bluuebunny/crossref_metadata_2025 huggingface dataset:
Glyceraldehyde-3-Phosphate Dehydrogenase Is a GABAAReceptor Kinase Linking Glycolysis to Neuronal Inhibition
Authors: Laschet Jacques J. , Minier Frédéric , Kurcewicz Irène , Bureau Michel H. , Trottier Suzanne , Jeanneteau Freddy , Griffon Nathalie , Samyn Bart , Van Beeumen Jozef , Louvel Jacques , Sokoloff Pierre , Pumain René
Published: September 2004

Protein phosphorylation is crucial for regulating synaptic transmission. We describe a novel mechanism for the phosphorylation of the GABAAreceptor, which mediates fast inhibition in the brain. A protein copurified and coimmunoprecipitated with the phosphorylated receptor α1 subunit; this receptor-associated protein was identified by purification and microsequencing as the key glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Molecular constructs demonstrated that GAPDH directly phosphorylates the long intracellular loop of GABAAreceptor α1 subunit at identified serine and threonine residues. GAPDH and the α1 subunit were found to be colocalized at the neuronal plasma membrane. In keeping with the GAPDH/GABAAreceptor molecular association, glycolytic ATP produced locally at plasma membranes was consumed for this α1 subunit phosphorylation, possibly within a single macrocomplex. The membrane-attached GAPDH is thus a dual-purpose enzyme, a glycolytic dehydrogenase, and a receptor-associated kinase. In acutely dissociated cortical neurons, the rundown of the GABAAresponses was essentially attributable to a Mg2+-dependent phosphatase activity, which was sensitive to vanadate but insensitive to okadaic acid or fluoride. Rundown was significantly reduced by the addition of GAPDH or its reduced cofactor NADH and nearly abolished by the addition of its substrate glyceraldehyde-3-phosphate (G3P). The prevention of rundown by G3P was abolished by iodoacetamide, an inhibitor of the dehydrogenase activity of GAPDH, indicating that the GABAAresponses are maintained by a glycolysis-dependent phosphorylation. Our results provide a molecular mechanism for the direct involvement of glycolysis in neurotransmission.
Muscarinic Receptor Modulation of Slow Afterhyperpolarization and Phasic Firing in Rat Supraoptic Nucleus Neurons
Authors: Ghamari-Langroudi Masoud , Bourque Charles W.
Published: September 2004

A slow posttrain afterhyperpolarization (sAHP) was studied in rat magnocellular neurosecretory cells (MNCs)in vitro. The sAHP was isolated from other afterpotentials by blocking the depolarizing afterpotential (DAP) with Cs+and the medium afterhyperpolarization (mAHP) with apamin. The sAHP amplitude increased logarithmically with activity (∼3 mV pere-fold increase in number of impulses) and, when firing stopped, decayed exponentially with a time constant of 2 sec. The sAHP was associated with increased membrane conductance, and its amplitude varied linearly with voltage, reversing at the K+equilibrium potential. The sAHP was blocked by Cd2+but not by charybdotoxin or iberiotoxin, blockers of intermediate- and big-conductance-type Ca2+-dependent K+(KCa) channels. The sAHP was reversibly inhibited by muscarine, an effect antagonized by atropine, indicating involvement of muscarinic cholinergic receptors. Muscarine did not affect Ca2+-dependent features of action potentials, DAPs, or the mAHP in MNCs, indicating selective modulation of KCachannels causing the sAHP. Muscarinic inhibition of the sAHP enhanced plateau potentials and increased the mean firing rate and duration of afterdischarges that followed spike trains evoked from voltages near threshold. Similarly, the frequency and duration of the spontaneous phasic bursts that characterize physiologically activated vasopressin-releasing MNCs were enhanced by muscarine. MNCs thus express apamin- and voltage-insensitive KCachannels that mediate an sAHP. The activity dependence and kinetics of the sAHP cause it to mask DAPs in a manner that attenuates the amplitude of plateau potentials. Muscarinic inhibition of the sAHP provides an effective mechanism for promoting phasic firing in MNCs.
Selective Neurotoxic Lesions of Basolateral and Central Nuclei of the Amygdala Produce Differential Effects on Fear Conditioning
Authors: Koo Ja Wook , Han Jung-Soo , Kim Jeansok J.
Published: September 2004

