bluuebunny/crossref_metadata_2025_split huggingface dataset:
The polymorphism in MUC1 gene in Nelore cattle
Authors: De Souza F. R. P. , Dentillo D. B. , Meola J. , Biase F. H. , Andréa M. V. , Vozzi P. A. , Lôbo R. B. , Martelli L. R. 
Published: February 2007

SummaryMUC1 is a transmembrane glycoprotein expressed on the apical surfaces of the uterine epithelial tissue with predicted functions in protection and cell–cell adhesion. These properties are closely related with the repetitive region [variable number of tandem repeats (VNTR)] of the extracellullar domain and with the O‐glycosylation in their serine and threonine residues. This study describes a polymerase chain reaction (PCR) protocol to analyse MUC1 bovine genetic polymorphism and demonstrates the existence of a VNTR within the sites for O‐glycosylation. Oligonucleotide primers based on the Bos taurus mucin (MUC1) gene sequence GenBank AF399757 were used to amplify five VNTR MUC1 alleles from a study group of 56 pure Nelore bovines. The number of repeats varied between 10 and 24, being more prevalent than the alleles with less number of repeats. The DNA sequence analysis revealed two repeats and one of them presented 100% homology with the bovine consensus sequence already reported. The second repeat showed codons that translate to serine and proline amino acids, which are conserved in the MUC1 of several species. This study is the first description of allelic variation and the VNTR structure in the Nelore breed MUC1 gene, and we suggest that this genetic variability can be tested for association with variation in reproductive traits in Nelore cattle.
An insertion/deletion in the porcine FGFR2 gene
Authors: Aldenhoven J. , Spötter A. , Distl O. 
Published: February 2007

SummaryThe 7000‐rad INRA‐University of Minnesota porcine Radiation Hybrid panel was used to localize the FGFR2 gene on Sus scrofa chromosome 14 (SSC14). An insertion/deletion mutation of approximately 240 bp was detected in the porcine FGFR2 gene. This mutation consists of a repeat motif of 48 bp. In a short and long variant of this polymorphism, the motif was repeated either six or 11 times. The mutation was shown to follow a Mendelian mode of inheritance in 10 families including 48 pigs of Large White × Duroc origin.
Genetic and phenotypic parameters for conformation and yield traits in three Swiss dairy cattle breeds
Authors: De Haas Y. , Janss L.L.G. , Kadarmideen H.N. 
Published: February 2007

SummaryThis study presents genetic parameters for conformation traits and their genetic and phenotypic correlations with milk production traits and somatic cell score (SCS) in three Swiss dairy cattle breeds. Data on first lactations from Holstein (67 839), Brown Swiss (173 372) and Red & White breeds (53 784) were available. Analysed conformation traits were stature and heart girth (both in cm), and linear scores of body depth, rump width, dairy character or muscularity, and body condition score (only in Holstein). A sire model, with relationships among sires, was used for all breeds and traits and variance components were estimated using AS‐REML. Heritabilities for stature were high (0.6–0.8), and for the linear type traits ranged from 0.3 to 0.5, for all breeds. Genetic correlations with production traits (milk, fat and protein yield) and SCS differed between the dairy breeds. Most markedly, stronger correlations were found between SCS and some conformation traits in Brown Swiss and Red & White, indicating that a focus on a larger and more ‘dairy’ type in these breeds would lead to increased SCS. Another marked difference was that rump width correlated positively with milk yield traits in Holstein and Red & White, but negative in Brown Swiss. Results indicate that conformation traits generally can be used as predictors for various purposes in dairy cattle breeding, but may require specific adaptation for each breed.
Analysis of FMO genes and off flavour in pork
Authors: Glenn K.L. , Ramos A.M. , Rothschild M.F. 
Published: February 2007

