bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Affecting Postmortem Tooth Loss
Authors: Duriဗ M , Rakocevic Z , Tuller H 
Published: August 2004

Abstract
Unassociated human bones are a particular problem during the exhumation of mass graves and a factor that limits anthropological and paleopathological analyses from archaeological contexts. Extensive anthropological literature has focused on the complex taphonomic factors that influences bone assemblages, but little attention has been paid to postmortem tooth loss and factors affecting this process. The following study focuses upon the influence of different factors on postmortem tooth loss. Three samples were investigated in the study: a medieval church cemetery containing 110 individual skeletal remains, and two samples from a series of mass graves made within the same time period in 1999, containing 402 bodies. The frequency of postmortem tooth loss was analyzed relative to postmortem interval for each sample, excavation methods, age distribution, and presence of bone loss associated with periodontal disease. Our results indicate that the degree of alveolar bone loss significantly affected both antemortem and postmortem tooth loss and that the frequency of postmortem tooth loss has the strongest correlation to time since death. These findings suggest that additional care should be taken when exhuming remains from older contexts.
Defining Event Reconstruction of Digital Crime Scenes
Authors: Carrier BD , Spafford EH 
Published: August 2004

Abstract
Event reconstruction plays a critical role in solving physical crimes by explaining why a piece of physical evidence has certain characteristics. With digital crimes, the current focus has been on the recognition and identification of digital evidence using an object's characteristics, but not on the identification of the events that caused the characteristics. This paper examines digital event reconstruction and proposes a process model and procedure that can be used for a digital crime scene. The model has been designed so that it can apply to physical crime scenes, can support the unique aspects of a digital crime scene, and can be implemented in software to automate part of the process. We also examine the differences between physical event reconstruction and digital event reconstruction.
Detecting Selection in Noncoding Regions of Nucleotide Sequences
Authors: Wong Wendy S W , Nielsen Rasmus 
Published: August 2004

Abstract
We present a maximum-likelihood method for examining the selection pressure and detecting positive selection in noncoding regions using multiple aligned DNA sequences. The rate of substitution in noncoding regions relative to the rate of synonymous substitution in coding regions is modeled by a parameter ζ. When a site in a noncoding region is evolving neutrally ζ = 1, while ζ &gt; 1 indicates the action of positive selection, and ζ &lt; 1 suggests negative selection. Using a combined model for the evolution of noncoding and coding regions, we develop two likelihood-ratio tests for the detection of selection in noncoding regions. Data analysis of both simulated and real viral data is presented. Using the new method we show that positive selection in viruses is acting primarily in protein-coding regions and is rare or absent in noncoding regions.
Mapping Sites of Positive Selection and Amino Acid Diversification in the HIV Genome
Authors: de Oliveira Tulio , Salemi Marco , Gordon Michelle , Vandamme Anne-Mieke , van Rensburg Estrelita Janse , Engelbrecht Susan , Coovadia Hoosen M , Cassol Sharon 
Published: August 2004

AbstractA safe and effective HIV-1 vaccine is urgently needed to control the worldwide AIDS epidemic. Traditional methods of vaccine development have been frustratingly slow, and it is becoming increasingly apparent that radical new approaches may be required. Computational and mathematical approaches, combined with evolutionary reasoning, may provide new insights for the design of an efficacious AIDS vaccine. Here, we used codon-based substitution models and maximum-likelihood (ML) methods to identify positively selected sites that are likely to be involved in the immune control of HIV-1. Analysis of subtypes B and C revealed widespread adaptive evolution. Positively selected amino acids were detected in all nine HIV-1 proteins, including Env. Of particular interest was the high level of positive selection within the C-terminal regions of the immediate-early regulatory proteins, Tat and Rev. Many of the amino acid replacements were associated with the emergence of novel (or alternative) myristylation and casein kinase II (CKII) phosphorylation sites. The impact of these changes on the conformation and antigenicity of Tat and Rev remains to be established. In rhesus macaques, a single CTL-associated amino substitution in Tat has been linked to escape from acute SIV infection. Understanding the relationship between host-driven positive selection and antigenic variation may lead to the development of novel vaccine strategies that preempt the escape process.
The Effects of Intraspecific Competition and Stabilizing Selection on a Polygenic TraitThis article is dedicated to the memory of Sasha Gimelfarb, who died May 11, 2004.
Authors: Bürger Reinhard , Gimelfarb Alexander 
Published: August 2004

