bluuebunny/crossref_metadata_2025 huggingface dataset:
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization
Authors: Chen Hung-I Harry , Hsu Fang-Han , Jiang Yuan , Tsai Mong-Hsun , Yang Pan-Chyr , Meltzer Paul S. , Chuang Eric Y. , Chen Yidong
Published: July 2008

Motivation: Genomic instability is one of the fundamental factors in tumorigenesis and tumor progression. Many studies have shown that copy-number abnormalities at the DNA level are important in the pathogenesis of cancer. Array comparative genomic hybridization (aCGH), developed based on expression microarray technology, can reveal the chromosomal aberrations in segmental copies at a high resolution. However, due to the nature of aCGH, many standard expression data processing tools, such as data normalization, often fail to yield satisfactory results.

Results: We demonstrated a novel aCGH normalization algorithm, which provides an accurate aCGH data normalization by utilizing the dependency of neighboring probe measurements in aCGH experiments. To facilitate the study, we have developed a hidden Markov model (HMM) to simulate a series of aCGH experiments with random DNA copy number alterations that are used to validate the performance of our normalization. In addition, we applied the proposed normalization algorithm to an aCGH study of lung cancer cell lines. By using the proposed algorithm, data quality and the reliability of experimental results are significantly improved, and the distinct patterns of DNA copy number alternations are observed among those lung cancer cell lines.

Contact:  chuangey@ntu.edu.tw

Supplementary information: Source codes and.gures may be found at http://ntumaps.cgm.ntu.edu.tw/aCGH_supplementary
TRITON: a graphical tool for ligand-binding protein engineering
Authors: Prokop Martin , Adam Jan , Kříž Zdeněk , Wimmerová Michaela , Koča Jaroslav
Published: July 2008

Summary: The new version of the TRITON program provides user-friendly graphical tools for modeling protein mutants using the external program MODELLER and for docking ligands into the mutants using the external program AutoDock. TRITON can now be used to design ligand-binding proteins, to study protein–ligand binding mechanisms or simply to dock any ligand to a protein.

Availability: Executable files of TRITON are available free of charge for academic users at http://ncbr.chemi.muni.cz/triton/

Contact: triton@chemi.muni.cz

Supplementary information: Supplementary data are available at Bioinformatics online.
A new modeling method in feature construction for the HSQC spectra screening problem
Authors: Arai Hiromi , Watanabe Satoru , Kigawa Takanori , Yamamura Masayuki
Published: July 2008

Motivation: Large-scale biological analyses produce huge amounts of data. As a consequence, automation in the data analysis process is needed. Sample screening problems in NMR high-throughput protein structure analysis are the typical examples. Especially, screening by protein 1H−15N heteronuclear single quantum coherence (HSQC) spectra must be done quantitatively by a human expert. One popular solution for this problem is data mining. Machine learning methods can automatically extract rules and achieve high accuracy in prediction when a good quality training dataset is prepared. However, they tend to be a black box and the learned machines suffer the risk of overfitting to the dataset.

Results: We propose a model which evaluates HSQC spectra for feature construction. The model calculates similarity between the measured chemical shifts and those of a random coil peak model. We applied our feature construction method for the machine learning discrimination of folded protein HSQC spectra from unfolded ones, and compared our model-based features with those of conventional sequence-based features and image recognition features. The results revealed that our method has sufficient discrimination power and less overfits on training data, as compared to the other methods. In addition, our method succeeded reduction of input data complexity towards further investigation.

Contact:  arai@es.dis.titech.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bioimage informatics: a new area of engineering biology
Authors: Peng Hanchuan
Published: July 2008

In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community. There has been an increasing focus on developing novel image processing, data mining, database and visualization techniques to extract, compare, search and manage the biological knowledge in these data-intensive problems. This emerging new area of bioinformatics can be called ‘bioimage informatics’. This article reviews the advances of this field from several aspects, including applications, key techniques, available tools and resources. Application examples such as high-throughput/high-content phenotyping and atlas building for model organisms demonstrate the importance of bioimage informatics. The essential techniques to the success of these applications, such as bioimage feature identification, segmentation and tracking, registration, annotation, mining, image data management and visualization, are further summarized, along with a brief overview of the available bioimage databases, analysis tools and other resources.

Contact:  pengh@janelia.hhmi.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Two Cheers for Discrimination: Deregulation and Efficiency in the Reform of U.S. Freight Transportation, 1976–1998
Authors: Levinson Marc
Published: July 2008

Nondiscrimination was the bedrock of U.S. transport regulation for nearly a century. The Interstate Commerce Act of 1887, the federal government's first major regulatory initiative, barred “unreasonable discrimination” in rates and service to keep railroads from aiding one businesses or community over another. As regulation developed, similar obligations were imposed on ship lines, truck lines, and air carriers. Most freight transportation companies were forced to operate as “common carriers,” publishing a rate applicable to each commodity and applying that rate to every shipment. Equal treatment of all customers, based strictly on posted prices and terms of service, was widely considered essential to keeping the transportation market “fair.”
Nonlinear Euler buckling
Authors: Goriely Alain , Vandiver Rebecca , Destrade Michel
Published: July 2008

