bluuebunny/crossref_metadata_2025 huggingface dataset:
Raman spectroscopy of nanocrystalline and amorphous GaN
Authors: Trodahl H. J. , Budde F. , Ruck B. J. , Granville S. , Koo A. , Bittar A.
Published: April 2005

We report Raman measurements on thin films of strongly disordered GaN and GaN:O prepared by ion-assisted deposition. The incident photon energies used in the experiments ranged from 1.95 to 3.8eV, spanning the interband edge. Under subgap excitation the signal resembles the crystalline GaN vibrational density-of-modes, with significant broadening as expected for disordered material. There is a strong resonant behavior at the interband edge of the same mode for which a strong resonance is found in crystalline GaN, with a width suggesting that the entire vibrational branch contributes to the signal. Even nanocrystalline material is found to display Raman spectra characteristic of very short-range (<1n) translational symmetry, in agreement with x-ray diffraction evidence for the random stacking nature of the 3nm diameter crystallites. The presence of oxygen at even 25at.% has only a subtle effect on Raman spectra at the network vibrational frequencies below 800cm−1, but its presence is signaled by the appearance of an oxygen mode at 1000cm−1. An N2 line at 2360cm−1 correlates with a nitrogen excess introduced during growth.
Laminarization of minimal plane Couette flow: Going beyond the basin of attraction of turbulence
Authors: Kawahara Genta
Published: April 2005

Laminarization of minimal plane Couette turbulence is achieved numerically through short-time imposition of weak spanwise system rotation. A laminarization strategy presented in this Letter is inspired by investigation of the phase-space structure in the vicinity of a recently found unstable periodic orbit [G. Kawahara and S. Kida, “Periodic motion embedded in plane Couette turbulence: regeneration cycle and burst,” J. Fluid Mech. 449, 291 (2001)]. The periodic orbit, which a turbulent state occasionally approaches, and its local stable manifold are found to form the separatrix between the basin of attraction of turbulent and laminar flows. The introduction of the slight rotation during its approach to the periodic orbit enables the state to go beyond the basin of attraction of the turbulence toward the laminar flow. The global stabilization of the unstable periodic orbit by the method of controlling chaos is also performed to accomplish the laminarization without waiting until the natural approach.
Low-temperature synthesis of ZnSe nanowires and nanosaws by catalyst-assisted molecular-beam epitaxy
Authors: Colli A. , Hofmann S. , Ferrari A. C. , Ducati C. , Martelli F. , Rubini S. , Cabrini S. , Franciosi A. , Robertson J.
Published: April 2005

Single-crystal ZnSe nanowires are grown on a prepatterned gold catalyst by molecular-beam epitaxy. Optimum selectivity and maximum nanowire densities are obtained for growth temperatures in the range 400–450°C, but gold-assisted growth is demonstrated for temperatures as low as 300°C. This suggests a diffusion process on/through the catalyst particle in the solid state, in contrast to the commonly assumed liquid phase growth models. Straight wires, as thin as 10nm, nucleate together with thicker and saw-like structures. A gold particle is always found at the tip in both cases.
Nd 3 + -doped lead lanthanum zirconate titanate transparent ferroelectric ceramic as a laser material: Energy transfer and stimulated emission
Authors: de Camargo A. S. S. , Botero É. R. , Garcia D. , Eiras J. A. , Nunes L. A. O.
Published: April 2005

An investigation of the spectroscopic characteristics of high optical quality Nd3+-doped lead lanthanum zirconate titanate transparent ferroelectric ceramics was done to evaluate its potentiality as a near-infrared laser active host. Nonradiative losses that could compromise laser action were quantified in terms of the Judd-Ofelt theory, the Dexter model for ion–ion energy transfer and by measuring excited state absorptions. It was verified that under low power 0.8μm diode pumping, ion–ion energy transfers are negligible and the system presents η=0.87. Stimulated emission was observed at 1.06μm (σSE=3.5×10−20cm2) with no influence of ESA transitions.
Field emission from AlN nanorod array
Authors: Tang Y. B. , Cong H. T. , Zhao Z. G. , Cheng H. M.
Published: April 2005

Single-crystalline mushroom-like AlN nanorod array has been synthesized. The AlN nanorods, with diameters of 50–200nm and lengths of several micrometers, are distributed uniformly with density of 107–108rods∕cm2. The field emission measurements show that the turn-on field is 8.8V∕μm at a field emission current density (J) of 10μA∕cm2, and the J (10.31mA∕cm2) fluctuation is as small as 2% within an hour. The relationship between the nanostructure and field emission properties is discussed. The low turn-on field and high current stability demonstrate that the mushroom-like AlN nanorod array is a promising field emission material.
Simultaneous current-, force-, and work-function measurement with atomic resolution
Authors: Herz M. , Schiller Ch. , Giessibl F. J. , Mannhart J.
Published: April 2005

The local work function of a surface determines the spatial decay of the charge density at the Fermi level normal to the surface. Here, we present a method that enables simultaneous measurements of local work-function and tip-sample forces. A combined dynamic scanning tunneling microscope and atomic force microscope is used to measure the tunneling current between an oscillating tip and the sample in real time as a function of the cantilever’s deflection. Atomically resolved work-function measurements on a silicon (111)−(7×7) surface are presented and related to concurrently recorded tunneling current and force measurements.
Electrical conductivity of single CdS nanowire synthesized by aqueous chemical growth
Authors: Long Yunze , Chen Zhaojia , Wang Wenlong , Bai Fenglian , Jin Aizi , Gu Changzhi
Published: April 2005

