bluuebunny/crossref_metadata_2025 huggingface dataset:
Finding a cold needle in a warm haystack: infrared imaging applied to locating cryocooled crystals in loops
Authors: Snell Edward H. , van der Woerd Mark J. , Miller Mitchell D. , Deacon Ashley M.
Published: January 2005

The use of infrared imaging to locate crystals mounted in cryoloops and cryopreserved in a nitrogen gas stream at 100 K is demonstrated. In the home laboratory, crystals are clearly seen in the infrared images with light transmitting through the sample while irradiating the crystal from behind, and with illumination from a direction perpendicular to the direction of view. The crystals transmit and reflect infrared radiation at different levels to the surrounding mother liquor and loop. Because of differences in contrast between crystals and their surrounding mother liquor, it is possible to identify the crystal position. At the synchrotron, with robotically mounted crystals, the small depth of field of the lens required the recording of multiple images at different focal points. Image processing techniques were then used to construct a clear image of the crystal. The resulting infrared images and intensity profiles show that infrared imaging can be a powerful complement to visual imaging in locating crystals in cryocooled loops.
SAXS of self-assembled nanocomposite films with oriented two-dimensional cylinder arrays: an advanced method of evaluation
Authors: Ruland Wilhelm , Smarsly Bernd
Published: January 2005

In a recent paper [Ruland & Smarsly (2002).J. Appl. Cryst.35, 624–633], an advanced method for the evaluation of the small-angle X-ray scattering (SAXS) from oriented lamellar systems was presented. In the present work, a comparable method is developed for the study of oriented cylinder arrays. Basic differences between the two methods are found in the way in which the preferred orientation affects the intensity distribution. The method is applied to the SAXS of SiO2-surfactant nanocomposite films which contain highly oriented arrays of cylinders. It is shown that up to eight structural parameters can be obtained by this method which characterize size, imperfection and preferred orientation of the two-dimensional hexagonal lattice formed by the cylinders, the radius and the polydispersity of the cylinders, and the interface boundary.
The intersect distribution of the regular tetrahedron
Authors: Ciccariello Salvino
Published: January 2005

A calculation of the intersect distribution of the regular tetrahedron is given throughout its full range of distances. This splits into five intervals where the closed algebraic expressions of the chord distribution are explicitly calculated. The resulting expressions are surprisingly simple within the three inner intervals and not particularly involved in the two outer ones. The implications of these expressions for the asymptotic behaviour of the scattering intensity are briefly discussed.
Bainite and stress-induced martensite in an AISI type 300 steel: an X-ray diffraction study of the microstructure by the Rietveld method
Authors: Sahu P.
Published: January 2005

The present study concerns the X-ray characterization of the microstructure of an AISI type 300 stainless steel with composition Fe–17Cr–8Ni–1Mn–0.1C (wt%), undergoing stress-induced martensite and bainite transformations following γ(f.c.c.) → α(b.c.c.) transformation reactions. The methodology applied is a Rietveld whole X-ray profile fitting technique, adopting the recently developed softwareMAUD(Materials Analysis Using Diffraction) which incorporates the Popa model for crystallite size and microstrain [root mean square (r.m.s.) strain] and the preferred orientation of the crystallites. The analysis also considers the lattice-defect-related features of the evolved microstructures, namely stacking-fault probabilities and dislocation-density values. The study revealed a high degree of stress-induced martensitic transformation (∼94%) in the cold-worked (hand-filed powder) state of the material. However, no low-temperature martensitic transformation could be observed in this class of materials at temperatures below the martensite start temperature (Ms). On isothermal aging at 673 K for different periods of time (1, 3 and 6 h), the austenite transforms partially into bainite with continuously varying volume fractions (17, 42 and 44%) and the corresponding microhardness values are 218, 230 and 233 kg mm−2. The size–strain–shape analysis adopting the Popa model reveals anisotropic and almost isotropic values of the crystallite sizes and r.m.s. strains in the austenite and bainite microstructures, respectively. High values of the dislocation density (∼1016 m−2) were observed in the bainite due to the plastic deformation of the austenite induced by the shape change of the growing bainite. The values of all the above defect parameters have been evaluated and compared in order to elucidate the structure–property relationships.
Characterization of a hybrid Monte Carlo search algorithm for structure determination
Authors: Markvardsen Anders J. , Shankland Kenneth , David William I. F. , Didlick Gareth
Published: January 2005

A hybrid Monte Carlo (HMC) search algorithm has recently been shown to be a promising method for structure determination from powder diffraction data [Johnston, David, Markvardsen & Shankland (2002).Acta Cryst.A58, 441–447]. Here, the performance of the algorithm on a number of different crystal structures is investigated as a function of its control parameters. This detailed analysis required the use of a system for distributed computing in order to keep the calculation times within a reasonable time frame. The results obtained confirm previous findings and a detailed discussion of the effect of the control parameters on the efficiency of the HMC method is provided. The results suggest a method for setting these parameters automatically, which is an essential step if HMC is to find routine use in the determination of crystal structures.
In situanomalous small-angle X-ray scattering from metal particles in supported-metal catalysts. I. Theory
Authors: Brumberger H. , Hagrman D. , Goodisman J. , Finkelstein K. D.
Published: January 2005

