bluuebunny/crossref_metadata_2025 huggingface dataset:
Children's developing understanding of differences between their own intentional action and passive movement
Authors: Montgomery Derek E. , Lightner Melisa
Published: August 2004

Four studies examined 3‐ and 4‐year‐olds' ability to judge accurately whether they acted intentionally. Children self‐initiated action to attain an outcome, or their arm was moved by the experimenter to create an outcome. In Experiment 3, children in both age groups accurately claimed they were agents of self‐guided action but not of passive movement. In contrast, in Experiments 1, 2 and 4, children in both age groups found it difficult to deny they intended to bring about the outcome, even though their movement was passive and, in some cases, the outcome was unexpected. They were consistently successful only when exclusively involved in creating one of two outcomes and asked which one they intended (Experiment 4). In sum, 3‐and 4‐year‐olds can distinguish when their movements are self‐directed and when they are passive. They are limited, however, in applying this distinction to self‐judgments concerning whether they acted intentionally. These findings are discussed with respect to linguistic and cognitive limitations that may influence the role first‐person knowledge plays in theory‐of‐mind development.
Indicating when you do not know the answer: The effect of question format and interviewer knowledge on children's ‘don't know’ responses
Authors: Waterman Amanda H. , Blades Mark , Spencer Christopher
Published: August 2004

Children are interviewed in a variety of contexts, for example, in the legal setting and in experimental research. In these situations, it is often very important that children indicate when they do not know the answer to a question, rather than guess. In the present experiment, one hundred and forty‐nine 5‐ to 9‐year‐olds witnessed a staged event in one of two conditions. The interviewer was either present at the event (knowledgeable interviewer) or absent from the event (uninformed interviewer). Children were then interviewed using yes/no questions and wh‐questions. Within each type of question, half were answerable based on the information provided; the other half were not answerable (i. e. the correct answer was ‘don't know’). The children performed consistently well with the answerable questions. With the unanswerable questions, there was an effect of format and interviewer knowledge. Children were more likely correctly to indicate that they did not know the answer to an unanswerable wh‐question than an unanswerable yes/no question. Also, children were more likely correctly to say ‘don't know’ to unanswerable questions when the interviewer had been absent from the event.
Sex differences in reactions to outperforming same‐sex friends
Authors: Benenson Joyce F. , Schinazi Joy
Published: August 2004

The current studies were designed to examine whether female adolescents have more negative reactions than male adolescents to achieving more than their same‐sex friends. In Study 1, 51 females and 48 males from grades 8 and 10 were administered questions assessing their reactions to performing better than their closest same‐sex friends in four domains. Across domains, females reported more negative reactions than males. Further, compared with males, female participants believed that their same‐sex friends would have more negative reactions if they performed better than their friends. In Study 2, 48 females and 49 males age 18 years were asked how they felt about performing better than and equal to their closest same‐sex friends in the domains of romance and academics in both hypothetical and actual situations. Females reported feeling more positive when they received the same outcomes as opposed to better outcomes than their friends. Males did not differ in the valence of their responses to the two outcomes. The implications for sex differences in achievement and friendship are discussed.
New evidence for infant colour categories
Authors: Franklin Anna , Davies Ian R.L.
Published: August 2004

Bornstein, Kessen, and Weiskopf (1976) reported that pre‐linguistic infants perceive colour categorically for primary boundaries: Following habituation, dishabituation only occurred if the test stimulus was from a different adult category to the original. Here, we replicated this important study and extended it to include secondary boundaries, with a crucial modification: The separations between habituated and novel stimuli were equated in a perceptually uniform metric (Munsell), rather than in wavelength. Experiment 1 found Categorical Perception and no within‐category novelty preference for primary boundary blue‐green and secondary boundary blue‐purple. Experiment 2 replicated the categorical effect for blue‐purple and found no within‐category novelty preference with increased stimulus separation. Experiment 3 showed category effects for a lightness/saturation boundary, pink‐red. Novelty preference requires a categorical difference between the habituated and novel stimulus. The implications for the origin of linguistic colour categories are discussed.
Parental reports of global physical health at ages 3 and 6 predict self‐reported depressive symptoms 17 years later
Authors: Räikkönen Katri , Schubert Carla , Pesonen Anu‐Katriina , Heinonen Kati , Viikari Jorma , Keltikangas‐Järvinen Liisa
Published: August 2004