In this Letter, we report on the temperature-dependent conductivity and current-voltage curve of a single CdS nanowire, which was synthesized by a simple aqueous chemical growth method. A pair of platinum microleads was fabricated on the single CdS nanowire by focused ion-beam deposition. The room-temperature conductivity and the band gap of the single CdS wire are 0.82Ω−1cm−1 and 0.055eV, respectively. When the applied electric field is larger than 1090Vcm−1, the CdS nanowire shows a nonlinear I-V curve at room temperature.
Intermediates in the oxygenation of a nonheme diiron(II) complex, including the first evidence for a bound superoxo species
Authors: Shan Xiaopeng , Que Lawrence
Published: April 2005

The reaction of [Fe
2
(μ-OH)
2
(6-Me
3
-TPA)
2
]
2+
(1) [6-Me
3
-TPA, Tris(6-methyl-2-pyridylmethyl)amine] with O
2
in CH
2
Cl
2
at –80°C gives rise to two new intermediates, 2 and 3, before the formation of previously characterized [Fe
2
(O)(O
2
)(6-Me
3
-TPA)
2
]
2+
(4) that allow the oxygenation reaction to be monitored one electron-transfer step at a time. Raman evidence assigns 2 and 3 as a diiron–superoxo species and a diiron–peroxo species, respectively. Intermediate 2 exhibits its ν(O–O) at 1,310 cm
–1
with a –71-cm
–1
18
O isotope shift. A doublet peak pattern for the
16
O
18
O isotopomer of 2 in mixed-isotope Raman experiments strongly suggests that the superoxide ligand of 2 is bound end-on. This first example of a nonheme iron–superoxo intermediate exhibits the highest frequency ν(O–O) yet observed for a biomimetic metal–dioxygen adduct. The bound superoxide of 2, unlike the bound peroxide of 4, is readily reduced by 2,4-di-
tert
-butylphenol via a proton-coupled electron-transfer mechanism, emphasizing that metal–superoxo species may serve as oxidants in oxygen activation mechanisms of metalloenzymes. The discovery of intermediates 2 and 3 allows us to dissect the initial steps of dioxygen binding at a diiron center leading to its activation for substrate oxidation.
Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites
Authors: Holman Alexander G. , Coffin John M.
Published: April 2005

To investigate retroviral integration targeting on a nucleotide scale, we examined the base frequencies directly surrounding cloned
in vivo
HIV-1, murine leukemia virus, and avian sarcoma/leukosis virus integrations. Base preferences of up to 2-fold the expected frequencies were found for three viruses, representing
P
values down to <10
-100
and defining what appear to be preferred integration sequences. Offset symmetry reflecting the topology of the integration reaction was found for HIV-1 and avian sarcoma/leukosis virus but not murine leukemia virus, suggesting fundamental differences in the way different retroviral integration complexes interact with host-cell DNA.
Differential shuffling of native genetic diversity across introduced regions in a brown alga: Aquaculture vs. maritime traffic effects
Authors: Voisin Marie , Engel Carolyn R. , Viard Frédérique
Published: April 2005

Worldwide marine invaders, such as the brown algaUndaria pinnatifida, offer challenging models for unraveling the apparent paradox of sustainable settlement of exotic species over a large spectrum of environments. Two intergenic noncoding mitochondrial loci were found to be highly informative at the within-species level. Twenty-five haplotypes were found over the whole dataset (333 base pairs, 524 individuals, and 24 populations). The native range showed striking population genetic structure stemming from low diversity within and high differentiation among populations, a pattern not observed in the introduced range of this seaweed. Contrary to classical expectations of founding effects associated with accidental introduction of exotic species, most of the introduced populations showed high genetic diversity. At the regional scale, genetic diversity and sequence divergence showed contrasting patterns in the two main areas of introduction (Europe and Australasia), suggesting different processes of introduction in the two regions. Gene genealogy analyses point to aquaculture as a major vector of introduction and spread in Europe but implicate maritime traffic in promoting recurrent migration events from the native range to Australasia. The multiplicity of processes and genetic signatures associated with the successful invasion confirms that multiple facets of global change, e.g., aquaculture practices, alteration of habitats, and increased traffic, act in synergy at the worldwide level, facilitating successful pandemic introductions.
A latent consolidation phase in auditory identification learning: Time in the awake state is sufficient
Authors: Roth Daphne Ari-Even , Kishon-Rabin Liat , Hildesheimer Minka , Karni Avi
Published: April 2005

Large gains in performance, evolving hours after practice has terminated, were reported in a number of visual and some motor learning tasks, as well as recently in an auditory nonverbal discrimination task. It was proposed that these gains reflect a latent phase of experience-triggered memory consolidation in human skill learning. It is not clear, however, whether and when delayed gains in performance evolve following training in an auditory verbal identification task. Here we show that normal-hearing young adults trained to identify consonant–vowel stimuli in increasing levels of background noise showed significant, robust, delayed gains in performance that became effective not earlier than 4 h post-training, with most participants improving at more than 6 h post-training. These gains were retained for over 6 mo. Moreover, although it has been recently argued that time including sleep, rather than time per se, is necessary for the evolution of delayed gains in human perceptual learning, our results show that 12 h post-training in the waking state were as effective as 12 h, including no less than 6 h night's sleep. Altogether, the results indicate, for the first time, the existence of a latent, hours-long, consolidation phase in a human auditory verbal learning task, which occurs even during the awake state.
An MT1-MMP-PDGF receptor-β axis regulates mural cell investment of the microvasculature
Authors: Lehti Kaisa , Allen Edward , Birkedal-Hansen Henning , Holmbeck Kenn , Miyake Yasuhiro , Chun Tae-Hwa , Weiss Stephen J.
Published: April 2005