The buckling of hyperelastic incompressible cylindrical tubes of arbitrary length and thickness under compressive axial load is considered within the framework of nonlinear elasticity. Analytical and numerical methods for bifurcation are developed using the exact solution of Wilkes for the linearized problem within the Stroh formalism. Using these methods, the range of validity of the Euler buckling formula and its first nonlinear corrections are obtained for third-order elasticity. The values of the geometric parameters (tube thickness and slenderness) where a transition between buckling and barrelling is observed are also identified.
The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery
Authors: Evans D.J.W , Lawford P.V , Gunn J , Walker D , Hose D.R , Smallwood R.H , Chopard B , Krafczyk M , Bernsdorf J , Hoekstra A
Published: July 2008

The inherent complexity of biomedical systems is well recognized; they are multiscale, multiscience systems, bridging a wide range of temporal and spatial scales. While the importance of multiscale modelling in this context is increasingly recognized, there is little underpinning literature on the methodology and generic description of the process. The COAST (complex autonoma simulation technique) project aims to address this by developing a multiscale, multiscience framework, coined
complex autonoma
(CxA), based on a hierarchical aggregation of coupled cellular automata (CA) and agent-based models (ABMs). The key tenet of COAST is that a multiscale system can be decomposed into
N
single-scale CA or ABMs that mutually interact across the scales. Decomposition is facilitated by building a scale separation map on which each single-scale system is represented according to its spatial and temporal characteristics. Processes having well-separated scales are thus easily identified as the components of the multiscale model. This paper focuses on methodology, introduces the concept of the CxA and demonstrates its use in the generation of a multiscale model of the physical and biological processes implicated in a challenging and clinically relevant problem, namely coronary artery in-stent restenosis.
Mitral valve finite-element modelling from ultrasound data: a pilot study for a new approach to understand mitral function and clinical scenarios
Authors: Votta Emiliano , Caiani Enrico , Veronesi Federico , Soncini Monica , Montevecchi Franco Maria , Redaelli Alberto
Published: July 2008

In the current scientific literature, particular attention is dedicated to the study of the mitral valve and to comprehension of the mechanisms that lead to its normal function, as well as those that trigger possible pathological conditions. One of the adopted approaches consists of computational modelling, which allows quantitative analysis of the mechanical behaviour of the valve by means of continuum mechanics theory and numerical techniques. However, none of the currently available models realistically accounts for all of the aspects that characterize the function of the mitral valve. Here, a new computational model of the mitral valve has been developed from
in vivo
data, as a first step towards the development of patient-specific models for the evaluation of annuloplasty procedures. A structural finite-element model of the mitral valve has been developed to account for all of the main valvular substructures. In particular, it includes the real geometry and the movement of the annulus and papillary muscles, reconstructed from four-dimensional ultrasound data from a healthy human subject, and a realistic description of the complex mechanical properties of mitral tissues. Preliminary simulations allowed mitral valve closure to be realistically mimicked and the role of annulus and papillary muscle dynamics to be quantified.
From mitochondrial ion channels to arrhythmias in the heart: computational techniques to bridge the spatio-temporal scales
Authors: Plank Gernot , Zhou Lufang , Greenstein Joseph L , Cortassa Sonia , Winslow Raimond L , O'Rourke Brian , Trayanova Natalia A
Published: July 2008

Computer simulations of electrical behaviour in the whole ventricles have become commonplace during the last few years. The goals of this article are (i) to review the techniques that are currently employed to model cardiac electrical activity in the heart, discussing the strengths and weaknesses of the various approaches, and (ii) to implement a novel modelling approach, based on physiological reasoning, that lifts some of the restrictions imposed by current state-of-the-art ionic models. To illustrate the latter approach, the present study uses a recently developed ionic model of the ventricular myocyte that incorporates an excitation–contraction coupling and mitochondrial energetics model. A paradigm to bridge the vastly disparate spatial and temporal scales, from subcellular processes to the entire organ, and from sub-microseconds to minutes, is presented. Achieving sufficient computational efficiency is the key to success in the quest to develop multiscale realistic models that are expected to lead to better understanding of the mechanisms of arrhythmia induction following failure at the organelle level, and ultimately to the development of novel therapeutic applications.
Neural mechanisms underlying the vulnerability to develop compulsive drug-seeking habits and addiction
Authors: Everitt Barry J , Belin David , Economidou Daina , Pelloux Yann , Dalley Jeffrey W , Robbins Trevor W
Published: July 2008