Abstract
The equilibrium properties of an additive multilocus model of a quantitative trait under frequency- and density-dependent selection are investigated. Two opposing evolutionary forces are assumed to act: (i) stabilizing selection on the trait, which favors genotypes with an intermediate phenotype, and (ii) intraspecific competition mediated by that trait, which favors genotypes whose effect on the trait deviates most from that of the prevailing genotypes. Accordingly, fitnesses of genotypes have a frequency-independent component describing stabilizing selection and a frequency- and density-dependent component modeling competition. We study how the equilibrium structure, in particular, number, degree of polymorphism, and genetic variance of stable equilibria, is affected by the strength of frequency dependence, and what role the number of loci, the amount of recombination, and the demographic parameters play. To this end, we employ a statistical and numerical approach, complemented by analytical results, and explore how the equilibrium properties averaged over a large number of genetic systems with a given number of loci and average amount of recombination depend on the ecological and demographic parameters. We identify two parameter regions with a transitory region in between, in which the equilibrium properties of genetic systems are distinctively different. These regions depend on the strength of frequency dependence relative to pure stabilizing selection and on the demographic parameters, but not on the number of loci or the amount of recombination. We further study the shape of the fitness function observed at equilibrium and the extent to which the dynamics in this model are adaptive, and we present examples of equilibrium distributions of genotypic values under strong frequency dependence. Consequences for the maintenance of genetic variation, the detection of disruptive selection, and models of sympatric speciation are discussed.
Regulation of the Drosophila Epidermal Growth Factor-Ligand Vein Is Mediated by Multiple Domains
Authors: Donaldson Timothy , Wang Shu-Huei , Jacobsen Thomas L , Schnepp Bruce , Price Jessica , Simcox Amanda 
Published: August 2004

Abstract
Vein (Vn), a ligand for the Drosophila epidermal growth factor receptor (Egfr), has a complex structure including a PEST, Ig, and EGF domain. We analyzed the structure-function relationships of Vn by assaying deletion mutants. The results show that each conserved domain influences Vn activity. A PEST deletion increases Vn potency and genetic evidence suggests that Vn is regulated by proteasomal degradation. The Ig deletion causes toxic effects not seen following expression of native Vn, but the Ig domain is not required for Vn localization or for the activation of Egfr signaling in wing vein patterning. Remarkably, when the EGF domain is deleted, Vn functions as a dominant negative ligand, implying that Vn normally physically interacts with another factor to promote its activity. We identified additional highly conserved sequences and found several regions that affect Vn potency and one that may mediate the effect of dominant negative Vn molecules. Together the results show that the activity of Vn is controlled both positively and negatively, demonstrating the existence of additional levels at which Egfr signaling can be regulated.
Diverse Evolutionary Mechanisms Shape the Type III Effector Virulence Factor Repertoire in the Plant Pathogen Pseudomonas syringae
Authors: Rohmer Laurence , Guttman David S , Dangl Jeffery L 
Published: August 2004

Abstract
Many gram-negative pathogenic bacteria directly translocate effector proteins into eukaryotic host cells via type III delivery systems. Type III effector proteins are determinants of virulence on susceptible plant hosts; they are also the proteins that trigger specific disease resistance in resistant plant hosts. Evolution of type III effectors is dominated by competing forces: the likely requirement for conservation of virulence function, the avoidance of host defenses, and possible adaptation to new hosts. To understand the evolutionary history of type III effectors in Pseudomonas syringae, we searched for homologs to 44 known or candidate P. syringae type III effectors and two effector chaperones. We examined 24 gene families for distribution among bacterial species, amino acid sequence diversity, and features indicative of horizontal transfer. We assessed the role of diversifying and purifying selection in the evolution of these gene families. While some P. syringae type III effectors were acquired recently, others have evolved predominantly by descent. The majority of codons in most of these genes were subjected to purifying selection, suggesting selective pressure to maintain presumed virulence function. However, members of 7 families had domains subject to diversifying selection.
Epistasis of Quantitative Trait Loci Under Different Gene Action Models
Authors: Yang Rong-Cai 
Published: August 2004