In the fear conditioning literature, it is generally hypothesized that neurons in the basolateral amygdalar complex (BLA) (lateral and basal nuclei) support the formation of conditioned fear memory and project to neurons in the central nucleus (CeA) for the expression of conditioned fear responses. According to this serial processing-transmission view, damage to either BLA or CeA would comparably disrupt the expression of a variety of conditioned fear responses. In the present study, we further investigated the roles of BLA and CeA in fear conditioning by concurrently assessing freezing and 22 kHz ultrasonic vocalization (USV) as dependent measures of fear in rats. Selective neurotoxins, NMDA for the BLA and ibotenic acid for the CeA, were used to destroy intrinsic neurons [evidenced by thionin dye and NeuN (neuronal nuclei) antibody stainings] without damaging the fibers of passage (confirmed by myelin staining). During the 10 tone-footshock paired training, postshock freezing and USV responses were significantly impaired in BLA-lesioned animals, whereas CeA-lesioned animals exhibited only mild deficits. Similarly, conditioned fear responses assessed 24 hr after training were severely reduced in BLA-lesioned animals but not in CeA-lesioned animals. In contrast to ibotenic lesions of the CeA, small electrolytic lesions of the CeA strongly affected both postshock and conditioned freezing and USV. Together, these results do not support the currently espoused BLA-to-CeA serial processing-transmission view of fear conditioning. Instead, the expression of conditioned fear appears to primarily involve BLA projections that course through the CeA en route to downstream fear response structures.
The Type IV-Specific Phosphodiesterase Inhibitor Rolipram and Its Effect on Hippocampal Long-Term Potentiation and Synaptic Tagging
Authors: Navakkode Sheeja , Sajikumar Sreedharan , Frey Julietta Uta
Published: September 2004

We investigated the effects of rolipram, a selective cAMP phosphodiesterase (PDE) inhibitor, on late plastic events during functional CA1 plasticityin vitroin rat hippocampal slices. We present data showing that an early form of long-term potentiation (LTP) (early-LTP) that normally decays within 2-3 hr can be converted to a lasting LTP (late-LTP) if rolipram is applied during tetanization. This rolipram-reinforced LTP (RLTP) was NMDA receptor and protein synthesis dependent. cAMP formation in region CA1 during late-LTP requires dopaminergic receptor activity (Frey et al., 1989, 1990). Thus, we studied whether RLTP was influenced by inhibitors of the D1/D5receptor. Application of the specific D1/D5antagonistSCH23390(0.1 μm) did not prevent RLTP, suggesting that the phosphodiesterase inhibitor acts downstream of the D1/D5receptors. We also studied whether rolipram can interact with processes of synaptic tagging, because RLTP was also dependent on protein synthesis, similar to late-LTP. Inhibition of PDE and subsequent induction of RLTP in one synaptic population were able to transform early-LTP into late-LTP in a second, independent synaptic population of the same neurons. This supports our hypothesis that cAMP-dependent processes are directly involved in the synthesis of plasticity-related proteins.
Noradrenergic Inputs Mediate State Dependence of Auditory Responses in the Avian Song System
Authors: Cardin Jessica A. , Schmidt Marc F.
Published: September 2004

Norepinephrine (NE) plays a complex role in the behavioral state-dependent regulation of sensory processing. However, the role of forebrain NE action in modulating high-order sensory activity has not been directly addressed. In this study, we take advantage of the discrete, feedforward organization of the avian song system to identify a site and mechanism of NE action underlying state-dependent modulation of sensory processing. We have developed an experimental paradigm in which brief arousal repeatedly suppresses song system auditory responsiveness. Using pharmacological manipulationsin vivo, we show that infusion of α-adrenergic antagonists into the NIf (nucleus interfacialis of the nidopallium), an auditory forebrain area, blocks this state-dependent modulation. We also demonstrate dose-dependent enhancement and suppression of song system auditory response properties by NE and adrenergic agonists. Our results demonstrate that noradrenergic release in a single forebrain area is a mechanism underlying behavioral state-dependent regulation of auditory processing in a neural system specialized for vocal learning.
The Expression of Matrix Metalloproteinase-12 by Oligodendrocytes Regulates Their Maturation and Morphological Differentiation
Authors: Larsen Peter H. , Yong V. Wee
Published: September 2004

Matrix metalloproteinases (MMPs) have important roles in many processes of the developing CNS requiring proteolytic activity such as the migration of neuronal precursors, axonal outgrowth, and vascularization. Another developmental event involving proteolysis is myelin formation, whereby the extensive processes elaborated from oligodendrocytes (OLs) enwrap axons. Here we find MMP-12 transcripts to be produced by OLs in much higher levels than other MMP members examined. MMP-12 activity correlated with the ability of OLs to extend processesin vitro, suggesting a role for MMP-12 in the morphological differentiation of OLs. This was corroborated by results that OL lineage cells from MMP-12 null mice were retarded in their ability to differentiate morphologically and that this deficiency was overcome by the exogenous addition of active MMP-12. Finally, the maturation of oligodendrocyte precursor cells (OPCs) to OLs was significantly reduced in cultures from MMP-12 null mice compared with wild-type controls. We conclude that OL lineage cells express MMP-12 during their maturation and that MMP-12 activity has functional involvement both in maturation of OPCs and in the ability of OPCs and OLs to extend processes.
Severe Defects in Dorsal Thalamic Development in Low-Density Lipoprotein Receptor-Related Protein-6 Mutants
Authors: Zhou Cheng-Ji , Pinson Kathleen I. , Pleasure Samuel J.
Published: September 2004