A supported-metal catalyst can be considered as a mixture of three homogeneous phases: support, void and metal. Information about the metal phase alone can be obtained using anomalous small-angle X-ray scattering (ASAXS), which requires measuring the SAXS for two different wavelengths near the metal's absorption edge. Herein, the conditions that must be obtained so that the difference between the two scattering profiles gives the scattering of the metal alone are presented. In a following contribution, the analysis will be applied toin situASAXS measurements made on mordenite impregnated with platinum metal while the temperature and composition of gas in the sample cell are changed. The metal particles are assumed to be randomly distributed spheres withN(R)dRbeing the number of spheres with radii betweenRandR+ dR. FromN(R) one can obtain the average value ofR.
X-ray scattering from unilamellar lipid vesicles
Authors: Brzustowicz Michael R. , Brunger Axel T.
Published: January 2005

An improved small-angle X-ray scattering (SAXS) method for determining asymmetric lipid bilayer structure in unilamellar vesicles is presented. From scattering theory, analytic expressions are derived for the bilayer form factor over flat and spherical geometries, assuming the lipid bilayer electron density to be composed of a series of Gaussian shells. This is in contrast to both classic diffraction and Guinier hard-shell SAXS methods which, respectively, are capable only of ascertaining symmetric bilayer structure and limited-resolution asymmetric structure. Using model fitting and direct calculation of the form factor, using only one equation, an asymmetric electron density profile of the lipid vesicle is obtained with high accuracy, as well as the average radius. The analysis suggests that the inner leaflet of a unilamellar lipid vesicle is `rougher' than the outer one.
The defect structure of Y- and N-doped zirconia
Authors: Kaiser-Bischoff Ines , Boysen Hans , Frey Friedrich , Hoffmann Jens-Uwe , Hohlwein Dietmar , Lerch Martin
Published: January 2005

The diffuse scattering of a single crystal of the quaternary system Zr–Y–O–N (Zr0.96Y0.04O1.64N0.223) has been recorded by neutron diffraction in different layers of the [1\bar{1}0] and [100] zones to study the short-range order originating from anion vacancies. A new model is proposed with uncorrelated anion vacancies and radial shifts of the surrounding ions towards or away from the vacancies. The parameters of the model were refined by fitting to the diffuse scattering intensities. The shortest Zr–anion distance is reduced, indicating covalent contributions.
Automated detection of disulfide bridges in electron density maps using linear discriminant analysis
Authors: Ioerger Thomas R.
Published: January 2005

The ability to recognize disulfide bridges automatically in electron density maps would be useful to both protein crystallographers and automated model-building programs. A computational method is described for recognizing disulfide bridges in uninterpreted maps based on linear discriminant analysis. For each localized spherical region in a map, a vector of rotation-invariant numeric features is calculated that captures various aspects of the local pattern of density. These features values are then input into a linear equation, with coefficients computed to optimize discrimination of a set of training examples (disulfides and non-disulfides), and compared with a decision threshold. The method is shown to be highly accurate at distinguishing disulfides from non-disulfides in both the original training data and in real (experimental) electron density maps of other proteins.
Analysis of the mosaic structure of an ordered (Al,Ga)N layer
Authors: Kirste L. , Pavlov K. M. , Mudie S. T. , Punegov V. I. , Herres N.
Published: January 2005

The mosaic structure of an (Al,Ga)N layer grown on (0001) sapphire showing natural ordering was studied by high-resolution X-ray diffraction (HRXRD) reciprocal-space mapping. The direction-dependent mosaicity of the layer has been elaborated using maps of symmetrical and asymmetrical reflections. The reciprocal-lattice points show significant broadening depending on the direction in reciprocal space, the diffraction order and the reflection type (fundamental or superstructural). The evaluation followed two paths: (i) a procedure based on the Williamson–Hall plot and (ii) a new approach based on the statistical diffraction theory (SDT). Here, the transformed Takagi equations were implemented for the simulation of the reciprocal-space maps (RSM) for symmetrical and asymmetrical reflections. The reconstruction comprised the mosaic block size, their average rotation angle and the spatial distribution of some components of the microdistortion tensor. The results based on the SDT modelling agree well with those obtained by the Williamson–Hall method, while providing a higher degree of precision and detail.
VALTOPO: a program for the determination of atomic and molecular properties from experimental electron densities
Authors: Bianchi Riccardo , Forni Alessandra
Published: January 2005

VALTOPOis a program for the multipole refinement of accurate X-ray diffraction data and for the determination of electrostatic properties. It is a new version ofVALRAY, including the quantum theory of atoms in molecules analysis as implemented in theTOPOND98program. Two test structures, L-alanine and the complex of (E)-1,2-bis(4-pyridyl)ethylene with 1,4-diiodotetrafluorobenzene, have been analysed in order to illustrate some of the potentialities of the program.
X-ray absorption, refraction and resonant scattering tensors in selenated protein crystals: implications for data collection strategies in macromolecular crystallography
Authors: Bricogne G. , Capelli S. C. , Evans G. , Mitschler A. , Pattison P. , Roversi P. , Schiltz M.
Published: January 2005