Platelet-derived growth factor (PDGF)/PDGFRβ-dependent investment of the vascular endothelium by mural cells (i.e., pericytes and vascular smooth muscle cells; VSMCs) is critical for normal vessel wall structure and function. In the developing vasculature, mural cell recruitment is associated with the functionally undefined expression of the type I transmembrane proteinase, membrane-type 1 matrix metalloproteinase (MT1-MMP). In this paper, using VSMCs and tissues isolated from gene-targeted mice, we identify MT1-MMP as a PDGF-B-selective regulator of PDGFRβ-dependent signal transduction and mural cell function. In VSMCs, catalytically active MT1-MMP associates with PDGFRβ in membrane complexes that support the efficient induction of mitogenic signaling by PDGF-B in a matrix metalloproteinase inhibitor-sensitive fashion. In contrast, MT1-MMP-deficient VSMCs display PDGF-B-selective defects in chemotaxis and proliferation as well as ERK1/2 and Akt activation that can be rescued in tandem fashion following retroviral transduction with the wild-type protease. Consistent with these in vitro findings, MT1-MMP-deficient brain tissues display a marked reduction in mural cell density as well as abnormal vessel wall morphology similar to that reported in mice expressing PDGF-B or PDGFRβ hypomorphic alleles. Together, these data identify MT1-MMP as a novel proteolytic modifier of PDGF-B/PDGFRβ signal transduction that cooperatively regulates vessel wall architecture in vivo.
Ddb1 controls genome stability and meiosis in fission yeast
Authors: Holmberg Christian , Fleck Oliver , Hansen Heidi A. , Liu Cong , Slaaby Rita , Carr Antony M. , Nielsen Olaf
Published: April 2005

The human UV-damaged DNA-binding protein Ddb1 associates with cullin 4 ubiquitin ligases implicated in nucleotide excision repair (NER). These complexes also contain the signalosome (CSN), but NER-relevant ubiquitination targets have not yet been identified. We report that fission yeast Ddb1, Cullin 4 (Pcu4), and CSN subunits Csn1 and Csn2 are required for degradation of the ribonucleotide reductase (RNR) inhibitor protein Spd1. Ddb1-deficient cells have >20-fold increased spontaneous mutation rate. This is partly dependent on the error-prone translesion DNA polymerases. Spd1 deletion substantially reduced the mutation rate, suggesting that insufficient RNR activity accounts for ∼50% of observed mutations. Epistasis analysis indicated that Ddb1 contributed to mutation avoidance and tolerance to DNA damage in a pathway distinct from NER. Finally, we show that Ddb1/Csn1/Cullin 4-mediated Spd1 degradation becomes essential when cells differentiate into meiosis. These results suggest that Ddb1, along with Cullin 4 and the signalosome, constitute a major pathway controlling genome stability, repair, and differentiation via RNR regulation.
ECgene: Genome-based EST clustering and gene modeling for alternative splicing
Authors: Kim Namshin , Shin Seokmin , Lee Sanghyuk
Published: April 2005

With the availability of the human genome map and fast algorithms for sequence alignment, genome-basedESTclustering became a viable method for gene modeling. We developed a novel gene-modeling method, ECgene (Gene modeling by EST Clustering), which combines genome-based EST clustering and the transcript assembly procedure in a coherent and consistent fashion. Specifically, ECgene takes alternative splicing events into consideration. The position of splice sites (i.e., exon–intron boundaries) in the genome map is utilized as the critical information in the whole procedure. Sequences that share any splice sites are grouped together to define an EST cluster in a manner similar to that of the genome-based version of the UniGene algorithm. Transcript assembly is achieved using graph theory that represents the exon connectivity in each cluster as a directed acyclic graph (DAG). Distinct paths along exons correspond to possible gene models encompassing all alternative splicing events. EST sequences in each cluster are subclustered further according to the compatibility with gene structure of each splice variant, and they can be regarded as clone evidence for the corresponding isoform. The reliability of each isoform is assessed from the nature of cluster members and from the minimum number of clones required to reconstruct all exons in the transcript.
Comparing low coverage random shotgun sequence data fromBrassica oleraceaandOryza sativagenome sequence for their ability to add to the annotation ofArabidopsis thaliana
Authors: Katari Manpreet S. , Balija Vivekanand , Wilson Richard K. , Martienssen Robert A. , McCombie W. Richard
Published: April 2005

