bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of PRKAG1 coding sequence and mapping of PRKAG1 and PRKAG2 relatively to porcine back fat thickness QTL
Authors: Demeure O. , Liaubet L. , Riquet J. , Milan D. 
Published: March 2004

Summary PRKAG1, PRKAG2 and PRKAG3 encode three isoforms of AMP‐activated protein kinase γ chain. A major effect on meat quality and a medium effect on back fat thickness of the RN− mutation in the PRKAG3 gene has previously been reported. We have now mapped PRKAG1 and PRKAG2 at expected locations on SSC5 and SSC18 by analysis of radiation hybrids (IMpRH panel). PRKAG2 has been mapped in a region where no quantitative trait loci (QTL) has been reported. PRKAG1 has been mapped close to (but probably outside) a region containing a QTL influencing fatness traits. We have determined the full coding sequence of PRKAG1. No missense mutation was identified when comparing the coding sequence of one Meishan and one Large White boars. Further work is, however, required to determine if a polymorphism in PRKAG1 could be responsible for a part of the variability observed on fatness traits.
Differential expression of iodothyronine deiodinase type 2 in growth plates of chickens divergently selected for incidence of tibial dyschondroplasia
Authors: Shen S. , Berry W. , Jaques S. , Pillai S. , Zhu J. 
Published: March 2004

SummaryTibial dyschondroplasia (TD) is a genetic leg defect in broilers with a lesion of avascular, non‐calcified cartilage below the growth plate of the proximal tibiatarsus. This disease is considered to result from the inability of chondrocytes to undergo terminal differentiation. Thyroid hormones are required for chondrocyte differentiation. The thyroid gland produces and secrets mostly l‐thyroxine or T4, and T4 plays most of its biological activities through conversion to triiodothyronine or T3 in local tissues by iodothyronine deiodinases type 1 or type 2, which are tissue specific. In this study, no differences were found in the plasma concentrations of total T3 and T4 between two chicken lines divergently selected for the incidence of TD. Plasma T4 was higher than T3, especially in older chickens. Younger birds had much higher T3 than older birds, but there were no significant age differences in T4. The expression level of deiodinase type 2 in the growth plates of broilers with TD was one‐eighth of those birds without the disease. The expression levels of deiodinase type 2 (DIO2) in commercial broilers without the disease were much higher than those with TD and lower than those without the disease in the susceptible and resistant lines, respectively. These results indicate that the inadequate expression of DIO2 in the growth plates contributes to the pathogenesis of TD in broilers and that TD is a tissue‐specific hypothyroidism.
Characterization of a new BAC library for rainbow trout: evidence for multi‐locus duplication
Authors: Palti Y. , Gahr S. A. , Hansen J. D. , Rexroad C. E. 
Published: March 2004

SummaryA 10X rainbow trout bacterial artificial chromosome (BAC) library was constructed to aid in the physical and genetic mapping efforts of the rainbow trout genome. The library was derived from the Swanson clonal line (YY male) and consists of 184 704 clones with an average insert size of 137 500 bp (PFGE) or 118 700 bp (DNA fingerprinting). The clones were gridded onto 10 large nylon membranes to produce high‐density arrays for screening the library by hybridization. The library was probed with 11 cDNAs from the NCCCWA EST project chosen because of interest in their homology to known gene sequences, seven known genes, and a Y‐specific sex marker. Putative positive clones identified by hybridization were re‐arrayed and gridded for secondary confirmation. FPC analysis of HindIII and EcoRV DNA fingerprinting was used to estimate the level of redundancy in the library, to construct BAC contigs and to detect duplicated loci in the semi‐duplicated rainbow trout genome. A good correlation (R2 = 0.7) was found between the number of hits per probe and the number of contigs that were assembled from the positive BACs. The average number of BACs per contig was 9.6, which is in good agreement with 10X genome coverage of the library. Two‐thirds of the loci screened were predicted to be duplicated as the positive BACs for those genes were assembled into two or three different contigs, which suggests that most of the rainbow trout genome is duplicated.
Assignment of the appaloosa coat colour gene (LP) to equine chromosome 1
Authors: Terry R. B. , Archer S. , Brooks S. , Bernoco D. , Bailey E. 
Published: March 2004