Research studies testing longitudinal relations between childhood physical health measures and adulthood sub‐clinical depressive symptoms are rare. In the Cardiovascular Risk in Young Finns Study, longitudinal relations of parental reports of the global physical health of the child (1 = good, 2 = moderately good, 3 = average/not good) and of absent days from daycare due to physical illness during the past year (1 = no absent days, 2 = 1–5 days, 3 = 6–10 days, 4 = 11 days or more) with self‐reported depressive symptoms (a modified version of the Beck Depression Inventory) were studied over 17 years. The sample was population‐based, consisting at the study entry of 3‐ and 6‐year‐olds (n = 567) free of any chronic physical or mental illnesses. The results indicated that parent‐reported global physical health of the child during the childhood period significantly predicted the participant's self‐reported depressive symptom scores at follow‐up 12 and 17 years from the baseline (ps < .03). The risk of having depressive symptom scores at the top quartile of age‐ and gender‐specific distributions at follow‐up 12 and 17 years from the baseline, and both follow‐ups simultaneously was 1.97‐ to 4.49‐fold (95% confidence intervals: 1.15–11.96) for participants with a moderately good to average/not good global physical health at the study entry relative to participants with a good global physical health. Absent days from daycare were not associated with depressive symptoms. Despite its subjectivity, the results support the validity of parental reports and suggest that parent‐reported global physical health rating of the child early in development may indicate a risk for later depressive symptoms.
Lonely in the crowd: Recollections of bullying
Authors: Schäfer Mechthild , Korn Stefan , Smith Peter K. , Hunter Simon C. , Mora‐Merchán Joaqún A. , Singer Monika M. , Van der Meulen Kevin
Published: August 2004

This study examined the long‐term correlates of victimization in school with aspects of functioning in adult life, using a specially designed Retrospective Bullying Questionnaire, which also included questions about short‐term effects (e. g. suicidal ideation and intrusive memories) and victimization experiences in adulthood. Current relationship quality was assessed in terms of self‐perception, attachment style and friendship quality. In total, 884 adults (35% male) from two occupations (teacher, student) and three countries (Spain, Germany, UK) participated. Victims and especially stable victims (in both primary and secondary school) scored lower on general self‐esteem and higher on emotional loneliness, and reported more difficulties in maintaining friendships, than non‐victims. Victims in secondary school had a lower self‐esteem in relation to the opposite sex and were more often fearfully attached. The data revealed additional differences by gender, occupation and country level, but no further interactions with victim status. This indicates a general association between victimization in school and quality of later life predominately robust to variations in gender, occupation and country. Possible limitations caused by the retrospective nature of victimization reports are acknowledged.
Identity formation and parent‐child value congruence in adolescence
Authors: Knafo Ariel , Schwartz Shalom H.
Published: August 2004

We examine relations between identity formation and parent‐child value congruence. A total of 267 adolescents reported their own values and the values they perceive their parents to hold, and parents reported their values for their children. We measured identity formation by location in one of the four Marcia (1966) identity statuses (diffusion, foreclosure, moratorium and achievement). Adolescents in the two statuses characterized by exploration, achievement and moratorium, perceived their parents' values more accurately. Adolescents in the two high‐commitment statuses, achievement and foreclosure, were more accepting of the values they perceived their parents to hold. The four identity statuses did not differ in level of parent‐child value congruence. Implications for the process of value achievement are discussed.
Further Evidence to Show Population Specificity of Discriminant Function Equations for Sex Determination Using the Talus of South African Blacks
Authors: Bidmos M A , Dayal M R
Published: August 2004

Several studies have shown that osteometric differences exist between different population groups. Thus, discriminant function equations derived for the determination of sex from skeletal elements are population specific. In a previous study, the authors derived such equations from nine measurements of the talus of South African whites with high levels of average accuracies. The validity of some of the equations was tested on data collected from a South African black sample that consisted of 120 tali, equally distributed by sex, derived from the Raymond A. Dart Collection of Human Skeletons. The average accuracies dropped significantly. This necessitated the derivation of new equations for the South African black population and the average accuracies obtained ranged between 80% and 89%. The validity of the equations derived from the present study was tested using the leave-one-out classification and two independent samples (1 and 2). The applicability of the equations with very high classification rate from the present study was tested on Independent sample 1 of 10 white tali with poor results. The result of the validity of these equations on an Independent sample 2 of 10 black tali revealed acceptably high average accuracies in correct classification thereby supporting earlier observations on population specificity of discriminant function equations.
Rapid Screening of Selected Organic Explosives by High Performance Liquid Chromatography Using Reversed-Phase Monolithic Columns
Authors: Paull B , Roux C , Dawson M , Doble P
Published: August 2004