Abstract
Modeling and detecting nonallelic (epistatic) effects at multiple quantitative trait loci (QTL) often assume that the study population is in zygotic equilibrium (i.e., genotypic frequencies at different loci are products of corresponding single-locus genotypic frequencies). However, zygotic associations can arise from physical linkages between different loci or from many evolutionary and demographic processes even for unlinked loci. We describe a new model that partitions the two-locus genotypic values in a zygotic disequilibrium population into equilibrium and residual portions. The residual portion is of course due to the presence of zygotic associations. The equilibrium portion has eight components including epistatic effects that can be defined under three commonly used equilibrium models, Cockerham's model, F2-metric, and F∞-metric models. We evaluate our model along with these equilibrium models theoretically and empirically. While all the equilibrium models require zygotic equilibrium, Cockerham's model is the most general, allowing for Hardy-Weinberg disequilibrium and arbitrary gene frequencies at individual loci whereas F2-metric and F∞-metric models require gene frequencies of one-half in a Hardy-Weinberg equilibrium population. In an F2 population with two unlinked loci, Cockerham's model is reduced to the F2-metric model and thus both have a desirable property of orthogonality among the genic effects; the genic effects under the F∞-metric model are not orthogonal but they can be easily translated into those under the F2-metric model through a simple relation. Our model is reduced to these equilibrium models in the absence of zygotic associations. The results from our empirical analysis suggest that the residual genetic variance arising from zygotic associations can be substantial and may be an important source of bias in QTL mapping studies.
The GAR-3 Muscarinic Receptor Cooperates With Calcium Signals to Regulate Muscle Contraction in the Caenorhabditis elegans Pharynx
Authors: Steger Katherine A , Avery Leon 
Published: August 2004

Abstract
Muscarinic acetylcholine receptors regulate the activity of neurons and muscle cells through G-protein-coupled cascades. Here, we identify a pathway through which the GAR-3 muscarinic receptor regulates both membrane potential and excitation-contraction coupling in the Caenorhabditis elegans pharyngeal muscle. GAR-3 signaling is enhanced in worms overexpressing gar-3 or lacking GPB-2, a G-protein β-subunit involved in RGS-mediated inhibition of Goα- and Gqα-linked pathways. High levels of signaling through GAR-3 inhibit pharyngeal muscle relaxation and impair feeding—but do not block muscle repolarization—when worms are exposed to arecoline, a muscarinic agonist. Loss of gar-3 function results in shortened action potentials and brief muscle contractions in the pharyngeal terminal bulb. High levels of calcium entry through voltage-gated channels also impair terminal bulb relaxation and sensitize worms to the toxic effects of arecoline. Mutation of gar-3 reverses this sensitivity, suggesting that GAR-3 regulates calcium influx or calcium-dependent processes. Because the effects of GAR-3 signaling on membrane depolarization and muscle contraction can be separated, we conclude that GAR-3 regulates multiple calcium-dependent processes in the C. elegans pharyngeal muscle.
Wide-Cross Whole-Genome Radiation Hybrid Mapping of Cotton (Gossypium hirsutum L.)
Authors: Gao Wenxiang , Chen Z Jeffrey , Yu John Z , Raska Dwaine , Kohel Russell J , Womack James E , Stelly David M 
Published: August 2004

