bluuebunny/crossref_metadata_2025 huggingface dataset:
Depth-dependent variation in condition and length-at-age of Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence
Authors: Chouinard G A , Swain D P
Published: October 2002

We describe depth-dependent variation in the condition and length-at-age of southern Gulf of St. Lawrence cod (Gadus morhua) on their feeding grounds in September 19712000. Bathymetric variation in condition appears to be linked to abundance. In periods of low abundance, condition was relatively uniform over shallow and intermediate depths (<100125 m). During periods of high abundance, condition was highest in the shallowest waters and declined steadily as depth increased to 100 m. In all periods, condition was low in deep water. Bathymetric trends in length-at-age contrasted with those in condition. Length-at-age was high in the deep waters where condition was low. Length-at-age also tended to increase from minimum values at intermediate depths to high values in shallow waters. This tendency was most striking in the 1990s, a period when condition was uniform over this depth range. We discuss the ecological, bioenergetic, and sampling implications of these patterns.
The effects of reduced pH on chemical alarm signalling in ostariophysan fishes
Authors: Brown Grant E , Adrian, Jr. James C , Lewis Michael G , Tower Jon M
Published: October 2002

Under laboratory conditions, we examined the effects of acute exposure to weakly acidic conditions (pH 6.0) on the ability of fathead minnows (Pimephales promelas) and finescale dace (Phoxinus neogaeus) to detect and respond to conspecific and artificial alarm pheromones. Initially, minnows and dace exhibited normal antipredator responses when exposed to conspecific alarm pheromones under normal (pH 8.0) conditions. When retested at pH 6.0, we observed no significant antipredator response. However, when returned to normal pH conditions, both exhibited normal antipredator responses. Minnows exposed to the putative ostariophysan alarm pheromone (hypoxanthine-3-N-oxide) exhibited a similar trend in behavioural response. Finally, we manipulated the pH of minnow skin extract and hypoxanthine-3-N-oxide to determine the chemical mechanism responsible for this observed loss of response. Minnows exhibited significant antipredator responses to natural and artificial alarm pheromones at normal pH conditions, but did not respond to either stimulus once they had been buffered to pH 6.0 or acidified and rebuffered to pH 7.5. These data suggest that the ability of minnows and dace to detect and respond to alarm pheromones is impaired under weakly acidic conditions and that this loss of response is due to a nonreversible covalent change to the alarm pheromone molecule itself.
Respiratory strategy is a major determinant of [3H]water and [14C]chlorpyrifos uptake in aquatic insects
Authors: Buchwalter D B , Jenkins J J , Curtis L R
Published: October 2002

Despite the extensive use of aquatic insects to evaluate freshwater ecosystem health, little is known about the underlying factors that result in sensitivity differences between taxa. Organismal characteristics (respiratory strategy and body size) were used to explore the rates of [3H]H2O and [14C]chlorpyrifos accumulation in aquatic insects. Ten aquatic insect taxa, including ephemeropteran, trichopteran, dipteran, hemipteran, and coleopteran species, were exposed to [14C]chlorpyrifos (240 ng·L1) and [3H]H2O for up to 12 h. Because exchange epithelial surfaces on the integument are permeable to water, [3H]H2O was used as a quantitative surrogate for exposed cellular surface area. [14C]Chlorpyrifos uptake rates were highly correlated with water permeability in all 10 taxa tested and largely covaried with body size and respiratory strategy. Rates were highest among smaller organisms on a per-weight basis and in taxa with relatively large external cellular surfaces such as gills. Air-breathing taxa were significantly less permeable to both [3H]H20 and [14C]chlorpyrifos. A method for labeling exposed epithelial surfaces with a fluorescent dye was developed. This technique allowed discrimination between exchange epithelium and barrier tissue on the integument. Fluorescent dye distributions on the body surface provided a rapid method for estimating exposed epithelium consistent with [3H]H20 and [14C]chlorpyrifos accumulation.
Reference priors for Bayesian fisheries models
Authors: Millar Russell B
Published: October 2002

Bayesian models require the specification of prior distributions for all unknown parameters, and this formal utilization of prior knowledge (if any) can be used to great advantage in some fisheries. However, regardless of whether prior knowledge about model parameters is available, specification of prior distributions is seldom unequivocal. This work addresses the problem of specifying default priors for several common fisheries models. To maintain consistency of terminology with the statistical literature, such priors are herein called reference priors to recognize that they can be interpreted as providing a sensible reference point against which the implications of alternative priors can be compared. Here, the Jeffreys' prior is demonstrated for the Ricker and BevertonHolt stockrecruit curves, von Bertalanffy growth curve, Schaefer surplus production model, and sequential population analysis. The Jeffreys' priors for relevant derived parameters are demonstrated, including the steepness parameter of the BevertonHolt stockrecruit curve. The sequential population analysis example is used to show that the Jeffreys' prior should not be automatically accepted as a reference prior in all modelsthis needs to be decided on a case-by-case basis.
Landscape allometry: from tidal channel hydraulic geometry to benthic ecology
Authors: Hood W Gregory
Published: October 2002