Mice with mutations in the Wnt coreceptor low-density lipoprotein receptor-related protein-6 (LRP6) have a smaller and severely disorganized dorsal thalamus and lack thalamocortical projections. Using molecular markers, we showed that most dorsal thalamic and epithalamic neurons were missing, and most of the major dorsal thalamic nuclei were not identifiable. However, the ventral thalamus was essentially unaffected, although the dorsal thalamic defect leads to rostral displacement of portions of the ventral thalamus. Analysis of younger embryos showed that epithalamic and dorsal thalamic neurons were not produced at early stages of development, whereas ventral thalamic neurons were still produced. These defects were accompanied by improper formation of the boundary between dorsal and ventral thalamus, the zona limitans interthalamica (ZLI). Furthermore, the expression of an early marker of posterior forebrain development that marks the compartment from the midbrain-hindbrain junction to the ZLI (including the future dorsal thalamus, pretectum, and midbrain) was disrupted, supporting the idea that diencephalic development is abnormal from very early in embryogenesis. This study provides compellingin vivoevidence that thalamic development requires normal activity of the LRP6-mediated canonical Wnt signaling pathway.
An Element in the α1-Tubulin Promoter Is Necessary for Retinal Expression during Optic Nerve Regeneration But Not after Eye Injury in the Adult Zebrafish
Authors: Senut Marie-Claude , Gulati-Leekha Abhilasha , Goldman Daniel
Published: September 2004

We have shown previously that a 1.696 kb upstream fragment of the goldfish α1-tubulin promoter was capable of driving green fluorescent protein (GFP) expression in the developing and regenerating zebrafish CNS in a pattern closely mimicking the endogenous α1-tubulin gene. Comparison of fish and rat α1-tubulin promoters identified a 64 bp region with a conserved repetitive homeodomain (HD) consensus sequence core (TAAT) and a nearby basic helix—loop-helix binding E-box sequence (CANNTG), which led us to speculate that it could be of importance for regulating α1-tubulin gene transcription. To address this issue, we examined the ability of deletion mutants of the 1.696 kb promoter to drive expression of GFP in zebrafish retinal cells under normal conditions and after injury. Interestingly, although wild-type 1.696 kb and mutant promoters, lacking the E-box and/or HD sequences, exhibited rather similar patterns of GFP expression in the developing retina, significant differences were noticed in the mature retina. First, although the 1.696 kb promoter directed transgene expression to retinal neurons and progenitor cells, the activity of mutant promoters was drastically reduced. Second, we found that the E-box and HD sequences were necessary for transgene reinduction during optic nerve regeneration, but were not as important for transgene expression in regenerating retinal neurons after eye injury. In this latter lesion model, remarkably, both 1.696 kb and mutant promoters targeted GFP expression to Müller glia-like cells, some of which re-entered the cell cycle. These new findings will be useful for identifying the molecular signals necessary for successful CNS regeneration.
Visual Neurons in the Pigeon Brain Encode the Acceleration of Stimulus Motion
Authors: Cao Peng , Gu Yong , Wang Shu-Rong
Published: September 2004

Seeing target motion is a vital capability of the visual system in humans and animals. Physically, motion is described by its acceleration, speed, and direction. Motion-sensitive neurons in all the visual areas examined to date are selective for the direction and speed of motion. Here, we show by single-unit recording that one-third of motion-sensitive neurons in the pigeon's pretectal nucleus also encode the acceleration of stimulus motion. These neurons are characterized by plateau-shaped speed-tuning curves in which the firing rate is the same over a wide range of speeds, a feature that allows these neurons to encode unambiguously the rate of change of speed over time. Acceleration-sensitive neurons also show transient responses to the offset of motion in the preferred and/or nonpreferred directions; acceleration-insensitive neurons do not. We observed the same sensitivity to target acceleration for brief ramps of stimulus speed and for sinusoidal modulation of speed. The locations of acceleration-sensitive and -insensitive neurons are segregated in the pretectal nucleus. The visual responses of pretectal neurons indicate that the visual and vestibular systems share not only a spatial but also a temporal reference frame that can detect the acceleration produced by self-motion of an organism.
UmamiTaste Responses Are Mediated by α-Transducin and α-Gustducin
Authors: He Wei , Yasumatsu Keiko , Varadarajan Vijaya , Yamada Ayako , Lem Janis , Ninomiya Yuzo , Margolskee Robert F. , Damak Sami
Published: September 2004