This study presents the rapid screening of various high grade explosives by high performance liquid chromatography (HPLC) with monolithic stationary phases. Two gradient methods were developed, the first for quantitative analysis of eleven explosives: HMX; RDX; Tetryl; TNT; 2,3-DNT; 2,6-DNT; 3,4-DNT; 2-NT; 3-NT; 4-NT; and PETN in under 14 min. The second method separated seven explosives in under two min and is suitable for rapid screening to determine the presence of specific and/or class of explosive. The rapid screening methods were successfully applied to soils spiked with known amounts of target explosives. This technology showed excellent potential for forensic explosives detection and analysis.
Factors Affecting Postmortem Tooth Loss
Authors: Duriဗ M , Rakocevic Z , Tuller H
Published: August 2004

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

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.
LIM Genes Parcellate the Embryonic Amygdala and Regulate Its Development
Authors: Remedios Ryan , Subramanian Lakshmi , Tole Shubha
Published: August 2004

The mechanisms that regulate the development of the amygdaloid complex are as yet poorly understood. Here, we show that in the absence of the LIM-homeodomain (LIM-HD) geneLhx2, a particular amygdaloid nucleus, the nucleus of the lateral olfactory tract (nLOT), is selectively disrupted. LIM family members are well suited for multiple roles in the development of complex structures because they participate in regulatory interactions that permit a diversity of function. To investigate the possible role for other LIM-HD genes as well as LIM-only (Lmo) genes in the developing amygdala, we examined their expression in the embryo. We show that amygdaloid nuclei upregulate distinct patterns of LIM gene expression from embryonic stages. This supports the hypothesis that LIM genes may participate in the mechanisms that control the development of the amygdala. The disruption of the nLOT in theLhx2mutant is the first evidence of a role for LIM-HD genes in the development of the amygdaloid complex. The combinatorial expression patterns of LIM genes suggest a comprehensive mechanism for patterning this structure.
Glutamate Released from Glial Cells Synchronizes Neuronal Activity in the Hippocampus
Authors: Angulo María Cecilia , Kozlov Andreï S. , Charpak Serge , Audinat Etienne
Published: August 2004

Glial cells of the nervous system directly influence neuronal and synaptic activities by releasing transmitters. However, the physiological consequences of this glial transmitter release on brain information processing remain poorly understood. We demonstrate here in hippocampal slices of 2- to 5-week-old rats that glutamate released from glial cells generates slow transient currents (STCs) mediated by the activation of NMDA receptors in pyramidal cells. STCs persist in the absence of neuronal and synaptic activity, indicating a nonsynaptic origin of the source of glutamate. Indeed, STCs occur spontaneously but can also be induced by pharmacological tools known to activate astrocytes and by the selective mechanical stimulation of single nearby glial cells. Bath application of the inhibitor of the glutamate uptakedl-threo-β-benzyloxyaspartate increases both the frequency of STCs and the amplitude of a tonic conductance mediated by NMDA receptors and probably also originated from glial glutamate release. By using dual recordings, we observed synchronized STCs in pyramidal cells having their soma distant by <100 μm. The degree of precision (<100 msec) of this synchronization rules out the involvement of calcium waves spreading through the glial network. It also indicates that single glial cells release glutamate onto adjacent neuronal processes, thereby controlling simultaneously the excitability of several neighboring pyramidal cells. In conclusion, our results show that the glial glutamate release occurs spontaneously and synchronizes the neuronal activity in the hippocampus.
Multiple Sites of Adaptive Plasticity in the Owl's Auditory Localization Pathway
Authors: DeBello William M. , Knudsen Eric I.
Published: August 2004