Polarized fluorescence spectra were recorded in the vicinity of the Se and BrKedges on crystals of the selenated protein aldose reductase in complex with a brominated inhibitor molecule. The X-ray absorption, refraction and resonant scattering tensors as a function of X-ray energy were derived from these data. Substantial dichroism and anisotropy of resonant scattering were observed in these crystals. It is predicted that these effects are present in many resonant scattering experiments in macromolecular crystallography and are likely to affect the diffraction data. As a consequence, the anomalous phasing signal in single- or multi-wavelength anomalous diffraction experiments can be optimized simply by choosing a judicious orientation of the crystal with respect to the polarization direction of the incident X-ray beam. A simple procedure is presented to achieve this, prior to any knowledge about the selenium sites.
Likelihood weighting of partial structure factors using spline coefficients
Authors: Cowtan Kevin
Published: January 2005

A method for the weighting of structure factors from an incomplete and inaccurate model is described which relies on the fitting of smooth spline functions of resolution. The use of smooth spline functions avoids the problems of discontinuities introduced when performing calculations in resolution shells. The complexity of the functions to be fit may be varied by changing the number of spline parameters. This approach is used to investigate the stability of the problem when data are limited.
Abinitiostructure solution of nucleic acids and proteins by direct methods: reciprocal-space and real-space approach
Authors: Chowdhury Krishna , Bhattacharya Soma , Mukherjee Monika
Published: January 2005

Anab initiomethod for solving macromolecular structures is described. The heavy atom(s) or some disulfide bridge in the structure are located from the phase sets selected on the basis of a figure of merit of a reciprocal-space-based multiple-solution direct method. Subsequent weighted Fourier recycling reveals recognizable structures for two nucleic acids where data resolution is 1.3 Å or better. With lower than 1.3 Å data resolution or sulfur as the heaviest atom in the structure, the phase refinement has been carried out using the density modification procedure (PERP) operating in direct space. The resulting electron density map can readily be interpreted. The methodology has been illustrated with six known nucleic acids and proteins crystallizing in different space groups. It has proved to be fast, simple to use and a very effective tool for solving macromolecular structures with data resolution up to 1.7 Å.
Lipid content and fatty acid composition of target tissues in wild Perca fluviatilis females in relation to hepatic status and gonad maturation
Authors: Blanchard G. , Druart X. , Kestemont P.
Published: January 2005

Variation in liver ultra‐structure and composition in relation to energy mobilization was investigated in female perch Perca fluviatilis from the Meuse River between August 2001 and June 2002. In April, just before spawning, the lipo‐somatic index (IF) was 0·3%, the gonado‐somatic index (IG) was 28% and the total lipid content of the liver was 2·53%. The average areas of lipid droplets and mitochondria were 0·05 and 0·06 μm2, respectively. Glycogen supply reached 7·9% of the total area of the hepatocyte. During the sexual resting period, females accumulated energy in perivisceral fat and in the liver to reach 1·6%IF and 4·85% of liver lipid content in August with lipid droplets average size of 0·09 μm2 and glycogen average area of 15%. Liver cells contained a weakly developed rough endoplasmic reticulum (RER) and a great number of small mitochondria (average size 0·02 μm2). The IG was 0·6% at this time. During the whole annual cycle, the average lipid content of female liver never exceeded 3·9 ± 1·9%. The concentration of docosahexaenoic (DHA), linolenic and linoleic acids increased in mature gonads while linolenic and linoleic acids decreased in the liver during the same period. Fatty acid composition of muscles of perch was characterized by a high content of DHA.
Migration of hatchery‐reared Atlantic salmon and wild anadromous brown trout post‐smolts in a Norwegian fjord system
Authors: Finstad B. , Økland F. , Thorstad E. B. , BjØrn P. A. , McKinley R. S.
Published: January 2005

Hatchery‐reared Atlantic salmon Salmo salar(n = 25) and wild anadromous brown trout (sea trout) Salmo trutta(n = 15) smolts were tagged with coded acoustic transmitters and released at the mouth of the River Eira on the west coast of Norway. Data logging receivers recorded the fish during their outward migration at 9, 32, 48 and 77 km from the release site. Seventeen Atlantic salmon (68%) and eight sea trout (53%) were recorded after release. Mean migratory speeds between different receiver sites ranged from 0·49 to 1·82 body lengths (total length) per second (bl s−1) for Atlantic salmon and 0·11–2·60 bl s−1 for sea trout. Atlantic salmon were recorded 9, 48 and 77 km from the river mouth on average 28, 65 and 83 h after release, respectively. Sea trout were recorded 9 km from the release site 438 h after release. Only four (23%) sea trout were detected in the outer part of the fjord system, while the rest of the fish seemed to stay in the inner fjord system. The Atlantic salmon stayed for a longer time in the inner part than in the outer parts of the fjord system, but distinct from sea trout, migrated through the whole fjord system into the ocean.
The use of PIT telemetry to study movements of ammocoetes and metamorphosing sea lampreys in river beds
Authors: Quintella B. R. , Andrade N. O. , Espanhol R. , Almeida P. R.
Published: January 2005

