Martien A M , Griffin Darren K 
Published: August 2004

Abstract
Chicken genome mapping is important for a range of scientific disciplines. The ability to distinguish chromosomes of the chicken and other birds is thus a priority. Here we describe the molecular cytogenetic characterization of each chicken chromosome using chromosome painting and mapping of individual clones by FISH. Where possible, we have assigned the chromosomes to known linkage groups. We propose, on the basis of size, that the NOR chromosome is approximately the size of chromosome 22; however, we suggest that its original assignment of 16 should be retained. We also suggest a definitive chromosome classification system and propose that the probes developed here will find wide utility in the fields of developmental biology, DT40 studies, agriculture, vertebrate genome organization, and comparative mapping of avian species.
Nucleotide Diversity in Gorillas
Authors: Yu Ning , Jensen-Seaman Michael I , Chemnick Leona , Ryder Oliver , Li Wen-Hsiung 
Published: August 2004

Abstract
Comparison of the levels of nucleotide diversity in humans and apes may provide valuable information for inferring the demographic history of these species, the effect of social structure on genetic diversity, patterns of past migration, and signatures of past selection events. Previous DNA sequence data from both the mitochondrial and the nuclear genomes suggested a much higher level of nucleotide diversity in the African apes than in humans. Noting that the nuclear DNA data from the apes were very limited, we previously conducted a DNA polymorphism study in humans and another in chimpanzees and bonobos, using 50 DNA segments randomly chosen from the noncoding, nonrepetitive parts of the human genome. The data revealed that the nucleotide diversity (π) in bonobos (0.077%) is actually lower than that in humans (0.087%) and that π in chimpanzees (0.134%) is only 50% higher than that in humans. In the present study we sequenced the same 50 segments in 15 western lowland gorillas and estimated π to be 0.158%. This is the highest value among the African apes but is only about two times higher than that in humans. Interestingly, available mtDNA sequence data also suggest a twofold higher nucleotide diversity in gorillas than in humans, but suggest a threefold higher nucleotide diversity in chimpanzees than in humans. The higher mtDNA diversity in chimpanzees might be due to the unique pattern in the evolution of chimpanzee mtDNA. From the nuclear DNA π values, we estimated that the long-term effective population sizes of humans, bonobos, chimpanzees, and gorillas are, respectively, 10,400, 12,300, 21,300, and 25,200.
Heritability and Segregation Analysis of Deafness in U.S. Dalmatians
Authors: Cargill E J , Famula T R , Strain G M , Murphy K E 
Published: August 2004

Abstract
Hereditary loss of hearing affects many breeds of the domestic dog, but the Dalmatian has the highest prevalence. Approximately 30% are affected in the United States (U.S.) population. It is widely accepted that a relationship exists between deafness and pigmentation in the dog and also in other animals. While the Dalmatian exemplifies this relationship, the genetic origin and mode of inheritance of deafness in this breed are unknown. The goals of this study were to: (1) estimate the heritability of deafness in an extended kindred of U.S. Dalmatians and (2) determine, through complex segregation analysis, whether there is a major segregating locus that has a large effect on the expression of deafness. A kindred of 266 Dalmatians was assembled, of which 199 had been diagnosed using the brainstem auditory evoked response to determine auditory status. Of these, 74.4% (N = 148) had normal hearing, 18.1% (N = 36) were unilaterally deaf, and 7.5% (N = 15) were bilaterally deaf. A heritability of 0.73 was estimated considering deafness a dichotomous trait and 0.75 considering it as a trichotomous trait. Although deafness in the Dalmatian is clearly heritable, the evidence for the presence of a single major gene affecting the disorder is not persuasive.
Genetics of Postzygotic Isolation in Eucalyptus: Whole-Genome Analysis of Barriers to Introgression in a Wide Interspecific Cross of Eucalyptus grandis and E. globulus
Authors: Myburg Alexander A , Vogl Claus , Griffin A Rod , Sederoff Ronald R , Whetten Ross W 
Published: August 2004