We hypothesize that drug addiction can be viewed as the endpoint of a series of transitions from initial voluntary drug use through the loss of control over this behaviour, such that it becomes habitual and ultimately compulsive. We describe evidence that the switch from controlled to compulsive drug seeking represents a transition at the neural level from prefrontal cortical to striatal control over drug-seeking and drug-taking behaviours as well as a progression from ventral to more dorsal domains of the striatum, mediated by its serially interconnecting dopaminergic circuitry. These neural transitions depend upon the neuroplasticity induced by chronic self-administration of drugs in both cortical and striatal structures, including long-lasting changes that are the consequence of toxic drug effects. We further summarize evidence showing that impulsivity, a spontaneously occurring behavioural tendency in outbred rats that is associated with low dopamine D
2/3
receptors in the nucleus accumbens, predicts both the propensity to escalate cocaine intake and the switch to compulsive drug seeking and addiction.
Positron emission tomography imaging studies of dopamine receptors in primate models of addiction
Authors: Nader Michael A , Czoty Paul W , Gould Robert W , Riddick Natallia V
Published: July 2008

Animal models have provided valuable information related to trait and state variables associated with vulnerability to drug addiction. Our brain imaging studies in monkeys have implicated D2receptors in cocaine addiction. For example, an inverse relationship between D2receptor availability and rates of cocaine self-administration has been documented. Moreover, environmental variables, such as those associated with formation of the social hierarchy, can impact receptor availability and sensitivity to the abuse-related effects of cocaine. Similarly, both D2receptor availability and cocaine self-administration can be altered by chronic drug administration and fluctuations in hormone levels. In addition, cocaine self-administration can be altered in an orderly fashion by presentation of an acute stressor, such as acting as an intruder into an unfamiliar social group, which can shift the cocaine dose–response curve to the left in subordinate monkeys and to the right in dominant animals, suggesting an interaction between social variables and acute stressors. Conversely, irrespective of social rank, acute environmental enrichment, such as increasing the size of the living space, shifts the cocaine dose–response curve to the right. These findings highlight a pervasive influence of the environment in modifying the reinforcing effects of cocaine and strongly implicate brain D2receptors.
Neurobiology of nicotine dependence
Authors: Markou Athina
Published: July 2008

Nicotine is a psychoactive ingredient in tobacco that significantly contributes to the harmful tobacco smoking habit. Nicotine dependence is more prevalent than dependence on any other substance. Preclinical research in animal models of the various aspects of nicotine dependence suggests a critical role of glutamate, γ-aminobutyric acid (GABA), cholinergic and dopamine neurotransmitter interactions in the ventral tegmental area and possibly other brain sites, such as the central nucleus of the amygdala and the prefrontal cortex, in the effects of nicotine. Specifically, decreasing glutamate transmission or increasing GABA transmission with pharmacological manipulations decreased the rewarding effects of nicotine and cue-induced reinstatement of nicotine seeking. Furthermore, early nicotine withdrawal is characterized by decreased function of presynaptic inhibitory metabotropic glutamate 2/3 receptors and increased expression of postsynaptic glutamate receptor subunits in limbic and frontal brain sites, while protracted abstinence may be associated with increased glutamate response to stimuli associated with nicotine administration. Finally, adaptations in nicotinic acetylcholine receptor function are also involved in nicotine dependence. These neuroadaptations probably develop to counteract the decreased glutamate and cholinergic transmission that is hypothesized to characterize early nicotine withdrawal. In conclusion, glutamate, GABA and cholinergic transmission in limbic and frontal brain sites are critically involved in nicotine dependence.
Genetics of addictions: strategies for addressing heterogeneity and polygenicity of substance use disorders
Authors: Wong Chloe C.Y , Schumann Gunter
Published: July 2008

Addictions are common psychiatric disorders that exert high cost to the individual and to society. Addictions are a result of the interplay of multiple genetic and environmental factors. They are characterized by phenotypic and genetic heterogeneity as well as polygenicity, implying a contribution of different neurobiological mechanisms to the clinical diagnosis. Therefore, treatments for most substance use disorders are often only partially effective, with a substantial proportion of patients failing to respond. To address heterogeneity and polygenicity, strategies have been developed to identify more homogeneous subgroups of patients and to characterize genes contributing to their phenotype. These include genetic linkage and association studies as well as functional genetic analysis using endophenotypes and animal behavioural experimentation. Applying these strategies in a translational context aims at improving therapeutic response by the identification of subgroups of addiction patients for individualized, targeted treatment strategies. This article aims to discuss strategies addressing heterogeneity and polygenicity of substance use disorders by presenting results of recent research on genetic and environmental components of addiction. It will also introduce the European IMAGEN study that aims to integrate methodical approaches discussed in order to identify the genetic and neurobiological basis of behavioural traits relevant to the development of addictions.
Roosting behavior of a Neotropical migrant songbird, the northern waterthrush Seiurus noveboracensis, during the non‐breeding season
Authors: Smith Joseph A. M. , Reitsma Leonard R. , Rockwood Larry L. , Marra Peter P.
Published: July 2008