The use of hydraulic geometry and other geomorphic indices has been recommended for habitat restoration and creation of estuarine tidal channels. Although such an approach provides design guidance for tidal channel form, it does not provide guidance for the ecological consequences of channel form. This study investigates the potential linkage of the scaling of tidal channel form with ecological patterns and processes in estuarine tidal channels of the lower Chehalis River, Washington, U.S.A. Ebb tide surface velocity was related to channel size, as was exit time and export probability of tiny drogues, which mimic floating allochthonous detritus. Consequently, the amount of organic material in channel sediments scaled negatively with channel size as did the abundance of benthic surface deposit feeders. These observations suggest that the highest concentrations of fish feeding in estuarine tidal channels may be in smaller channels or in the smaller and more distal portions of large channels. Scaling of ecological patterns and processes with tidal channel size may be an example of a more general ecological scaling with landscape form, i.e., landscape allometry.
Regional analysis of body size and population density in stream fish assemblages: testing predictions of the energetic equivalence rule
Authors: Knouft Jason H
Published: October 2002

The energetic equivalence rule predicts that body mass (W) and population density (β) within an assemblage are negatively correlated and will exhibit a W0.75 = β relationship. Bergmann's rule predicts that body size among species will increase with increasing latitude. If species body size increases with latitude, the shape of the body size  population density distribution among assemblages may also vary. This change in the body size  population density distribution, when viewed in the context of the energetic equivalence rule, may indicate an alteration in the use of available energy by individuals of different sizes within an assemblage. Twenty-eight streams were sampled across four geographically distinct regions to determine if stream fish assemblages conform to the prediction of the energetic equivalence rule. Body size in stream fish assemblages did not support the pattern predicted by Bergmann's rule, but rather was negatively correlated with latitude. Stream fish assemblages generally did not conform to the relationship predicted by the energetic equivalence rule. Moreover, these results, coupled with the predictions of the energetic equivalence rule, suggest that larger individuals tended to control a disproportionately greater amount of energy than smaller individuals in stream fish assemblages, which may be partially due to predation pressure on smaller individuals.
Impact of fertilization and stocking on trophic interactions and growth of juvenile sockeye salmon (Oncorhynchus nerka)
Authors: Mazumder Asit , Edmundson Jim A
Published: October 2002

Using 16 years of data on nutrients, plankton, and sockeye fry and smolts from Packers Lake, Alaska, we test the impact of nutrients and fry stocking on the growth and productivity of juvenile sockeye salmon (Oncorhynchus nerka). To enhance sockeye production, this lake was fertilized (19831996) and stocked annually (19871996) with sockeye fry. Before fertilization, the density of sockeye fry was low (<0.20 fry·m2), the size and biomass of Daphnia were low, and sockeye smolts were relatively small. Before stocking, all trophic levels responded positively to fertilization. The biomass and mean size of Daphnia increased significantly. The average size of age-1 and age-2 smolts increased three- to four-fold. Fry stocking produced dramatic declines in both biomass and mean length of Daphnia and in size of smolts. When large-sized (>1 mm) Daphnia were significantly reduced in density under heavy predation by sockeye fry, the growth of juvenile sockeye declined, even under continued fertilization. We show that fry density and associated food web structure are major determinants of juvenile sockeye responses to fertilization and stocking. This study probably provides the first long-term experimental results linking limnological and nutrient  food web concepts to trophodynamics and productivity of juvenile sockeye salmon.
Least median of squares: a suitable objective function for stock assessment models?
Authors: Shertzer Kyle W , Prager Michael H
Published: October 2002

Robust fitting methods, intended for data sets possibly contaminated with invalid observations, are gaining increased use in analysis of fishery data. In particular, the method of least median of squares (LMS) has attracted attention. Its hallmark is high statistical resistance, which makes it immune to up to 50% contamination in the data. However, the same property makes it inefficient and can cause faulty fitting of typical fishery data. The LMS fit can be in conflict with important sections of a time series, a problem we illustrate by fitting a biomass dynamic (surplus production) model to simulated and actual fishery data. Additionally, we illustrate that LMS parameter estimates can be highly sensitive to small perturbations in the data. Other robust methods, like the method of least absolute values (LAV), appear less prone to such problems. A key reference on LMS recommends using the method as part of an exploratory procedure to identify outliers, rather than as an objective function for final model fitting. We concur with that recommendation.
From continua to patches: examining stream community structure over large environmental gradients
Authors: Wright Kristopher K , Li Judith L
Published: October 2002

We present an approach that integrates a conceptual framework with multivariate ordination techniques and traditional parametric analyses to examine biotic and abiotic gradients in stream ecosystems. Ordinations were used to examine multivariate patterns along an environmental gradient, with individual variables used to interpret those patterns across spatial scales. The conceptual framework provides a consistent context to compare community distributions and consequently allows for hypothesis testing using ordinations. To illustrate the approach, we examined the physical template, fish and benthic macroinvertebrate communities, and algal biomass and production along a 1st- through 5th-order stream gradient in eastern Oregon. We hypothesized that longitudinal distributions of physical habitat characteristics, fishes, macroinvertebrates, and periphyton would reflect highly variable, discontinuous gradients. Multivariate patterns were determined by rotating nonparametric ordinations to a common set of variables and comparing them to conceptual models of (i) an ideal continuum, (ii) a random distribution, and (iii) discrete patches. Physical habitat and fishes reflected strong longitudinal gradients, macroinvertebrates were the most patchy, and algal biomass and production were highly variable. Distributions of individual variables from site and stream-order perspectives revealed how different factors, potentially influencing stream communities, may be continuous or patchy depending on spatial scale.
Allozyme and microsatellite diversity in natural and domestic populations of turbot (Scophthalmus maximus) in comparison with other Pleuronectiformes
Authors: Bouza C , Presa P , Castro J , Sánchez L , Martínez P
Published: October 2002

