bluuebunny/crossref_metadata_2025 huggingface dataset:
Inverse free electron lasers and laser wakefield acceleration driven by CO
2
lasers
Authors: Kimura W.D , Andreev N.E , Babzien M , Ben-Zvi I , Cline D.B , Dilley C.E , Gottschalk S.C , Hooker S.M , Kusche K.P , Kuznetsov S.V , Pavlishin I.V , Pogorelsky I.V , Pogosova A.A , Steinhauer L.C , Ting A , Yakimenko V , Zigler A , Zhou F
Published: January 2006

The staged electron laser acceleration (STELLA) experiment demonstrated staging between two laser-driven devices, high trapping efficiency of microbunches within the accelerating field and narrow energy spread during laser acceleration. These are important for practical laser-driven accelerators. STELLA used inverse free electron lasers, which were chosen primarily for convenience. Nevertheless, the STELLA approach can be applied to other laser acceleration methods, in particular, laser-driven plasma accelerators. STELLA is now conducting experiments on laser wakefield acceleration (LWFA). Two novel LWFA approaches are being investigated. In the first one, called pseudo-resonant LWFA, a laser pulse enters a low-density plasma where nonlinear laser/plasma interactions cause the laser pulse shape to steepen, thereby creating strong wakefields. A witness
e
-beam pulse probes the wakefields. The second one, called seeded self-modulated LWFA, involves sending a seed
e
-beam pulse into the plasma to initiate wakefield formation. These wakefields are amplified by a laser pulse following shortly after the seed pulse. A second
e
-beam pulse (witness) follows the seed pulse to probe the wakefields. These LWFA experiments will also be the first ones driven by a CO
2
laser beam.
Bubble regime of wake field acceleration: similarity theory and optimal scalings
Authors: Pukhov A , Gordienko S
Published: January 2006

A similarity theory is developed for ultra-relativistic laser–plasmas. It is used to compare and optimize possible regimes of three-dimensional wake field acceleration. The optimal scalings for laser wake field electron acceleration are obtained analytically. The main message of the present work is that the bubble acceleration regime [see Pukhov A. & Meyer-ter-Vehn J. 2002.
Appl. Phys. B
74
, 355] satisfies these optimal scalings.
Electron and photon beams interacting with plasma
Authors: Reitsma Albert , Jaroszynski Dino
Published: January 2006

A comparison is made between the interaction of electron bunches and intense laser pulses with plasma. The laser pulse is modelled with
photon kinetic theory
, i.e. a representation of the electromagnetic field in terms of classical quasi-particles with space and wave number coordinates, which enables a direct comparison with the phase space evolution of the electron bunch. Analytical results are presented of the plasma waves excited by a propagating electron bunch or laser pulse, the motion of electrons or photons in these plasma waves and collective effects, which result from the self-consistent coupling of the particle and plasma wave dynamics.
The generation of mono-energetic electron beams from ultrashort pulse laser–plasma interactions
Authors: Mangles S.P.D , Krushelnick K , Najmudin Z , Wei M.S , Walton B , Gopal A , Dangor A.E , Fritzler S , Murphy C.D , Thomas A.G.R , Mori W.B , Gallacher J , Jaroszynski D , Norreys P.A , Viskup R
Published: January 2006

The physics of the interaction of high-intensity laser pulses with underdense plasma depends not only on the interaction intensity but also on the laser pulse length. We show experimentally that as intensities are increased beyond 10
20
 W cm
−2
the peak electron acceleration increases beyond that which can be produced from single stage plasma wave acceleration and it is likely that direct laser acceleration mechanisms begin to play an important role. If, alternatively, the pulse length is reduced such that it approaches the plasma period of a relativistic electron plasma wave, high-power interactions at much lower intensity enable the generation of quasi-mono-energetic beams of relativistic electrons.
Radiation sources based on laser–plasma interactions
Authors: Jaroszynski D.A , Bingham R , Brunetti E , Ersfeld B , Gallacher J , van der Geer B , Issac R , Jamison S.P , Jones D , de Loos M , Lyachev A , Pavlov V , Reitsma A , Saveliev Y , Vieux G , Wiggins S.M
Published: January 2006

Plasma waves excited by intense laser beams can be harnessed to produce femtosecond duration bunches of electrons with relativistic energies. The very large electrostatic forces of plasma density wakes trailing behind an intense laser pulse provide field potentials capable of accelerating charged particles to high energies over very short distances, as high as 1 GeV in a few millimetres. The short length scale of plasma waves provides a means of developing very compact high-energy accelerators, which could form the basis of compact next-generation light sources with unique properties. Tuneable X-ray radiation and particle pulses with durations of the order of or less than 5 fs should be possible and would be useful for probing matter on unprecedented time and spatial scales. If developed to fruition this revolutionary technology could reduce the size and cost of light sources by three orders of magnitude and, therefore, provide powerful new tools to a large scientific community. We will discuss how a laser-driven plasma wakefield accelerator can be used to produce radiation with unique characteristics over a very large spectral range.
High-intensity laser-driven proton acceleration: influence of pulse contrast
Authors: McKenna Paul , Lindau Filip , Lundh Olle , Neely David , Persson Anders , Wahlström Claes-Göran
Published: January 2006