Passive integrated transponder (PIT) tags were surgically implanted in 118 sea lamprey Petromyzon marinus ammocoetes which were left to recover in the laboratory for 2 months. During this period 55 individuals started to metamorphose. In the late summer of 2002 the tagged animals were released in a small tributary of the River Mondego, Portugal, and were regularly monitored for a period of 2 months using a portable PIT tag reader. The distribution of the released animals changed from an initial uniform pattern to a random distribution, and then to an aggregated pattern. At the end of the first week 60% of the tagged sea lampreys had already left the study area, indicating their dynamic behaviour. Ammocoetes were more active than metamorphosing sea lampreys, and downstream movements were more frequent when compared to the upstream ones, which were usually a short distance. In order to determine the influence of the dark‐light cycle in the diel activity rhythms, 10 tagged sea lamprey ammocoetes were released in a tank (2000 l capacity) and their position monitored twice a day, for a period of 1 month. Ammocoetes locomotor activity appeared to be conditioned by circadian rhythms, and they were particularly active during darkness.
Juvenile Sparus aurata L. on the south coast of Ireland
Authors: Fahy E. , Green P. , Quigley D.T.G.
Published: January 2005

Records of gilthead sea bream Sparus aurata L. in Irish and British waters since 1967 are provided together with the first observations on the ecology of 0 year group gilthead sea bream in these islands.
Changes in size and age at maturity in a population of kokanee Oncorhynchus nerka during a period of declining growth conditions
Authors: Grover M. C.
Published: January 2005

Trends in size distributions and age at maturity of spawning kokanee Oncorhynchus nerka during a 5 year period of declining growth conditions at Bucks Lake, California, U.S.A. were consistent with the hypothesis that reductions in growth rates in successive cohorts induce a shift to an older age at maturity. This forestalls decreases in size at maturity during a transitional period characterized by an increasing proportion of individuals that delay maturation. During the course of the study, kokanee first began declining in size at maturity, and then shifted from a 3 year to a 4 year egg to adult cycle. Individuals that spawned during their fourth year (age 3 years) were significantly larger, on average, than members of their cohort that spawned during their third year (age 2 years). This difference was greatest when age 2 year adults were smallest. The shift to an older age at maturity prevented a steady decline in size at maturity, even though age‐specific size was steadily declining over time. Size at maturity, however, began to decline again once the transition to a 4 year cycle was complete. In addition, there was a general trend of decreasing length‐specific mass. The data indicate that there is a range of growth trajectories over which delayed maturity can prevent a temporal pattern of decreasing size at maturity as growth rates decline.
Gape limitation and piscine prey size‐selection by yellow perch in the extreme southern area of Lake Michigan, with emphasis on two exotic prey items
Authors: Truemper H. A. , Lauer T. E.
Published: January 2005

The trophic linkage between yellow perch Perca flavescens and two exotic prey items, alewife Alosa pseudoharengus and round goby Neogobius melanostomus, was investigated in the extreme southern area of Lake Michigan during the summer of 2002. Yellow perch ≥100 mm total length, LT(n = 1293) exhibited size selective feeding, with 148 fish containing round gobies and 120 fish containing alewives. The mean round goby LT, preyed on by yellow perch, was 23% of the predator LT, with a range of 7 to 47%, and mean alewife LT was 32% of yellow perch LT, with a range of 18 to 46%. Although the selection of prey size by yellow perch increased proportionally with yellow perch LT, prey consumed appeared smaller than theoretically possible based on gape size.
Home range areas and activity centres in six species of Caribbean wrasses (Labridae)
Authors: Jones K. M. M.
Published: January 2005

In six Caribbean wrasse (Labridae) species:Halichoeres bivittatus,Halichoeres garnoti,Halichoeres maculipinna,Halichoeres poeyi,Halichoeres radiatusandThalassoma bifasciatum, home range area (AHR) was positively correlated with fish total length (LT) and this relationship was not significantly different amongH. bivittatus,H. garnoti,H. radiatusandT. bifasciatum. The data for three of these species (H. radiatuswas excluded because only juveniles were investigated) were pooled and the relationship betweenLTandAHRwas analysed for juveniles and initial phase (IP) adults separately. This analysis found that once individuals of these two species become IP adults, theAHRreached a plateau, despite continued fish growth. In a separate analysis including all six wrasse species, after accounting for differences inLTusing ANOVA, it was found that IP adults required larger areas than juveniles, and terminal phase (TP) adults required largerAHRthan IP adults. Upon analysis of the distribution of activity throughoutAHRfor all species studied, it was found that 50% of the observation points (defined as the activity centre) were found in 13 to 24% of theAHR.
Energy reserves during food deprivation and compensatory growth in juvenile roach: the importance of season and temperature
Authors: Van Dijk P. L. M. , Hardewig I. , HÖlker F.
Published: January 2005