The sense of taste comprises at least five distinct qualities: sweet, bitter, sour, salty, andumami, the taste of glutamate. For bitter, sweet, andumamicompounds, taste signaling is initiated by binding of tastants to G-protein-coupled receptors in specialized epithelial cells located in the taste buds, leading to the activation of signal transduction cascades. α-Gustducin, a taste cell-expressed G-protein α subunit closely related to the α-transducins, is a key mediator of sweet and bitter tastes. α-Gustducin knock-out (KO) mice have greatly diminished, but not entirely abolished, responses to many bitter and sweet compounds. We set out to determine whether α-gustducin also mediatesumamitaste and whether rod α-transducin (αt-rod), which is also expressed in taste receptor cells, plays a role in any of the taste responses that remain in α-gustducin KO mice. Behavioral tests and taste nerve recordings of single and double KO mice lacking α-gustducin and/or αt-rodconfirmed the involvement of α-gustducin in bitter (quinine and denatonium) and sweet (sucrose and SC45647) taste and demonstrated the involvement ofα-gustducin inumami[monosodium glutamate (MSG), monopotassium glutamate (MPG), and inosine monophosphate (IMP)] taste as well. We found that αt-rodplayed no role in taste responses to the salty, bitter, and sweet compounds tested or to IMP but was involved in theumamitaste of MSG and MPG.Umamidetection involving α-gustducin and αt-rodoccurs in anteriorly placed taste buds, however taste cells at the back of the tongue respond toumamicompounds independently of these two G-protein subunits.
Phenotypic Variation Resulting From a Deficiency of Epidermal Growth Factor Receptor in Mice Is Caused by Extensive Genetic Heterogeneity That Can Be Genetically and Molecularly Partitioned
Authors: Strunk Karen E , Amann Vicky , Threadgill David W
Published: September 2004

The timing of lethality caused by homozygosity for a null allele of the epidermal growth factor receptor (Egfrtm1Mag) in mice is strongly dependent on genetic background. Initial attempts to genetically map background modifiers using Swiss-derived, outbred CD-1 mice were unsuccessful. To investigate the genetic architecture contributing to survival of Egfrtm1Mag homozygous embryos, the genetic variability segregating within the outbred population was partitioned by surveying viability of Egfrtm1Mag mutants using intercrosses between 129S6/SvEvTAC-Egfrtm1Mag and nine Swiss-derived, inbred strains: ALR/LtJ, ALS/LtJ, APN, APS, ICR/HaRos, NOD/LtJ, NON/LtJ, SJL/J, and SWR/J. The observations showed that these strains support varying levels of survival of Egfrtm1Mag homozygous embryos, suggesting that genetic heterogeneity within the CD-1 stock contributed to the original lack of Egfrtm1Mag modifier detection. Similar to the Swiss-derived intercrosses, nine congenic strains, derived from 129S6/SvEvTAC, AKR/J, APN, BALB/cJ, BTBR-T+ tf/tf, C3H/HeJ, C57BL/6J, DBA/2J, and FVB/NJ inbred backgrounds, also supported varying levels of survival of Egfrtm1Mag mutants. By intercrossing the congenic lines to create hybrid F1 embryos, different genetic backgrounds were found to have complementary modifiers. Analysis of the congenic lines argues against heterosis of outbred backgrounds contributing to Egfrtm1Mag phenotypic variability. A detailed analysis of the crosses suggests that modifiers function at three distinct stages of development. One class of modifiers supports survival of Egfrtm1Mag homozygous embryos to mid-gestation, another class supports development through the mid-gestation transition from yolk-sac to placental-derived nutrient sources, and a third class supports survival through later stages of gestation. Data from microarray analysis using RNA from wild-type and Egfrtm1Mag mutant placentas support the existence of extensive genetic heterogeneity and suggest that it can be molecularly partitioned. This method should be generally useful to partition heterogeneity contributing to other complex traits.
Conditional Probability Methods for Haplotyping in Pedigrees
Authors: Gao Guimin , Hoeschele Ina , Sorensen Peter , Du Fengxing
Published: September 2004