Proton acceleration from the interaction of ultra-short laser pulses with thin foil targets at intensities greater than 10
18
 W cm
−2
is discussed. An overview of the physical processes giving rise to the generation of protons with multi-MeV energies, in well defined beams with excellent spatial quality, is presented. Specifically, the discussion centres on the influence of laser pulse contrast on the spatial and energy distributions of accelerated proton beams. Results from an ongoing experimental investigation of proton acceleration using the 10 Hz multi-terawatt Ti : sapphire laser (35 fs, 35 TW) at the Lund Laser Centre are discussed. It is demonstrated that a window of amplified spontaneous emission (ASE) conditions exist, for which the direction of proton emission is sensitive to the ASE-pedestal preceding the peak of the laser pulse, and that by significantly improving the temporal contrast, using plasma mirrors, efficient proton acceleration is observed from target foils with thickness less than 50 nm.
Binding of a novel SMG-1–Upf1–eRF1–eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay
Authors: Kashima Isao , Yamashita Akio , Izumi Natsuko , Kataoka Naoyuki , Morishita Ryo , Hoshino Shinichi , Ohno Mutsuhito , Dreyfuss Gideon , Ohno Shigeo
Published: February 2006

Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that degrades mRNA containing premature termination codons (PTCs). In mammalian cells, recognition of PTCs requires translation and depends on the presence on the mRNA with the splicing-dependent exon junction complex (EJC). While it is known that a key event in the triggering of NMD is phosphorylation of the trans-acting factor, Upf1, by SMG-1, the relationship between Upf1 phosphorylation and PTC recognition remains undetermined. Here we show that SMG-1 binds to the mRNA-associated components of the EJC, Upf2, Upf3b, eIF4A3, Magoh, and Y14. Further, we describe a novel complex that contains the NMD factors SMG-1 and Upf1, and the translation termination release factors eRF1 and eRF3 (SURF). Importantly, an association between SURF and the EJC is required for SMG-1-mediated Upf1 phosphorylation and NMD. Thus, the SMG-1-mediated phosphorylation of Upf1 occurs on the association of SURF with EJC, which provides the link between the EJC and recognition of PTCs and triggers NMD.
Function and Characterization of Starch Synthase I Using Mutants in Rice
Authors: Fujita Naoko , Yoshida Mayumi , Asakura Noriko , Ohdan Takashi , Miyao Akio , Hirochika Hirohiko , Nakamura Yasunori
Published: January 2006

Four starch synthase I (SSI)-deficient rice (Oryza sativa) mutant lines were generated using retrotransposon Tos17 insertion. The mutants exhibited different levels of SSI activities and produced significantly lower amounts of SSI protein ranging from 0% to 20% of the wild type. The mutant endosperm amylopectin showed a decrease in chains with degree of polymerization (DP) 8 to 12 and an increase in chains with DP 6 to 7 and DP 16 to 19. The degree of change in amylopectin chain-length distribution was positively correlated with the extent of decrease in SSI activity in the mutants. The structural changes in the amylopectin increased the gelatinization temperature of endosperm starch. Chain-length analysis of amylopectin in the SSI band excised from native-polyacrylamide gel electrophoresis/SS activity staining gel showed that SSI preferentially synthesized DP 7 to 11 chains by elongating DP 4 to 7 short chains of glycogen or amylopectin. These results show that SSI distinctly generates DP 8 to 12 chains from short DP 6 to 7 chains emerging from the branch point in the A or B1 chain of amylopectin. SSI seemingly functions from the very early through the late stage of endosperm development. Yet, the complete absence of SSI, despite being a major SS isozyme in the developing endosperm, had no effect on the size and shape of seeds and starch granules and the crystallinity of endosperm starch, suggesting that other SS enzymes are probably capable of partly compensating SSI function. In summary, this study strongly suggested that amylopectin chains are synthesized by the coordinated actions of SSI, SSIIa, and SSIIIa isoforms.
A Role for Mitochondria in the Establishment and Maintenance of the Maize Root Quiescent Center
Authors: Jiang Keni , Ballinger Tracy , Li Daisy , Zhang Shibo , Feldman Lewis
Published: January 2006

Mitochondria in the oxidizing environment of the maize (Zea mays) root quiescent center (QC) are altered in function, but otherwise structurally normal. Compared to mitochondria in the adjacent, rapidly dividing cells of the proximal root tissues, mitochondria in the QC show marked reductions in the activities of tricarboxylic acid cycle enzymes. Pyruvate dehydrogenase activity was not detected in the QC. Use of several mitochondrial membrane potential (ΔΨm) sensing probes indicated a depolarization of the mitochondrial membrane in the QC, which suggests a reduction in the capacity of QC mitochondria to generate ATP and NADH. We postulate that modifications of mitochondrial function are central to the establishment and maintenance of the QC.
Effects of Feeding Spodoptera littoralis on Lima Bean Leaves. III. Membrane Depolarization and Involvement of Hydrogen Peroxide
Authors: Maffei Massimo E. , Mithöfer Axel , Arimura Gen-Ichiro , Uchtenhagen Hannes , Bossi Simone , Bertea Cinzia M. , Cucuzza Laura Starvaggi , Novero Mara , Volpe Veronica , Quadro Stefano , Boland Wilhelm
Published: January 2006