In the midbrain auditory localization pathway of the barn owl, a map of auditory space is relayed from the external nucleus of the inferior colliculus (ICX) to the deep and intermediate layers of the optic tectum (OT) and from these layers to the superficial layers. Within the OT, the auditory space map aligns with a visual map of space. Raising young barn owls with a prismatic displacement of the visual field leads to progressive changes in auditory tuning in the OT that tend to realign the auditory space map with the prismatically displaced visual space map. The only known site of this adaptive plasticity is in the ICX, in which the auditory system first creates a map of space. In this study, we identified an additional site of plasticity in the OT. In owls that experienced prisms beginning late in the juvenile period, adaptive shifts in auditory tuning in the superficial layers of the OT exceeded the adaptive shifts that occurred in the deep layers of the OT or in the ICX. Anatomical results from these owls demonstrated that the topography of intrinsic OT connections was systematically altered in the adaptive direction. In juvenile owls, plasticity in the OT increased as plasticity in the ICX decreased. Because plasticity at both sites has been shown to decline substantially in adults, these results suggest that an age-dependent decrease in auditory map plasticity occurs first in the ICX and later at the higher level, in the OT.
The Sleep Slow Oscillation as a Traveling Wave
Authors: Massimini Marcello , Huber Reto , Ferrarelli Fabio , Hill Sean , Tononi Giulio
Published: August 2004

During much of sleep, virtually all cortical neurons undergo a slow oscillation (<1 Hz) in membrane potential, cycling from a hyperpolarized state of silence to a depolarized state of intense firing. This slow oscillation is the fundamental cellular phenomenon that organizes other sleep rhythms such as spindles and slow waves. Using high-density electroencephalogram recordings in humans, we show here that each cycle of the slow oscillation is a traveling wave. Each wave originates at a definite site and travels over the scalp at an estimated speed of 1.2-7.0 m/sec. Waves originate more frequently in prefrontal-orbitofrontal regions and propagate in an anteroposterior direction. Their rate of occurrence increases progressively reaching almost once per second as sleep deepens. The pattern of origin and propagation of sleep slow oscillations is reproducible across nights and subjects and provides a blueprint of cortical excitability and connectivity. The orderly propagation of correlated activity along connected pathways may play a role in spike timing-dependent synaptic plasticity during sleep.
Surface Targeting of the Dopamine Transporter Involves Discrete Epitopes in the Distal C Terminus But Does Not Require Canonical PDZ Domain Interactions
Authors: Bjerggaard Christian , Fog Jacob U. , Hastrup Hanne , Madsen Kenneth , Loland Claus J. , Javitch Jonathan A. , Gether Ulrik
Published: August 2004

The human dopamine transporter (hDAT) contains a C-terminal type 2 PDZ (postsynaptic density 95/Discs large/zona occludens 1) domain-binding motif (LKV) known to interact with PDZ domain proteins such as PICK1 (protein interacting with C-kinase 1). As reported previously, we found that, after deletion of this motif, hDAT was retained in the endoplasmic reticulum (ER) of human embryonic kidney (HEK) 293 and Neuro2A cells, suggesting that PDZ domain interactions might be critical for hDAT targeting. Nonetheless, substitution of LKV with SLL, the type 1 PDZ-binding sequence from the β2-adrenergic receptor, did not disrupt plasma membrane targeting. Moreover, the addition of an alanine to the hDAT C terminus (+Ala), resulting in an LKVA termination sequence, or substitution of LKV with alanines (3xAla_618-620) prevented neither plasma membrane targeting nor targeting into sprouting neurites of differentiated N2A cells. The inability of +Ala and 3xAla_618-620 to bind PDZ domains was confirmed by lack of colocalization with PICK1 in cotransfected HEK293 cells and by the inability of corresponding C-terminal fusion proteins to pull down purified PICK1. Thus, although residues in the hDAT C terminus are indispensable for proper targeting, PDZ domain interactions are not required. By progressive substitutions with β2-adrenergic receptor sequence, and by triple-alanine substitutions in the hDAT C terminus, we examined the importance of epitopes preceding the LKV motif. Substitution of RHW615-617with alanines caused retention of the transporter in the ER despite preserved ability of this mutant to bind PICK1. We propose dual roles of the hDAT C terminus: a role independent of PDZ interactions for ER export and surface targeting, and a not fully clarified role involving PDZ interactions with proteins such as PICK1.
Putting Fear in Its Place: Remapping of Hippocampal Place Cells during Fear Conditioning
Authors: Moita Marta A. P. , Rosis Svetlana , Zhou Yu , LeDoux Joseph E. , Blair Hugh T.
Published: August 2004