Several species of Nearctic‐Neotropical migratory songbirds appear to form roosting aggregations while on their wintering grounds but little is understood about the ecology of this behavior. We studied roosting behavior and patterns of roost habitat selection in the northern waterthrush Seiurus noveboracensis, during three winter years (2002–2004) in Puerto Rico using radio telemetry. Overall, red mangrove was selected for roosting disproportionately to its availability. Regardless of diurnal habitat used, 87% (n=86) of northern waterthrush selected dense stands of coastal red mangrove for roost sites. Individuals traveled up to 2 km to access roost sites in this habitat on a daily basis. The majority (8 of 14) of individuals roosted alone, while others roosted in loose aggregations near communal roosts of gray kingbirds Tyrannus dominicensis. Patterns of roost site selection did not vary by sex. Individuals showing aggressive response to playback during the day, however, selected roost sites significantly closer to the coast. Several additional migratory and resident bird species also used red mangrove for night‐time roosting habitat. Red mangrove may be a critical nocturnal roosting habitat for bird populations that live in proximity to coastal areas in the Neotropics. The benefits of nocturnal roosting behavior as well as why individuals appear to select red mangrove remain poorly understood.
Genome size variation in parrots: longevity and flying ability
Authors: Costantini David , Racheli Luigi , Cavallo Delia , Dell'Omo Giacomo
Published: July 2008

Several hypotheses have been proposed to explain genome size variation in birds. However, no general consensus has been reached thus far. In this study, we analysed the inter‐ and intraspecific variation of genome size in some parrot species, and we tested the hypotheses that (1) weaker fliers have larger genomes, and (2) long‐living species have lower DNA content. In general, parrots have a mean genome size (2.93 pg/nucleus) comparable to that of other avian orders. Amazona ochrocephala tresmariae has the highest genome size (4.30 pg/nucleus) among parrots. As expected, weaker flyers have larger genomes than better ones. In contrast to our prediction, we found a positive correlation between genome size and longevity. Finally, the species‐group Amazona has a higher DNA content than the two groups Ara and Cacatua. Since oxidative stress is causally related to longevity, we suggest that DNA oxidative damage could have acted to some extent as a constraint on GS variation in parrots and perhaps also in other avian orders.
A multigene phylogeny of Galliformes supports a single origin of erectile ability in non‐feathered facial traits
Authors: Kimball Rebecca T. , Braun Edward L.
Published: July 2008

Many species in the avian order Galliformes have bare (or “fleshy”) regions on their head, ranging from simple featherless regions to specialized structures such as combs or wattles. Sexual selection for these traits has been demonstrated in several species within the largest galliform family, the Phasianidae, though it has also been suggested that such traits are important in heat loss. These fleshy traits exhibit substantial variation in shape, color, location and use in displays, raising the question of whether these traits are homologous. To examine the evolution of fleshy traits, we estimated the phylogeny of galliforms using sequences from four nuclear loci and two mitochondrial regions. The resulting phylogeny suggests multiple gains and/or losses of fleshy traits. However, it also indicated that the ability to erect rapidly the fleshy traits is restricted to a single, well‐supported lineage that includes species such as the wild turkeyMeleagris gallopavoand ring‐necked pheasantPhasianus colchicus. The most parsimonious interpretation of this result is a single evolution of the physiological mechanisms that underlie trait erection despite the variation in color, location, and structure of fleshy traits that suggest other aspects of the traits may not be homologous.
Foraging areas of breeding blue‐footed boobies Sula nebouxii in northern Peru, as determined by direction recorders
Authors: Zavalaga Carlos B. , Benvenuti Silvano , Dall'Antonia Luigi , Emslie Steven D.
Published: July 2008

The association between the distribution of blue‐footed boobies Sula nebouxii (BFB) and marine productivity around their breeding grounds is unclear. In Peru, they breed in a region seasonally influenced by the cold, nutrient rich Humboldt Current, and by warm, nutrient poor oceanic waters. The foraging range of BFB in Peru is unknown, although some evidence suggest that they may feed in warm offshore waters. During the austral winter 2002 and summer 2003, we tracked 26 BFBs breeding on Isla Lobos de Tierra, Peru (located approximately 15 km west of the mainland), during 59 feeding trips using small direction recorders to determine their marine habitat use. BFBs preferentially moved to the east of the island and foraged over the continental shelf in cold water masses where marine productivity and the abundance of the main prey, the Peruvian anchovy Engraulis ringens, are usually higher than in other areas. Overall, the median maximum foraging distance from the colony was 39 km (range 3–109 km), with 90% of all trips located within 30 km from the mainland, and enclosed in an area of 13,113 km2. These results reveal that BFBs exploit the productive waters of the Peruvian Coastal Upwelling System, rather than open oceanic waters as previously suggested. BFBs travelled a greater distance, dispersed in a broader area, and visited more offshore waters during the winter 2002, than during the summer 2003, following the typical seasonal horizontal dispersion of the Peruvian anchovy.
Age‐related differences in plumage characteristics of male tree swallows Tachycineta bicolor: hue and brightness signal different aspects of individual quality
Authors: Bitton Pierre‐Paul , Dawson Russell D.
Published: July 2008