Twelve microsatellite and 28 allozyme loci were employed to analyse genetic diversity in natural and domestic populations of turbot (Scophthalmus maximus) from northwest Spain in comparison with other flatfish species with similar habitat, life history, and geographic distributionthe brill (Scophthalmus rhombus) and the flounder (Platichthys flesus). These species had shown much higher allozyme diversity than turbot in previous studies, and were used as a reference to check for putative historical bottlenecks in turbot. Significantly lower genetic variability in turbot than in brill and flounder was confirmed with allozymes, but not with the highly variable microsatellite loci. This intermarker discrepancy could be explained by different mutation rates in relation with historical bottlenecks along turbot evolution. A significantly lower genetic diversity was observed in a domestic strain of turbot than in natural populations of this species. This sample evidenced a strong family structure from microsatellite data, which suggests caution against the use of commercial batches for broodstock foundation in turbot farming. A strong concordance was found across the two categories of markers used when analysing the pattern of genetic subdivision at a local scale within the three species analysed, low and nonsignificant genetic differentiation being observed between Atlantic and Cantabric areas.
Marine ecosystem assessment in a fisheries management context
Authors: Link Jason S , Brodziak Jon K.T , Edwards Steve F , Overholtz William J , Mountain David , Jossi Jack W , Smith Tim D , Fogarty Michael J
Published: October 2002

We examined a suite of abiotic, biotic, and human metrics for the northeast U.S. continental shelf ecosystem at the aggregate, community, and system level (>30 different metrics) over three decades. Our primary goals were to describe ecosystem status, to improve understanding of the relationships between key ecosystem processes, and to evaluate potential reference points for ecosystem-based fisheries management (EBFM). To this end, empirical indicators of ecosystem status were examined and standard multivariate statistical methods were applied to describe changes in the system. We found that (i) a suite of metrics is required to accurately characterize ecosystem status and, conversely, that focusing on a few metrics may be misleading; (ii) assessment of ecosystem status is feasible for marine ecosystems; (iii) multivariate points of reference can be determined for EBFM; and (iv) the concept of reference directions could provide an ecosystem level analog to single-species reference points.
Controls on fish distribution and abundance in temporary wetlands
Authors: Baber Matthew J , Childers Daniel L , Babbitt Kimberly J , Anderson David H
Published: October 2002

Our main goal was to determine if fish distribution and adundance in temporary wetlands were shaped primarily by large-scale (landscape) or small-scale (local) characteristics and to investigate the influence of cattle ranching on fish assemblages. A total of 24 temporary ponds were selected at the Kissimmee Prairie Sanctuary and the Mac Arthur Agro-Ecology Research Center. Each wetland was sampled for fish using throw traps and dip nets during 1999. Landscape processes (connectivity to permanent water bodies) predominately influenced fish assemblages, although local processes (depthhydroperiod) were also important. Furthermore, no colonizing species went locally extinct before wetlands began to dry. Our findings suggest that large-scale processes that influence colonization dynamics are of more importance than small-scale processes that influence extinction dynamics. Finally, hydrological changes (ditching) associated with agriculture (cattle ranching) have adversely affected temporary wetland fish assemblages by reducing wetland hydroperiods and connectivity.
The effects of environmental heat stress on heat-shock mRNA and protein expression in Miramichi Atlantic salmon (Salmo salar) parr
Authors: Lund Susan G , Caissie Daniel , Cunjak Richard A , Vijayan Mathilakath M , Tufts Bruce L
Published: October 2002

This study combines laboratory experiments with temperature monitoring and fish sampling in the wild to determine if Atlantic salmon (Salmo salar) parr from the Miramichi River in New Brunswick are currently experiencing significant sublethal heat stress during the warm summer months. Laboratory experiments indicated that Hsp 70 mRNA and protein and Hsp 30 mRNA were all significantly induced in Atlantic salmon parr between 22°C and 25°C. Field sampling during moderate spring temperatures and a high-temperature event in summer further indicated that the threshold for mRNA induction of both Hsp 70 and Hsp 30 is around 23°C, but Hsp 70 protein levels were only significantly elevated in the field at 27°C. Hsc 70 mRNA and protein levels were not significantly increased during heat stress under laboratory conditions. In the field, however, Hsc 70 mRNA was significantly increased at 23°C and both Hsc 70 mRNA and protein levels were elevated at 27°C. Taken together, the results of this investigation suggest that Atlantic salmon parr from the Miramichi River are currently experiencing temperatures that will cause significant protein damage and induce a heat-shock response for about 30 days each summer.
A regional meta-model for stockrecruitment analysis using an empirical Bayesian approach
Authors: Chen D G , Holtby L Blair
Published: October 2002

