bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel patterns of genome rearrangement and their association with survival in breast cancer
Authors: Hicks James , Krasnitz Alexander , Lakshmi B. , Navin Nicholas E. , Riggs Michael , Leibu Evan , Esposito Diane , Alexander Joan , Troge Jen , Grubor Vladimir , Yoon Seungtai , Wigler Michael , Ye Kenny , Børresen-Dale Anne-Lise , Naume Bjørn , Schlicting Ellen , Norton Larry , Hägerström Torsten , Skoog Lambert , Auer Gert , Månér Susanne , Lundin Pär , Zetterberg Anders
Published: December 2006

Representational Oligonucleotide Microarray Analysis (ROMA) detects genomic amplifications and deletions with boundaries defined at a resolution of ∼50 kb. We have used this technique to examine 243 breast tumors from two separate studies for which detailed clinical data were available. The very high resolution of this technology has enabled us to identify three characteristic patterns of genomic copy number variation in diploid tumors and to measure correlations with patient survival. One of these patterns is characterized by multiple closely spaced amplicons, or “firestorms,” limited to single chromosome arms. These multiple amplifications are highly correlated with aggressive disease and poor survival even when the rest of the genome is relatively quiet. Analysis of a selected subset of clinical material suggests that a simple genomic calculation, based on the number and proximity of genomic alterations, correlates with life-table estimates of the probability of overall survival in patients with primary breast cancer. Based on this sample, we generate the working hypothesis that copy number profiling might provide information useful in making clinical decisions, especially regarding the use or not of systemic therapies (hormonal therapy, chemotherapy), in the management of operable primary breast cancer with ostensibly good prognosis, for example, small, node-negative, hormone-receptor-positive diploid cases.
Associative memory in three aplysiids: Correlation with heterosynaptic modulation
Authors: Hoover Brian A. , Nguyen Hoang , Thompson Laura , Wright William G.
Published: December 2006

Much recent research on mechanisms of learning and memory focuses on the role of heterosynaptic neuromodulatory signaling. Such neuromodulation appears to stabilize Hebbian synaptic changes underlying associative learning, thereby extending memory. Previous comparisons of three related sea-hares (Mollusca, Opisthobranchia) uncovered interspecific variation in neuromodulatory signaling: strong inAplysia californica,immeasureable inDolabrifera dolabrifera,and intermediate inPhyllaplysia taylori.The present study addressed whether this interspecific variation in neuromodulation is correlated with memory of associative (classical conditioning) learning. We differentially conditioned the tail-mantle withdrawal reflex of each of the three species: Mild touch to one side of the tail was paired with a noxious electrical stimulus to the neck. Mild touch to the other side served as an internal control. Post-training reflex amplitudes were tested 15–30 min after training and compared with pre-test amplitudes. All three species showed conditioning: training increased the paired reflex more than the unpaired reflex. However, the temporal pattern of conditioning varied between species.Aplysiashowed modest conditioning that grew across the post-test period.Dolabriferashowed distinctly short-lived conditioning, present only on the first post-test. The time course of memory inPhyllaplysiawas intermediate, although not statistically distinguishable from the other two species. Taken together, these experiments suggest that evolutionary changes in nonassociative heterosynaptic modulation may contribute to evolutionary changes in the stability of the memory of classical conditioning.
Microstimulation reveals opposing influences of prelimbic and infralimbic cortex on the expression of conditioned fear
Authors: Vidal-Gonzalez Ivan , Vidal-Gonzalez Benjamín , Rauch Scott L. , Quirk Gregory J.
Published: December 2006

Recent studies using lesion, infusion, and unit-recording techniques suggest that the infralimbic (IL) subregion of medial prefrontal cortex (mPFC) is necessary for the inhibition of conditioned fear following extinction. Brief microstimulation of IL paired with conditioned tones, designed to mimic neuronal tone responses, reduces the expression of conditioned fear to the tone. In the present study we used microstimulation to investigate the role of additional mPFC subregions: the prelimbic (PL), dorsal anterior cingulate (ACd), and medial precentral (PrCm) cortices in the expression and extinction of conditioned fear. These are tone-responsive areas that have been implicated in both acquisition and extinction of conditioned fear. In contrast to IL, microstimulation of PL increased the expression of conditioned fear and prevented extinction. Microstimulation of ACd and PrCm had no effect. Under low-footshock conditions (to avoid ceiling levels of freezing), microstimulation of PL and IL had opposite effects, respectively increasing and decreasing freezing to the conditioned tone. We suggest that PL excites amygdala output and IL inhibits amygdala output, providing a mechanism for bidirectional modulation of fear expression.
Dopaminergic modulation of the persistence of one-trial hippocampus-dependent memory
Authors: O’Carroll Colin M. , Martin Stephen J. , Sandin Johan , Frenguelli Bruno , Morris Richard G.M.
Published: December 2006