In response to herbivore (Spodoptera littoralis) attack, lima bean (Phaseolus lunatus) leaves produced hydrogen peroxide (H2O2) in concentrations that were higher when compared to mechanically damaged (MD) leaves. Cellular and subcellular localization analyses revealed that H2O2 was mainly localized in MD and herbivore-wounded (HW) zones and spread throughout the veins and tissues. Preferentially, H2O2 was found in cell walls of spongy and mesophyll cells facing intercellular spaces, even though confocal laser scanning microscopy analyses also revealed the presence of H2O2 in mitochondria/peroxisomes. Increased gene and enzyme activations of superoxide dismutase after HW were in agreement with confocal laser scanning microscopy data. After MD, additional application of H2O2 prompted a transient transmembrane potential (V  m) depolarization, with a V  m depolarization rate that was higher when compared to HW leaves. In transgenic soybean (Glycine max) suspension cells expressing the Ca2+-sensing aequorin system, increasing amounts of added H2O2 correlated with a higher cytosolic calcium ([Ca2+]cyt) concentration. In MD and HW leaves, H2O2 also triggered the increase of [Ca2+]cyt, but MD-elicited [Ca2+]cyt increase was more pronounced when compared to HW leaves after addition of exogenous H2O2. The results clearly indicate that V  m depolarization caused by HW makes the membrane potential more positive and reduces the ability of lima bean leaves to react to signaling molecules.
GOLD HULL AND INTERNODE2 Encodes a Primarily Multifunctional Cinnamyl-Alcohol Dehydrogenase in Rice
Authors: Zhang Kewei , Qian Qian , Huang Zejun , Wang Yiqin , Li Ming , Hong Lilan , Zeng Dali , Gu Minghong , Chu Chengcai , Cheng Zhukuan
Published: January 2006

Lignin content and composition are two important agronomic traits for the utilization of agricultural residues. Rice (Oryza sativa) gold hull and internode phenotype is a classical morphological marker trait that has long been applied to breeding and genetics study. In this study, we have cloned the GOLD HULL AND INTERNODE2 (GH2) gene in rice using a map-based cloning approach. The result shows that the gh2 mutant is a lignin-deficient mutant, and GH2 encodes a cinnamyl-alcohol dehydrogenase (CAD). Consistent with this finding, extracts from roots, internodes, hulls, and panicles of the gh2 plants exhibited drastically reduced CAD activity and undetectable sinapyl alcohol dehydrogenase activity. When expressed in Escherichia coli, purified recombinant GH2 was found to exhibit strong catalytic ability toward coniferaldehyde and sinapaldehyde, while the mutant protein gh2 completely lost the corresponding CAD and sinapyl alcohol dehydrogenase activities. Further phenotypic analysis of the gh2 mutant plants revealed that the p-hydroxyphenyl, guaiacyl, and sinapyl monomers were reduced in almost the same ratio compared to the wild type. Our results suggest GH2 acts as a primarily multifunctional CAD to synthesize coniferyl and sinapyl alcohol precursors in rice lignin biosynthesis.
Characterization of low phosphorus insensitive Mutants Reveals a Crosstalk between Low Phosphorus-Induced Determinate Root Development and the Activation of Genes Involved in the Adaptation of Arabidopsis to Phosphorus Deficiency
Authors: Sánchez-Calderón Lenin , López-Bucio José , Chacón-López Alejandra , Gutiérrez-Ortega Abel , Hernández-Abreu Esmeralda , Herrera-Estrella Luis
Published: January 2006

Low phosphorus (P) availability is one of the most limiting factors for plant productivity in many natural and agricultural ecosystems. Plants display a wide range of adaptive responses to cope with low P stress, which generally serve to enhance P availability in the soil and to increase its uptake by roots. In Arabidopsis (Arabidopsis thaliana), primary root growth inhibition and increased lateral root formation have been reported to occur in response to P limitation. To gain knowledge of the genetic mechanisms that regulate root architectural responses to P availability, we designed a screen for identifying Arabidopsis mutants that fail to arrest primary root growth when grown under low P conditions. Eleven low phosphorus insensitive (lpi) mutants that define at least four different complementation groups involved in primary root growth responses to P availability were identified. The lpi mutants do not show the typical determinate developmental program induced by P stress in the primary root. Other root developmental aspects of the low P rescue system, including increased root hair elongation and anthocyanin accumulation, remained unaltered in lpi mutants. In addition to the insensitivity of primary root growth inhibition, when subjected to P deprivation, lpi mutants show a reduced induction in the expression of several genes involved in the P starvation rescue system (PHOSPHATE TRANSPORTER 1 and 2, PURPLE ACID PHOSPHATASE 1, ACID PHOSPHATASE 5, and INDUCED BY PHOSPHATE STARVATION 1). Our results provide genetic support for the role of P as an important signal for postembryonic root development and root meristem maintenance and show a crosstalk in developmental and biochemical responses to P deprivation.
Phytochrome B Represses Teosinte Branched1 Expression and Induces Sorghum Axillary Bud Outgrowth in Response to Light Signals
Authors: Kebrom Tesfamichael H. , Burson Byron L. , Finlayson Scott A.
Published: January 2006