Abstract
The genetic architecture of hybrid fitness characters can provide valuable insights into the nature and evolution of postzygotic reproductive barriers in diverged species. We determined the genome-wide distribution of barriers to introgression in an F1 hybrid of two Eucalyptus tree species, Eucalyptus grandis (W. Hill ex Maiden.) and E. globulus (Labill.). Two interspecific backcross families (N = 186) were used to construct comparative, single-tree, genetic linkage maps of an F1 hybrid individual and two backcross parents. A total of 1354 testcross AFLP marker loci were evaluated in the three parental maps and a substantial proportion (27.7% average) exhibited transmission ratio distortion (α= 0.05). The distorted markers were located in distinct regions of the parental maps and marker alleles within each region were all biased toward either of the two parental species. We used a Bayesian approach to estimate the position and effect of transmission ratio distorting loci (TRDLs) in the distorted regions of each parental linkage map. The relative viability of TRDL alleles ranged from 0.20 to 0.72. Contrary to expectation, heterospecific (donor) alleles of TRDLs were favored as often as recurrent alleles in both backcrosses, suggesting that positive and negative heterospecific interactions affect introgression rates in this wide interspecific pedigree.
Large Retrotransposon Derivatives: Abundant, Conserved but Nonautonomous Retroelements of Barley and Related Genomes
Authors: Kalendar Ruslan , Vicient Carlos M , Peleg Ofer , Anamthawat-Jonsson Kesara , Bolshoy Alexander , Schulman Alan H 
Published: August 2004

Abstract
Retroviruses and LTR retrotransposons comprise two long-terminal repeats (LTRs) bounding a central domain that encodes the products needed for reverse transcription, packaging, and integration into the genome. We describe a group of retrotransposons in 13 species and four genera of the grass tribe Triticeae, including barley, with long, ∼4.4-kb LTRs formerly called Sukkula elements. The ∼3.5-kb central domains include reverse transcriptase priming sites and are conserved in sequence but contain no open reading frames encoding typical retrotransposon proteins. However, they specify well-conserved RNA secondary structures. These features describe a novel group of elements, called LARDs or large retrotransposon derivatives (LARDs). These appear to be members of the gypsy class of LTR retrotransposons. Although apparently nonautonomous, LARDs appear to be transcribed and can be recombinationally mapped due to the polymorphism of their insertion sites. They are dispersed throughout the genome in an estimated 1.3 × 103 full-length copies and 1.16 × 104 solo LTRs, indicating frequent recombinational loss of internal domains as demonstrated also for the BARE-1 barley retrotransposon.
The Maizemacrohairless1Locus Specifically Promotes Leaf Blade Macrohair Initiation and Responds to Factors Regulating Leaf Identity
Authors: Moose Stephen P , Lauter Nick , Carlson Shawn R 
Published: August 2004

AbstractThe leaf surfaces of almost all plant species possess specialized epidermal cell types that form hairs or trichomes. Maize leaves produce three distinct types of hairs, the most prominent being the macrohairs that serve as a marker for adult leaf identity and may contribute to insect resistance. This report describes the maize macrohairless1 (mhl1) locus, which promotes macrohair initiation specifically in the leaf blade. Each of seven recessive mhl1 mutant alleles significantly reduces or eliminates macrohairs in the leaf blade. The mhl1 mutations block macrohair initiation rather than interfering with macrohair morphogenesis. Genetic mapping placed mhl1 within bin 4 on chromosome 9. A second independently segregating locus was found to partially suppress the mhl1 mutant phenotype in certain genetic backgrounds. Macrohair density was observed to increase during early adult vegetative development and then progressively decline, suggesting macrohair initiation frequency is affected by factors that act throughout shoot development. Genetic analyses demonstrated that mhl1 acts in the same pathway but downstream of factors that either promote or repress adult leaf identity. Thus, mhl1 plays a key role in integrating developmental programs that regulate leaf identity during shoot development with those that specify macrohair initiation within the leaf blade.
A Sequence-Based Genetic Map ofMedicago truncatulaand Comparison of Marker Colinearity withM. sativa
Authors: Choi Hong-Kyu , Kim Dongjin , Uhm Taesik , Limpens Eric , Lim Hyunju , Mun Jeong-Hwan , Kalo Peter , Penmetsa R Varma , Seres Andrea , Kulikova Olga , Roe Bruce A , Bisseling Ton , Kiss Gyorgy B , Cook Douglas R 
Published: August 2004