SummaryA single autosomal dominant locus, leopard complex (LP) controls the presence of appaloosa pigmentation patterns in the horse. The causative gene for LP is unknown. This study was undertaken to map LP in the horse. Two paternal half sib families segregating for the LP locus and including a total of 47 offspring were used to perform a genome scan which localized LP to horse chromosome 1 (ECA1). LP was linked to ASB08 (LOD = 9.99 at Θ = 0.02) and AHT21 (LOD = 5.03 at Θ = 0.14). To refine the map position of LP, eight microsatellite markers on ECA1 (UM041, LEX77, 1CA41, TKY374, COR046, 1CA32, 1CA43, and TKY002) were analysed in the two half sib families. Results from this linkage analysis showed LP was located in the interval between ASB08 and 1CA43. Tight junction protein (TJP1), which lies within the LP interval on ECA1, was used to determine the homologous chromosomes in humans (HSA15) and mice (mouse chromosome 7). We propose that the pink eyed dilution (p) gene and transient receptor potential cation channel subfamily M, member 1 (TRPM1) are positional candidate genes for LP.
Phosphate regime structures species composition in cultured phototrophic biofilms
Authors: Van der Grinten E. , Janssen M. , Simis S. G. H. , Barranguet C. , Admiraal W. 
Published: March 2004

Summary1. The effect of phosphate on species composition in biofilms was studied under three different phosphate regimes (0.5, 5 and 50 μm) in two different multi species communities: one composed of the four diatom species Melosira varians, Nitzschia perminuta, Navicula trivialis and Achnanthes lanceolata and one containing these diatom species plus the two cyanobacterial species Leptolyngbya foveolarum and Cylindrospermum stagnale.2. Algal growth in monocultures and mixtures was measured as chlorophyll a and PAM fluorimetry was applied to document density and physiological condition of the two main groups of photosynthetic organisms in mixed cultures.3. In phosphate‐replete communities, a single species dominated the community (N. perminuta in the diatom mixture and L. foveolarum in the all species mixture), while in the phosphate‐deprived communities several species persisted, in spite of severe phosphate limitation.4. We conclude that high supply of phosphate enables the species L. foveolarum, and to a lesser extent N. perminuta, to overgrow biofilm consortia, facilitated by their filamentous growth form, motility or the excretion of inhibitors. The persistence of several species under a low phosphate regime is explained by a less intense interspecific interaction in low‐density biofilms. This clarifies field observations published previously.
Depth distribution of Daphnia in response to a deep‐water algal maximum: the effect of body size and temperature gradient
Authors: Kessler Kirsten , Lampert Winfried 
Published: March 2004

Summary1. In the absence of fish predation, Daphnia exploiting a deep‐water algal maximum are faced with a trade‐off. They can either dwell in the epilimnion where development in the warm water is fast, but food shortage causes low egg production, or in the hypolimnion, where food availability is high but development is slow because of low temperatures.2. We tested the hypotheses that (i) depth distributions of various ontogenetic stages (size classes and egg‐bearing females) differ because daphnids react to light with size‐specific diel vertical migration (DVM) even in the absence of fish (residual predator avoidance hypothesis) and (ii) differently sized daphnids select different depths because the relative importance of temperature and food varies for ontogenetic stages (physiological hypothesis). We used large indoor mesocosms (Plankton Towers) to test these hypotheses experimentally.3. Temperature was the strongest factor governing the distribution, with larger proportions of the population dwelling in the food‐rich hypolimnion if the temperature gradient was shallow. There were small but significant differences between ontogenetic stages during the day, but not at night. This suggested the existence of a ‘residual’ effect of light on depth distribution in the absence of a fish cue.4. Although large individuals exhibited greater amplitude of DVM, the physiological hypothesis had to be rejected. A stage‐specific physiological effect is unlikely to be directly triggered by light, hence vertical movement of the individuals should not be synchronised. Rather, being forced into deeper layers by the residual light response during the day, large and egg‐bearing females experience a lower average temperature during day than juveniles. They probably compensate for this by spending longer time periods in warm waters at night.
Scale and the detection of land‐use effects on morphology, vegetation and macroinvertebrate communities of grassland streams
Authors: Townsend Colin R. , Downes Barbara J. , Peacock Kathi , Arbuckle Chris J. 
Published: March 2004