Efficient haplotyping in pedigrees is important for the fine mapping of quantitative trait locus (QTL) or complex disease genes. To reconstruct haplotypes efficiently for a large pedigree with a large number of linked loci, two algorithms based on conditional probabilities and likelihood computations are presented. The first algorithm (the conditional probability method) produces a single, approximately optimal haplotype configuration, with computing time increasing linearly in the number of linked loci and the pedigree size. The other algorithm (the conditional enumeration method) identifies a set of haplotype configurations with high probabilities conditional on the observed genotype data for a pedigree. Its computing time increases less than exponentially with the size of a subset of the set of person-loci with unordered genotypes and linearly with its complement. The size of the subset is controlled by a threshold parameter. The set of identified haplotype configurations can be used to estimate the identity-by-descent (IBD) matrix at a map position for a pedigree. The algorithms have been tested on published and simulated data sets. The new haplotyping methods are much faster and provide more information than several existing stochastic and rule-based methods. The accuracies of the new methods are equivalent to or better than those of these existing methods.
In Vivo Interaction Between Mitochondria Carrying mtDNAs From Different Mouse Species
Authors: Sato Akitsugu , Nakada Kazuto , Shitara Hiroshi , Yonekawa Hiromichi , Hayashi Jun-Ichi
Published: September 2004

Mitochondrial disease model mice, mitomice, were created using zygotes of B6mtspr strain mice carrying mitochondrial DNA (mtDNA) from Mus spretus as recipients of exogenous mitochondria carrying wild-type and a deletion mutant mtDNA (ΔmtDNA) of M. musculus domesticus. In these experiments, mtDNAs from different mouse species were used for identification of exo- and endogenous wild-type mtDNAs in the mitomice. Results showed transmission of exogenous ΔmtDNA, but not exogenous wild-type mtDNA, of M. m. domesticus to following generations through the female germ line. Complete elimination of exogenous wild-type mtDNA would be due to stochastic segregation, whereas transmission of exogenous ΔmtDNA would be due to its smaller size leading to a propagational advantage. Tissues in mitomice of the F3 generation carrying exogenous ΔmtDNA showed protection from respiration defects until ΔmtDNA accumulated predominantly. This protection from expression of mitochondrial dysfunction was attained with the help of endogenous wild-type mtDNA of M. spretus, since mitomice did not possess exogenous wild-type mtDNA of M. m. domesticus. These observations provide unambiguous evidence for the presence of interaction between exogenous mitochondria carrying ΔmtDNA and endogenous mitochondria carrying M. spretus wild-type mtDNA.
Multiple-Interval Mapping for Quantitative Trait Loci Controlling Endosperm Traits
Authors: Kao Chen-Hung
Published: September 2004

Endosperm traits are trisomic inheritant and are of great economic importance because they are usually directly related to grain quality. Mapping for quantitative trait loci (QTL) underlying endosperm traits can provide an efficient way to genetically improve grain quality. As the traditional QTL mapping methods (diploid methods) are usually designed for traits under diploid control, they are not the ideal approaches to map endosperm traits because they ignore the triploid nature of endosperm. In this article, a statistical method considering the triploid nature of endosperm (triploid method) is developed on the basis of multiple-interval mapping (MIM) to map for the underlying QTL. The proposed triploid MIM method is derived to broadly use the marker information either from only the maternal plants or from both the maternal plants and their embryos in the backcross and F2 populations for mapping endosperm traits. Due to the use of multiple intervals simultaneously to take multiple QTL into account, the triploid MIM method can provide better detection power and estimation precision, and as shown in this article it is capable of analyzing and searching for epistatic QTL directly as compared to the traditional diploid methods and current triploid methods using only one (or two) interval(s). Several important issues in endosperm trait mapping, such as the relation and differences between the diploid and triploid methods, variance components of genetic variation, and the problems if effects are present and ignored, are also addressed. Simulations are performed to further explore these issues, to investigate the relative efficiency of different experimental designs, and to evaluate the performance of the proposed and current methods in mapping endosperm traits. The MIM-based triploid method can provide a powerful tool to estimate the genetic architecture of endosperm traits and to assist the marker-assisted selection for the improvement of grain quality in crop science. The triploid MIM FORTRAN program for mapping endosperm traits is available on the worldwide web (http://www.stat.sinica.edu.tw/chkao/).
CDC7/DBF4 Functions in the Translesion Synthesis Branch of the RAD6 Epistasis Group in Saccharomyces cerevisiae
Authors: Pessoa-Brandão Luis , Sclafani Robert A
Published: September 2004