Age‐related differences in plumage characteristics of birds can be the result of differential survival of more ornamented individuals, within‐individual changes in plumage attributes with age, or a combination of both. In this study, we investigated age‐class related differences in plumage attributes of male tree swallows Tachycineta bicolor by performing both cross‐sectional and longitudinal analyses. Male tree swallows in their first breeding season do not display delayed plumage maturation, and possess, like experienced breeders, metallic green to metallic blue iridescent plumage on their dorsal surface. Our results showed that, at the population level, older males were brighter and reflected light maximally at shorter wavelengths (i.e. were more blue). Differences in plumage brightness were most likely caused by changes within individuals as males increased in brightness between the first time they were captured and the subsequent year. Differences in hue, however, were not due to within‐individual changes, but rather appear to be the result of greener individuals having lower survival and/or nest site fidelity. Indeed, relatively dull, greener birds had a lower probability of being recaptured the subsequent year. In contrast, we found that if birds captured in their first year as breeding adults were relatively bright, hue was not related to the probability of recapture. These results suggest that plumage attributes in male tree swallows have the potential of being honest signals of quality. Furthermore, plumage brightness and plumage hue might signal different aspects of male quality in this species.
Eggshell coloration in relation to male ornamentation, female condition and egg quality in the collared flycatcherFicedula albicollis
Authors: Hargitai Rita , Herényi Márton , Török János
Published: July 2008

The blue‐green eggshell pigment biliverdin is an efficient antioxidant, the deposition of which may be costly and act as a handicap to the female's antioxidant capacity. Thus, it is hypothesized that there exists a positive correlation between the degree of eggshell coloration and the condition and health state of the mother. In this study, we measured the blue‐green chroma of collared flycatcherFicedula albicolliseggs, and investigated the associations between egg colour and parental characteristics, laying date, clutch size and laying order. We also analysed the possible correlations between egg size, yolk carotenoid and antibody levels and eggshell pigmentation. Our results revealed no significant relationships between egg colour and female age, morphological and serological variables. Blue‐green colour intensity of eggs increased throughout the breeding season, which could be the result of either a proximate constraint or an adaptive strategy. We found a positive association between egg colour saturation and yolk lutein concentration. This relationship could be the result of the seasonal improvement of caterpillar supply, which could influence the deposition of both components into the egg. Furthermore, we found that females mated to lower‐quality males produced eggs with higher biliverdin pigmentation. It is possible that deposition of biliverdin is correlated to some unmeasured aspect of egg quality that could enhance the viability of offspring of lower‐quality fathers. We found that intensity of blue‐green coloration increased with laying order between the first and fifth eggs.
Conservation genetics and phylogeography of southern dunlins Calidris alpina schinzii
Authors: Wennerberg Liv , Marthinsen Gunnhild , Lifjeld Jan T.
Published: July 2008

Breeding populations of southern dunlin Calidris alpina schinzii in South Fennoscandia and the Baltic are severely fragmented and declining dramatically. Information on the genetic structure and diversity is therefore of importance for the conservation and management of these populations. Here we present the results of comparative genetic analyses of these populations with other populations of the schinzii, alpina and arctica subspecies in northern Europe. We sequenced the mitochondrial DNA control region and the Z‐chromosome intron VLDLR‐9, and analyzed microsatellites and AFLPs, for analyses of within‐population genetic diversity. We also extended previous analyses of the phylogeographic structure of dunlins in northern Europe with a larger sample of individuals and populations. Our results revealed no evidence of reduced genetic diversity or increased levels of inbreeding in the small and fragmented populations around the Baltic Sea as compared to the more vital and larger populations elsewhere. Nevertheless, their small population sizes and presumably high degree of isolation may lead to local extinctions, indicating that demographic and ecological factors may pose a greater threat to the survival of these populations than purely genetic factors. Phylogeographically, the schinzii populations in Scandinavia and the Baltic do not form a separate genetic clade, but are part of larger cline of genetic variation encompassing several recognized subspecies of dunlins in the western Palearctic region. Only the Icelandic population showed some distinctiveness in genetic structure and might therefore be considered a separate management unit. Our study highlights the general problem of lack of genetic support for subspecies in avian taxonomy and conservation genetics.
The cost of being alone: the fate of floaters in a population of cooperatively breeding pied babblers Turdoides bicolor
Authors: Ridley Amanda R. , Raihani Nichola J. , Nelson‐Flower Martha J.
Published: July 2008

The occurrence of group‐living behaviour has often been explained by the benefits individuals receive through cooperation; including increased reproductive output, vigilance against predators, and load‐lightening behaviour. However, to fully understand the benefits of group‐living, it is important to quantify the costs of living alone. Here, we look at the fate of floaters (individuals who have no fixed territory and remain alone for extended periods) in a population of cooperatively breeding pied babblers Turdoides bicolor. We found that individuals spent less time foraging and more time vigilant for predators when found as a floater compared to when they were in a group. Consequently, they suffered a continuous loss of body mass, with long‐term floaters suffering the highest losses. This had a long‐term effect: floaters that eventually did regain a position in a group usually entered as helpers, in contrast to dispersers, who usually entered a new group as breeders. This high cost of living alone highlights the benefits of group‐living and may help to understand patterns of delayed dispersal in some social species.
African cichlid Pseudotropheus spp. males moan to females during foreplay
Authors: Simões J. M. , Fonseca P. J. , Turner G. F. , Amorim M. C. P.
Published: July 2008