Light is one of the environmental signals that regulate the development of shoot architecture. Molecular mechanisms regulating shoot branching by light signals have not been investigated in detail. Analyses of light signaling mutants defective in branching provide insight into the molecular events associated with the phenomenon. It is well documented that phytochrome B (phyB) mutant plants display constitutive shade avoidance responses, including increased plant height and enhanced apical dominance. We investigated the phyB-1 mutant sorghum (Sorghum bicolor) and analyzed the expression of the sorghum Teosinte Branched1 gene (SbTB1), which encodes a putative transcription factor that suppresses bud outgrowth, and the sorghum dormancy-associated gene (SbDRM1), a marker of bud dormancy. Buds are formed in the leaf axils of phyB-1; however, they enter into dormancy soon after their formation. The dormant state of phyB-1 buds is confirmed by the high level of expression of the SbDRM1 gene. The level of SbTB1 mRNA is higher in the buds of phyB-1 compared to wild type, suggesting that phyB mediates the growth of axillary shoots in response to light signals in part by regulating the mRNA abundance of SbTB1. These results are confirmed by growing wild-type seedlings with supplemental far-red light that induces shade avoidance responses. We hypothesize that active phyB (Pfr) suppresses the expression of the SbTB1 gene, thereby inducing bud outgrowth, whereas environmental conditions that inactivate phyB allow increased expression of SbTB1, thereby suppressing bud outgrowth.
Cinnamate Metabolism in Ripening Fruit. Characterization of a UDP-Glucose:Cinnamate Glucosyltransferase from Strawberry
Authors: Lunkenbein Stefan , Bellido MariLuz , Aharoni Asaph , Salentijn Elma M.J. , Kaldenhoff Ralf , Coiner Heather A. , Muñoz-Blanco Juan , Schwab Wilfried
Published: January 2006

Strawberry (Fragaria × ananassa) fruit accumulate (hydroxy)cinnamoyl glucose (Glc) esters, which may serve as the biogenetic precursors of diverse secondary metabolites, such as the flavor constituents methyl cinnamate and ethyl cinnamate. Here, we report on the isolation of a cDNA encoding a UDP-Glc:cinnamate glucosyltransferase (Fragaria × ananassa glucosyltransferase 2 [FaGT2]) from ripe strawberry cv Elsanta that catalyzes the formation of 1-O-acyl-Glc esters of cinnamic acid, benzoic acid, and their derivatives in vitro. Quantitative real-time PCR analysis indicated that FaGT2 transcripts accumulate to high levels during strawberry fruit ripening and to lower levels in flowers. The levels in fruits positively correlated with the in planta concentration of cinnamoyl, p-coumaroyl, and caffeoyl Glc. In the leaf, high amounts of Glc esters were detected, but FaGT2 mRNA was not observed. The expression of FaGT2 is negatively regulated by auxin, induced by oxidative stress, and by hydroxycinnamic acids. Although FaGT2 glucosylates a number of aromatic acids in vitro, quantitative analysis in transgenic lines containing an antisense construct of FaGT2 under the control of the constitutive 35S cauliflower mosaic virus promoter demonstrated that the enzyme is only involved in the formation of cinnamoyl Glc and p-coumaroyl Glc during ripening.
Imagination and the imaginary
Authors: Colman Warren
Published: February 2006

Abstract:  This paper argues that real imagination depends on the capacity to acknowledge the absence of what is imagined from the world of material actuality. This leads on to a view of symbol formation as the operation of the transcendent function between the opposites of presence and absence. ‘The imaginary’ is contrasted with this as a defensive misuse of imagination that attempts to deny ‘negation’ where negation is defined as all those aspects of the world that constitute a check to the omnipotence of fantasy—e.g., absence, loss, difference, otherness etc. Parallels are drawn with theoretical antecedents in analytical psychology and psychoanalysis, with particular attention to papers published in the Journal of Analytical Psychology (JAP) in the 1960s on the relation between active imagination, transference and ego development. A clinical example is given to show the use of the imaginary as a means of warding off the unbearable pain of Oedipal disappointment.
Repeated antipredator conditioning: a pathway to habituation or to better avoidance?
Authors: Vilhunen S.
Published: January 2006

Hatchery‐reared juveniles of Arctic charr Salvelinus alpinus were conditioned to the odours of Arctic charr‐fed pikeperch Sander lucioperca in the absence of any other cues. Accordingly, there was no physical threat of capture for the Arctic charr. It was evident from the subsequent survival tests that a single exposure to predator odours was enough to increase Arctic charr survival compared to predator‐naïve control fish whist under direct threat from live predators. Instead of habituating to predator odours, the fish conditioned repeatedly (four times) improved their spatial avoidance of predator cues in the course of training. The repeated conditioning also further enhanced the survival of the test fish as compared to the singly conditioned fish. The economical and ethical advantages of training with chemical cues, combined with its high reliability, could promote the success of fish reintroductions especially through repeated antipredator conditioning.
Diet of brown trout in relation to variation in abundance and size of pelagic fish prey
Authors: Hyvärinen P. , Huusko A.
Published: January 2006

The seasonal diet of a predator, brown trout Salmo trutta[total length (LT) 17–69 cm] and simultaneous density and size‐structure of prey populations, vendace Coregonus albula and smelt Osmerus eperlanus(4–16 cm LT), in a large boreal lake were analysed and compared in 2001 and 2002. The upper LT limit for consumed prey was c. 40% of the predator LT. All brown trout, however, preferred small (<10 cm LT) and avoided large (≥10 cm LT) prey. The results also suggested that equal densities of similar‐sized (4–10 cm LT) fish of the two prey species led to random foraging on these species by brown trout, but if either one of the prey species predominated (>50%) in the lake, brown trout shifted to foraging on this species almost exclusively. Brown trout diets thus reflected the density dynamics of the two alternative prey species.
An evaluation of the otolith characteristics ofConger congerduring metamorphosis
Authors: Correia A. T. , Antunes C. , Wilson J. M. , Coimbra J.
Published: January 2006