The persistence of new memory traces in the hippocampus, encoded following appropriate activation of glutamatergic receptors and the induction of synaptic plasticity, can be influenced by heterosynaptic activation of neuromodulatory brain systems. We therefore investigated the effects of a hippocampus-specific blockade of dopamine D1/D5 receptors on the persistence of spatial memory encoded in one trial using a delayed matching-to-place (DMP) task in a watermaze in which rats learn a new escape location each day. A within-subjects design was used such that both short (20 min) and long (6 h) retention intervals, and both drug (SCH23390, a D1/D5 receptor antagonist) and vehicle (aCSF) infusions were tested on different days in the same animals. Bilateral intrahippocampal infusion of SCH23390 (5 μg in 1 μL per side) prior to trial 1 (encoding) caused a differential impairment as a function of memory delay—with no effect during trial 2 (memory retrieval) after a 20-min interval, but a block of memory at 6 h. Further experiments revealed that infusion of SCH23390 immediately after trial 1 had no effect on retention 6 h later, and the poor memory seen at long retention intervals when the drug was present at encoding was not due to a state-dependent failure of retrieval. These results suggest that activation of D1/D5 receptors during memory encoding is necessary for the formation of a persistent memory trace in the hippocampus. The complementary effects of D1/D5 receptor blockade on the persistence of LTP and the duration of memory are consistent with the idea that changes in synaptic strength underlie memory.
Chronically increased Gsα signaling disrupts associative and spatial learning
Authors: Bourtchouladze Rusiko , Patterson Susan L. , Kelly Michele P. , Kreibich Arati , Kandel Eric R. , Abel Ted
Published: December 2006

The cAMP/PKA pathway plays a critical role in learning and memory systems in animals ranging from mice to Drosophila to Aplysia. Studies of olfactory learning in Drosophila suggest that altered expression of either positive or negative regulators of the cAMP/PKA signaling pathway beyond a certain optimum range may be deleterious. Here we provide genetic evidence of the behavioral and physiological effects of increased signaling through the cAMP/PKA pathway in mice. We have generated transgenic mice in which the expression of a constitutively active form of Gsα (Gsα* Q227L), the G protein that stimulates adenylyl cyclase activity, is driven in neurons within the forebrain by the promoter from the CaMKIIα gene. Despite significantly increased adenylyl cyclase activity, Gsα* transgenic mice exhibit PKA-dependent decreases in levels of cAMP due to a compensatory up-regulation in phosphodiesterase activity. Interestingly, Gsα* transgenic mice also exhibit enhanced basal synaptic transmission. Consistent with a role for the cAMP/PKA pathway in learning and memory, Gsα* transgenic mice show impairments in spatial learning in the Morris water maze and in contextual and cued fear conditioning tasks. The learning deficits observed in these transgenic mice suggest that associative and spatial learning requires regulated Gsα protein signaling, much as does olfactory learning in Drosophila.
Sound sequence discrimination learning motivated by reward requires dopaminergic D2 receptor activation in the rat auditory cortex
Authors: Kudoh Masaharu , Shibuki Katsuei
Published: December 2006

We have previously reported that sound sequence discrimination learning requires cholinergic inputs to the auditory cortex (AC) in rats. In that study, reward was used for motivating discrimination behavior in rats. Therefore, dopaminergic inputs mediating reward signals may have an important role in the learning. We tested the possibility in the present study. Rats were trained to discriminate sequences of two sound components, and licking behavior in response to one of the two sequences was rewarded with water. To identify the dopaminergic inputs responsible for the learning, dopaminergic afferents to the AC were lesioned with local injection of 6-hydroxydopamine (6-OHDA). The injection attenuated sound sequence discrimination learning, while it had no effect on discrimination between the sound components of the sequence stimuli. Local injection of 6-OHDA into the nucleus accumbens attenuated sound discrimination learning. However, not only discrimination learning of sound sequence but also that of the sound components were impaired. SCH23390 (0.2 mg/kg, i.p.), a D1 receptor antagonist, had no effect on sound sequence discrimination learning, while it attenuated the licking behavior to unfamiliar stimuli. Haloperidol (0.5 mg/kg, i.p.), a D2 family antagonist, attenuated sound sequence discrimination learning, while it had no clear suppressive effect on discrimination of two different sound components and licking. These results suggest that D2 family receptors activated by dopaminergic inputs to the AC are required for sound sequence discrimination learning.
Conditioned fear extinction and reinstatement in a human fear-potentiated startle paradigm
Authors: Norrholm Seth D. , Jovanovic Tanja , Vervliet Bram , Myers Karyn M. , Davis Michael , Rothbaum Barbara O. , Duncan Erica J.
Published: December 2006

The purpose of this study was to analyze fear extinction and reinstatement in humans using fear-potentiated startle. Participants were fear conditioned using a simple discrimination procedure with colored lights as the conditioned stimuli (CSs) and an airblast to the throat as the unconditioned stimulus (US). Participants were extinguished 24 h after fear conditioning. Upon presentation of unsignaled USs after extinction, participants displayed significant fear reinstatement. In summary, these procedures produced robust fear-potentiated startle, significant CS+/CS− discrimination, within-session extinction, and significant reinstatement. This is the first demonstration of fear extinction and reinstatement in humans using startle measures.
Temporary basolateral amygdala lesions disrupt acquisition of socially transmitted food preferences in rats
Authors: Wang Yunyan , Fontanini Alfredo , Katz Donald B.
Published: December 2006