Since the completion of theArabidopsis thalianagenome sequence, there is an ongoing effort to annotate the genome as accurately as possible. Comparing genome sequences of related species complements the current annotation strategies by identifying genes and improving gene structure. A total of 595,321Brassica oleraceashotgun reads were sequenced by TIGR (The Institute for Genome Research) and the collaboration of Washington University and Cold Spring Harbor. Vicogenta (a genome viewer based on GMOD and GBrowse) was created to view the current annotation and sequence alignments forArabidopsis. Brassicareads were compared with theArabidopsisgenome and proteome databases using BLAST. Hypothetical genes and conserved unannotated regions on the short arm of chromosome 4 fromArabidopsiswere experimentally verified using RT–PCR. We were able to improve theArabidopsisannotation by identifying 25 genes that were missed, and confirming expression of 43 hypothetical genes inArabidopsis. We were also able to detect conservation in genes whose transcription is normally suppressed due to methylation. We also examined how useful theO. sativagenome and ESTs from other species are, compared withBrassica, in improving theArabidopsisannotation.
Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions
Authors: Wei Chaochun , Lamesch Philippe , Arumugam Manimozhiyan , Rosenberg Jennifer , Hu Ping , Vidal Marc , Brent Michael R.
Published: April 2005

The genome of Caenorhabditis elegans was the first animal genome to be sequenced. Although considerable effort has been devoted to annotating it, the standard WormBase annotation contains thousands of predicted genes for which there is no cDNA or EST evidence. We hypothesized that a more complete experimental annotation could be obtained by creating a more accurate gene-prediction program and then amplifying and sequencing predicted genes. Our approach was to adapt the TWINSCAN gene prediction system to C. elegans and C. briggsae and to improve its splice site and intron-length models. The resulting system has 60% sensitivity and 58% specificity in exact prediction of open reading frames (ORFs), and hence, proteins–the best results we are aware of any multicellular organism. We then attempted to amplify, clone, and sequence 265 TWINSCAN-predicted ORFs that did not overlap WormBase gene annotations. The success rate was 55%, adding 146 genes that were completely absent from WormBase to the ORF clone collection (ORFeome). The same procedure had a 7% success rate on 90 Worm Base “predicted” genes that do not overlap TWINSCAN predictions. These results indicate that the accuracy of WormBase could be significantly increased by replacing its partially curated predicted genes with TWINSCAN predictions. The technology described in this study will continue to drive the C. elegans ORFeome toward completion and contribute to the annotation of the three Caenorhabditis species currently being sequenced. The results also suggest that this technology can significantly improve our knowledge of the “parts list” for even the best-studied model organisms.
Comparative genome analyses of Arabidopsis spp.: Inferring chromosomal rearrangement events in the evolutionary history of A. thaliana
Authors: Yogeeswaran Krithika , Frary Amy , York Thomas L. , Amenta Alison , Lesser Andrew H. , Nasrallah June B. , Tanksley Steven D. , Nasrallah Mikhail E.
Published: April 2005

Comparative genome analysis is a powerful tool that can facilitate the reconstruction of the evolutionary history of the genomes of modern-day species. The model plant Arabidopsis thaliana with its n = 5 genome is thought to be derived from an ancestral n = 8 genome. Pairwise comparative genome analyses of A. thaliana with polyploid and diploid Brassicaceae species have suggested that rapid genome evolution, manifested by chromosomal rearrangements and duplications, characterizes the polyploid, but not the diploid, lineages of this family. In this study, we constructed a low-density genetic linkage map of Arabidopsis lyrata ssp. lyrata (A. l. lyrata; n = 8, diploid), the closest known relative of A. thaliana (MRCA ∼5 Mya), using A. thaliana-specific markers that resolve into the expected eight linkage groups. We then performed comparative Bayesian analyses using raw mapping data from this study and from a Capsella study to infer the number and nature of rearrangements that distinguish the n = 8 genomes of A. l. lyrata and Capsella from the n = 5 genome of A. thaliana. We conclude that there is strong statistical support in favor of the parsimony scenarios of 10 major chromosomal rearrangements separating these n = 8 genomes from A. thaliana. These chromosomal rearrangement events contribute to a rate of chromosomal evolution higher than previously reported in this lineage. We infer that at least seven of these events, common to both sets of data, are responsible for the change in karyotype and underlie genome reduction in A. thaliana.
CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models
Authors: Kurata Hiroyuki , Masaki Kouichi , Sumida Yoshiyuki , Iwasaki Rei
Published: April 2005

We have developed the CADLIVE (Computer-Aided Design of LIVing systEms) Simulator that provided a rule-based automatic way to convert biochemical network maps into dynamic models, which enables simulating their dynamics without going through all of the reactions down to the details of exact kinetic parameters. The simulator supports the biochemical reaction maps that are generated by the previously developed GUI editor. Notice that the part of the GUI editor had been previously published, but, as yet, not the simulator. To directly link biochemical network maps to dynamic simulation, we have created the strategy of three layers and two stages with the efficient conversion rules in an XML representation. This strategy divides a molecular network into three layers, i.e., gene, protein, and metabolic layers, and partitions the conversion process into two stages. Once a biochemical map is provided, CADLIVE automatically builds a mathematical model, thereby facilitating one to simulate and analyze it. In order to demonstrate the feasibility of CADLIVE, we analyzed theEscherichia colinitrogen-assimilation system (64 equations with 64 variables) that consists of multiple and complicated negative and positive feedback loops. CADLIVE predicted that theglnKgene is responsible for hysteresis or reversibility of nitrogen-related (Ntr) gene expression with respect to the ammonia concentration, supporting the experimental observation of the runaway expression of theNtrgenes.
Olfactory blocking and odorant similarity in the honeybee
Authors: Guerrieri Fernando , Lachnit Harald , Gerber Bertram , Giurfa Martin
Published: April 2005