A sample of 20 metamorphosing conger eelConger congerleptocephali were collected from the Minho River, Portugal, in February 1999 and their sagittal otoliths were analysed by scanning electron microscopy. Four different etching agents were applied along both sagittal and frontal sections during otolith preparation to examine the microstructural growth in this species. Otolith growth increments were visible throughout the increment countable zone using all four treatments, but a permanent peripheral diffuse zone, where the daily increments were unclear, appeared on all otoliths, preventing accurate age estimation. To understand more about the nature of the diffuse zone, otoliths of 10 other metamorphosing leptocephali reared in aquaria were marked by immersion in tetracycline hydrochloride. The distance between the fluorescent marks and otolith edge, measured over a fixed period of time, was used to estimate the otolith growth rate. The application of this technique led to an anomalously high estimated otolith growth rate, probably as a result of the capture, marking and handling stress.
Changes of taxonomic and trophic structure of fish assemblages along an environmental gradient in the Upper Beni watershed (Bolivia)
Authors: Pouilly M. , Barrera S. , Rosales C.
Published: January 2006

The distribution and the diet of 28 fish species were evaluated, during the dry season, in 12 streams of the Upper Beni watershed (Amazon basin, Bolivia). The 12 streams were of similar size (stream width and water depth) but situated on a gradient of altitude in the Andean and sub‐Andean areas. The environmental conditions in the stream changed in relation to the altitude. As altitude decreased, slope and water velocity also decreased, while temperature, conductivity, pH and the proportion of pools increased. Although the diets of the species were mainly based on two aquatic autochthonous food resources, invertebrates and sediment, species were classified into five trophic guilds: detritivores, algivores, piscivores, invertivores‐omnivores and aquatic specialist invertivores. In all streams invertivores dominated or co‐dominated with detritivores. The trophic structure of the assemblages, however, changed in relation to the environmental gradient. The fish species richness increased and the trophic composition became more diverse at lower altitudes, when slope decreased and temperature increased. At the same time, the relative number of invertivore species decreased, whereas the relative number of detritivore, algivore and piscivore species increased. Decreasing altitude appeared to play a role similar to increasing stream size along the longitudinal gradient. This could be explained by geomorphological and temperature variations that may generate environmental conditions favourable to an increase of productivity.
Vulnerability of seamount fish to fishing: fuzzy analysis of life‐history attributes
Authors: Morato T. , Cheung W. W. L. , Pitcher T. J.
Published: January 2006

Despite rather broad definitions, global analysis showed that seamount fishes, particularly seamount‐aggregating fishes, had higher intrinsic vulnerability than other groups of fishes. The pattern was similar when considering only commercially exploited species. Biological characteristics leading to greater vulnerability included a longer life span, later sexual maturation, slower growth and lower natural mortality. The results supported the contention that seamount fishes, especially those that aggregate on seamounts, are highly vulnerable to exploitation and that fishing on seamounts may not be sustainable at current levels and with current methods. A number of seamount populations have already been depleted; more depletion, extirpations, and even species extinctions may follow if fishing on seamounts is not reduced.
A sex cord‐like structure and some remarkable features in early gonadal sex differentiation in the marine teleost Siganus guttatus(Bloch)
Authors: Komatsu T. , Nakamura S. , Nakamura M.
Published: January 2006

Several notable features of early gonadal sex differentiation in the golden rabbitfish Siganus guttatus are described including the first report among teleosts of a distinctive dual structure, consisting of somatic cells directly enclosing germ cells (sex cord‐like structure, SCS) and outer somatic tissue surrounding the SCS, in both undifferentiated and early differentiated gonads. Germ cells occurred and proliferated exclusively in the SCS during the process of ovarian and testicular differentiation. A second remarkable characteristic was the delayed germinal cell proliferation for oogenesis in the ovary, that commenced simultaneously with that in the testis, a relatively long time after the onset of somatic development. These observations suggest the possibility that sex differentiation of germ cells is preceded by some sex specific changes in somatic components of the SCS that are light‐microscopically indistinguishable between the sexes. The third unique feature was the detachment of gonadal tissue, including both somatic and germ cells, into the ovarian cavity in the ovary and into the seminiferous lobules and main seminal duct in the testis. This phenomenon occurred in the testis, forming the efferent duct network after 73 days post‐hatch (DPH), and in the ovaries, forming the ovigerous lamellae and regulating the number of oocytes attaining full maturation at c. 129 DPH.
Development of a microtitre plate indirect ELISA for measuring cortisol in teleosts, and evaluation of stress responses in rainbow trout and gilthead sea bream
Authors: Tintos A. , Míguez J. M. , Mancera J. M. , Soengas J. L.
Published: January 2006