AbstractA core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an F2 population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence tags, and 67 resistance gene analogs, covering 513 cM. In the case of EST-based markers we used an intron-targeted marker strategy with primers designed to anneal in conserved exon regions and to amplify across intron regions. Polymorphisms were significantly more frequent in intron vs. exon regions, thus providing an efficient mechanism to map transcribed genes. Genetic and cytogenetic analysis produced eight well-resolved linkage groups, which have been previously correlated with eight chromosomes by means of FISH with mapped BAC clones. We anticipated that mapping of conserved coding regions would have utility for comparative mapping among legumes; thus 60 of the EST-based primer pairs were designed to amplify orthologous sequences across a range of legume species. As an initial test of this strategy, we used primers designed against M. truncatula exon sequences to rapidly map genes in M. sativa. The resulting comparative map, which includes 68 bridging markers, indicates that the two Medicago genomes are highly similar and establishes the basis for a Medicago composite map.
The Maintenance of Extreme Amino Acid Diversity at the Disease Resistance Gene, RPP13, in Arabidopsis thaliana
Authors: Rose Laura E , Bittner-Eddy Peter D , Langley Charles H , Holub Eric B , Michelmore Richard W , Beynon Jim L 
Published: August 2004

Abstract
We have used the naturally occurring plant-parasite system of Arabidopsis thaliana and its common parasite Peronospora parasitica (downy mildew) to study the evolution of resistance specificity in the host population. DNA sequence of the resistance gene, RPP13, from 24 accessions, including 20 from the United Kingdom, revealed amino acid sequence diversity higher than that of any protein coding gene reported so far in A. thaliana. A significant excess of amino acid polymorphism segregating within this species is localized within the leucine-rich repeat (LRR) domain of RPP13. These results indicate that single alleles of the gene have not swept through the population, but instead, a diverse collection of alleles have been maintained. Transgenic complementation experiments demonstrate functional differences among alleles in their resistance to various pathogen isolates, suggesting that the extreme amino acid polymorphism in RPP13 is maintained through continual reciprocal selection between host and pathogen.
The Effective Size of Mixed Sexually and Asexually Reproducing Populations
Authors: Yonezawa Katsuei , Ishii Takuro , Nagamine Tsukasa 
Published: August 2004

AbstractUsing the transition matrix of inbreeding and coancestry coefficients, the inbreeding (NeI), variance (NeV), and asymptotic (Neλ) effective sizes of mixed sexual and asexual populations are formulated in terms of asexuality rate (δ), variance of asexual (C) and sexual (K) reproductive contributions of individuals, correlation between asexual and sexual contributions (ρck), selfing rate (β), and census population size (N). The trajectory of NeI toward Neλ changes crucially depending on δ, N, and β, whereas that of NeV is rather consistent. With increasing asexuality, Neλ either increases or decreases depending on C, K, and ρck. The parameter space in which a partially asexual population has a larger Neλ than a fully sexual population is delineated. This structure is destroyed when N(1 –δ) &lt; 1 or δ&gt; 1 –1/N. With such a high asexuality, tremendously many generations are required for the asymptotic size Neλ to be established, and Neλ is extremely large with any value of C, K, and ρck because the population is dominated eventually by individuals of the same genotype and the allelic diversity within the individuals decays quite slowly. In reality, the asymptotic state would occur only occasionally, and instantaneous rather than asymptotic effective sizes should be practical when predicting evolutionary dynamics of highly asexual populations.
A General Framework for Analyzing the Genetic Architecture of Developmental Characteristics
Authors: Wu Rongling , Ma Chang-Xing , Lin Min , Casella George 
Published: August 2004

AbstractThe genetic architecture of growth traits plays a central role in shaping the growth, development, and evolution of organisms. While a limited number of models have been devised to estimate genetic effects on complex phenotypes, no model has been available to examine how gene actions and interactions alter the ontogenetic development of an organism and transform the altered ontogeny into descendants. In this article, we present a novel statistical model for mapping quantitative trait loci (QTL) determining the developmental process of complex traits. Our model is constructed within the traditional maximum-likelihood framework implemented with the EM algorithm. We employ biologically meaningful growth curve equations to model time-specific expected genetic values and the AR(1) model to structure the residual variance-covariance matrix among different time points. Because of a reduced number of parameters being estimated and the incorporation of biological principles, the new model displays increased statistical power to detect QTL exerting an effect on the shape of ontogenetic growth and development. The model allows for the tests of a number of biological hypotheses regarding the role of epistasis in determining biological growth, form, and shape and for the resolution of developmental problems at the interface with evolution. Using our newly developed model, we have successfully detected significant additive × additive epistatic effects on stem height growth trajectories in a forest tree.
The Effect of Gene Conversion on the Divergence Between Duplicated Genes
Authors: Teshima Kosuke M , Innan Hideki 
Published: August 2004