The effect of 21 days of starvation, followed by a period of compensatory growth during refeeding, was studied in juvenile roach Rutilus rutilus during winter and summer, at 4, 20 and 27° C acclimation temperature and at a constant photoperiod (12L : 12D). Although light conditions were the same during summer and winter experiments and fish were acclimated to the same temperatures, there were significant differences in a range of variables between summer and winter. Generally winter fish were better prepared to face starvation than summer fish, especially when acclimated at a realistic cold season water temperature of 4° C. In winter, the cold acclimated fish had a two to three‐fold larger relative liver size with an approximately double fractional lipid content, in comparison to summer animals at the same temperature. Their white muscle protein and glycogen concentration, but not their lipid content, were significantly higher. Season, independent of photoperiod or reproductive cycle, was therefore an important factor that determined the physiological status of the animal, and should generally be taken into account when fish are acclimated to different temperature regimes. There were no significant differences between seasons with respect to growth. Juvenile roach showed compensatory growth at all three acclimation temperatures with maximal rates of compensatory growth at 27° C. The replenishment of body energy stores, which were utilized during the starvation period, was responsible for the observed mass gain at 4° C. The contribution of the different energy resources (protein, glycogen and lipid) was dependent on acclimation temperature. In 20 and 27° C acclimated roach, the energetic needs during food deprivation were met by metabolizing white muscle energy stores. While the concentration of white muscle glycogen had decreased after the fasting period, the concentrations of white muscle lipid and protein remained more or less constant. The mobilization of protein and fat was revealed by the reduced size of the muscle after fasting, which was reflected in a decrease in condition factor. At 20° C, liver lipids and glycogen were mobilized, which caused a decrease both in the relative liver size and in the concentration of these substrates. Liver size was also decreased after fasting in the 4° C acclimated fish, but the substrate concentrations remained stable. This experimental group additionally utilized white muscle glycogen during food deprivation. Almost all measured variables were back at the control level within 7 days of refeeding.
Moon phase and nocturnal density of Atlantic salmon parr in the Sainte‐Marguerite River, Québec
Authors: Imre I. , Boisclair D.
Published: January 2005

Nocturnal underwater counts of Atlantic salmon Salmo salar parr were made on four consecutive occasions (two lunar cycles, samplings at both the full and new moon) at four 40 m long sites in the Sainte‐Marguerite River, Québec, Canada, between 30 June and 14 August 2003. Atlantic salmon parr counts did not differ significantly between moon phases. Cloud cover ranged from 0 to 100% during the study, and had no significant effect on parr counts. There were significantly more Atlantic salmon parr in the near shore than in the midstream areas. The findings of this study suggest that the sampling strategy of summer studies aimed at assessing population abundance or developing habitat quality models can be designed without taking moon phase or cloud cover into consideration, but it should account for the higher relative abundance of Atlantic salmon parr in the near shore areas as compared to areas closer to the middle of streams.
Haematology of juvenile Acipenser oxyrinchus and Acipenser brevirostrum at rest and following forced activity
Authors: Baker D. W. , Wood A. M. , Litvak M. K. , Kieffer J. D.
Published: January 2005

In vivo experiments were conducted to examine the haematology of juveniles from two relic bony fishes, Atlantic sturgeon Acipenser oxyrhinchus and shortnose sturgeon Acipenser brevirostrum. Oxygen transport characteristics (haematocrit, haemoglobin and mean erythrocytic haemoglobin concentration), ionic composition (Na+, Cl−, K+ and osmolality), metabolite concentration (lactate, cortisol and glucose) and protein content in blood were measured or calculated at rest and during recovery from forced activity. Under resting conditions, plasma osmolality and concentrations of Na+, Cl−, lactate, cortisol and total protein were significantly different between Atlantic and shortnose sturgeon. All other resting variables were not different between species. Following forced activity, plasma lactate levels were significantly higher in both species than at rest. Plasma cortisol levels in both species were only significantly higher 1 h following forced activity compared to resting values. Plasma lactate levels were significantly higher in Atlantic sturgeon than in shortnose sturgeon, but these levels returned to resting levels by 1 h in both species. Cortisol increases were greater in shortnose sturgeon than in Atlantic sturgeon. In general, oxygen transport characteristics, blood glucose, plasma protein and plasma osmolality were not altered by forced activity in either sturgeon species. Overall, both species had reduced responses (i.e. the magnitude of changes in measured variables) to forced activity compared with teleosts.
Glycoconjugate distribution in gastric fundic mucosa of Umbrina cirrosa L. revealed by lectin histochemistry
Authors: Pedini V. , Dall’Aglio C. , Parillo F. , Scocco P.
Published: January 2005

The stomach of adult shi drum Umbrina cirrosa was investigated using a battery of nine horseradish peroxidase‐conjugated lectins combined with enzymatic treatment, in order to distinguish glycoconjugate sugar residues. Epithelial cells showed the presence of galactosyl(β1→4)N‐acetylglucosamine, mannose, N‐acetylgalactosamine, N‐acetylglucosamine, fucose and sialic acid‐galactosyl(β1→3)N‐acetylgalactosamine residues. Gastric pits had similar sugar residues with the exception of N‐acetylgalactosamine which was less diffused. Gastric glands were characterized by the presence of glycoconjugates containing galactosyl(β1→3)N‐acetylgalactosamine, N‐acetylglucosamine, galactosyl(β1→4) N‐acetylglucosamine, N‐acetylgalactosamine and a small amount of sialic acid linked to N‐acetylgalactosamine.
Behaviour impairment in captured and released sablefish: ecological consequences and possible substitute measures for delayed discard mortality
Authors: Davis M. W.
Published: January 2005