A microtitre plate indirect enzyme‐linked immunoassay (ELISA) was developed for measuring plasma cortisol levels in rainbow trout Oncorhynchus mykiss, gilthead sea bream Sparus auratus sea bass Dicentrarchus labrax and Senegalese sole Solea senegalensis. Covalink microplates pretreated with disuccinimidyl suberate were coated with bovine serum albumin (BSA) conjugated to cortisol‐3‐carboxymethyl oxime. After blocking with BSA, competition was started by addition of plasma samples and anti‐cortisol antibody raised in rabbit. Goat anti‐rabbit IgG conjugated‐peroxidase was added as second antibody and then incubated with orthophenylenediamine as substrate. Reaction was stopped with 0·1 M HCl and absorbance was read at 450 nm in an automatic plate reader. The standard curve was linear from the lower limit of sensitivity of the assay (c. 0·3 ng ml−1) to c. 3000 ng ml−1. Dose‐response inhibition curves using serially diluted plasma samples of four species consistently showed parallelism with the standard curve using cortisol. The ELISA satisfied the strictest criteria of specificity (cross‐reactivity of anti‐cortisol antibody with testosterone, progesterone and 17ß‐oestradiol was negligible, cross‐reactivity with cortisone, corticosterone and 11‐deoxycortisol, was 1·5, 1 and 0·1%, respectively), reproducibility (interassay CV <6%), precision (intra‐assay CV <4%), and accuracy (average recovery >98%). Plasma cortisol concentration in rested fishes was in the range of 5–30 ng ml−1. To physiologically validate the technique, changes in plasma cortisol concentrations were also measured in plasma of rainbow trout and gilthead sea bream following an acute 15 min chasing or 3 min air‐exposure stress, respectively. In both species plasma concentrations of cortisol, glucose and lactate rose significantly with respect to controls, showing concentrations similar to those reported previously for these species under similar stress conditions. Furthermore, gilthead sea bream chronically stressed by maintaining for 14 days under increased stocking density conditions also showed increased concentrations of plasma cortisol and glucose. These results validate the indirect ELISA technique developed for use in the evaluation of plasma cortisol concentration of at least four fish species.
Promiscuous spawning behaviour of the tropical herring Spratelloides gracilis
Authors: Takeuchi N. , Gushima K.
Published: January 2006

Spawning behaviour of the blue sprat Spratelloides gracilis was observed at shallow reefs of Kuchierabu‐jima Island, southern Japan. The fish carried out promiscuous spawning behaviour on substrata covered with algal mats mainly in the intertidal region of a shallow inlet. The spawning events occurred only at predawn (20–50 min before sunrise) and daily for c. 25 days from mid‐June to mid‐July.
A new method to evaluate egg‐to‐fry survival in salmonids, trials with Atlantic salmon
Authors: Dumas J. , Marty S.
Published: January 2006

A new method to estimate the survival of salmonids from egg fertilization to fry emergence is described. Fine mesh screen cylindrical capsules, 12 cm3 in volume, filled with batches of 10 eggs of Atlantic salmon Salmo salar were implanted in the substratum using small removable guiding tubes inserted with a metal spike. The method was compared with two other commonly used techniques, capping redds with fry‐traps and fine mesh screen incubation‐emergence boxes buried into the gravel. Egg‐to‐fry survival was recorded for the three methods run in parallel in artificial redds created on three sites of the Nivelle River watershed (south‐west of France), two in the stream and one in an experimental spawning channel. In the channel, survival to the eyed stage and to hatching in capsules and incubation‐emergence boxes was also compared. The implant of capsules proved easier and faster to use than other methods, the structure of the surrounding substratum was less disturbed and the capsules were less vulnerable to spates. This technique provided survival values largely free of the bias induced by other methods and intermediate between that of incubators and of traps.
Nitrogen controls in planta expression of Cladosporium fulvum Avr9 but no other effector genes
Authors: THOMMA BART P. H. J. , BOLTON MELVIN D. , CLERGEOT PIERRE‐HENRI , DE WIT PIERRE J. G. M.
Published: January 2006

During growth on its host tomato, the apoplast‐colonizing fungal pathogen Cladosporium fulvum secretes several effector proteins. The expression of the Avr9 gene encoding one of these effector proteins has previously been shown to be strongly induced in vitro during nitrogen deprivation. This led to the hypothesis that expression of additional effector genes in C. fulvum could be triggered by nitrogen starvation conditions that are encountered in the host. We now show that expression of most effectors is not affected by varying levels of nitrogen supplementation in vitro. In addition, we demonstrate that the nitrogen response regulator Nrf1 only regulates Avr9 expression during infection of the host, whereas none of the other known effectors is significantly controlled by this transcription factor in planta. Deletion of Nrf1, but not of Avr9, significantly reduces C. fulvum virulence. Therefore, it is concluded that Nrf1 controls, in addition to Avr9, unidentified effector genes that are required for full virulence of C. fulvum.
The phytopathogen Rhodococcus fascians breaks apical dominance and activates axillary meristems by inducing plant genes involved in hormone metabolism
Authors: SIMÓN‐MATEO CARMEN , DEPUYDT STEPHEN , DE OLIVEIRA MANES CARMEM LARA , CNUDDE FILIP , HOLSTERS MARCELLE , GOETHALS KOEN , VEREECKE DANNY
Published: January 2006