Blocking occurs when previous training with a stimulus A reduces (blocks)
subsequent learning about a stimulus B, when A and B are trained in compound.
The question of whether blocking exists in olfactory conditioning of proboscis
extension reflex (PER) in honeybees is under debate. The last published
accounts on blocking in honeybees state that blocking occurs when odors A and
B are similar (the “similarity hypothesis”). We have tested this
hypothesis using four odors (1-octanol, 1-nonanol, eugenol, and limonene)
chosen on the basis of their chemical and physiological similarity (experiment
1). We established a generalization matrix that measured perceptual
similarity. Bees in the “block group” were first trained with an
odor A and, in the second phase, with the mixture AB. Bees in the “novel
group” (control group) were first trained with an odor N and, in the
second phase, with the mixture AB. After conditioning, bees in both groups
were tested for their response to B. We assayed all 24 possible combinations
for the four odors standing for A, B, and N. We found blocking in four cases,
augmentation in two cases, and no difference in 18 cases; odor similarity
could not account for these results. We also repeated the experiments with
those six odor combinations that gave rise to the similarity hypothesis
(experiment 2: 1-hexanol, 1-octanol, geraniol) and found augmentation in one
and no effect in five cases. Thus, blocking is not a consistent phenomenon,
nor does it depend on odor similarity.
Transgenic mice expressing a truncated form of CREB-binding protein (CBP) exhibit deficits in hippocampal synaptic plasticity and memory storage
Authors: Wood Marcelo A. , Kaplan Michael P. , Park Alice , Blanchard Edward J. , Oliveira Ana M.M. , Lombardi Thomas L. , Abel Ted
Published: April 2005

Deletions, translocations, or point mutations in the CREB-binding protein (CBP) gene have been associated with Rubinstein-Taybi Syndrome; a human developmental disorder characterized by retarded growth and reduced mental function. To examine the role of CBP in memory, transgenic mice were generated in which the CaMKIIα promoter drives expression of an inhibitory truncated CBP protein in forebrain neurons. Examination of hippocampal long-term potentiation (LTP), a form of synaptic plasticity thought to underlie memory storage, revealed significantly reduced late-phase LTP induced by dopamine-regulated potentiation in hippocampal slices from CBP transgenic mice. However, four-train induced late-phase LTP is normal. Behaviorally, CBP transgenic mice exhibited memory deficits in spatial learning in the Morris water maze and deficits in long-term memory for contextual fear conditioning, two hippocampus-dependent tasks. Together, these results demonstrate that CBP is involved in specific forms of hippocampal synaptic plasticity and hippocampus-dependent long-term memory formation.
Unfolding of Green Fluorescent Protein mut2 in wet nanoporous silica gels
Authors: Campanini Barbara , Bologna Sara , Cannone Fabio , Chirico Giuseppe , Mozzarelli Andrea , Bettati Stefano
Published: April 2005

Many of the effects exerted on protein structure, stability, and dynamics by molecular crowding and confinement in the cellular environment can be mimicked by encapsulation in polymeric matrices. We have compared the stability and unfolding kinetics of a highly fluorescent mutant of Green Fluorescent Protein, GFPmut2, in solution and in wet, nanoporous silica gels. In the absence of denaturant, encapsulation does not induce any observable change in the circular dichroism and fluorescence emission spectra of GFPmut2. In solution, the unfolding induced by guanidinium chloride is well described by a thermodynamic and kinetic two‐state process. In the gel, biphasic unfolding kinetics reveal that at least two alternative conformations of the native protein are significantly populated. The relative rates for the unfolding of each conformer differ by almost two orders of magnitude. The slower rate, once extrapolated to native solvent conditions, superimposes to that of the single unfolding phase observed in solution. Differences in the dependence on denaturant concentration are consistent with restrictions opposed by the gel to possibly expanded transition states and to the conformational entropy of the denatured ensemble. The observed behavior highlights the significance of investigating protein function and stability in different environments to uncover structural and dynamic properties that can escape detection in dilute solution, but might be relevant for proteins in vivo.
The P5 protein from bacteriophage phi‐6 is a distant homolog of lytic transglycosylases
Authors: Pei Jimin , Grishin Nick V.
Published: April 2005

Peptidases are classical objects of enzymology and structural studies. However, a few protein families with experimentally characterized proteolytic activity, but unknown catalytic mechanism and three‐dimensional structures, still exist. Using comparative sequence analysis, we deduce spatial structure for one of such families, namely, U40, which contains just one P5 protein from bacteriophage phi‐6. We show that this singleton sequence possesses conserved sequence motifs characteristic of lysozymes and is a distant homolog of lytic transglycosylases that cleave bacterial peptidoglycan. The structure of the P5 protein is therefore predicted to adopt the lysozyme‐like fold shared by T4, λ, C‐type, G‐type lysozymes, and lytic transglycosylases. Since previous biochemical experiments with P5 of phi‐6 have indicated that the purified enzyme possesses endopeptidase activity and not glycosidase activity, our results point to the possibility of a newly evolved molecular function and call for further experimental characterization of this unusual P5 protein.
Characterization of the HslU chaperone affinity for HslV protease
Authors: Azim M. Kamran , Goehring Walter , Song Hyun Kyu , Ramachandran Ravishankar , Bochtler Matthias , Goettig Peter
Published: April 2005