Lesions of the basolateral amygdala (BLA) have long been associated with abnormalities of taste-related behaviors and with failure in a variety of taste- and odor-related learning paradigms, including taste-potentiated odor aversion, conditioned taste preference, and conditioned taste aversion. Still, the general role of the amygdala in chemosensory learning remains somewhat controversial. In particular, it has been suggested that the amygdala may not be involved in a form of chemosensory learning that has recently received a substantial amount of study—socially transmitted food preference (STFP). Here, we provide evidence for this involvement by pharmacologically inactivating the basolateral amygdala bilaterally during STFP training. The same inactivation sites that impaired taste aversion learning eliminated the normally conditioned preference for a food smelled on a conspecific’s breath. Impairments of learned preference persisted even in testing sessions in which BLA was not inactivated, and learning was normal when the BLA was inactivated only during testing sessions; thus, the impairment was a true acquisition deficit. In conjunction with previous results from other paradigms, therefore, our data suggest that the amygdala is vital for learning procedures involving pairings of potent and arbitrary chemosensory stimuli.
Dopamine D1 receptors in the anterior cingulate cortex regulate effort-based decision making
Authors: Schweimer Judith , Hauber Wolfgang
Published: December 2006

The anterior cingulate cortex (ACC) has been implicated in encoding whether or not an action is worth performing in view of the expected benefit and the cost of performing the action. Dopamine input to the ACC may be critical for this form of effort-based decision making; however, the role of distinct ACC dopamine receptors is yet unknown. Therefore, we examined in rats the effects of an intra-ACC D1 and D2 receptor blockade on effort-based decision making tested in a T-maze cost-benefit task. In this task, subjects could either choose to climb a barrier to obtain a high reward in one arm or a low reward in the other arm without a barrier. Unlike vehicle-treated rats, rats with intra-ACC infusion of the D1 receptor antagonist SCH23390 exhibited a reduced preference for the high-cost– high-reward response option when having the choice to obtain a low reward with little effort. In contrast, in rats with intra-ACC infusion of the D2 receptor antagonist eticlopride, the preference for the high-cost–high-reward response option was not altered relative to vehicle-treated rats. These data provide the first evidence that D1 receptors in the ACC regulate effort-based decision making.
Freeze-Thaw Lysis for Extraction of Proteins from Mammalian Cells
Authors: Tansey William P.
Published: December 2006

INTRODUCTION

This protocol describes the extraction of proteins from mammalian cells grown in 6- or 10-cm tissue-culture dishes. It is useful for making very concentrated extracts for Western blotting, and is particularly helpful when low-abundance proteins such as Myc are being studied.
Detection of Ubiquitylated Proteins in Yeast
Authors: Tansey William P.
Published: December 2006

INTRODUCTION

This assay is performed to detect ubiquitylated proteins in yeast. Yeast that have been transformed with a vector expressing polyhistidine-tagged ubiquitin (Ub) under the control of a copper-inducible promoter are grown, induced with copper, and harvested. Total ubiquitylated proteins are then recovered by nickel-affinity chromatography, and specific proteins are detected by Western blotting.
Constructing and Expressing GFP Fusion Proteins
Authors: Spector David L. , Goldman Robert D.
Published: December 2006

INTRODUCTION

GFP (green fluorescent protein) fusion proteins have been used to address a wide range of questions in individual cells, as well as in tissues of a particular organism. GFP fusion proteins can be transiently or stably expressed. Although transient expression is quick and can provide informative results, in many cases it is beneficial and/or essential to develop stable cell lines expressing the fusion protein of interest. In addition to providing more native levels of expression, individual clones can be generated from single cells, the integration site of the plasmid mapped, and the copy number determined. Because every cell in the population is expressing the fusion protein, cell cycle analyses and biochemical fractionation are significantly easier to accomplish. The following protocol can be used for the development of stable cell lines expressing GFP fusion proteins. Although optimal transfection procedures (e.g., calcium phosphate, electroporation, or FuGENE 6 [Roche Applied Science]) vary depending on cell type, this general transfection procedure has been successful for stable transfection of HeLa, A-431, U2OS, BHK, and HT1080 cells.
Gene Delivery by Direct Injection (Microinjection) Using a Controlled-Flow System
Authors: Dean David A.
Published: December 2006

INTRODUCTION

This protocol describes a method for constant-flow microinjection using the Pneumatic PicoPump (World Precision Instruments). This type of system is very simple and can be assembled on a relatively low budget. In this method, a constant flow of sample is delivered from the tip of the pipette, and the amount of sample injected into the cell is determined by how long the pipette remains in the cell. A typical system is composed of a pressure regulator that can be adjusted for two pressures (back pressure and injection pressure), a capillary holder, and a coarse and fine micromanipulator.
Silver Staining, Digestion, and Extraction of Peptides from an Acrylamide Gel for MS Analysis
Authors: Niessen Sherry , Mcleod Ian , Yates John R.
Published: December 2006

INTRODUCTION

Individual components of protein complexes separated by sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) are visualized by silver (or Coomassie) staining. For subsequent analysis by mass spectrometry (MS), it is important to use silver staining protocols with no glutaraldehyde, as this reagent chemically modifies the protein and inhibits subsequent steps. The individual stained protein bands are excised from the gel, the proteins are enzymatically digested into peptides, and the peptides are extracted. The peptides from each protein can be subsequently analyzed by high-pressure liquid chromatography (HPLC) fractionation and electrospray ionization (ESI) MS. This generates a mass fingerprint of the peptides that comprise the unknown protein. Further structural data for peptides can be obtained by fragmenting the ionized peptides to generate a tandem mass spectrum. Alternatively, a mass fingerprint of the peptides is obtained by matrix-assisted laser desorption/ionization in combination with a time-of-flight instrument (MALDI/TOF).
Direct Enzymatic Digestion of Protein Complexes for MS Analysis
Authors: Niessen Sherry , Mcleod Ian , Yates John R.
Published: December 2006