Sablefish Anoplopoma fimbria aged 1+ and 2+ years were towed for 4 h in a net, transferred to air for either 15 or 30 min, and then held in tanks for up to 35 days for observation of physical injury, immediate mortality, behaviour impairment, delayed mortality and total mortality. Behaviour was impaired for at least 3 h and returned to normal levels by 24 h after stress induction. Behaviour impairment was correlated with delayed mortality in 2+ year fish but not in 1+ year fish which showed greater variation in stress responses. The results of this study and a review of past discard and escapee studies showed that substitute measures for delayed mortality in the field should include physical injury and behaviour impairment. These two measures integrate the effects of capture‐related stressors which can produce and magnify physical and physiological injury, resulting in changes in fish condition and delayed mortality.
The anal fin complex in a weakly discharging electric fish, Gnathonemus petersii(Mormyridae)
Authors: Greisman L. , Moller P.
Published: January 2005

An examination of the permanent bony structures of the anal fin complex in the mormyrid fish, Gnathonemus petersii, revealed two new structural sexual dimorphisms: longer proximal pterygiophores and wider anal fin rays in males than in females. Both structures are thought to facilitate the male’s courtship‐associated anal fin reflex. Adult male mormyrid fishes are characterized by a dorsally directed indentation of the posterior body wall (anal fin indentation). The expression of this indentation in males, presumably driven by anal fin musculature, was correlated with the fish’s gonadal state: large indentations were associated with high gonado‐somatic indices and small indentations with low indices.
Characterization of bovine FAS‐associated death domain gene1
Authors: Szperka M. E. , Connor E. E. , Paape M. J. , Williams J. L. , Bannerman D. D.
Published: January 2005

The FAS‐associated death domain (FADD) protein is an adapter/signaling molecule that has been shown to function in human cells to promote apoptosis and to inhibit NF‐κB activation. Because of the critical role that apoptosis and NF‐κB play in a variety of disease states, we mapped the bovine FADD gene, sequenced bovine FADD cDNA, and characterized its expression in endothelial cells (EC). Sequencing of bovine FADD revealed approximately 65 and 58% amino acid sequence identity to its human and murine homologues, respectively. Bovine FADD was mapped to chromosome 29 by radiation hybrid mapping. In addition, the functionality of bovine FADD was studied. Expression of a bovine FADD dominant‐negative construct blocked bacterial lipopolysaccharide (LPS)‐ and TNF‐α‐induced apoptosis in bovine EC consistent with previous studies of human FADD. In contrast to human FADD, elevated expression of bovine FADD had no effect on LPS‐ or TNF‐α‐induced upregulation of NF‐κB‐dependent gene products as assayed by E‐selectin expression. Thus, while the role of FADD in mediating apoptosis is conserved across species, its role in regulating NF‐κB‐dependent gene expression is not.
Detection of quantitative trait loci for androstenone, skatole and boar taint in a cross between Large White and Meishan pigs
Authors: Lee G. J. , Archibald A. L. , Law A. S. , Lloyd S. , Wood J. , Haley C. S.
Published: January 2005

‘Boar taint’ is a strong perspiration‐like, urine‐like unpleasant odour given off upon heating or cooking of meat from some intact (uncastrated) male pigs. Data from the F2 generation of a Large White (LW) × Meishan (MS) crossbred population were analysed to detect quantitative trait loci (QTL) for traits associated with boar taint. Fat samples from 178 intact male pigs slaughtered at 85 ± 5 kg were analysed for the major contributors to boar taint (androstenone, indole and skatole). Fat and lean samples from cooked meat were scored for boar, abnormal and pork flavour and odour by a trained sensory panel (SP). A scan with 117 markers covering the whole genome was performed in the F2 individuals, together with their F1 parents and purebred grandparents. At the 5% chromosomal significance threshold (approximately equal to the genome‐wide suggestive significance threshold), QTL were detected for the laboratory estimate of androstenone on chromosomes 2, 4, 6, 7 and 9. However, only on chromosome 6 were there QTL for boar flavour (BF) traits in the same or adjacent marker intervals as a QTL for the laboratory estimate of androstenone. On chromosome 14, QTL were detected for the laboratory estimates of indole and skatole, the SP score for skatole and the scores for BF in lean and BF in fat. In all five cases, the MS allele generally increased the estimate or score, compared with the LW allele, but it appeared that desirable and undesirable alleles were present in both breeds. This locus on chromosome 14 has considerable potential for use to reduce the incidence of boar taint, especially if further research can identify the causative polymorphism or strongly associated markers.
Using mitochondrial nucleotide sequences to investigate diversity and genealogical relationships within common carp (Cyprinus carpio L.)
Authors: Thai B. T. , Burridge C. P. , Pham T. A. , Austin C. M.
Published: January 2005

Direct sequencing of mitochondrial DNA (mtDNA) D‐loop (745 bp) and MTATPase6/MTATPase8 (857 bp) regions was used to investigate genetic variation within common carp and develop a global genealogy of common carp strains. The D‐loop region was more variable than the MTATPase6/MTATPase8 region, but given the wide distribution of carp the overall levels of sequence divergence were low. Levels of haplotype diversity varied widely among countries with Chinese, Indonesian and Vietnamese carp showing the greatest diversity whereas Japanese Koi and European carp had undetectable nucleotide variation. A genealogical analysis supports a close relationship between Vietnamese, Koi and Chinese Color carp strains and to a lesser extent, European carp. Chinese and Indonesian carp strains were the most divergent, and their relationships do not support the evolution of independent Asian and European lineages and current taxonomic treatments.
Mapping and association studies of diabetes related genes in the pig
Authors: Otieno C. J. , Bastiaansen J. , Ramos A. M. , Rothschild M. F.
Published: January 2005