A regional stockrecruitment meta-model is developed using a hierarchical Bayesian framework to combine information from multiple fish populations. The use of the meta-model is illustrated through analysis of the regional stockrecruitment parameters of the coho salmon (Oncorhynchus kisutch) within two large fisheries management units in southern and northern British Columbia. We construct our regional prior distribution from an analysis of all stock-recruitment data rather than by the more usual approach of assuming a prior distribution. That preliminary analysis indicated that the regional prior distribution for the two parameters of the Ricker model was bivariate normallognormal (NLN) with a high degree of correlation between the two Ricker parameters. Because this distribution had not been fully developed, we formulated the density function for the NLN distribution and proved some of its important properties. An empirical Bayesian approach was then used to estimate the regional distributions of the Ricker parameters and derived management parameters. Characterization of the distributional properties of productivity within management regions is a necessary step for resource managers seeking to prosecute mixed-stock fisheries while conserving population diversity.
Intra- and inter-specific competition for winter concealment habitat in juvenile salmonids
Authors: Harwood A J , Metcalfe N B , Griffiths S W , Armstrong J D
Published: October 2002

The availability of streambed refuges has previously been shown to be of critical importance to the survival of overwintering juvenile salmonids. We used semi-natural stream channels to quantify intra- and inter-specific competition for daytime refuges and the willingness of Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) to share available shelter. Refuge use was frequently associated with aggressive behaviour when two fish were provided with only one shelter, with intra- and inter-specific competition being similar in intensity. Resident individuals were less likely to leave the refuge than were intruders, and sharing of refuges was uncommon, both when competing for one shelter (experiment I) and when these were provided in excess (experiment II). Fish showed greater preferences for foraging habitat during the night than for the location of daytime shelters and were therefore willing to shift habitats to find adequate shelter. Overall, these results suggest that winter competition for refuges, both within and between species of salmonid, is likely to be intense if refuge availability is limited in the wild.
Using nonlinear hierarchical models for analyzing annulus-based size-at-age data
Authors: Schaalje G Bruce , Shaw Jared L , Belk Mark C
Published: October 2002

Size-at-age data for fish (derived from otoliths or other structures) are valuable but statistically messy. The data are typically serially correlated and unbalanced, with both time-independent and time-varying covariates. Appropriate growth models are typically nonlinear, with an unknown functional form. We recommend the use of nonlinear hierarchical models for the analysis of such data. We illustrate the use of these methods by applying the recently introduced SAS procedure NLMIXED (SAS Institute Inc., Cary, N.C.) to otolith-based estimated standard lengths of Utah chub (Gila atraria) collected in four locations with predators and four locations without predators.
Algal production and trihalomethane formation potential: an experimental assessment and inter-river comparison
Authors: Jack Jeffrey , Sellers Tim , Bukaveckas Paul A
Published: October 2002

Trihalomethanes (THMs) are byproducts produced during the disinfection of drinking water. We combined survey and experimental approaches to identify factors that influence THM formation potential (THMFP) in the Ohio River drainage basin. Two surveys of the Ohio River and its five principal tributaries were conducted to characterize spatial variation in THMFP in relation to algal abundance and suspended organic matter. We performed three experiments by placing Ohio River water in 2000-L outdoor mesocosms and manipulating algal senescence and bloom development by shading. Increases in THMFP among high- and low-light and dark tanks suggest that algal production, algal senescence, and possibly photolysis increased THMFP by as much as 50% over 36 days. Comparable yields of THMs (per unit of chlorophyll) were observed in both survey and experimental settings. Comparison of input waters with outputs indicates that the Ohio River at times acts to attenuate downstream transport of THM precursors. Our findings suggest that both watershed-scale and internal processes regulating THMFP should be considered as utilities develop strategies to meet new drinking water guidelines.
Functional plasticity of benthic macroinvertebrates: implications for trophic dynamics in acid streams
Authors: Dangles Olivier
Published: October 2002

Functional plasticity of benthic macroinvertebrates was investigated over one year in four acid streams in the Vosges Mountains (northeastern France). The trophic position of macroinvertebrate species within the benthic food web was determined using gut content analyses. Diet analyses revealed that only 2436% of biomass of putative shredders consumed leaf fragments, whereas up to 44% consumed benthic algae and bryophytes. Although most Nemouromorpha stoneflies were generalist consumers, several other taxa (e.g., Brachyptera seticornis, Chaetopterygopsis maclachlani) specialised on benthic algae and bryophytes. Our study showed that acid streams unexpectedly had very few specialised leaf-shredding species (e.g., Chaetopteryx villosa) that could explain the slow leaf detritus processing rates observed in these systems. Primary producers appear to be an alternative resource for shredders, playing an important role in supporting food webs in forested acid streams. The food web built in this study suggests that overlooking species-specific functional plasticity of invertebrates may result in a misconception of invertebrate community structure in acid streams.
Comparison of equilibrium and nonequilibrium estimators for the generalized production model
Authors: Williams Erik H , Prager Michael H
Published: October 2002