INTRODUCTION

The individual components of a purified protein complex can be determined by MS. Components can be separated by SDS-PAGE and subsequently digested, or the entire protein complex can be digested by chemical agents or by proteases. The mixture of peptides that results from digestion without prior separation is more complex than that obtained from the digestion of a single protein, and can best be resolved subsequently using HPLC in combination with a biphasic column. Protein complexes can be digested directly using several different protocols. Common methods include a double digest with endoproteinase Lys-C and trypsin, or a triple digest with elastase, subtilisin, and trypsin. Endoproteinase Lys-C cleaves carboxy-terminal to lysine residues, while trypsin cleaves carboxy-terminal to lysine and arginine residues. The triple digest uses the relatively nonspecific proteases elastase and subtilisin to create a large number of overlapping peptides for the analysis of post-translational modifications. The double and triple digest protocols begin with the reduction and alkylation of cysteine residues to disrupt disulfide bonds and, therefore, higher-order protein structure.
HPLC Separation of Digested Proteins and Preparation for Matrix-Assisted Laser Desorption/Ionization Analysis
Authors: Niessen Sherry , Mcleod Ian , Yates John R.
Published: December 2006

INTRODUCTION

Two types of columns are commonly used for the separation of peptides by HPLC. A single-phase column contains the reverse-phase resin C18, which interacts with the hydrophobic moieties of the peptides. Peptides resulting from digestion of simple mixtures of proteins are loaded onto the single-phase column and eluted into the mass analyzer using an increasing gradient of an organic solvent. Peptides resulting from the digestion of more complex mixtures of proteins are resolved using a biphasic column. This column integrates both a strong cation exchange SCX resin, which interacts with peptides as a result of their positive charge, and a reverse-phase C18 resin, packed in tandem. Peptides initially interact with the SCX resin and are eluted into the C18 resin by ammonium acetate that competes for the peptide-binding sites. Peptides are then eluted from the C18 resin into the mass analyzer. This process is repeated using increasing concentrations of ammonium acetate to differentially elute peptides in a stepwise fashion. The biphasic column also uses an additional C18 reverse-phase resin linked through an Inline MicroFilter Assembly (Upchurch) to desalt the peptides prior to loading onto the SCX. The desalting and biphasic columns are combined to give an integrated desalting/biphasic column.
Transformation of Agrobacterium Using the Freeze-Thaw Method
Authors: Weigel Detlef , Glazebrook Jane
Published: December 2006

INTRODUCTION

This protocol describes a method for transforming Agrobacterium with plasmid DNA using a freeze-thaw technique. Although the transformation efficiency for Agrobacterium is lower than that for Escherichia coli, it is possible to obtain adequate numbers of transformants with this technique.
In Planta Transformation of Arabidopsis
Authors: Weigel Detlef , Glazebrook Jane
Published: December 2006

INTRODUCTION

A breakthrough in Arabidopsis research was the invention of the vacuum-infiltration procedure, a simple and reliable method of obtaining transformants at high efficiency while avoiding the use of tissue culture. The plant transformation procedures described here involve floral dip, vacuum infiltration, and spraying. They yield transformants at frequencies ranging up to several percent, with the most common frequency being 0.1%-1%.
Kanamycin Selection of Transformed Arabidopsis
Authors: Weigel Detlef , Glazebrook Jane
Published: December 2006

INTRODUCTION

The most commonly used markers for selection of transgenic Arabidopsis are resistance to the antibiotic kanamycin and to the herbicide glufosinate ammonium. Resistance to kanamycin is conferred by a bacterial gene encoding the enzyme neomycin phosphotransferase (NPT). In this protocol, kanamycin-resistant seedlings are selected on solid medium.
Glufosinate Ammonium Selection of Transformed Arabidopsis
Authors: Weigel Detlef , Glazebrook Jane
Published: December 2006

INTRODUCTION

One of the most commonly used markers for the selection of transgenic Arabidopsis is resistance to glufosinate ammonium, an herbicide that is sold under a variety of trade names including Basta and Finale. Resistance to glufosinate ammonium is conferred by the bacterial bialophos resistance gene (BAR) encoding the enzyme phosphinotricin acetyl transferase (PAT). This protocol describes the use of glufosinate ammonium to select transformed Arabidopsis plants. The major advantage of glufosinate ammonium selection is that it can be performed on plants growing in soil and does not require the use of sterile techniques.
PlantN-Glycan Processing Enzymes Employ Different Targeting Mechanisms for Their Spatial Arrangement along the Secretory Pathway
Authors: Saint-Jore-Dupas Claude , Nebenführ Andreas , Boulaflous Aurélia , Follet-Gueye Marie-Laure , Plasson Carole , Hawes Chris , Driouich Azeddine , Faye Loïc , Gomord Véronique
Published: December 2006