The mitogen‐activated protein kinase 8 (MAPK8), resistin (RETN), 11 beta hydroxysteroid dehydrogenase isoform 1 (HSD11B1) and protein kinase B Akt2 (AKT2) genes are all genes known to affect insulin signalling and have been implicated in the progression of obesity and type 2 diabetes in humans. In this study, polymorphisms in the porcine diabetes related MAPK8, RETN, HSD11B1 and AKT2 genes were identified, mapped and their associations with phenotypic measurements in swine were analysed. Polymorphisms detected in the MAPK8, RETN and HSD11B1 loci were used to genotype a Berkshire–Yorkshire pig breed reference family. Using linkage analysis, RETN, HSD11B1 and MAPK8 genes were mapped to pig chromosomes 2, 9 and 14, respectively, while the AKT2 gene was physically mapped to pig chromosome 6q21. Results presented here suggest associations between the polymorphisms in the MAPK8, RETN and HSD11B1 genes with several phenotypic measurements, including fat deposition traits in the pig. Because these genes have been implicated in obesity and diabetes in humans, and this study suggests associations with fat related traits, further research on these genes in swine may provide useful information on genetic factors underlying lean pork production.
Genetic variation within and among domesticated Atlantic salmon broodstocks in British Columbia, Canada
Authors: Withler R. E. , Supernault K. J. , Miller K. M.
Published: January 2005

Atlantic salmon have been reared in the British Columbia, Canada aquaculture industry since the early 1980s. No breeding programmes spanned the entire production period and pedigree records were not kept for broodstocks prior to or since importation. Of the three recognized industry strains, two are of European ancestry (‘Mowi’ from Norway and ‘McConnell’ from Scotland) and one is of North American heritage (‘Cascade’ from Gaspé, Quebec). We evaluated the amount and distribution of genetic variation within industry broodstocks by surveying microsatellite variation at 11 loci in 20 broodstock groups sampled from major production facilities. Allelic richness averaged 10.9 (range 5.8–13.8), compared with a value of 20.3 obtained for a North American wild population. Pairwise genetic distances (DS) between samples within strains were generally less than those between strains, with samples attributed to the same strain clustering together in a neighbour‐joining dendrogram. Nevertheless, average distances between samples within the European strains were high (0.41 for Mowi; 0.71 for McConnell) but lower (0.06) for the Cascade strain. The reduced intra‐sample and increased intra‐strain genetic variation observed for the BC domesticated samples compared with wild populations was similar to observations for European domesticated Atlantic salmon. Evidence of introgression of the Cascade strain into European broodstocks was provided by the presence of large Ssa202 alleles (confined to North America in wild populations) in some Mowi and McConnell samples. Introgression likely also contributed to the decreased intercontinental genetic distance for the domesticated samples of this study compared with that observed for wild populations.
Sequence analysis of 0.4 megabases of the rabbit germline immunoglobulin kappa1 light chain locus
Authors: Ros F. , Reichenberger N. , Dragicevic T. , Van Schooten W. C. A. , Buelow R. , Platzer J.
Published: January 2005

Two rabbit germline bacterial artificial chromosome (BAC) libraries from animals with the b5 and b4 allotype were screened with probes specific for the immunoglobulin kappa1 light chain locus. Two partially overlapping BAC clones containing Vκ elements of b5 allotype were isolated from the b5 library and one BAC clone containing Jκ1, Cκ and Vκ was isolated from the b4 library. These three BAC clones were sequenced. They span about 0.4 MB of the rabbit Ig κ1 light chain locus including 36 Vκ elements, five J elements and the coding region of Cκ1. The organization of the locus and the potential function of newly identified functional and structural elements are discussed.
Effects of polymorphic microsatellites in the regulatory region of IGF1 and GHR on growth and carcass traits in beef cattle
Authors: Curi R. A. , de Oliveira H. N. , Silveira A. C. , Lopes C. R.
Published: January 2005

Growth hormone (GH), insulin‐like growth factors 1 and 2 (IGF1 and IGF2) and their associated binding proteins and transmembrane receptors (GHR, IGF1R and IGF2R) play an important role in the physiology of mammalian growth. The objectives of the present study were to estimate the allele and genotype frequencies of microsatellite markers located in the 5′‐regulatory region of the IGF1 and GHR genes in beef cattle belonging to different genetic groups and to determine effects of these markers on growth and carcass traits in these animals under an intensive production system. For this purpose, genotyping was performed on 384 bulls including 79 Nellore, 30 Canchim (5/8 Charolais + 3/8 Zebu) and 275 crossbred animals originating from crosses of Simmental (1/2 Simmental, n = 30) and Angus (1/2 Angus, n = 245) sires with Nellore females. The effects of substituting L allele for S allele of GHR microsatellite across Nellore, Canchim and 1/2 Angus were significant for weight gain and body weight (P < 0.05). The IGF1 microsatellite allele substitutions of 229 for 225 within Nellore group and of 225 for 229 within 1/2 Angus were not significant for any of the traits.
Myostatinand its implications on animal breeding: a review
Authors: Bellinge R. H. S. , Liberles D. A. , Iaschi S. P. A. , O'Brien P. A. , Tay G. K.
Published: January 2005