The HslVU complex is a bacterial two‐component ATP‐dependent protease, consisting of HslU chaperone and HslV peptidase. Investigation of protein–protein interactions using SPR in Escherichia coli HslVU and the protein substrates demonstrates that HslU and HslV have moderate affinity (Kd = 1 μM) for each other. However, the affinity of HslU for HslV fivefold increased (Kd ∼0.2 μM) after binding with the MBP∼SulA protein indicating the formation of a “ternary complex” of HslV–HslU–MBP∼SulA. The molecular interaction studies also revealed that HslU strongly binds to MBP∼SulA with 10−9 M affinity but does not associate with nonstructured casein. Conversely, HslV does not interact with the MBP–SulA whereas it strongly binds with casein (Kd = 0.2 μM) requiring an intact active site of HslV. These findings provide evidence for “substrate‐induced” stable HslVU complex formation. Presumably, the binding of HslU to MBP∼SulA stimulates a conformational change in HslU to a high‐affinity form for HslV.
Comparisons between the age structures, growth and reproductive biology of two co‐occurring sillaginids, Sillago robusta and S. bassensis, in temperate coastal waters of Australia
Authors: Hyndes G. A. , Potter I. C.
Published: April 2005

Sillago robusta and S. bassensis occupy the open sandy areas of the deeper waters (20–35 m) of the inner continental shelf of the lower west coast of Australia. Comparisons were made of their age and size compositions, growth rates, ages and sizes at first maturity, and spawning times. Most S. robusta were less than 3 years old (maximum 7 years), while S. bassensis often reached 7 years of age (maximum 10 years). The maximum length of S. robusta (200 mm) was far shorter than S. bassensis (328 mm), whereas the reverse pertained for the von Bertalanffy growth coeffcient (K), i.e. c. 1.0 v. c. 0.3. Differences in K reflect the fact that c. 80% of the asymptotic length is achieved by S. robusta after 2 years, but not until 6 years of age by S. bassensis. Sexual maturity was reached by up to 50% of S. robusta at the end of their first year of life, and by almost all fish at the end of their second year of life. Most S. bassensis did not reach maturity until the end of their third year of life. In both species, those individuals that reached maturity early, were significantly longer than those that did not reach maturity at the same age. The gonadosomatic indices and proportions of mature gonads, and the numbers of vitellogenic and hydrated oocytes and post‐ovulatory follicles, were relatively high in ovaries of both species between December and March. Although both species spawn in these 4 months, some S. bassensis also spawn between September and November and in March and April. In the middle of the spawning period, the ovaries of S. robusta and S. bassensis frequently contained oocytes that ranged widely in size and development, together with post‐ovulatory follicles, suggesting that both species are multiple spawners. Juveniles of S. robusta remain in the deeper waters of the inner continental shelf, whereas those of S. bassensis migrate inshore to their nursery areas in surf zones. As S. robusta reaches sexual maturity at an earlier age and smaller size than S. bassensis, it is probably more advantageous for the juveniles of this species to remain in deeper water, and thereby conserve energy for gonadal maturation, rather than migrating into shallow waters for only a very few months.
Ultrastructure of the glandular epidermis on the fins of male estuarine triplefins Forsterygion nigripenne
Authors: Northcott S. J. , James M. A.
Published: April 2005

Male estuarine triplefins Forsterygion nigripenne develop enlarged fin tips during the breeding season. Using light microscopy and scanning and transmission electron microscopy the fins of males and females were compared. Tall columnar cells proliferated in the fin epidermis of males but were absent in females. The columnar cells were packed with proteinaceous granules that were bound by a double membrane. Three stages of development of columnar cells could be distinguished; the most mature expanded and ruptured to release its content. The function of the glandular epidermis is unknown but behavioural observations suggested that the secretion was applied to the egg mass and thus may protect it from infection.
Piscine predation on juvenile fishes on a Scottish sandy beach
Authors: Gibson R. N. , Robb L.
Published: April 2005

Predation by larger fishes is a major cause of mortality for the populations of juvenile fishes on a sandy beach on the west coast of Scotland. Predation was concentrated on the most numerous species (0‐group Pleuronectes platessa) in June but with the decline in numbers and growth in size of this species, the fish predators had changed their diet in August to feed principally on small sandeels (Ammodytidae). Six major predatory species had taken 95 per cent of all fish found in predators' stomachs and could be roughly divided into three categories according to their piscivorous tendencies and their abundance. (1) Common species in which fishes formed the main item of their diet (Gadus morhua). (2) Species in which fishes formed only a relatively minor constituent of the diet but which, by virtue of their abundance, potentially had a significant predatory impact (I‐group P. platessa). (3) less abundant species whose diet consisted principally of fishes. The intensity of predation was generally greatest at night for G. morhua but during the day for I‐group P. platessa. The distributions and movements of the dominant prey species can be interpreted in the light of their predator‐prey relationships. The most common benthic species, 0‐group P. platessa, move off ‐and onshore with the ebb and flow of the tides and concentrate in shallow water at night. Such movements would have the effect of maintaining the majority of the population in depths where predation pressure from nocturnally onshore‐migrating gadoids and other predators is likely to be minimized.
Annual changes in the nutritive state of North Sea dab
Authors: Saborowski R. , Buchholz F.
Published: April 2005