CDC7 and DBF4 encode the essential Cdc7-Dbf4 protein kinase required for DNA replication in eukaryotes from yeast to human. Cdc7-Dbf4 is also required for DNA damage-induced mutagenesis, one of several postreplicational DNA damage tolerance mechanisms mediated by the RAD6 epistasis group. Several genes have been determined to function in separate branches within this group, including RAD5, REV3/REV7 (Pol ζ), RAD30 (Pol η), and POL30 (PCNA). An extensive genetic analysis of the interactions between CDC7 and REV3, RAD30, RAD5, or POL30 in response to DNA damage was done to determine its role in the RAD6 pathway. CDC7, RAD5, POL30, and RAD30 were found to constitute four separate branches of the RAD6 epistasis group in response to UV and MMS exposure. CDC7 is also shown to function separately from REV3 in response to MMS. However, they belong in the same pathway in response to UV. We propose that the Cdc7-Dbf4 kinase associates with components of the translesion synthesis pathway and that this interaction is dependent upon the type of DNA damage. Finally, activation of the DNA damage checkpoint and the resulting cell cycle delay is intact in cdc7Δ mcm5-bob1 cells, suggesting a direct role for CDC7 in DNA repair/damage tolerance.
The Genetic Architecture of the Behavioral Ontogeny of Foraging in Honeybee Workers
Authors: Rueppell Olav , Pankiw Tanya , Nielsen David I , Fondrk M Kim , Beye Martin , Page Robert E
Published: September 2004

The initiation of foraging during the life course of honeybee workers is of central interest to understanding the division of labor in social insects, a central theme in sociobiology and behavioral research. It also provides one of the most complex phenotypic traits in biological systems because of the interaction of various external, social, and individual factors. This study reports on a comprehensive investigation of the genetic architecture of the age of foraging initiation in honeybees. It comprises an estimation of genetic variation, the study of candidate loci, and two complementary quantitative trait loci (QTL) maps using two selected, continually bred lines of honeybees. We conclude that considerable genetic variation exists between the selected lines for this central life history component. The study reveals direct pleiotropic and epistatic effects of candidate loci (including previously identified QTL for foraging behavior). Furthermore, two maps of the honeybee genome were constructed from over 400 AFLP markers. Both maps confirm the extraordinary recombinational size of the honeybee genome. On the basis of these maps, we report four new significant QTL and two more suggestive QTL that influence the initiation of foraging.
Evidence for Multiple Alleles at the DGAT1 Locus Better Explains a Quantitative Trait Locus With Major Effect on Milk Fat Content in Cattle
Authors: Kühn Christa , Thaller Georg , Winter Andreas , Bininda-Emonds Olaf R P , Kaupe Bernhard , Erhardt Georg , Bennewitz Jörn , Schwerin Manfred , Fries Ruedi
Published: September 2004

A quantitative trait locus (QTL) for milk fat percentage has been mapped consistently to the centromeric region of bovine chromosome 14 (BTA14). Two independent studies have identified the nonconservative mutation K232A in the acylCoA-diacylglycerol-acyltransferase 1 (DGAT1) gene as likely to be causal for the observed variation. Here we provide evidence for additional genetic variability at the same QTL that is associated with milk fat percentage variation within the German Holstein population. Namely, we show that alleles of the DGAT1 promoter derived from the variable number of tandem repeat (VNTR) polymorphism are associated with milk fat content in animals homozygous for the allele 232A at DGAT1. Our results present another example for more than two trait-associated alleles being involved in a major gene effect on a quantitative trait. The segregation of multiple alleles affecting milk production traits at the QTL on BTA14 has to be considered whenever marker-assisted selection programs are implemented in dairy cattle. Due to the presence of a potential transcription factor binding site in the 18mer element of the VNTR, the variation in the number of tandem repeats of the 18mer element might be causal for the variability in the transcription level of the DGAT1 gene.
Simultaneous Detection of Linkage Disequilibrium and Genetic Differentiation of Subdivided Populations
Authors: Kitada Shuichi , Kishino Hirohisa
Published: September 2004

We propose a new method for simultaneously detecting linkage disequilibrium and genetic structure in subdivided populations. Taking subpopulation structure into account with a hierarchical model, we estimate the magnitude of genetic differentiation and linkage disequilibrium in a metapopulation on the basis of geographical samples, rather than decompose a population into a finite number of random-mating subpopulations. We assume that Hardy-Weinberg equilibrium is satisfied in each locality, but do not assume independence between marker loci. Linkage states remain unknown. Genetic differentiation and linkage disequilibrium are expressed as hyperparameters describing the prior distribution of genotypes or haplotypes. We estimate related parameters by maximizing marginal-likelihood functions and detect linkage equilibrium or disequilibrium by the Akaike information criterion. Our empirical Bayesian model analyzes genotype and haplotype frequencies regardless of haploid or diploid data, so it can be applied to most commonly used genetic markers. The performance of our procedure is examined via numerical simulations in comparison with classical procedures. Finally, we analyze isozyme data of ayu, a severely exploited fish species, and single-nucleotide polymorphisms in human ALDH2.
Estimating the Frequency of Events That Cause Multiple-Nucleotide Changes
Authors: Whelan Simon , Goldman Nick
Published: September 2004