This study describes a new courtship sound (moan) produced by Pseudotropheus spp. males, not previously reported for cichlids. Moans are short tonal sounds often showing frequency modulation. This sound type is of very low amplitude and is produced when males swim in close proximity to a female, usually before performing more exuberant behavioural exhibitions, such as darting, quivering the body and growling.
Size‐independent growth in fishes: patterns, models and metrics
Authors: Sigourney D. B. , Letcher B. H. , Obedzinski M. , Cunjak R. A.
Published: July 2008

A combination of a dynamic energy budget (DEB) model, field data on Atlantic salmon Salmo salar and brown trout Salmo trutta and laboratory data on Atlantic salmon was used to assess the underlying assumptions of three different metrics of growth including specific growth rate (G), standardized mass‐specific growth rate (GS) and absolute growth rate in length (GL) in salmonids. Close agreement was found between predictions of the DEB model and the assumptions of linear growth in length and parabolic growth in mass. Field data comparing spring growth rates of age 1+ year and 2+ year Atlantic salmon demonstrated that in all years the larger age 2+ year fish exhibited a significantly lower G, but differences in growth in terms of GS and GL depended on the year examined. For brown trout, larger age 2+ year fish also consistently exhibited slower growth rates in terms of G but grew at similar rates as age 1+ year fish in terms of GS and GL. Laboratory results revealed that during the age 0+ year (autumn) the divergence in growth between future Atlantic salmon smolts and non‐smolts was similar in terms of all three metrics with smolts displaying higher growth than non‐smolts, however, both GS and GL indicated that smolts maintain relatively fast growth into the late autumn where G suggested that both smolts and non‐smolts exhibit a sharp decrease in growth from October to November. During the spring, patterns of growth in length were significantly decoupled from patterns in growth in mass. Smolts maintained relatively fast growth though April in length but not in mass. These results suggest GS can be a useful alternative to G as a size‐independent measure of growth rate in immature salmonids. In addition, during certain growth stanzas, GS may be highly correlated with GL. The decoupling of growth in mass from growth in length over ontogeny, however, may necessitate a combination of metrics to adequately describe variation in growth depending on ontogenetic stage particularly if life histories differ.
Alternative migration and host parasitism strategies and their long‐term stability in river lampreys from the River Endrick, Scotland
Authors: Adams C. E. , Bissett N. , Newton J. , Maitland P. S.
Published: July 2008

The stability of a discrete body size dimorphism of sexually mature river lamprey Lampetra fluviatilis from the River Endrick, Scotland, was examined over a 21 year period. Stable isotope analysis was used to test the hypothesis that the two size forms comprise individuals with differing migration and parasitic foraging strategies. Maturing river lamprey and the brook lamprey Lampetra planeri were trapped over 3 months each year in the periods 1983–1984 and 2004–2005. Brook lamprey catches and catches of both species combined showed no significant trend in catch rate with time. The catch rate of small body size river lamprey declined between 1983–1984 and 2004–2005 (although the difference did not reach statistical significance; P = 0·055). In contrast, there was a significant increase in the catch rate of the large body size river lamprey and as a consequence, a significant change in the relative proportion of each of the two river lamprey morphs over the study period. Analysis of the stable isotopes of C and N in muscle tissue showed that brook lamprey tissue derived its carbon from a freshwater source and had a δ13C more consistent with that of the River Endrick than with Loch Lomond. δ15N values for this species showed it to be feeding at the base of the food chain, consistent with filter feeding as an ammocoete. The large body size and the small body size river lamprey adults differed substantially in their δ13C values, with the small body size δ13C signature indicative of a freshwater carbon source and the large body size morph of a marine source. The small body size morph had a δ13C signature that was consistent with that of Loch Lomond powan Coregonus lavaretus suggesting that they share a common carbon source. The large body size morph was clearly feeding at a higher trophic level than the small body size morph. A single small body size river lamprey individual with typical morphology for that group, however, had C and N signatures that clustered with those of the large body size morphs. This individual had either migrated to sea to forage, as is typical for the species, or had been feeding on an anadromous fish with a strong marine C signature in fresh water. It is concluded that the body size dimorphism is indicative of a differential migration and foraging strategy in the parasitic phase of the life cycle of river lamprey at this site.
Habitat and abundance of Balitoridae in small rivers of central Thailand
Authors: Beamish F. W. H. , Sa‐ardrit P. , Cheevaporn V.
Published: July 2008