Myostatin, or growth and differentiation factor 8 (GDF8), has been identified as the factor causing a phenotype known as double muscling, in which a series of mutations render the gene inactive, and therefore, unable to regulate muscle fibre deposition. This phenotype occurs at a high frequency in some breeds of cattle such as Belgian Blue and Peidmontese. Phylogenetic analysis has shown that there has been positive selection pressure for non‐synonymous mutations within themyostatingene family, around the time of the divergence of cattle, sheep and goats, and these positive selective pressures on non‐ancestralmyostatinare relatively recent. To date, there have been reports of nine mutations in coding regions ofmyostatinthat cause non‐synonymous changes, of which three cause missense mutations, including two in exon 1 and one in exon 2. The remaining six mutations, located in exons 2 and 3, result in premature stop codons, which are the mutations responsible for the double‐muscling phenotype. Unfortunately, breed management problems exist for double‐muscled cattle, such as birthing difficulties, which can be overcome through genetically controlled breeding programmes, as shown in this review.
The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers
Authors: Fang M. , Hu X. , Jiang T. , Braunschweig M. , Hu L. , Du Z. , Feng J. , Zhang Q. , Wu C. , Li N.
Published: January 2005

A genetic study of 32 local Chinese, three foreign pig breeds [Duroc (DU), Landrace and Yorkshire], and two types of wild boar (Hainan and Dongbei wild boar) based on 34 microsatellite loci was carried out to clarify the phylogeny of Chinese indigenous pig breeds. The allele frequencies, effective numbers of alleles, and the average heterozygosity within populations were calculated. The results showed that the genetic variability of the Lingao pig was the largest, while the Jiaxing pig was the lowest. The greatest distance between domestic pigs was found between Shanggao and DU pig and the shortest was found between Wuzhishan and Lingao pig, respectively. A neighbour‐joining tree constructed from Modified Cavalli‐Sforza genetic distances divided Chinese pigs into two clusters; four subclusters were also identified. Our results only partly agree with the traditional types of classification and also provide a new relationship among Chinese local pig breeds. Our data also confirmed that Chinese pig breeds have a different origin from European/American breeds and can be utilized in programmes that aim to maintain Chinese indigenous pig breeds.
Localizing the X‐linked orange colour phenotype using feline resource families
Authors: Grahn R. A. , Lemesch B. M. , Millon L. V. , Matise T. , Rogers Q. R. , Morris J. G. , Fretwell N. , Bailey S. J. , Batt R. M. , Lyons L. A.
Published: January 2005

Many genes influencing mammalian coat colours are well conserved. While genes responsible for pelage phenotypes in one species provide strong evidence for a candidate gene in a different species, the X‐linked orange phenotype of the domestic cat is unique within mammals. The orange locus (O) undergoes X‐inactivation, producing females that express both wildtype black (wt) and orange (variant) phenotypes when heterozygous (tortoiseshell). The orange locus has not yet been localized on the X chromosome. Tortoiseshell male cats have been identified but have been shown to be sex chromosome trisomies (XXY). To localize the cat orange locus, 10 feline‐derived X‐linked microsatellites were analysed in two extended cat pedigrees consisting of 79 and 55 individuals, respectively, segregating for the orange phenotype. Linkage analyses excluded close association of orange in the vicinity of the nine informative X‐linked microsatellites. One marker was not polymorphic within either family. Several markers suggested exclusion (Z < −2.0) at distances of 7.5–33 cM. Exclusion analyses suggested a possible location for orange a 14 cM region near Xcen. Recombination distances of markers in the segregating feline pedigrees were reduced as compared with the feline interspecies backcross family. Thus, the presented pedigrees may be useful as reference families for the domestic cat because more accurate recombination rates for domestic cats can be determined.
Measuring health state preferences for hemophilia: development of a disease‐specific utility instrument
Authors: Wasserman J. , Aday L. A. , Begley C. E. , Ahn C. , Lairson D. R.
Published: January 2005

Summary.  Generic and disease‐specific instruments have been used to assess health‐related quality of life (HRQoL) in hemophilia. However, HRQoL measures also need to reflect patient preferences for various hemophilia health states. The goal of this project was to develop a disease‐specific utility instrument that measures patient preferences for various health states unique to hemophilia. The visual analog scale (VAS) and the standard gamble (SG) methods were used. Study participants (n = 128) were tested and stratified into paediatric and adult groups. Test–retest reliability was demonstrated for both instruments, with r = 0.91 for the VAS and r = 0.79 for the SG. When comparing results by age group, statistically significant differences were observed between paediatric and adult participants with the SG instrument (P = 0.045), with older participants taking more risk overall. However, no significant differences based on age were seen when using the VAS (P = 0.636). Statistically significant differences were observed between the VAS and SG instruments within both the paediatric and adult groups (P < 0.0001). In general, the SG yielded higher preference scores than the VAS for the majority of health states. Results derived from the SG instrument indicate that age can influence patients’ preferences regarding their state of health. This can have implications for considering treatment options based on the mean age of the population under consideration. Both instruments demonstrated reliability and validity indicating that they could be used to assess patient preferences in hemophilia. However, preference score differences indicate that the two measures may not be interchangeable.