Existing mathematical models of DNA sequence evolution assume that all substitutions derive from point mutations. There is, however, increasing evidence that larger-scale events, involving two or more consecutive sites, may also be important. We describe a model, denoted SDT, that allows for single-nucleotide, doublet, and triplet mutations. Applied to protein-coding DNA, the SDT model allows doublet and triplet mutations to overlap codon boundaries but still permits data to be analyzed using the simplifying assumption of independence of sites. We have implemented the SDT model for maximum-likelihood phylogenetic inference and have applied it to an alignment of mammalian globin sequences and to 258 other protein-coding sequence alignments from the Pandit database. We find the SDT model's inclusion of doublet and triplet mutations to be overwhelmingly successful in giving statistically significant improvements in fit of model to data, indicating that larger-scale mutation events do occur. Distributions of inferred parameter values over all alignments analyzed suggest that these events are far more prevalent than previously thought. Detailed consideration of our results and the absence of any known mechanism causing three adjacent nucleotides to be substituted simultaneously, however, leads us to suggest that the actual evolutionary events occurring may include still-larger-scale events, such as gene conversion, inversion, or recombination, or a series of rapid compensatory changes.
Pervasive Genomic Recombination of HIV-1 in VivoSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY496645, AY496646, AY496647, AY496648, AY496649, AY496650, AY496651, AY496652, AY496653, AY496654, AY496655, AY496656, AY496657, AY496658, AY496659, AY496660, AY496661, AY496662, AY496663, AY496664, AY496665, AY496666, AY496667, AY496668, AY496669, AY496670, AY496671, AY496672, AY496673, AY496674, AY496675, AY496676, AY496677, AY496678, AY496679, AY496680, AY496681, AY496682, AY496683, AY496684.
Authors: Shriner Daniel , Rodrigo Allen G , Nickle David C , Mullins James I
Published: September 2004

Recombinants of preexisting human immunodeficiency virus type 1 (HIV-1) strains are now circulating globally. To increase our understanding of the importance of these recombinants, we assessed recombination within an individual infected from a single source by studying the linkage patterns of the auxiliary genes of HIV-1 subtype B. Maximum-likelihood phylogenetic techniques revealed evidence for recombination from topological incongruence among adjacent genes. Coalescent methods were then used to estimate the in vivo recombination rate. The estimated mean rate of 1.38 × 10−4 recombination events/adjacent sites/generation is ∼5.5-fold greater than the reported point mutation rate of 2.5 × 10−5/site/generation. Recombination was found to be frequent enough to mask evidence for purifying selection by Tajima's D test. Thus, recombination is a major evolutionary force affecting genetic variation within an HIV-1-infected individual, of the same order of magnitude as point mutational change.
The Role of cis-acting Sequences Governing Catabolite Repression Control of lacS Expression in the Archaeon Sulfolobus solfataricus
Authors: Hoang Viet , Bini Elisabetta , Dixit Vidula , Drozda Melissa , Blum Paul
Published: September 2004

The archaeon Sulfolobus solfataricus uses a catabolite repression-like system to control production of several glycoside hydrolases. To better understand this regulatory system, studies of the regulation of expression of the β-glycosidase gene (lacS) were conducted. Expression of lacS varies in response to medium composition and to mutations at an unlinked gene called car. Despite gene overlap, expression of the lacS promoter proximal gene, SSO3017, exhibited coregulation but not cotranscription with lacS. Measurements of mRNA half-life excluded differential stability as a factor in lacS regulation. Chromosomal repositioning by homologous recombination of a lacS deletion series clarified critical cis-acting sequences required for lacS regulation. lacS repositioned at amyA exhibited increased lacS expression and compromised the response to medium composition independently of lacS 5′ flanking sequence composition. In contrast, regulation of lacS by the car mutation was dependent on sequences upstream of the archaeal TATA box. Expression of a promoter fusion between lacS and the car-independent malA promoter integrated either at amyA or at the natural lacS locus was insensitive to the allelic state of car. In contrast, the promoter fusion retained a response to medium composition only at the lacS locus. These results indicate that car acts at the lacS promoter and that the response to medium composition involves locus-specific sequences exclusive of those present 5′ to lacS or within the lacS transcription unit.
Genes Encoding Subunits of Stable Complexes Are Clustered on the Yeast Chromosomes
Authors: Teichmann Sarah Amalia , Veitia Reiner Albert
Published: September 2004