Parameter estimation for the logistic (Schaefer) production model commonly uses an observation-error estimator, here termed the NM estimator, combining nonlinear-function minimization and forward projection of estimated population state. Although the NM estimator can be used to fit the generalized (PellaTomlinson) production model, an equilibrium approximation method (EA) is often used, despite calls in the literature to abandon equilibrium estimators. We examined relative merits of NM and EA estimators for the generalized model by fitting 48 000 simulated data sets describing five basic stock trajectories and widely varying population characteristics. Simulated populations followed the generalized production model exactly but were observed with random error. Both estimators were used on each data set to estimate several quantities of management interest. The estimates from NM were usually more accurate and precise than EA estimates, and overall, NM outperformed EA. This is the most comprehensive study of the question to datethe first to examine the generalized production modeland it demonstrates clearly why equilibrium estimators should be abandoned. Although valuable when introduced, they are no longer computationally necessary, they are no less demanding of data, and their performance is poor.
Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes
Authors: Ming Ray , Del Monte Terrye A. , Hernandez Eduardo , Moore Paul H , Irvine James E , Paterson Andrew H
Published: October 2002

Quantitative trait loci (QTLs) affecting plant height and flowering were studied in the two Saccharum species from which modern sugarcane cultivars are derived. Two segregating populations derived from interspecific crosses between Saccharum officinarum and Saccharum spontaneum were genotyped with 735 DNA markers. Among the 65 significant associations found between these two traits and DNA markers, 35 of the loci were linked to sugarcane genetic maps and 30 were unlinked DNA markers. Twenty-one of the 35 mapped QTLs were clustered in eight genomic regions of six sugarcane homologous groups. Some of these could be divergent alleles at homologous loci, making the actual number of genes implicated in these traits much less than 35. Four QTL clusters controlling plant height in sugarcane corresponded closely to four of the six plant-height QTLs previously mapped in sorghum. One QTL controlling flowering in sugarcane corresponded to one of three flowering QTLs mapped in sorghum. The correspondence in locations of QTLs affecting plant height and flowering in sugarcane and sorghum reinforce the notion that the simple sorghum genome is a valuable "template" for molecular dissection of the much more complex sugarcane genome.Key words: DNA markers, genetic map, quantitative trait loci, Saccharum.
AFLP markers linked to resistance againstStriga gesnerioidesrace 1 in cowpea (Vigna unguiculata)
Authors: Ouédraogo Jeremy T , Tignegre Jean-Baptiste , Timko Michael P , Belzile François J
Published: October 2002

Amplified fragment length polymorphism (AFLP) analysis was used in combination with bulked segregant analysis (BSA) to identify molecular markers linked to two cowpea (Vigna unguiculata (L.) Walp.) genes conferring resistance to Striga gesnerioides race 1. After AFLP analysis of an F2population derived from a cross between the resistant cultivar Gorom and the susceptible cultivar Tvx 3236, seven AFLP markers were identified that are linked to Rsg3, the gene conferring race 1 resistance in 'Gorom'. The distances between these markers and Rsg3 ranged from 9.9 to 2.5 cM, with two markers, E-AGA/M-CTA460and E-AGA/M-CAG300, flanking Rsg3 at 2.5 and 2.6 cM, respectively. Analysis of a second F2population derived from the cross between 'Tvx 3236' and the resistant cultivar IT81D-994 identified five AFLP markers linked to the race 1 resistance gene 994-Rsg present in 'IT81D-994'. The two markers showing the tightest linkage to the994-Rsg locus were E-AAG/M-AAC450and E-AAG/M-AAC150at 2.1 and 2.0 cM, respectively. Two of the markers linked to 994-Rsg, E-AGA/M-CAG300and E-AGA/M-CAG450, were also linked to Rsg3. The identification of molecular markers in common between the two sources of race 1 resistance suggests that either Striga resistance genes are clustered in these plants or that these loci are allelic. Mapping of the resistance loci within the cowpea genome revealed that three markers linked to Rsg3 and (or) 994-Rsg are located on linkage group 6.Key words: cowpea, AFLP markers, Striga resistance, bulked segregant analysis.
Expression and genomic organization of the zebrafish chaperonin gene complex
Authors: Martin C Cristofre , Tsang Cemaine H , Beiko Robert G , Krone Patrick H
Published: October 2002

Chaperonin 10 and chaperonin 60 monomers exist within the multimeric mitochondrial chaperonin folding complex with a stoichiometry of 2:1. This complex is located in the mitochondrial matrix, where it aids in the folding and acquisition of the tertiary structure of proteins. We have previously isolated the cpn10 cDNA in zebrafish (Danio rerio), and demonstrated that it is ubiquitously expressed during embryonic development and transcriptionally upregulated after exposure to heat shock. In the present study, we have isolated a cDNA encoding chaperonin 60 (cpn60) from zebrafish, and have shown that it is similarly expressed uniformly and ubiquitously throughout early embryonic development of zebrafish. Upregulation of cpn60 expression was also observed after exposure of zebrafish embryos to a heat shock of 1 h at 37°C compared with control embryos raised at 27°C. The induction of the cpn60 heat shock response was greatest after 1 h of heat shock, whereas significant decreases of cpn60 mRNA were observed within 2 h following a return to 27°C. We subsequently isolated genomic DNA sequences for both of these genes, and show that they are also arranged in a head-to-head organization and share a common bidirectional promoter that contains a single heat shock element (HSE). Our database analysis shows that this head-to-head organization is also found in human (Homo sapiens), rat (Rattus norvegicus), pufferfish (Fugu rubripes), and Caenorhabditis elegans, but not in Drosophila or yeast (Saccharomyces cerevisiae). The data suggest that the genomic organization of the cpn gene complex has been conserved across the vertebrates.Key words: zebrafish, chaperones, heat shock, promoter, chaperonin.
Development and characterization of polymorphic microsatellite markers in taro (Colocasia esculenta)
Authors: Mace Emma S , Godwin Ian D
Published: October 2002