The processing of N-linked oligosaccharides in the secretory pathway requires the sequential action of a number of glycosidases and glycosyltransferases. We studied the spatial distribution of several type II membrane-bound enzymes from Glycine max, Arabidopsis thaliana, and Nicotiana tabacum. Glucosidase I (GCSI) localized to the endoplasmic reticulum (ER), α-1,2 mannosidase I (ManI) and N-acetylglucosaminyltransferase I (GNTI) both targeted to the ER and Golgi, and β-1,2 xylosyltransferase localized exclusively to Golgi stacks, corresponding to the order of expected function. ManI deletion constructs revealed that the ManI transmembrane domain (TMD) contains all necessary targeting information. Likewise, GNTI truncations showed that this could apply to other type II enzymes. A green fluorescent protein chimera with ManI TMD, lengthened by duplicating its last seven amino acids, localized exclusively to the Golgi and colocalized with a trans-Golgi marker (ST52-mRFP), suggesting roles for protein–lipid interactions in ManI targeting. However, the TMD lengths of other plant glycosylation enzymes indicate that this mechanism cannot apply to all enzymes in the pathway. In fact, removal of the first 11 amino acids of the GCSI cytoplasmic tail resulted in relocalization from the ER to the Golgi, suggesting a targeting mechanism relying on protein–protein interactions. We conclude that the localization of N-glycan processing enzymes corresponds to an assembly line in the early secretory pathway and depends on both TMD length and signals in the cytoplasmic tail.
Two Cytosolic Glutamine Synthetase Isoforms of Maize Are Specifically Involved in the Control of Grain Production
Authors: Martin Antoine , Lee Judy , Kichey Thomas , Gerentes Denise , Zivy Michel , Tatout Christophe , Dubois Frédéric , Balliau Thierry , Valot Benoît , Davanture Marlène , Tercé-Laforgue Thérèse , Quilleré Isabelle , Coque Marie , Gallais André , Gonzalez-Moro María-Begoña , Bethencourt Linda , Habash Dimah Z. , Lea Peter J. , Charcosset Alain , Perez Pascual , Murigneux Alain , Sakakibara Hitoshi , Edwards Keith J. , Hirel Bertrand
Published: December 2006

The roles of two cytosolic maize glutamine synthetase isoenzymes (GS1), products of the Gln1-3 and Gln1-4 genes, were investigated by examining the impact of knockout mutations on kernel yield. In the gln1-3 and gln1-4 single mutants and the gln1-3 gln1-4 double mutant, GS mRNA expression was impaired, resulting in reduced GS1 protein and activity. The gln1-4 phenotype displayed reduced kernel size and gln1-3 reduced kernel number, with both phenotypes displayed in gln1-3 gln1-4. However, at maturity, shoot biomass production was not modified in either the single mutants or double mutants, suggesting a specific impact on grain production in both mutants. Asn increased in the leaves of the mutants during grain filling, indicating that it probably accumulates to circumvent ammonium buildup resulting from lower GS1 activity. Phloem sap analysis revealed that unlike Gln, Asn is not efficiently transported to developing kernels, apparently causing reduced kernel production. When Gln1-3 was overexpressed constitutively in leaves, kernel number increased by 30%, providing further evidence that GS1-3 plays a major role in kernel yield. Cytoimmunochemistry and in situ hybridization revealed that GS1-3 is present in mesophyll cells, whereas GS1-4 is specifically localized in the bundle sheath cells. The two GS1 isoenzymes play nonredundant roles with respect to their tissue-specific localization.
CONSTANS and the CCAAT Box Binding Complex Share a Functionally Important Domain and Interact to Regulate Flowering ofArabidopsis
Authors: Wenkel Stephan , Turck Franziska , Singer Kamy , Gissot Lionel , Le Gourrierec José , Samach Alon , Coupland George
Published: December 2006

The CCT (for CONSTANS, CONSTANS-LIKE, TOC1) domain is found in 45 Arabidopsis thaliana proteins involved in processes such as photoperiodic flowering, light signaling, and regulation of circadian rhythms. We show that this domain exhibits similarities to yeast HEME ACTIVATOR PROTEIN2 (HAP2), which is a subunit of the HAP2/HAP3/HAP5 trimeric complex that binds to CCAAT boxes in eukaryotic promoters. Moreover, we demonstrate that CONSTANS (CO), which promotes Arabidopsis flowering, interacts with At HAP3 and At HAP5 in yeast, in vitro, and in planta. Mutations in CO that delay flowering affect residues highly conserved between CCT and the DNA binding domain of HAP2. Taken together, these data suggest that CO might replace At HAP2 in the HAP complex to form a trimeric CO/At HAP3/At HAP5 complex. Flowering was delayed by overexpression of At HAP2 or At HAP3 throughout the plant or in phloem companion cells, where CO is expressed. This phenotype was correlated with reduced abundance of FLOWERING LOCUS T (FT) mRNA and no change in CO mRNA levels. At HAP2 or At HAP3 overexpression may therefore impair formation of a CO/At HAP3/At HAP5 complex leading to reduced expression of FT. During plant evolution, the number of genes encoding HAP proteins was greatly amplified, and these proteins may have acquired novel functions, such as mediating the effect of CCT domain proteins on gene expression.
A Ferroxidation/Permeation Iron Uptake System Is Required for Virulence inUstilago maydis
Authors: Eichhorn Heiko , Lessing Franziska , Winterberg Britta , Schirawski Jan , Kämper Jörg , Müller Philip , Kahmann Regine
Published: December 2006