Abstract
Nonindependent evolution of duplicated genes is called concerted evolution. In this article, we study the evolutionary process of duplicated regions that involves concerted evolution. The model incorporates mutation and gene conversion: the former increases d, the divergence between two duplicated regions, while the latter decreases d. It is demonstrated that the process consists of three phases. Phase I is the time until d reaches its equilibrium value, d0. In phase II d fluctuates around d0, and d increases again in phase III. Our simulation results demonstrate that the length of concerted evolution (i.e., phase II) is highly variable, while the lengths of the other two phases are relatively constant. It is also demonstrated that the length of phase II approximately follows an exponential distribution with mean τ, which is a function of many parameters including gene conversion rate and the length of gene conversion tract. On the basis of these findings, we obtain the probability distribution of the level of divergence between a pair of duplicated regions as a function of time, mutation rate, and τ. Finally, we discuss potential problems in genomic data analysis of duplicated genes when it is based on the molecular clock but concerted evolution is common.
Comparing Linkage Disequilibrium-Based Methods for Fine Mapping Quantitative Trait Loci
Authors: Grapes L , Dekkers J C M , Rothschild M F , Fernando R L 
Published: August 2004

Abstract
Recently, a method for fine mapping quantitative trait loci (QTL) using linkage disequilibrium was proposed to map QTL by modeling covariance between individuals, due to identical-by-descent (IBD) QTL alleles, on the basis of the similarity of their marker haplotypes under an assumed population history. In the work presented here, the advantage of using marker haplotype information for fine mapping QTL was studied by comparing the IBD-based method with 10 markers to regression on a single marker, a pair of markers, or a two-locus haplotype under alternative population histories. When 10 markers were genotyped, the IBD-based method estimated the position of the QTL more accurately than did single-marker regression in all populations. When 20 markers were genotyped for regression, as single-marker methods do not require knowledge of haplotypes, the mapping accuracy of regression in all populations was similar to or greater than that of the IBD-based method using 10 markers. Thus for populations similar to those simulated here, the IBD-based method is comparable to single-marker regression analysis for fine mapping QTL.
Decomposing Multilocus Linkage Disequilibrium
Authors: Gorelick Root , Laubichler Manfred D 
Published: August 2004

Abstract
We present a mathematically precise formulation of total linkage disequilibrium between multiple loci as the deviation from probabilistic independence and provide explicit formulas for all higher-order terms of linkage disequilibrium, thereby combining J. Dausset et al.'s 1978 definition of linkage disequilibrium with H. Geiringer's 1944 approach. We recursively decompose higher-order linkage disequilibrium terms into lower-order ones. Our greatest simplification comes from defining linkage disequilibrium at a single locus as allele frequency at that locus. At each level, decomposition of linkage disequilibrium is mathematically equivalent to number theoretic compositions of positive integers; i.e., we have converted a genetic decomposition into a mathematical decomposition.
Yeast Mn2+ Transporter, Smf1p, Is Regulated by Ubiquitin-Dependent Vacuolar Protein Sorting
Authors: Eguez Lorena , Chung Young-Sook , Kuchibhatla Ajay , Paidhungat Madan , Garrett Stephen 
Published: August 2004

Abstract
Conditional cdc1(Ts) mutants of S. cerevisiae arrest with a phenotype similar to that exhibited by Mn2+-depleted cells. Sequence similarity between Cdc1p and a class of Mn2+-dependent phosphoesterases, as well as the observation that conditional cdc1(Ts) growth can be ameliorated by Mn2+ supplement, suggests that Cdc1p activity is sensitive to intracellular Mn2+ levels. This article identifies several previously uncharacterized cdc1(Ts) suppressors as class E vps (vacuolar protein sorting) mutants and shows that these, as well as other vps mutants, accumulate high levels of intracellular Mn2+. Yeast VPS genes play a role in delivery of membrane transporters to the vacuole for degradation, and we show that the vps mutants accumulate elevated levels of the high-affinity Mn2+ transporter Smf1p. cdc1(Ts) conditional growth is also alleviated by mutations, including doa4 and ubc4, that compromise protein ubiquitination, and these ubiquitination defects are associated with Smf1p accumulation. Epistasis studies show that these suppressors require functional Smf1p to alleviate the cdc1(Ts) growth defect, whereas Smf1p is dispensable for cdc1(Ts) suppression by a mutation (cos16/per1) that does not influence intracellular Mn2+ levels. Because Smf1p is ubiquitinated in vivo, we propose that Smf1p is targeted to the vacuole for degradation by ubiquitination-dependent protein sorting.