Microsatellite-containing sequences were isolated from enriched genomic libraries of taro (Colocasia esculenta (L.) Schott). The sequencing of 269 clones yielded 77 inserts containing repeat motifs. The majority of these (81.7%) were dinucleotide or trinucleotide repeats. The GT/CA repeat motif was the most common, accounting for 42% of all repeat types. From a total of 43 primer pairs designed, 41 produced markers within the expected size range. Sixteen (39%) were polymorphic when screened against a restricted set of taro genotypes from Southeast Asia and Oceania, with an average of 3.2 alleles detected on each locus. These markers represent a useful resource for taro germplasm management, genome mapping, and marker-assisted selection.Key words: Colocasia esculenta, microsatellite-enriched genomic library, simple sequence repeats, germplasm characterization.
Molecular analysis of the complete set of length mutations found in the plastomes ofTriticumAegilopsspecies
Authors: Ogihara Y , Ohsawa T
Published: October 2002

Precise location and nature of each of 14 length mutations detected among chloroplast DNAs of TriticumAegilops species by RFLP analysis were determined at the nucleotide sequence level. Each mutation was compared with at least three non-mutated wild-type plastomes as standards. These 14 length mutations were classified into 4 duplications and 10 deletions. One duplication occurred in the small single-copy region close to the border of the inverted repeat, and the remaining 13 length mutations took place in the large single-copy region. All length mutations occurred in the intergenic regions, suggesting that these length mutations do not affect plastid gene expression. Saltatory replication was the cause of all duplications, whereas intramolecular recombination mediated by short direct repeats played a substantial role in the deletions. Recurrent occurrences of certain deletion events were found in some AT-rich regions, which constituted hot spots for deletion. Out of four hypervariable regions detected among the grass plastomes, two (downstream of rbcL and a tRNA gene accumulated region) were still active after differentiation of Triticum and Aegilops complex.Key words: insertionsdeletions, plastome, TriticumAegilops, deletion hot spots, molecular mechanism.
Chromosome landing near avirulence gene vH13 in the Hessian fly
Authors: Rider, Jr. Stanley Dean , Sun Weilin , Ratcliffe Roger H , Stuart Jeffrey J
Published: October 2002

AFLP markers in linkage disequilibrium with vH13, an avirulence gene in the Hessian fly (Mayetiola destructor) that conditions avirulence to resistance gene H13 in wheat (Triticum spp.), were discovered by bulked segregant analysis. Five AFLPs were converted into codominant site-specific markers that genetically mapped within 13 cM of this gene. Flanking markers used as probes positioned vH13 near the telomere of the short arm of Hessian fly chromosome X2. These results suggest that the X-linked avirulence genes vH6, vH9, and vH13 are present on Hessian fly chromosome X2 rather than on chromosome X1 as reported previously. Genetic complementation demonstrated that recessive alleles of vH13 were responsible for the H13-virulence observed in populations derived from four different states in the U.S.A.: Georgia, Maryland, Virginia, and Washington. Results support the hypothesis that a gene-for-gene interaction exists between wheat and Hessian fly.Key words: bulked segregant analysis, gene-for-gene interaction, wheat, Triticum, Mayetiola destructor.
Localization of a new highly repeated DNA sequence of Lemur catta (Lemuridae, Strepsirhini)
Authors: Boniotto Michele , Ventura Mario , Cardone Maria Francesca , Boaretto Francesca , Archidiacono Nicoletta , Rocchi Mariano , Crovella Sergio
Published: October 2002

We have isolated and cloned an 800-bp highly repeated DNA (HRDNA) sequence from Lemur catta (LCA) and described its localization on LCA chromosomes. Lemur catta HRDNA sequences were localized by performing FISH experiments on standard and elongated metaphasic chromosomes using an LCA HRDNA probe (LCASAT). A complex hybridization pattern was detected. A strong pericentromeric hybridization signal was observed on most LCA chromosomes. Chromosomes 7 and 13 were lit in pericentromeric regions, as well as in the interspersed heterochromatin. Chromosomes 1, 3, 4, 17, 19, X, and microchromosomes (20, 25, 26, and 27) showed no signals in the pericentromeric region, but chromosomes 3 and 4 showed a positive hybridization in heterochromatic regions. The 800-bp L. catta HRDNA was species specific. We performed FISH experiments with the LCASAT probe on Eulemur macaco macaco (EMA) andEulemur fulvus fulvus (EFU) metaphases and no positive signal of hybridization was detected. These findings were also confirmed by Southern blot analysis and PCR.Key words: highly repeated DNA, FISH, chromosome rearrangements, heterochromatin, Malagasy lemurs.
Analysis of 106 kb of contiguous DNA sequence from the D genome of wheat reveals high gene density and a complex arrangement of genes related to disease resistance
Authors: Brooks Steven A , Huang Li , Gill Bikram S , Fellers John P
Published: October 2002