In the smut fungus Ustilago maydis, a tightly regulated cAMP signaling cascade is necessary for pathogenic development. Transcriptome analysis using whole genome microarrays set up to identify putative target genes of the protein kinase A catalytic subunit Adr1 revealed nine genes with putative functions in two high-affinity iron uptake systems. These genes locate to three gene clusters on different chromosomes and include the previously identified complementing siderophore auxotroph genes sid1 and sid2 involved in siderophore biosynthesis. Transcription of all nine genes plus three additional genes associated with the gene clusters was also coregulated by iron through the Urbs1 transcription factor. Two components of a high-affinity iron uptake system were characterized in more detail: fer2, encoding a high-affinity iron permease; and fer1, encoding an iron multicopper oxidase. Fer2 localized to the plasma membrane and complemented an ftr1 mutant of Saccharomyces cerevisiae lacking a high-affinity iron permease. During pathogenic development, fer2 expression was confined to the phase of hyphal proliferation inside the plant. fer2 as well as fer1 deletion mutants were strongly affected in virulence. These data highlight the importance of the high-affinity iron uptake system via an iron permease and a multicopper oxidase for biotrophic development in the U. maydis/maize (Zea mays) pathosystem.
SUPPRESSOR OF FRIGIDA4, Encoding a C2H2-Type Zinc Finger Protein, Represses Flowering by Transcriptional Activation ofArabidopsis FLOWERING LOCUS C
Authors: Kim Sanghee , Choi Kyuha , Park Chulmin , Hwang Hyun-Ju , Lee Ilha
Published: December 2006

FLOWERING LOCUS C (FLC), a strong floral repressor, is one of the central regulators of flowering in Arabidopsis thaliana. The expression of FLC is increased by FRIGIDA (FRI) but decreased by vernalization, a long period of cold exposure that accelerates flowering. Although many aspects of FLC regulation have been reported, it is not known how FLC is transcriptionally activated by FRI at the molecular level. We isolated suppressor of FRIGIDA4 (suf4), a mutant that flowers early as a result of low FLC expression. SUF4 encodes a nuclear-localized protein with two C2H2-type zinc finger motifs and a Pro-rich domain. SUF4 protein interacts with FRI and FRIGIDA-LIKE1 (FRL1), two genes for which single mutations have the same phenotype as suf4. SUF4 also bound to the promoter of FLC in a chromatin immunoprecipitation assay, suggesting that SUF4 acts as a transcriptional activator of FLC after forming a complex with FRI and FRL1. In addition, suf4 suppresses luminidependens (ld), a late-flowering mutation that causes an increase of FLC, and SUF4 protein directly interacts with LD. Thus, we propose that LD binds to SUF4 to suppress its activity in the absence of FRI.
Evidence for metapopulation structuring in cod from the west of Scotland and North Sea
Authors: Wright P. J. , Neat F. C. , Gibb F. M. , Gibb I. M. , Thordarson H.
Published: December 2006

The scale of population structuring in codGadus morhuafrom the west of Scotland (ICES stock area VIa) and northern North Sea was investigated using a combination of non‐genetic methods. Site fidelity of spawning aggregations was examined using historic tag‐recapture experiments and individual geolocation estimates from data storage tagged fish. The extent of movements from spawning areas indicated by these two tagging approaches was broadly similar. Between 67 and 97% of adult cod remained within 100 km of spawning areas throughout the year, suggesting resident spawning groups. A small proportion of cod, however, did appear to stray between spawning areas. A comparison of the elemental signature of the otoliths of 0 year‐group and the 0 year‐group component from the same year‐class at age 2 years indicated that most adults originate from local nursery areas. Moreover, there did not appear to be detectable exchange between spawning areas >200 km apart, such as the Clyde and Minch or Shetland and the Inner Hebrides. As such, population processes may operate at a smaller spatial scale than the stock level, with spawning aggregations functioning as local populations within a metapopulation. The relevance of this scale of dynamics is discussed in relation to recently imposed closed areas in the region.
Morphological and genetic differentiation in anadromous smelt Osmerus mordax (Mitchill): disentangling the effects of geography and morphology on gene flow
Authors: Bradbury I. R. , Coulson M. W , Campana S. E. , Bentzen P.
Published: December 2006

Morphological analyses were combined with genetic analyses at nine microsatellite loci to examine the determinants of gene flow at 21 spawning locations of rainbow smelt Osmerus mordax along the east coast of Canada. Associations between morphology, geography and gene flow were examined using a computational geometric approach and partial Mantel tests. Significant barriers to gene flow and discontinuities in morphology were observed between Newfoundland and mainland Canada, as well as within Newfoundland samples. On regional scales, contrasting patterns were present with restricted gene flow between Newfoundland populations (FST=c. 0·11) and high gene flow between mainland populations (FST=c. 0·017). Within Newfoundland populations, geographic distance was significantly associated with gene flow (r= 0·85, P < 0·001) contrasting mainland samples where gene flow was most associated with phenotypic divergence (r= 0·33, P < 0·001). At large spatial scales, weak (r= 0·19, P= 0·02) associations between gene flow and geographic distance were observed, and moderate associations were also observed between gene flow and morphology (r= 0·28, P < 0·001). The presence of significant genetic isolation by distance in Newfoundland samples and the clear discontinuity associated with the Cabot Strait suggest geography may be the primary determinant of gene flow. Interestingly, the association between genetic and morphological divergence within mainland samples and overall, supports the hypothesis that gene flow may be moderated by morphological divergence at larger spatial scales even in high gene flow environments.
Discriminating the impact of recent human mediated stock transfer from historical gene flow on genetic structure of European grayling Thymallus thymallus L.
Authors: Gum B. , Gross R. , Kuehn R.
Published: December 2006