Summary1. Land‐use studies are challenging because of the difficulty of finding catchments that can be used as replicates and because land‐use effects may be obscured by sources of variance acting over spatial scales smaller than the catchment. To determine the extent to which land‐use effects on stream ecosystems are scale dependent, we designed a whole‐catchment study of six matched pairs (pasture versus native tussock) of second‐order stream catchments, taking replicate samples from replicate bedforms (pools and riffles) in each stream.2. Pasture streams had a smaller representation of endemic riparian plant species, particularly tussock grasses, higher bank erosion, a somewhat deeper layer of fine sediment, lower water velocities in riffles, less moss cover and higher macroinvertebrate biodiversity. At the bedform scale, suspendable inorganic sediment (SIS) was higher in pools than riffles and in pasture streams there was a negative relationship between SIS and the percentage of the bed free of overhanging vegetation. Differences between stream reaches (including any interactions between land use and stream pair) were significant for SIS, substrate depth and characteristics of riparian vegetation. There were also significant differences between replicate bedforms in the same stream reaches in percentage exotic species in overhanging vegetation, percentage moss cover, QMCI (Quantitative Macroinvertebrate Community Index – a macroinvertebrate‐based stream health index) and macroinvertebrate density.3. Significant differences among stream reaches and among replicate bedform units within the same reach, as well as interactions between these spatial units and land‐use effects, are neither trivial nor ‘noise’ but represent real differences among spatial units that typically are unaccounted for in stream studies. Our multi‐scale study design, accompanied by an investigation of the explanatory power of different factors operating at different scales, provides an improved understanding of variability in nature.
Determinants of the distribution of juvenile fish in the littoral area of a shallow lake
Authors: Lewin Wolf‐Christian , Okun Nils , Mehner Thomas 
Published: March 2004

Summary1. Research has often focused on the pelagic areas of lakes; the littoral zone has received less attention. The few studies concerning fish distribution in littoral habitats have concentrated on stands of submersed macrophytes, whereas other littoral habitat types have seldom been investigated.2. This study aimed to predict the occurrence of juvenile fish in several littoral habitats of a shallow lake as a function of food availability, complexity of habitat structure, water depth and substrate. Habitats comprising reed, woody structures, and two open water areas differing in depth were sampled for fish and invertebrate biomasses on two shores, over 6 months and during both daylight and at night.3. The juvenile fish community consisted almost exclusively of 0+ and 1+ roach and perch. There was a strong diel component in habitat use, with a predominant occurrence of fish in complex habitats (mainly woody structures) during the day, and a partial migration towards the open habitats at night, more strongly expressed in roach than in perch.4. The diet of all fish groups was relatively constant over the seasonal cycle, and was independent of habitat. There was a higher degree of planktivory in roach than in perch, but both species fed on benthic macroinvertebrates to a substantial extent.5. According to a logistic regression model, the biomass of potential food organisms in the different habitats had little predictive effect on the spatial distribution of the fish, whereas the structural complexity of the habitats combined with the diel cycle explained about 28% of the occurrence patterns in 0+ and 1+ perch and 1+ roach.
Nitrogen stable isotope ratios in surface sediments, epilithon and macrophytes from upland lakes with differing nutrient status
Authors: Jones R. I. , King L. , Dent M. M. , Maberly S. C. , Gibson C. E. 
Published: March 2004

Summary1. Thirty small upland lakes in Cumbria, Wales, Scotland and Northern Ireland were each visited once during June and July 2000. From each lake, samples of surface sediment epilithon, macrophytes and total dissolved nitrogen (TDN) were collected for nitrogen stable isotope analysis. As part of a wider programme, samples were also collected for chemical analysis and bioassays.2. Considerable variation was found in δ15N values in all measured nitrogen compartments. Some regional variation was evident but was generally weak. Sediment and epilithon δ15N were positively correlated with δ15N of TDN, suggesting that baseline nitrogen isotope ratios influence those in some organic matter compartments in the lakes.3. Sediment δ15N was higher when inorganic nitrogen concentration in the water was low, possibly reflecting reduced isotope fractionation under these conditions. However, this was not the case for epilithon or macrophytes. Sediment δ15N values were also negatively related to annual nitrogen deposition.4. Sediment, epilithon and macrophyte δ15N values all showed significant relations to nutrient limitation in the lakes as determined by algal bioassays. We suggest that sediment δ15N might be developed as a simple integrating measure of the degree of nitrogen limitation in lakes.
Deforestation alters the resource base and biomass of endemic stream insects in eastern Madagascar
Authors: Benstead Jonathan P. , Pringle Catherine M. 
Published: March 2004