Vast differences exist in genome sizes of higher plants; however, gene count remains relatively constant among species. Differences observed in DNA content can be attributed to retroelement amplification leading to genome expansion. Cytological and genetic studies have demonstrated that genes are clustered in islands rather than distributed at random in the genome. Analysis of gene islands within highly repetitive genomes of plants like wheat remains largely unstudied. The objective of our work was to sequence and characterize a contiguous DNA sequence from chromosome 1DS of Aegilops tauschii. An RFLP probe that maps to the Lr21 region of 1DS was used to isolate a single BAC. The BAC was sequenced and is 106 kb in length. The contiguous DNA sequence contains a 46-kb retroelement-free gene island containing seven coding sequences. Within the gene island is a complex arrangement of resistance and defense response genes. Overall gene density in this BAC is 1 gene per 8.9 kb. This report demonstrates that wheat and its relatives do contain regions with gene densities similar to that of Arabidopsis.Key words: resistance gene block, nucleotide-binding site, pathogenesis-related genes.
Genome size and developmental parameters in the homeothermic vertebrates
Authors: Gregory T Ryan
Published: October 2002

Although unrelated to any intuitive notions of organismal complexity, haploid genome sizes (C values) are correlated with a variety of cellular and organismal parameters in different taxa. In some cases, these relationships are universal  notably, genome size correlates positively with cell size in each of the vertebrate classes. Other relationships are apparently relevant only in particular groups. For example, although genome size is inversely correlated with metabolic rate in both mammals and birds, no such relationship is found in amphibians. More recently, it has been suggested that developmental rate and (or) longevity are related to genome size in birds. In the present study, a large dataset was used to examine possible relationships between genome size and various developmental parameters in both birds and mammals. In neither group does development appear to be of relevance to genome size evolution (except perhaps indirectly in birds through the intermediation of body size and (or) within the rodents), a situation very different from that found in amphibians. These findings make it clear that genome size evolution cannot be understood without reference to the particular biology of the organisms under study.Key words: body size, C-value enigma, C-value paradox, fledging, gestation, growth, incubation, lactation, metabolism.
A method for assaying the sensitivity ofDrosophilareplication checkpoint mutants to anti-cancer and DNA-damaging drugs.
Authors: Radcliffe Colleen M , Silva Elizabeth A , Campbell Shelagh D
Published: October 2002

In multi-cellular organisms, failure to properly regulate cell-cycle progression can result in inappropriate cell death or uncontrolled cell division leading to tumor formation. To guard against such events, conserved regulatory mechanisms called "checkpoints" block progression into mitosis in response to DNA damage and incomplete replication, as well as in response to other signals. Checkpoint mutants in organisms as diverse as yeast and humans are sensitive to various chemical agents that inhibit DNA replication or cause DNA damage. This phenomenon is the primary rationale for chemotherapy, which uses drugs that preferentially target tumor cells with compromised checkpoints. In this study, we demonstrate the use of Drosophila checkpoint mutants as a system for assaying the effects of various DNA-damaging and anti-cancer agents in a developing multicellular organism. Dwee1, grp and mei-41 are genes that encode kinases that function in the DNA replication checkpoint. We tested zygotic mutants of each gene for sensitivity to the DNA replication inhibitor hydroxyurea (HU), methyl methanosulfonate (MMS), ara-C, cisplatin, and the oxygen radical generating compound paraquat. The mutants show distinct differences in their sensitivity to each of the drugs tested, suggesting an underlying complexity in the responses of individual checkpoint genes to genotoxic stress.Key words: hydroxyurea (HU), ara-C, cisplatin, methyl methane sulfonate (MMS), paraquat.
DNA methylation analysis of a male reproductive organ specific gene (MROS1) during pollen development
Authors: Janousek Bohuslav , Matsunaga Sachihiro , Kejnovsky Eduard , Zluvova Jitka , Vyskot Boris
Published: October 2002

Pollen grains of angiosperm plants represent a good model system for studies of chromatin structure and remodelling factors, but very little is known about the DNA methylation status of particular genes in pollen. In this study, we present an analysis of the DNA methylation patterns of the MROS1 gene, which is expressed in the late phases of pollen development in Silene latifolia (syn. Meladrium album). The genomic sequencing technique revealed similar DNA methylation patterns in leaves, binucleate pollen, and trinucleate pollen. Extremely high DNA methylation levels occurred in the CG dinucleotides of the upstream region (99%), whereas only a low level of CG methylation was observed in the transcribed sequence (7%). Low levels of methylation were also observed in asymmetric sequences (in both regions; 2% methylated). The results obtained in the MROS1 gene are discussed in consequence with the immunohistochemical data showing a hypermethylation of DNA in the vegetative nucleus.Key words: DNA methylation, genomic sequencing, immunocytology, pollen, Silene latifolia.
Towards the saturation of the pepper linkage map by alignment of three intraspecific maps including known-function genes
Authors: Lefebvre V , Pflieger S , Thabuis A , Caranta C , Blattes A , Chauvet J -C , Daubèze A -M , Palloix A
Published: October 2002