Microsatellite markers were first used to partition individuals of European grayling Thymallus thymallus, from the Danube, Rhine and Main, and Elbe drainage systems into subpopulations and to estimate individual immigrant ancestries over the last few generations. Subsequently, the studied populations were ‘purged’ from recent immigrants and the proportions of evolutionary lineages within the ‘purged’ populations were re‐estimated by applying mtDNA markers. The results confirmed a high level of admixture of the divergent mtDNA lineages (i.e. natural secondary contact) in populations sampled at the contact zones of the drainages. In addition, a substantial amount of introgression was observed for several populations that were known to be affected by stocking of European grayling from different origins.
The use of otolith shape and chemistry to determine stock structure of Mediterranean horse mackerel Trachurus mediterraneus (Steindachner)
Authors: Turan C.
Published: December 2006

Otolith shape and chemistry of Mediterranean horse mackerel Trachurus mediterraneus were simultaneously used to assess the feasibility of using these natural tags to discriminate populations throughout the Black, Marmara, Aegean and eastern Mediterranean Seas. Otolith shape and chemistry analyses showed a similar pattern of differentiation between T. mediterraneus stocks, revealing a clear discreteness of the middle Black Sea (Sinop) and Aegean Sea (Izmir) samples. Otolith upper side length and width, and Na, K, Mg and Ba, were the morphological traits and trace elements, respectively, differing most among groups. Overall assignment of individuals into their original sample was high for both otolith shape and chemistry. Highest reclassification rate was observed for the south‐middle Black Sea and Aegean Sea samples for both analyses. Hierarchical cluster analyses also supported high differentiation of the south‐middle Black Sea and Aegean Sea samples for both analyses. Mantel’s test revealed that the Euclidean distance both for otolith shape (r=−0·0917, P > 0·05) and chemistry (r=−0·1248, P > 0·05) between these populations were not significantly associated with their geographical distances.
Morphological differentiation in introduced pumpkinseedLepomis gibbosus(L.) occupying different habitat zones in Portuguese reservoirs
Authors: Bhagat Y. , Fox M. G. , Ferreira M. T.
Published: December 2006

Introduced pumpkinseedLepomis gibbosussampled from four habitat zones (fluvial pelagic, fluvial littoral, lacustrine pelagic and lacustrine littoral) in three Portuguese reservoirs were used to test the hypotheses that habitats with the least similar characteristics will show the most differentiation, and that morphological differences will relate to functional adaptations to flow and trophic habitats. Results from discriminant function analysis and ANCOVA showed that there were significant differences in external morphology in pumpkinseed captured from the four habitat zones in all three reservoirs. Littoral and pelagic differentiation was stronger than fluvial and lacustrine differentiation in all of the reservoirs, and the most significant variable that differentiated pumpkinseed from the littoral and pelagic habitats was body depth. The illustration of external morphological differentiation in pumpkinseed along both habitat dimensions demonstrates the high degree of morphological plasticity of this introduced species.
Temporal genetic differentiation: continuous v. discontinuous spawning runs in anadromous rainbow smelt Osmerus mordax (Mitchill)
Authors: Coulson M. W. , Bradbury I. R. , Bentzen P.
Published: December 2006

Genetic differentiation was greater between ‘early’ and ‘late’ spawning rainbow smelt Osmerus mordax separated by a hiatus in spawning activity compared to a continuously spawning population over a similar time period. This magnitude of temporal differentiation was comparable to that seen among spatially separated populations.
Stock structure of Icelandic cod Gadus morhua L. based on otolith chemistry
Authors: Jónsdóttir I. G. , Campana S. E. , Marteinsdottir G.
Published: December 2006

Otolith chemistry was used to study the stock structure of Icelandic cod Gadus morhua. Otoliths were collected from spawning cod at 12 and 17 different spawning locations around Iceland during the spawning season in 2002 and 2003, respectively. The otolith elemental composition of cod spawning north and south of Iceland differed substantially from each other, as did spawning cod below and above 125 m depth at the main spawning ground in the south of Iceland. Otolith chemistry differed more between locations than among years within a location, indicating temporal stability between the 2 years. The Icelandic cod stock is managed as a single stock. These results suggest, however, that optimal fisheries management may require different management units than are currently present.
Cod Gadus morhua L. populations as behavioural units: inference from time series on juvenile abundance in the eastern Skagerrak
Authors: Svedäng H. , Svenson A.
Published: December 2006

Abundance and distribution of cod Gadus morhua in various size intervals and age groups between 2000 and 2005 were followed in coastal trawl surveys. In spite of a reduction in fishing pressure in recent years and high cod recruitment in the Skagerrak region in 2001 and 2003, no recovery could be evidenced. The survey data clearly showed that low cod density areas were not recolonized, even though abundance of juvenile cod remained high for about a year after the recruitment episodes. Increased abundance of fish >400 mm total length was only discernible at some scattered locations where other studies also have suggested local populations still to be present. The intermittent high recruitment has been linked to an inflow of egg and larvae from the North Sea, a theory which also has gained support from genetic studies. It was thus argued that the disappearance of the juvenile cod from the inshore is an effect of a migratory behaviour; the fish of offshore origin eventually leave the coast for the open Skagerrak or the North Sea. These findings support a view on cod populations as essentially behavioural entities, whereas dispersal of early life stages may be less important as a structuring mechanism.
Spatial and temporal scales of adaptive divergence in marine fishes and the implications for conservation
Authors: Conover D. O. , Clarke L. M. , Munch S. B. , Wagner G. N.
Published: December 2006