Abstract
We report the development and characterization of a “wide-cross whole-genome radiation hybrid” (WWRH) panel from cotton (Gossypium hirsutum L.). Chromosomes were segmented by γ-irradiation of G. hirsutum (n = 26) pollen, and segmented chromosomes were rescued after in vivo fertilization of G. barbadense egg cells (n = 26). A 5-krad γ-ray WWRH mapping panel (N = 93) was constructed and genotyped at 102 SSR loci. SSR marker retention frequencies were higher than those for animal systems and marker retention patterns were informative. Using the program RHMAP, 52 of 102 SSR markers were mapped into 16 syntenic groups. Linkage group 9 (LG 9) SSR markers BNL0625 and BNL2805 had been colocalized by linkage analysis, but their order was resolved by differential retention among WWRH plants. Two linkage groups, LG 13 and LG 9, were combined into one syntenic group, and the chromosome 1 linkage group marker BNL4053 was reassigned to chromosome 9. Analyses of cytogenetic stocks supported synteny of LG 9 and LG 13 and localized them to the short arm of chromosome 17. They also supported reassignment of marker BNL4053 to the long arm of chromosome 9. A WWRH map of the syntenic group composed of linkage groups 9 and 13 was constructed by maximum-likelihood analysis under the general retention model. The results demonstrate not only the feasibility of WWRH panel construction and mapping, but also complementarity to traditional linkage mapping and cytogenetic methods.
The Caenorhabditis elegans pvl-5 Gene Protects Hypodermal Cells From ced-3-Dependent, ced-4-Independent Cell Death
Authors: Joshi Pradeep , Eisenmann David M 
Published: August 2004

Abstract
Programmed cell death (PCD) is regulated by multiple evolutionarily conserved mechanisms to ensure the survival of the cell. Here we describe pvl-5, a gene that likely regulates PCD in Caenorhabditis elegans. In wild-type hermaphrodites at the L2 stage there are 11 Pn.p hypodermal cells in the ventral midline arrayed along the anterior-posterior axis and 6 of these cells become the vulval precursor cells. In pvl-5(ga87) animals there are fewer Pn.p cells (average of 7.0) present at this time. Lineage analysis reveals that the missing Pn.p cells die around the time of the L1 molt in a manner that often resembles the programmed cell deaths that occur normally in C. elegans development. This Pn.p cell death is suppressed by mutations in the caspase gene ced-3 and in the bcl-2 homolog ced-9, suggesting that the Pn.p cells are dying by PCD in pvl-5 mutants. Surprisingly, the Pn.p cell death is not suppressed by loss of ced-4 function. ced-4 (Apaf-1) is required for all previously known apoptotic cell deaths in C. elegans. This suggests that loss of pvl-5 function leads to the activation of a ced-3-dependent, ced-4-independent form of PCD and that pvl-5 may normally function to protect cells from inappropriate activation of the apoptotic pathway.
Molecular Population Genetics of Male Accessory Gland Proteins in the Drosophila simulans Complex
Authors: Kern Andrew D , Jones Corbin D , Begun David J 
Published: August 2004

Abstract
Accessory gland proteins are a major component of Drosophila seminal fluid. These proteins have a variety of functions and may be subject to sexual selection and/or antagonistic evolution between the sexes. Most population genetic data from these proteins are from D. melanogaster and D. simulans. Here, we extend the population genetic analysis of Acp genes to the other simulans complex species, D. mauritiana and D. sechellia. We sequenced population samples of seven Acp's from D. mauritiana, D. sechellia, and D. simulans. We investigated the population genetics of these genes on individual simulans complex lineages and compared Acp polymorphism and divergence to polymorphism and divergence from a set of non-Acp loci in the same species. Polymorphism and divergence data from the simulans complex revealed little evidence for adaptive protein evolution at individual loci. However, we observed a dramatically inflated index of dispersion for amino acid substitutions in the simulans complex at Acp genes, but not at non-Acp genes. This pattern of episodic bursts of protein evolution in Acp's provides the strongest evidence to date that the population genetic mechanisms driving Acp divergence are different from the mechanisms driving evolution at most Drosophila genes.
The PGL Family Proteins Associate With Germ Granules and Function Redundantly in Caenorhabditis elegans Germline Development
Authors: Kawasaki Ichiro , Amiri Anahita , Fan Yuan , Meyer Nicole , Dunkelbarger Steve , Motohashi Tomoko , Karashima Takeshi , Bossinger Olaf , Strome Susan 
Published: August 2004