Three populations composed of a total of 215 doubled haploid lines and 151 F2individuals were used to design an intraspecific consensus map of pepper (Capsicum annuum L.). The individual maps varied from 685 to 1668 cM with 16 to 20 linkage groups (LGs). The alignment of the three individual maps permitted the arrangement of 12 consensus major linkage groups corresponding to the basic chromosome number of pepper and displaying a complex correspondence with the tomato map. The consensus map contained 100 known-function gene markers and 5 loci of agronomic interest (the disease-resistance loci L, pvr2, and Pvr4; the C locus, which determines capsaicin content; and the up locus, controlling the erect habit of the fruits). The locations of three other disease-resistance loci (Tsw, Me3, and Bs3) and the y locus, which determines the yellow fruit colour, were also found on this consensus map thanks to linked markers. Here we report on the first functional detailed map in pepper. The use of candidate gene sequences as genetic markers allowed us to localize four clusters of disease-resistance gene analogues and to establish syntenic relationships with other species.Key words: Capsicum annuum L., comparative mapping, molecular marker, candidate gene, Solanaceae.
Genetic diversity of root-knot nematodes from Brazil and development of SCAR markers specific for the coffee-damaging species
Authors: Randig Onivaldo , Bongiovanni Michel , Carneiro Regina M.D.G , Castagnone-Sereno Philippe
Published: October 2002

RAPD markers were used to characterize the genetic diversity and relationships of root-knot nematodes (RKN) (Meloidogyne spp.) in Brazil. A high level of infraspecific polymorphism was detected in Meloidogyne arenaria, Meloidogyne exigua, and Meloidogyne hapla compared with the other species tested. Phylogenetic analyses showed that M. hapla and M. exigua are more closely related to one another than they are to the other species, and illustrated the early divergence of these meiotically reproducing species from the mitotic ones. To develop a PCR-based assay to specifically identify RKN associated with coffee, three RAPD markers were further transformed into sequence-characterized amplified region (SCAR) markers specific for M. exigua, Meloigogyne incognita and Meloidogyne paranaensis, respectively. After PCR using the SCAR primers, the initial polymorphism was retained as the presence or absence of amplification. Moreover, multiplex PCR using the three pairs of SCAR primers in a single reaction enabled the unambiguous identification of each species, even in mixtures. Therefore, it is concluded that the method developed here has potential for application in routine diagnostic procedures.Key words: diagnostic, multiplex PCR, phylogeny, RAPD, root-knot nematodes.
Direct capture and cloning of receptor kinase and peroxidase genes from genomic DNA
Authors: Cheng Davis W , Armstrong Ken C
Published: October 2002

A direct DNA capture and cloning procedure with magnetic bead separation was used to isolate receptor kinase like and peroxidase genes from oat (Avena sativa) and wheat (Triticum aestivum L.) genomic DNA, respectively. In this procedure, the digoxigenin-labeled probe DNA and target genomic DNA fragments were mixed, denatured, and hybridized. The double-helix complexes formed were captured with anti-digoxigenin immunoglobulin-coated magnetic beads and then cloned into either the lambdaBlueSTAR or pUC18 vector. The effectiveness of this procedure was demonstrated by using two specific DNA probes to capture receptor-like kinase genes and surrounding sequences from oat genomic DNA and a peroxidase gene from wheat genomic DNA.Key words: magnetic beads, enrichment, oat, wheat, Avena sativa, Triticum aestivum.
Comparative analysis of different satellite DNAs in four Mytilus species
Authors: Martínez-Lage A , Rodríguez F , González-Tizón A , Prats E , Cornudella L , Méndez J
Published: October 2002

We report the characterization of three satellite DNAs in four species of mussel: Mytilus edulis, Mytilus galloprovincialis, Mytilus trossulus, and Mytilus californianus. The monomers of the Apa I satellite DNAs were 173, 161, and 166 bp long. These satellite monomers were used to construct phylogenetic trees to infer relationships among these species. The topologies obtained clearly indicate that M. californianus is the most divergent species with respect to the other three. Furthermore, localization of satellite DNAs on metaphase chromosomes was performed using fluorescent in situ hybridization (FISH). Fluorescent signals revealed a different organization and distribution of these three satellite DNAs.Key words: satellite DNA, phylogeny, mussel, Mytilus.
Photographic polytene chromosome maps forGlossina morsitans submorsitans(Diptera: Glossinidae): cytogenetic analysis of a colony with sex-ratio distortion
Authors: Gariou-Papalexiou A , Yannopoulos G , Zacharopoulou A , Gooding R H
Published: October 2002

Photographic polytene chromosome maps from trichogen cells of pharate adult Glossina morsitans submorsitans were constructed. Using the standard system employed to map polytene chromosomes of Drosophila, the characteristic landmarks were described for the X chromosome and the two autosomes (L1and L2). Sex-ratio distortion, which is expressed in male G. m. submorsitans, was found to be associated with an X chromosome (XB) that contains three inversions in each arm. Preliminary data indicate no differences in the fecundity of XAXAand XAXBfemales, but there are indications that G. m. submorsitans in colonies originating from Burkina Faso and Nigeria have genes on the autosomes and (or) the Y chromosome that suppress expression of sex-ratio distortion.Key words: tsetse, Glossina morsitans submorsitans, polytene chromosome maps, inversions, sex-ratio distortion.