The nutritive state of dab Limanda limanda was investigated over a 2‐year period at a fixed sampling site northwest of Helgoland (German Bight, North Sea), with respect to feeding habits and the accumulation of biochemical storage products. Ophiuroids formed the main weight of food organisms (50%) while polychaetes (10%), molluscs and crustaceans (<5% each) were less frequent. Feeding activity in males varied between summer and winter, while females fed more constantly. The condition factor and the hepatosomatic index showed characteristic seasonal cycles in both sexes. The glycogen content in the liver reached 40–60 mg g−1 FW in summer and fell to about 10–20 mg g−1 FW in late winter. Total lipids of the liver showed a distinct seasonal cycle with 400 mg g−1 FW in summer and a minimum of 50–100 mg g−1 FW in spring. The lipid content of the muscle ranged from 5 to 6 mg g−1 FW and did not vary significantly between seasons.
Prophylactic treatment of viral diseases in fish using native RNA linked to soluble and corpuscular carriers
Authors: Alikin Yu. S. , Shchelkunov I. S. , Shchelkunova T. I. , Kupinskaya O. A. , Masycheva V. I. , Klimenko V. P. , Fadina V. A.
Published: April 2005

The potential of double‐ (ds) and single‐stranded (ss) yeast RNA preparations for protection of carp Cyprinus carpio against experimental infection with Rhabdovirus carpio, the infectious agent of spring viraemia of carp, was studied. Prophylactic intraperitoneal injection of fish with dsRNA proved efficient while ssRNA had a much smaller effect. The protective effect of yeast dsRNA in 1‐year‐old carp lasted for at least 3 weeks. The efficacy of the preparations decreased considerably if they were administered by the bath method. Both insoluble and soluble carriers for dsRNA were studied to increase the preparation efficacy. Screening of the preparations revealed the importance of DEAE‐groups on the carriers. Their biological efficiency is confirmed by the method of phagocytosis of the mouse peritoneal macrophages.
Feeding and growth of juvenile sea bass: the effect of ration and temperature on growth rate and efficiency
Authors: Russell N. R. , Fish J. D. , Wootton R. J.
Published: April 2005

The effect of ration on the growth of pairs of juvenile sea bass Dicentrarchus labrax fed squid mantle was recorded at four temperatures: 6, 10, 14 and 18) C, covering the range typical of Welsh coastal waters. Initial weight of the fish ranged from 2.8 to 15.9 g. A predictive model for the maximum meal size (Mmax) at temperatures between 10 and 18) C, accounted for 95% of the variance in lnMmax. Even when offered excess food, bass at 6) C had a low rate of food consumption [0.19% body weight (BW) day−1] and lost weight (G=−0.04% day−1). Predictive regression models for specific growth rate (G) accounted for 86% of the variance at reduced rations and 70% at maximum meals. The relationship between G (calculated for total biomass per tank) and ration was a decelerating curve. G at maximum meals increased with temperature, at lower rations G decreased with temperature. For a pair of bass with a combined weight of 15 g, predicted maintenance ration ranged between 0.7 and 2.3% BW day−1 and increased with temperature. Maximum meal size was more sensitive to temperature than maintenance ration. At 18) C optimum ration was 7.4% BW day−1. At lower temperatures, the optimum ration was the maximum meal. The maximum gross growth efficiency was 17.4% at 18) C. Mean absorption efficiency was 94.8%. Ration level had no significant effect on absorption efficiency, which was lowest at 6) C. Condition indices (Fulton condition factor, wet and dry liver—somatic indices and body depth index) increased with meal size at all temperatures except 6) C. An increase in temperature between 10 and 18) C generally resulted in a decrease in condition indices at a given ration. When comparisons were made at a given standard length, gut and carcass weight increased with ration. Visceral fat and gut weight decreased with increased temperature.
Primary and secondary stress responses to line capture in the blue mao mao
Authors: Lowe T. E. , Wells R. M. G.
Published: April 2005

Primary and secondary stress responses were measured in wild Scorpis violaceus subjected to burst swimming from angling. Fish were blood sampled from 20 s to 30 min after hooking. Consequent rises in plasma adrenaline (14–316 nmol l−1), noradrenaline (25–345 nmol l−1), and cortisol (0.4–197 ng ml−1) correlated with time since capture, and plasma lactate (0.1–12.2 mmol l−1) reflected work done during intense exercise. Haemoglobin concentration and haematocrit also increased with exercise, and erythrocyte swelling occurred. Wild S. violaceus demonstrated a spontaneity and intensity of exercise not seen in fish acclimatized to aquarium conditions. By contrast, the stress responses of fish in captivity, despite careful husbandry, differed qualitatively and quantitatively from those in the wild. Cannulated fish had higher resting plasma cortisol concentrations (61.9±9.5 ng ml−1) than did rapidly caught wild fish (<5 ng ml−1) and these values were not significantly changed with burst swimming. Catecholamine secretion, possibly suppressed by cortisol, was insufficient to cause erythrocyte swelling. Erythrocyte nucleotides do not play a role in exercise, but are elevated in captive fish. It is hypothesized that primary endocrine responses are triggered by higher cortical processing of sensory information which is fundamentally different in the natural environment.
Population structure of Gobius bucchichii, in a Mediterranean marine reserve and in an unprotected area
Authors: Sasal P. , Faliex E. , Morand S.
Published: April 2005