Rhodococcus fascians is a Gram‐positive bacterium that interacts with many plant species and induces multiple shoots through a combination of activation of dormant axillary meristems and de novo meristem formation. Although phenotypic analysis of the symptoms of infected plants clearly demonstrates a disturbance of the phytohormonal balance and an activation of the cell cycle, the actual mechanism of symptom development and the targets of the bacterial signals are unknown. To elucidate the molecular pathways that are responsive to R. fascians infection, differential display was performed on Nicotiana tabacum as a host. Four differentially expressed genes could be identified that putatively encode a senescence‐associated protein, a gibberellin 2‐oxidase, a P450 monooxygenase and a proline dehydrogenase. The differential expression of the three latter genes was confirmed on infected Arabidopsis thaliana plants by quantitative reverse transcription polymerase chain reactions, supporting their general function in R. fascians‐induced symptom development. The role of these genes in hormone metabolism, especially of gibberellin and abscisic acid, in breaking apical dominance and in activating axillary meristems, which are processes associated with symptom development, is discussed.
Physiology and molecular aspects of Verticillium wilt diseases caused by V. dahliae and V. albo‐atrum
Authors: FRADIN EMILIE F. , THOMMA BART P. H. J.
Published: January 2006

Introduction:  Verticillium spp. are soil‐borne plant pathogens responsible for Verticillium wilt diseases in temperate and subtropical regions; collectively they affect over 200 hosts, including many economically important crops. There are currently no fungicides available to cure plants once they are infected.

Taxonomy:  Kingdom: Fungi, phylum: Ascomycota, subphylum, Pezizomycotina, class: Sordariomycetes, order: Phyllachorales, genus: Verticillium.

Host range and disease symptoms:  Over 200 mainly dicotyledonous species including herbaceous annuals, perennials and woody species are host to Verticillium diseases. As Verticillium symptoms can vary between hosts, there are no unique symptoms that belong to all plants infected by this fungus. Disease symptoms may comprise wilting, chlorosis, stunting, necrosis and vein clearing. Brown vascular discoloration may be observed in stem tissue cross‐sections.

Pathogenicity:  Verticillium spp. have been reported to produce cell‐wall‐degrading enzymes and phytotoxins that all have been implicated in symptom development. Nevertheless, evidence for a crucial role of toxins in pathogenicity is inconsistent and therefore not generally accepted. Microsclerotia and melanized mycelium play an important role in the disease cycle as they are a major inoculum source and are the primary long‐term survival structures.

Resistance:  Different defence responses in the prevascular and the vascular stage of Verticillium wilt diseases determine resistance. Although resistance physiology is well established, the molecular processes underlying this physiology remain largely unknown. Resistance against Verticillium largely depends on the isolation of the fungus in contained parts of the xylem tissues followed by subsequent elimination of the fungus. Although genetic resistance has been described in several plant species, only one resistance locus against Verticillium has been cloned to date.

Useful website:  http://cbr‐rbc.nrc‐cnrc.gc.ca/services/cogeme/
In vivo and in vitro studies of Chlamydia trachomatis TrpR:DNA interactions
Authors: Carlson John H. , Wood Heidi , Roshick Christine , Caldwell Harlan D. , McClarty Grant
Published: January 2006

We previously reported that Chlamydia trachomatis expresses the genes encoding tryptophan synthase (trpBA) and the tryptophan repressor (trpR). Here we employ primer extension analysis to identify the transcriptional origins of both trpR and trpBA, allowing for the identification of the putative operator sequences for both trpR and trpBA. Moreover we demonstrate that native recombinant chlamydial TrpR binds to the predicted operator sequence upstream of trpR. A restriction endonuclease protection assay was designed and used to demonstrate that 5‐fluorotryptophan was the only tryptophan analogue capable of activating binding of native recombinant chlamydial TrpR to its operator. Additionally, 5‐fluorotryptophan was the only analogue that repressed expression of trpBA at a level analogous to l‐tryptophan itself. Based on these findings, a mutant selection protocol was designed and a C. trachomatis isolate containing a frameshift mutation in trpR was isolated. This chlamydial mutant synthesizes a truncated TrpR protein that cannot regulate expression of trpBA and trpR in response to changes in tryptophan levels. These findings provide the first genetic proof that TrpR acts as a negative regulator of transcription in C. trachomatis.
The toxbox: specific DNA sequence requirements for activation of Vibrio cholerae virulence genes by ToxT
Authors: Withey Jeffrey H. , DiRita Victor J.
Published: January 2006

The Gram‐negative, curved rod Vibrio cholerae causes the severe diarrhoeal disease cholera. The two major virulence factors produced by V. cholerae during infection are the cholera toxin (CT) and the toxin‐coregulated pilus (TCP). Transcription of the genes encoding both CT and the components of the TCP is directly activated by ToxT, a transcription factor in the AraC/XylS family. ToxT binds upstream of the ctxAB genes, encoding CT, and upstream of tcpA, the first gene in a large operon encoding the components of the TCP. The DNA sequences upstream of ctxAB and tcpA that contain ToxT binding sites do not have any significant similarity other than being AT‐rich. Extensive site‐directed mutagenesis was performed on the region upstream of tcpA previously shown to be protected by ToxT, and we identified specific base pairs important for activation of tcpA transcription by ToxT. This genetic approach was complemented by copper‐phenanthroline footprinting experiments that showed protection by ToxT of the base pairs identified as most important for transcription activation in the mutagenesis experiments. Based on this new information and on previous work, we propose the presence of a ToxT‐binding motif – the ‘toxbox’– in promoters regulated by ToxT. At tcpA, two toxbox elements are present in a direct repeat configuration and both are required for activation of transcription by ToxT. The identity of only a few of the base pairs within the toxbox is important for activation by ToxT, and we term these the core toxbox elements. Lastly, we examined ToxT binding to a mutant having 5 bp inserted between the two toxboxes at tcpA and found that occupancy of both binding sites is retained regardless of the positions of the binding sites relative to each other on the face of the DNA. This suggests that ToxT binds independently as a monomer to each toxbox in the tcpA direct repeat, in accordance with what we observed previously with the inverted repeat ToxT sites between acfA and acfD.
A novel polar surface polysaccharide from Rhizobium leguminosarum binds host plant lectin
Authors: Laus Marc C. , Logman Trudy J. , Lamers Gerda E. , Van Brussel Anton A. N. , Carlson Russell W. , Kijne Jan W.
Published: January 2006