Balitorids were collected, by electrofishing, from small rivers across central Thailand between October 2000 and March 2004. Total balitorid abundance for the 18 species averaged 3·8% of the cumulative total for all fishes. Balitorid species numbers and abundance varied directly with elevation toc.400 m, substratum particle size and ambient silica concentration. Species numbers at stations were modest and few species were widely distributed. Species associations related significantly with elevation, temperature and ambient concentrations of dissolved oxygen and silica. Turbidity was also significant but probably an artefact. Habitat separation clearly occurs among some balitorids, particularly the less common species, and probably represents species‐specific direct and indirect habitat effects. The more common balitorid species tended to occur in similar habitats where the significant factors approximated average values. For these species, coexistence is suggested to occur through food resource sharing possibly facilitated through adaptations. Balitorid distributions in low‐order rivers are attributed to the direct and indirect influences of the environment on energy available for the performance of essential activities.
Effect of the exogenous soyabean phyto‐oestrogen genistein on sperm quality, ATP content and fertilization rates in channel catfish Ictalurus punctatus (Rafinesque) and walleye Sander vitreus (Mitchill)
Authors: Green C. C. , Kelly A. M.
Published: July 2008

This study examined whether the soya phyto‐oestrogen genistein would have an effect on spermatozoa quality and in vitro fertilization capacity in mature channel catfish Ictalurus punctatus or walleye Sander vitreus. For both species, motility time and motility rank were significantly different among treatment groups and control, with higher genistein concentrations producing significantly lower motility time and motility rank (P ≤ 0·01). Walleye and channel catfish ATP content was significantly lower compared to control treatments at several incubation concentrations and was significantly related to fertilization rate. Fertilization rate was significantly dependant on genistein incubation concentrations (P ≤ 0·01). Additionally, logistic regression showed a significant negative relation between genistein concentration and fertilization in channel catfish (P ≤ 0·01). These results establish that genistein could play a role in reproductive performance within aquaculture species. In addition, these findings warrant further examination of the impact of phyto‐oestrogens in broodstock feeds.
Feeding patterns of the dominant benthic and demersal fish community in a temperate estuary
Authors: Dolbeth M. , Martinho F. , Leitão R. , Cabral H. , Pardal M. A.
Published: July 2008

The diet and feeding relationships of the 12 most abundant benthic and demersal fish species of the Mondego Estuary, Portugal, were studied between June 2003 and May 2006. Fishes were caught during the night using a 2 m beam trawl. The stomach contents were analysed for prey identification, counting and weighing. According to prey importance in diets, three main feeding guilds were identified: (1) invertebrate feeders, (2) invertebrate and fish feeders and (3) plankton and invertebrate feeders. Besides these main feeding guilds, some fishes also presented fractions of algae and zooplankton in their stomach contents. The most abundant prey items were macroinvertebrates, with several polychaetes (Nephtys spp., Capitellidae, Spionidae and Eunicidae), Corophium spp. and Crangon crangon among the dominant prey. Pomatoschistus spp. were the most preyed on fishes. Several fish species showed a tendency for a specialized diet, but almost all also showed some degree of opportunistic feeding by preying on other food resources. High diet overlap was found between some fish species, yet exploitative competition could not be concluded.
Winter behaviour of juvenile Atlantic salmon Salmo salar L. in experimental stream channels: effect of substratum size and full ice cover on spatial distribution and activity pattern
Authors: Linnansaari T. , Cunjak R. A. , Newbury R.
Published: July 2008

Activity and choice of areas offering different cover (substratum or surface ice) for juvenile Atlantic salmon Salmo salar were studied in experimental stream channels during winter. Channels were completely ice covered between December and March. During this period, the ice thickness increased from 50 to 300 mm after which 50% of the ice was experimentally removed and followed by c. 2·5‐fold increase in discharge to simulate the effects of spring flood. Large substrata provided preferred habitats but areas with small substratum sizes were also used when full surface ice provided above‐stream cover and the stream discharge was relatively low. The fish remained nocturnal throughout the study but the level of day activity significantly increased as the surface ice became thicker. Maximum movement distance during a 24 h period and homing‐at‐dawn behaviour remained at a constant level throughout the main winter, but significantly changed during the simulated spring flood (mean ±s.e. maximum extent of movements within 24 h increased from 1·1 ± 0·1 to 3·0 ± 0·5 m; homing behaviour decreased from the highest level of 89·3 to 34·6% during spring flood). Overwinter survival was high (92·9%). Relative mass increase during the study ranged from –8·3 to 28·5%, and 84% of the juvenile Atlantic salmon gained mass. The highest rates of mass increase were associated with frequent movements between areas of different substratum size. The results indicate that during winter: (1) Atlantic salmon parr preferred large substratum cover compared with surface ice cover at the fish densities studied here, (2) juvenile Atlantic salmon were predominantly nocturnal but diurnal activity increased as surface ice became thicker and (3) increase in water discharge during spring altered the behaviour of juvenile Atlantic salmon and may have caused additional habitat shifts.
Compensatory growth of juvenile brown flounder Paralichthys olivaceus (Temminck & Schlegel) following thermal manipulation
Authors: Huang G. , Wei L. , Zhang X. , Gao T.
Published: July 2008