We recorded hippocampal place cells in two spatial environments: a training environment in which rats underwent fear conditioning and a neutral control environment. Fear conditioning caused many place cells to alter (or remap) their preferred firing locations in the training environment, whereas most cells remained stable in the control environment. This finding indicates that aversive reinforcement can induce place cell remapping even when the environment itself remains unchanged. Furthermore, contextual fear conditioning caused significantly more remapping of place cells than auditory fear conditioning, suggesting that place cell remapping was related to the rat's learned fear of the environment. These results suggest that one possible function of place cell remapping may be to generate new spatial representations of a single environment, which could help the animal to discriminate among different motivational contexts within that environment.
Detecting Selection in Noncoding Regions of Nucleotide Sequences
Authors: Wong Wendy S W , Nielsen Rasmus
Published: August 2004

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 > 1 indicates the action of positive selection, and ζ < 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

A 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

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

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

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

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

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

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

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

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

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

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

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.
Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis
Authors: Hey Jody , Nielsen Rasmus
Published: August 2004

The genetic study of diverging, closely related populations is required for basic questions on demography and speciation, as well as for biodiversity and conservation research. However, it is often unclear whether divergence is due simply to separation or whether populations have also experienced gene flow. These questions can be addressed with a full model of population separation with gene flow, by applying a Markov chain Monte Carlo method for estimating the posterior probability distribution of model parameters. We have generalized this method and made it applicable to data from multiple unlinked loci. These loci can vary in their modes of inheritance, and inheritance scalars can be implemented either as constants or as parameters to be estimated. By treating inheritance scalars as parameters it is also possible to address variation among loci in the impact via linkage of recurrent selective sweeps or background selection. These methods are applied to a large multilocus data set from Drosophila pseudoobscura and D. persimilis. The species are estimated to have diverged ∼500,000 years ago. Several loci have nonzero estimates of gene flow since the initial separation of the species, with considerable variation in gene flow estimates among loci, in both directions between the species.
Quantitative Trait Loci for Sexual Isolation Between Drosophila simulans and D. mauritiana
Authors: Moehring Amanda J , Li Jian , Schug Malcolm D , Smith Shelly G , deAngelis Matthew , Mackay Trudy F C , Coyne Jerry A
Published: August 2004

Sexual isolating mechanisms that act before fertilization are often considered the most important genetic barriers leading to speciation in animals. While recent progress has been made toward understanding the genetic basis of the postzygotic isolating mechanisms of hybrid sterility and inviability, little is known about the genetic basis of prezygotic sexual isolation. Here, we map quantitative trait loci (QTL) contributing to prezygotic reproductive isolation between the sibling species Drosophila simulans and D. mauritiana. We mapped at least seven QTL affecting discrimination of D. mauritiana females against D. simulans males, three QTL affecting D. simulans male traits against which D. mauritiana females discriminate, and six QTL affecting D. mauritiana male traits against which D. simulans females discriminate. QTL affecting sexual isolation act additively, are largely different in males and females, and are not disproportionately concentrated on the X chromosome: The QTL of greatest effect are located on chromosome 3. Unlike the genetic components of postzygotic isolation, the loci for prezygotic isolation do not interact epistatically. The observation of a few QTL with moderate to large effects will facilitate positional cloning of genes underlying sexual isolation.
The Quantitative Genetic Basis of Male Mating Behavior in Drosophila melanogaster
Authors: Moehring Amanda J , Mackay Trudy F C
Published: August 2004

Male mating behavior is an important component of fitness in Drosophila and displays segregating variation in natural popluations. However, we know very little about the genes affecting naturally occurring variation in mating behavior, their effects, or their interactions. Here, we have mapped quantitative trait loci (QTL) affecting courtship occurrence, courtship latency, copulation occurrence, and copulation latency that segregate between a D. melanogaster strain selected for reduced male mating propensity (2b) and a standard wild-type strain (Oregon-R). Mating behavior was assessed in a population of 98 recombinant inbred lines derived from these two strains and QTL affecting mating behavior were mapped using composite interval mapping. We found four QTL affecting male mating behavior at cytological locations 1A;3E, 57C;57F, 72A;85F, and 96F;99A. We used deficiency complementation mapping to map the autosomal QTL with much higher resolution to five QTL at 56F5;56F8, 56F9;57A3, 70E1;71F4, 78C5;79A1, and 96F1;97B1. Quantitative complementation tests performed for 45 positional candidate genes within these intervals revealed 7 genes that failed to complement the QTL: eagle, 18 wheeler, Enhancer of split, Polycomb, spermatocyte arrest, l(2)05510, and l(2)k02206. None of these genes have been previously implicated in mating behavior, demonstrating that quantitative analysis of subtle variants can reveal novel pleiotropic effects of key developmental loci on behavior.