Rhizobium bacteria produce different surface polysaccharides which are either secreted in the growth medium or contribute to a capsule surrounding the cell. Here, we describe isolation and partial characterization of a novel high molecular weight surface polysaccharide from a strain of Rhizobium leguminosarum that nodulates Pisum sativum (pea) and Vicia sativa (vetch) roots. Carbohydrate analysis showed that the polysaccharide consists for 95% of mannose and glucose, with minor amounts of galactose and rhamnose. Lectin precipitation analysis revealed high binding affinity of pea and vetch lectin for this polysaccharide, in contrast to the other known capsular and extracellular polysaccharides of this strain. Expression of the polysaccharide was independent of the presence of a Sym plasmid or the nod gene inducer naringenin. Incubation of R. leguminosarum with labelled pea lectin showed that this polysaccharide is exclusively localized on one of the poles of the bacterial cell. Vetch roots incubated with rhizobia and labelled pea lectin revealed that this bacterial pole is involved in attachment to the root surface. A mutant strain deficient in the production of this polysaccharide was impaired in attachment and root hair infection under slightly acidic conditions, in contrast to the situation at slightly alkaline conditions. Our data are consistent with the hypothesis that rhizobia can use (at least) two mechanisms for docking at the root surface, with use of a lectin–glycan mechanism under slightly acidic conditions.
Antibiotics and the ribosome
Authors: Tenson Tanel , Mankin Alexander
Published: January 2006

The ribosome is one of the main antibiotic targets in the cell. Recent years brought important insights into the mode of interaction of antibiotics with the ribosome and mechanisms of antibiotic action. Ribosome crystallography provided a detailed view of the interactions between antibiotics and rRNA. Advances in biochemical techniques let us better understand how the binding of small organic molecules can interfere with functions of an enzyme four orders of magnitude larger than the inhibitor. These and other achievements paved the way for the development of new ribosome‐targeting antibiotics, some of which have already entered medical practice. The recent progress, problems and new directions of research of ribosome‐targeting antibiotics are discussed in this review.
Bed forms in bimodal sand–gravel sediments: laboratory and field analysis
Authors: KUHNLE R. A. , HORTON J. K. , BENNETT S. J. , BEST J. L.
Published: January 2006

Bed forms were studied in Goodwin Creek and a laboratory flume channel. The bed sediment of the field site and flume had median diameters of 8·3 (modes of 0·4, 22·6 mm) and 1·82 mm (modes of 0·5, 5·6 mm), respectively. The laboratory and field channels had similar values of bimodal parameters, ratios of flow depth to median bed material diameter, and ratios of shear stress to critical shear stress and were judged to be comparable in the transport of bed load sediment and the resulting bed forms. Three groupings of bed forms from the laboratory flume experiments (ripple‐like bed forms, bed load sheets, low‐relief bed waves) were identified using the height and period of the bed forms. For the range of flow depths and discharges investigated in the flume, bed forms became higher and longer with increasing bed shear stress. Bed forms from Goodwin Creek were similar to those from the flume with comparable ratios between bed form length, height, and flow depth. The bed forms in the flume provide a positive link between rate and size fluctuations measured in the field and the bed forms. The smaller bed forms identified were sediment starved and are not considered to be dunes, while the largest bed forms in which all of the bed material sizes were mobilized in the field and laboratory were judged to be dunes.
Reduced inbreeding depression due to historical inbreeding in Drosophila melanogaster: evidence for purging
Authors: Swindell W. R. , Bouzat J. L.
Published: January 2006

An important issue in conservation biology and the study of evolution is the extent to which inbreeding depression can be reduced or reversed by natural selection. If the deleterious recessive alleles causing inbreeding depression can be ‘purged’ by natural selection, outbred populations that have a history of inbreeding are expected to be less susceptible to inbreeding depression. This expectation, however, has not been realized in previous laboratory experiments. In the present study, we used Drosophila melanogaster as a model system to test for an association between inbreeding history and inbreeding depression. We created six ‘purged’ populations from experimental lineages that had been maintained at a population size of 10 male–female pairs for 19 generations. We then measured the inbreeding depression that resulted from one generation of full-sib mating in the purged populations and in the original base population. The magnitude of inbreeding depression in the purged populations was approximately one-third of that observed in the original base population. In contrast to previous laboratory experiments, therefore, we found that inbreeding depression was reduced in populations that have a history of inbreeding. The large purging effects observed in this study may be attributable to the rate of historical inbreeding examined, which was slower than that considered in previous experiments.