Abstract
PGL-1 is a constitutive protein component of C. elegans germ granules, also known as P granules. Maternally supplied PGL-1 is essential for germline development but only at elevated temperature, raising the possibility that redundant factors provide sufficient function at lower temperatures. We have identified two PGL-1-related proteins, PGL-2 and PGL-3, by sequence analysis of the C. elegans genome and by a yeast two-hybrid screen for proteins that interact with PGL-1. PGL-3 is associated with P granules at all stages of development, while PGL-2 is associated with P granules only during postembryonic development. All three PGL proteins interact with each other in vitro. Furthermore, PGL-1 and PGL-3 are co-immunoprecipitated from embryo extracts, indicating that they are indeed in the same protein complex in vivo. Nevertheless, each PGL protein localizes to P granules independently of the other two. pgl-2 or pgl-3 single-mutant worms do not show obvious defects in germline development. However, pgl-1; pgl-3 (but not pgl-2; pgl-1) double-mutant hermaphrodites and males show significantly enhanced sterility at all temperatures, compared to pgl-1 alone. Mutant hermaphrodites show defects in germline proliferation and in production of healthy gametes and viable embryos. Our findings demonstrate that both PGL-2 and PGL-3 are components of P granules, both interact with PGL-1, and at least PGL-3 functions redundantly with PGL-1 to ensure fertility in both sexes of C. elegans.
A Misexpression Screen Reveals Effects of bag-of-marbles and TGFβ Class Signaling on the Drosophila Male Germ-Line Stem Cell Lineage
Authors: Schulz Cordula , Kiger Amy A , Tazuke Salli I , Yamashita Yukiko M , Pantalena-Filho Luiz C , Jones D Leanne , Wood Cricket G , Fuller Margaret T 
Published: August 2004

Abstract
Male gametes are produced throughout reproductive life by a classic stem cell mechanism. However, little is known about the molecular mechanisms for lineage production that maintain male germ-line stem cell (GSC) populations, regulate mitotic amplification divisions, and ensure germ cell differentiation. Here we utilize the Drosophila system to identify genes that cause defects in the male GSC lineage when forcibly expressed. We conducted a gain-of-function screen using a collection of 2050 EP lines and found 55 EP lines that caused defects at early stages of spermatogenesis upon forced expression either in germ cells or in surrounding somatic support cells. Most strikingly, our analysis of forced expression indicated that repression of bag-of-marbles (bam) expression in male GSC is important for male GSC survival, while activity of the TGFβ signal transduction pathway may play a permissive role in maintenance of GSCs in Drosophila testes. In addition, forced activation of the TGFβ signal transduction pathway in germ cells inhibits the transition from the spermatogonial mitotic amplification program to spermatocyte differentiation.
Characterization of Conditionally Expressed Mutants Affecting Age-Specific Survival in Inbred Lines of Drosophila melanogaster
Authors: Vermeulen C J , Bijlsma R 
Published: August 2004

Abstract
The specific genetic basis of inbreeding depression is poorly understood. To address this question, two conditionally expressed lethal effects that were found to cause line-specific life span reductions in two separate inbred lines of Drosophila melanogaster were characterized phenotypically and genetically in terms of whether the accelerated mortality effects are dominant or recessive. The mortality effect in one line (I4) is potentially a temperature-sensitive semilethal that expresses in adult males only and is partially dominant. The other line (I10) responds as one would expect for a recessive lethal. It requires a cold shock for expression and is cold sensitive. Flies exhibiting this lethal condition responded as pupae and freshly eclosed imagoes. The effect is recessive in both males and females. The expression of the lethal effects in both lines is highly dependent upon environmental conditions. These results will serve as a basis for more detailed and mechanistic genetic research on inbreeding depression and are relevant to sex- and environment-specific effects on life span observed in quantitative trait loci studies using inbred lines.