Summary1. Rainforest streams in eastern Madagascar have species‐rich and diverse endemic insect communities, while streams in deforested areas have relatively depauperate assemblages dominated by collector‐gatherer taxa. We sampled a suite of benthic insects and their food resources in three primary rainforest streams within Ranomafana National Park in eastern Madagascar and three agriculture streams in the park's deforested peripheral zone. We analysed gut contents and combined biomass and stable isotope data to examine stream community responses to deforestation in the region, which is a threatened and globally important hotspot for freshwater biodiversity.2. Gut analyses showed that most taxa depended largely on amorphous detritus, obtained either from biofilms (collector‐gatherers) or from seston (microfilterers). Despite different resource availability in forest versus agriculture streams, diets of each taxon did not differ between stream types, suggesting inflexible feeding modes. Carbon sources for forest stream insects were difficult to discern using δ13C. However, in agriculture streams dependence on terrestrial carbon sources was low relative to algal sources. Most insect taxa with δ13C similar to terrestrial carbon sources (e.g. the stonefly Madenemura, the caddisfly Chimarra sp. and Simulium blackflies) were absent or present at lower biomass in agriculture streams relative to forest streams. Conversely, collector‐gatherers (Afroptilum mayflies) relied on algal carbon sources and had much higher biomass in agriculture streams.3. Our analyses indicate that a few collector‐gatherer species (mostly Ephemeroptera) can take advantage of increased primary production in biofilms and consequently dominate biomass in streams affected by deforestation. In contrast, many forest stream insects (especially those in the orders Plecoptera, Trichoptera and Diptera) depend on terrestrial carbon sources (i.e. seston and leaf litter), are unable to track resource availability and consequently decline in streams draining deforested landscapes. These forest‐specialists are often micro‐endemic and particularly vulnerable to deforestation.4. The use of consumer biomass data in stable isotope research can help detect population‐level responses to shifts in basal resources caused by anthropogenic change. We also suggest that restoration of vegetated riparian zones in eastern Madagascar and elsewhere could mitigate the deleterious effects of deforestation on sensitive, endemic stream taxa that are dependent on terrestrial carbon sources.
Urinary compounds in autism
Authors: Alcorn A. , Berney T. , Bretherton K. , Mills M. , Savery D. , Shattock P. 
Published: March 2004

AbstractBackground  Although earlier claims to identify specific compounds in the urine of people with autism had been discredited, it was subsequently suggested that there might be biochemical characteristics that were specific to early childhood, particularly in those who also did not have a severe degree of intellectual disability This study was to establish whether autism might have a distinctive chromatographic profile on urinary analysis.Method  Thirty‐four prepubertal boys with autism were matched with two groups of boys without autism – one on ability and chronological age and the other on chronological age alone, being within the normal range of ability. Laboratory analysis of their urine samples was carried out blind as to the clinical diagnosis.Results  The analysis correctly identified 53% of the autism group as against misidentifying 33% and 18% of the other two groups. When children with a severe learning disability (both with and without autism) were excluded from the comparisons, the laboratory then identified 77% of the 13 boys left in the autism group and misidentified 8% and 18% of the other two groups.Conclusions  The results would support the idea of a biological marker in prepubertal children and that it may be absent in, or obscured by the presence of severe LD.
Understanding carbonate ramp dynamics using δ13C profiles: examples from the Neoproterozoic Buah Formation of Oman
Authors: Cozzi Andrea , Allen Philip A. , Grotzinger John P. 
Published: March 2004

AbstractThe Late Neoproterozoic Buah Formation (Nafun Group, Oman) is a carbonate unit outcropping in the Jabal Akhdar and Huqf areas. It is composed mostly of shallow‐water carbonates deposited on a distally steepened carbonate ramp. Correlation of two δ13C isotope shifts shows that in the Jabal Akhdar ramp differentiation into fast and slow subsiding areas was followed by lateral progradation. In the Huqf area, however, a uniform scenario of upward shallowing of the facies and lateral progradation is demonstrated by chemostratigraphic timelines cross‐cutting the facies belts. The chemostratigraphic profiles show that the Buah Formation was deposited during sea‐level highstand conditions and that ramp differentiation was due to synsedimentary tectonics. High‐resolution correlation of δ13C profiles from the same lithostratigraphic unit (whether Precambrian or Phanerozoic in age) lacking biostratigraphic data can shed light on carbonate systems dynamics, tectonic vs. eustatic controls on depositional sequences and basin subsidence.
Spill‐over of European Bat Lyssavirus Type 1 into a Stone Marten (Martes foina) in Germany
Authors: Müller T. , Cox J. , Peter W. , Schäfer R. , Johnson N. , McElhinney L. M. , Geue J. L. , Tjørnehøj K. , Fooks A. R. 
Published: March 2004