Gobius bucchichii, in a protected area lived longer than those outside the reserve. Our findings emphasize the cryptic role played by marine protected areas on ecosystems.
Pavement cell ultrastructural differences on Hoplias malabaricus, gill epithelia
Authors: Moron S. E. , Fernandes M. N.
Published: April 2005

Pavement cells from the leading and trailing edges of the gill filament of Hoplias malabaricus, exhibit a complex system of microridges, a long tight junction and a large number of desmosomes. Pavement cells from the secondary lamellae are smooth surfaced with clearly defined cell boundaries by a circular microridge. The junctional complex of these cells is short and it is characterized by an intense interdigitation between cells.
Observations on the agonistic behaviour of Lepadogaster lepadogaster purpurea (Pisces: Gobiesocidae)
Authors: Gonçlalves E. J. , Almada V. C. , Almeida S. P. , Gonçlalves D. M. , Repas M. , Simões N.
Published: April 2005

Agonistic behaviour of captive Lepadogaster lepadogaster purpurea, was described, forming the first record of such behaviour in the family Gobiesocidae. Both male and female engaged in similar behaviours. The agonistic interactions were related mainly to the control of shelter sites and larger fish tended to chase away and take over the shelter of smaller fish.
A comparison of food capture and ingestion in juveniles of two flatfish species, Pleuronectes platessa and Limanda limanda (Teleostei: Pleuronectiformes)
Authors: Bels V. L. , Davenport J.
Published: April 2005

Juvenile plaice, Pleuronectes platessa (n=6, 151–197 mm SL) and dab Limanda limanda (n=6, 119–180.5 mm SL) feeding on pieces of mussel flesh were studied by high‐speed (200 fields s−1) videophotography at 11) C. Prey capture cycles (involving jaw protrusion and opercular expansion) were described in both species. The capture cycle was followed by at least one cycle (similar to the capture cycle in all respects except food intake) which is believed to transport food to the oesophagus. The transport cycle (or cycles) was followed by a species‐specific number of normal respiratory cycles (7 or 8 in plaice, 11 or 12 in dab) and a final single cycle when food debris was violently ejected from the opercular cavity. The respiratory cycles and ejection cycle cleansed the orobranchial/opercular cavities and gills. Differences between the species were relatively minor, but plaice captured and transported food more quickly than dab.
The spermatogenetic process in Barbus longiceps, Capoeta damascina and their natural sterile hybrid (Teleostei, Cyprinidae)
Authors: Th. Stoumboudi M. , Abraham M.
Published: April 2005

Testicular ultrastructure was studied in Barbus longiceps, Capoeta damascina and their natural hybrid. The testes of these teleosts belong to the unrestricted or lobular type. Germ cell morphology is similar in the parental males. In the hybrid, spermatogenesis does not extend beyond the pachytene of the first meiotic division, probably due to the unsuccessful pairing of the homologous chromosomes. Hybrid testes are occupied mainly by degenerating primary spermatocytes, at the leptotene and pachytene stages. In both parents and the hybrid, Sertoli and Leydig cells are characterized by the presence of granular endoplasmic reticulum and of mitochondria with tubular cristae. Due to the arrest of spermatogenesis, the male germ cell protective barrier is absent in the hybrid. Germ cell nuclear size was measured by a computerized analysis system, using light‐microscopy images. In the parents and the hybrid, germ cells attain a uniform inter‐individual nuclear size when they reach the first meiotic prophase. The nuclear size of primary spermatocytes is similar among the three groups of fish, possibly reflecting their close genetic relationship.
A new species‐specific nuclear DNA marker for identification of hybrids between Atlantic salmon and brown trout
Authors: Gross R. , Nilsson J. , Schmitz M.
Published: April 2005

The banding pattern of Alu I‐digested prepro‐gonadotropin releasing hormone gene is species‐specific in Atlantic salmon and brown trout and can be applied for identification of their hybrids.
Contractile properties and the inheritance of myosin heavy chains in Oreochromis species with different temperature tolerances
Authors: Crockford T. , Johnston I. A. , McAndrew B. J. , Mutungi G.
Published: April 2005

Fast muscle fibres from Oreochromis andersonii generated higher isometric stresses at low temperature than fibres from O. niloticus, a less cold‐tolerant species. Hybrid fish showed codominant expression of myosin heavy chain sub‐units but the force generating characteristics of fibres resembled those of the O. niloticus phenotype.
Female reproductive biology of the sand smelt in brackish lagoons of southern France
Authors: Tomasini J. A. , Collart D. , Quignard J. P.
Published: April 2005

The breeding season of Atherina boyeri living in the brackish lagoons of Mauguio, Pérols and Méjean (Hérault, southern France) was very protracted (February‐September). The peak of the reproductive effort occurred in April, May and June. Larger fishes started spawning earlier, and stopped later, than smaller ones. Batch fecundity varied from 4 to 447 oocytes and was positively related to female length and weight. Monthly mean fecundity increased at the beginning of the breeding season and decreased between June and July. Individual mean oocyte diameter ranged from 1.34 to 1.94 mm and was not related to fish length. Monthly mean oocyte size declined throughout the breeding season as water temperature rose. There was no trade‐off between number and egg size. The strategy of these sand smelts seemed well adapted to ensure spawning success without endangering their survival. The highest reproductive effort period occurred in such a way that environmental conditions were suitable to the best survival and growth of hatched larvae. When breeding ceased, fishes, particularly the youngest ones, had enough time to improve their condition before overwintering.