The compensatory growth of juvenile brown flounder Paralichthys olivaceus (body mass c. 12 g) following different thermal exposure was investigated. Fish were exposed to one of the five temperatures: 8·5 (T8·5), 13·0 (T13·0), 17·5 (T17·5), 22·0 (T22·0) and 26·5° C (T26·5) for 10 days and fish grew best at 22·0° C. Then the water temperature in all treatments was equably adjusted to 22·0° C over 3 days. At the end of the following 30 days after temperature adjustment, there were no significant differences between body masses of fish in the different treatments (wet body mass at the end of the experiment ranged from 22·13 to 24·56 g). Results indicated that the juvenile P. olivaceus achieved complete compensatory growth. Analysis of the dynamics of the feeding rates and feed conversion efficiencies indicated that compensatory growth of the fish experienced low temperature (T8·5, T13·5 and T17·5) or high temperature (T26·5) exposure was mainly dependent on increasing feed intake (hyperphagia) and possibly by improvement in feed conversion efficiency. The moisture content was not affected by different temperature exposure significantly. The lipid and energy content of juvenile P. olivaceus in T8·5, however, were significantly lower than other treatment. Results of the current study indicate that a short period of low or high temperature exposure may not affect annual growth, but may affect lipid and energy deposition.
Auditory and olfactory abilities of larvae of the Indo‐Pacific coral trout Plectropomus leopardus (Lacepède) at settlement
Authors: Wright K. J. , Higgs D. M. , Belanger A. J. , Leis J. M.
Published: July 2008

Auditory and olfactory abilities of settlement‐stage larvae of the coral trout Plectropomus leopardus (Pisces: Serranidae) were tested electrophysiologically to determine if these senses are sufficiently developed to aid larvae in detection of settlement habitats on coral reefs. Plectropomus leopardus larvae detected sounds from 100 to 2000 Hz with hearing most sensitive at the frequencies of 100, 200 and 600 Hz. The olfactory response of P. leopardus was similar for the two amino acids tested and for the water conditioned by conspecifics. Auditory and olfactory abilities of P. leopardus are well developed at settlement‐stage, and apparently sufficient to detect auditory and olfactory cues from reefs.
Cage culture effects on mullets (Mugilidae) liver histology and blood chemistry profile
Authors: Coz‐Rakovac R. , Strunjak‐Perovic I. , Topicpopovic N. , Hacmanjek M. , Smuc T. , Jadan M. , Lipej Z. , Homen Z.
Published: July 2008

A comparative study of blood chemistry and histology was conducted on two groups of mullets (Mugilidae) living under different conditions with different feed sources. The aquaculture influenced mullet group (AIM), was collected near fish farms and the control group of mullet (CM) was caught in the waters without any aquaculture activities. Histological and biochemical procedures were employed to study liver histomorphology, plasma aspartate and alanine aminotransferase (AST, ALT), triglyceride (TRIG), cholesterol (CHOL), glucose (GLU) and total protein (TP) of both AIM and CM. Moderate histological changes (lipid infiltration) were observed in the liver of AIM. Significant changes in plasma variables were observed in AIM. Blood chemistry variables measured proved to be good indicators of artificial feed effects. Classical statistical approaches were applied to the blood chemistry and histopathology data. For the first time machine learning techniques were used to generate comprehensible classification models and to explore blood chemistry variable importance, strength, their mutual interactions or dependencies, and to investigate reliability of particular variables within the groups.
Substratum selection by juvenile flounder Platichthys flesus (L.): effect of ephemeral filamentous macroalgae
Authors: Carl J. D. , Sparrevohn C. R. , Nicolajsen H. , Støttrup J. G.
Published: July 2008

Selection of substrata representing habitats with or without filamentous vegetation by juvenile flounder Platichthys flesus was investigated in laboratory experiments and a field study to assess the effect of the increasing occurrence of ephemeral filamentous macroalgae in shallow nursery areas and its potential effect on flounder recruitment. In the laboratory experiments, 79% of juvenile flounder (24–99 mm total length, LT) preferred bare sand substrata in comparison to substrata with simulated filamentous vegetation. Substratum preference did not change with fish size. Field sampling using a drop trap (1 m2) in a vegetated (>50% coverage of ephemeral macroalgae) habitat in June, July and August showed small flounder (mean LT= 37·3 mm) were caught more often in samples with less vegetation. In contrast, larger flounder (mean LT= 57·2 and 79·7 mm in July and August, respectively) were more evenly distributed in relation to the distribution of vegetation. The results of this study indicate that the increase in ephemeral macroalgae observed in recent years potentially reduces the quantity and quality of suitable nursery habitats for juvenile flounder, which could have detrimental consequences to the overall recruitment of flounder in coastal areas.
The growth of a Welsh strain of Arctic charr Salvelinus alpinus (L.) and investigations into its aquaculture potential
Authors: Berrill I. K. , McCarthy I. D.
Published: July 2008

The growth in captivity of a wild Welsh strain (Llyn Cowlyd) of Arctic charr Salvelinus alpinus was compared to that of a commercial Scottish strain over the course of a 12 month experiment. At the conclusion of the study, the Welsh strain had a lower mass and condition factor than the commercial fish, but a similar length. Aspects of the growth and population structure of the Welsh strain imply that it could be a subject for aquaculture development, but such practises will be dependant on further work on selection and broodstock development.