Knowledge of geographic and temporal scales of adaptive genetic variation is crucial to species conservation, yet understanding of these phenomena, particularly in marine systems, is scant. Until recently, the belief has been that because most marine species have highly dispersive or mobile life stages, local adaptation could occur only on broad geographic scales. This view is supported by comparatively low levels of genetic variation among populations as detected by neutral markers. Similarly, the time scale of adaptive divergence has also been assumed to be very long, requiring thousands of generations. Recent studies of a variety of species have challenged these beliefs. First, there is strong evidence of geographically structured local adaptation in physiological and morphological traits. Second, the proportion of quantitative trait variation at the among‐population level (QST) is much higher than it is for neutral markers (FST) and these two metrics of genetic variation are poorly correlated. Third, evidence that selection is a potent evolutionary force capable of sustaining adaptive divergence on contemporary time scales is summarized. The differing spatial and temporal scales of adaptive v. neutral genetic divergence call for a new paradigm in thinking about the relationship between phenogeography (the geography of phenotypic variation) and phylogeography (the geography of lineages) in marine species. The idea that contemporary selective processes can cause fine‐scale spatial and temporal divergence underscores the need for a new emphasis on Darwinian fishery science.
Fish population structuring in the North Sea: understanding processes and mechanisms from studies of the movements of adults
Authors: Metcalfe J. D.
Published: December 2006

Few fish species form single, panmictic populations throughout their geographic range, most form subpopulations or ‘stocks’ with differing levels of interconnectivity. Different patterns of interconnectivity between subpopulations will give rise to different responses to exploitation and management, but they will also have different capacities to generate the genetic and phenotypic differences often used to discriminate between stocks. Consequently, knowledge of ontogenetic and seasonal patterns in the distribution, movement and behaviour of individuals is crucial to identifying population substructure. This paper considers the evidence gathered about movements and behaviour of adult fishes from mark‐recapture and electronic tagging studies for a number of fish species in the North Sea and elsewhere in U.K. waters in an attempt to understand population structure and the processes that may give rise to it.
Designing marine protected areas for migrating fish stocks
Authors: Stefansson G. , Rosenberg A. A.
Published: December 2006

This paper extends an earlier analysis and presents an investigation of how migration rates affect the performance of various types of management regimes with respect to economic yield and conservation benefits. Particular emphasis is placed on evaluating the geometric design of marine protected areas (MPAs). Earlier results have shown that MPAs are only likely to provide significant benefits when they are used in conjunction with direct catch or effort controls, unless they are quite large and cover most of the resource in question. Conversely, catch and effort controls are far more effective when protected areas are included in the management regime as a buffer against uncertainty. Dispersal of reproduction (recruitment) to other areas is an important expected benefit of protected areas, but such dispersal increases the variability of the effects of the area protection. If fishing mortality rates outside of the protected area are not controlled then dispersal can result in nullifying some of the benefits of the protected area. Similarly, adult migration increases the variability in the results when an area is protected and critically depends upon an overall control of fishing mortality outside the area. For both dispersal and migration separately or in combination, however, there are clear benefits to using MPAs in conjunction with catch or effort controls. These benefits are expressed in terms of long‐term yield and recovery probabilities. In addition, short‐term yield declines relatively slowly with increasing area protected. Design of the protected areas is seen to be important since using contiguous areas provide greater protection against overfishing than protected areas in isolation.
Edgeworth and Lindahl–Foley equilibria of a General Equilibrium Model with Private Provision of Pure Public Goods
Authors: FLORENZANO MONIQUE , Del MERCATO ELENA L.
Published: December 2006

In this paper, we propose a definition of Edgeworth equilibrium for a private ownership production economy with (possibly infinitely) many private goods and a finite number of pure public goods. We show that Edgeworth equilibria exist whatever be the dimension of the private goods space and can be decentralized, in the finite and infinite dimensional cases, as Lindahl–Foley equilibria. Existence theorems for Lindahl–Foley equilibria are a by‐product of our results.
Fixed Wages and Bonuses in Agency Contracts: The Case of a Continuous State Space
Authors: RACIONERO MARIA , QUIGGIN JOHN
Published: December 2006

In this paper, we extend the state‐contingent production approach to principal–agent problems to the case where the state space is an atomless continuum. The approach is modelled on the treatment of optimal tax problems. The central observation is that, under reasonable conditions, the optimal contract may involve a fixed wage with a bonus for above‐normal performance. This is analogous to the phenomenon of “bunching” at the bottom in the optimal tax literature.
Political Uncertainty and Policy Innovation
Authors: KOTSOGIANNIS CHRISTOS , SCHWAGER ROBERT
Published: December 2006

Conventional wisdom has it that outside sources of information enhance the capability of political institutions to separate selfish from benevolent incumbents. This paper investigates, in the presence of innovative public policies whose outcomes are uncertain, the role of outside information and shows that it is more involved than typically thought. While it is true that enhanced information helps in separating politicians, it also creates an externality that reduces the incentives to experiment with innovative public policies.