Genomic evidence for colocalization of functionally related genes on eukaryote chromosomes is mounting. Here we show that a statistically significant fraction of yeast genes coding for subunits of stable complexes are located within 10–30 kb of each other. Clustering of genes encoding subunits of complexes may ensure better coregulation and maintain the right stoichiometry of complexes upon duplication of chromosomal segments.
A Network of Stimulatory and Inhibitory Gα-Subunits Regulates Olfaction in Caenorhabditis elegans
Authors: Lans Hannes , Rademakers Suzanne , Jansen Gert
Published: September 2004

The two pairs of sensory neurons of C. elegans, AWA and AWC, that mediate odorant attraction, express six Gα-subunits, suggesting that olfaction is regulated by a complex signaling network. Here, we describe the cellular localization and functions of the six olfactory Gα-subunits: GPA-2, GPA-3, GPA-5, GPA-6, GPA-13, and ODR-3. All except GPA-6 localize to sensory cilia, suggesting a direct role in sensory transduction. GPA-2, GPA-3, GPA-5, and GPA-6 are also present in cell bodies and axons and GPA-5 specifically localizes to synaptic sites. Analysis of animals with single- to sixfold loss-of-function mutations shows that olfaction involves a balance between multiple stimulatory and inhibitory signals. ODR-3 constitutes the main stimulatory signal and is sufficient for the detection of odorants. GPA-3 forms a second stimulatory signal in the AWA and AWC neurons, also sufficient for odorant detection. In AWA, signaling is suppressed by GPA-5. In AWC, GPA-2 and GPA-13 negatively and positively regulate signaling, respectively. Finally, we show that only ODR-3 plays a role in cilia morphogenesis. Defects in this process are, however, independent of olfactory behavior. Our findings reveal the existence of a complex signaling network that controls odorant detection by C. elegans.
A Fast Algorithm for Functional Mapping of Complex Traits
Authors: Zhao Wei , Wu Rongling , Ma Chang-Xing , Casella George
Published: September 2004

By integrating the underlying developmental mechanisms for the phenotypic formation of traits into a mapping framework, functional mapping has emerged as an important statistical approach for mapping complex traits. In this note, we explore the feasibility of using the simplex algorithm as an alternative to solve the mixture-based likelihood for functional mapping of complex traits. The results from the simplex algorithm are consistent with those from the traditional EM algorithm, but the simplex algorithm has considerably reduced computational times. Moreover, because of its nonderivative nature and easy implementation with current software, the simplex algorithm enjoys an advantage over the EM algorithm in the dynamic modeling and analysis of complex traits.
Evolution of Specialists in an Experimental Microcosm
Authors: Dykhuizen Daniel E , Dean Antony M
Published: September 2004

The impact of adaptation on the persistence of a balanced polymorphism was explored using the lactose operon of Escherichia coli as a model system. Competition in chemostats for two substitutable resources, methylgalactoside and lactulose, generates stabilizing frequency-dependent selection when two different naturally isolated lac operons (TD2 and TD10) are used. The fate of this balanced polymorphism was tracked over evolutionary time by monitoring the frequency of fhuA−, a linked neutral genetic marker that confers resistance to the bacteriophage T5. In four out of nine chemostats the lac polymorphism persisted for 400–600 generations when the experiments were terminated. In the other five chemostats the fhuA polymorphism, and consequently the lac operon polymorphism, was lost between 86 and 219 generations. Four of 13 chemostat cultures monomorphic for the lac operon retained the neutral fhuA polymorphism for 450–550 generations until they were terminated; the remainder became monomorphic at fhuA between 63 and 303 generations. Specialists on each galactoside were isolated from chemostats that maintained the fhuA polymorphism, whether polymorphic or monomorphic at the lac operon. Strains isolated from three of four chemostats in which the lac polymorphism was preserved had switched their galactoside preference. Most of the chemostats where the fhuA polymorphism was lost also contained specialists. These results demonstrate that the initial polymorphism at lac was of little consequence to the outcome of long-term adaptive evolution. Instead, the fitnesses of evolved strains were dominated by mutations arising elsewhere in the genome, a fact confirmed by showing that operons isolated from their evolved backgrounds were alone unable to explain the presence of both specialists. Our results suggest that, once stabilized, ecological specialization prevented selective sweeps through the entire population, thereby promoting the maintenance of linked neutral polymorphisms.
Quantitative Trait Loci Associated With Adventitious Shoot Formation in Tissue Culture and the Program of Shoot Development in Arabidopsis
Authors: Lall Sonia , Nettleton Dan , DeCook Rhonda , Che Ping , Howell Stephen H
Published: September 2004

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

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

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

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

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