SummaryEuropean bat lyssavirus type 1 (EBLV‐1, genotype 5) is known to endemically circulate in insectivorous bat populations in Germany. In August 2001, a rabies suspect stone marten (Martes foina) was found in the city of Burg (Saxony‐Anhalt, Germany) and was sent to the regional veterinary laboratory for routine rabies diagnosis. Whereas brain samples repeatedly tested negative in the fluorescent antibody test for classical rabies virus (genotype 1), the mouse inoculation test and the rabies tissue culture inoculation test yielded positive results. Rabies viral RNA was also detected in the stone marten brain sample both by nested and heminested RT‐PCR specific for the nucleoprotein gene and for the nucleoprotein phosphoprotein junction of rabies virus. The amplification products were sequenced to genotype the isolate. Sequence data obtained from the first‐round RT‐PCR products were analysed and the suspect stone marten isolate was confirmed as a rabies related virus (EBLV‐1a). Phylogenetic comparison with sequences from recent genotype five isolates from Germany and Denmark showed that it was closely related to a previous isolate of EBLV‐1 from a serotine bat in Saxony‐Anhalt obtained in the same year in an area adjacent to the place where the EBLV‐1 infected stone marten was found. Both EBLV‐1 isolates share a 99.5% identity. This is the first report of an EBLV‐1a spill‐over from an insectivorous bat into wildlife in Europe.
Occurrence ofEscherichia coliO157 in Raw Material and Food in Czech Republic
Authors: Lukášová J. , Abraham B. , Cupáková Š. 
Published: March 2004

SummaryThe study was carried out to investigate the incidence ofEscherichia coliO157 in raw materials, foodstuffs and the agricultural environment. Of a total of 987 samples examined, 22 strains (2.2%) were identified asE. coliO157 and 10 of them asE. coliO157:H7. Cefixime‐Tellurite MacConkey sorbitol agar (CT‐SMAC) agar and Biosynth culture medium (BCM)E. coliO157:7 medium were used for the isolation. The virulence factors (stx1, stx2, eae, and ehxA genes) were identified by polymerase chain reaction (PCR). Most strains were isolated from the mechanically deboned poultry meat (nine), minced meat (six) and raw milk (four). One strain was isolated from beef carcass and two strains from waste water. No strains were were found in mass for sausages, refreshment salads, swabs of pork and poultry carcasses and faeces of cattle and pigs. Ten strains from the 22 identified proved to be positive for all factors of virulence. They were isolated from minced meat (four), raw milk (four), waste water (one) and swab from beef carcass (one). Sensitivity to the antimicrobial drugs ampicillin (AMS), ampicillin–sublactam (SAM), tetracycline (TET), ofloxacine (OFL), cefuroxime (CRX), chloramphenicol (CPM), gentamicine (GEN), colistin (COL), cephalozine (CLZ), cefoxitin (CXT), aztreonam (AZT), and sulphamethoxazole + trimethoprim (COT) was tested using the standard dilution technique and disc diffusion test. Minimum inhibitory concentrations (MIC) characteristics (MIC50, MIC90, MIC range) and inhibitory zone diameter were determined for each strain. As determined by MICs, the resistance to tested antibiotics inE. coliO157 isolates was found to AMS (90.9%), CLZ (81.8%), CRX (63.6%), CXT (72.7%), CPM (72.7%), TET (81.8%), SAM (59.1%), COT (9.1%), COL (63.61%), AZT (9%) and GEN (4.5%). The similar results were obtained using the disc diffusion method. The differences were found relating to SAM, CXT, CMO and TET. Resistance against one or more antibiotics was found in 95.4% ofE. coliO157. Only one strain was susceptible to all tested antibiotics. Most of the strains were resistant to ampicillin and cephalozine. Eight different resistance phenotypes were demonstrated inE. coliO157.