SummaryOff flavours in pork sometimes produce tastes such as sourness, fishy, metallic or other non‐typical flavours and are often caused by low pH. Loss of function mutations in flavin containing mono‐oxygenase 3 (FMO3) are known to be associated with a fishy off flavour in both chicken eggs and cow's milk and a similar autosomal recessive disorder is present in humans resulting in a fishy odour. FMO3 is a member of a gene family that is clustered on human chromosome 1. Comparative mapping suggested that FMO3 and the remaining FMO genes (ex. FMO1 and FMO5) might map to the orthologous region on pig chromosome 9 (SSC9) where a quantitative trait locus (QTL) for off flavour was previously identified. Primers were designed to amplify FMO1, FMO3 and FMO5 gene fragments and several SNPs were discovered and genotyping tests developed. The genotypes from the Iowa State University Berkshire × Yorkshire resource population were used to linkage map FMO1 and FMO3 to SSC9 and FMO5 to pig chromosome 4 (SSC4). QTL and associations analyses were performed using the map containing FMO1 and FMO3. Results demonstrated that FMO3 and FMO1 mapped less than 1 cM away from the peak for the off flavour QTL previously detected on SSC9 and provide indications of an association between the FMO3 polymorphism and off flavour in pork.
Estimation of phenotypic and genetic parameters for weight gain and weight at fixed ages in the double‐muscled Belgian Blue Beef breed using field records
Authors: Coopman F. , Krafft A. , Dewulf J. , Van Zeveren A. , Gengler N. 
Published: February 2007

SummaryIn the double‐muscled Belgian Blue beef (DM‐BBB) breed, selection focuses on muscular conformation and not on weight gain and higher weight. There are very few studies on growth in the DM‐BBB using field records. Therefore, farms have no available useful figures on weight at fixed ages and weight gain for the DM‐BBB. This study describes and evaluates live weights of DM‐BBB animals. All the data were gathered on farms in Belgium. It was found that a male DM‐BBB weighs an average of 51 kg at birth, 98 kg at 3 months, 242 kg at 7 months, 430 kg at 13 months and 627 kg at 20 months. Between the age of 7 and 20 months, weight gain is more than 1200 g a day. Females weigh 47 kg at birth, 96 kg at 3 months, 189 kg at 7 months and 332 kg at 13 months. For males, estimates of heritability for weights at 7, 13 and 20 months were between 0.21 and 0.36. The heritability for weight gain between 13 and 20 months was 0.13. This demonstrates that it is possible to select for higher weights and for increased growth between 13 and 20 months. Animals having high weights at a young age (7 and 13 months) tend to have also high weight at slaughtering age (20 months; rg between 0.81 and 0.98), but no additional growth between 13 and 20 months (rg between −0.09 and 0.00). High weight at 20 months is partially due to growth between 13 and 20 months (rg = 0.49).
Application of robust procedures for estimation of breeding values in multiple‐trait random regression test‐day model
Authors: Jamrozik J. , Fatehi J. , Schaeffer L.R. 
Published: February 2007

SummaryRobust procedures for estimation of breeding values were applied to multiple‐trait random regression test‐day (TD) model to reduce the influence of outliers on inferences. Robust estimation methods consisted of correcting selected observations (defined as outliers) in the process of solving mixed‐model equations in such a way that ‘new’ observations gave residuals (actual observation minus predicted) within k residual standard deviations for a given day in milk in 305‐day lactation. Data were 980 503 TD records on 63 346 Canadian Jersey cows. Milk, fat, protein and somatic cell score in the first three lactations were analysed jointly in the model that included fixed herd‐TD effect and regressions within region–age–season of calving, and regressions with random coefficients for animal genetic and permanent environmental effects. All regressions were orthogonal polynomials of order 4. Robust procedures for k = 1.5, 2.0, 2.5, 2.75 and 3.0 were contrasted with the regular best linear unbiased prediction (BLUP) method in terms of numbers and distributions of outliers, and estimated breeding values (EBV) of animals. Distributions of outliers were similar across traits and lactations. Early days in milk (from 5 to 15) were associated with larger frequency of outliers compared with the remaining part of lactation. Several, computationally simple, robust methods (for k > 2.0) reduced the influence of outlier observations in the model and improved the overall model performance. Differences in rankings of animals from robust evaluations were small compared with the regular BLUP method. No clear associations between changes in EBV (rankings) of top animals from different methods and the occurrence of outliers were detected.
Evaluation of association between polymorphism within the thyroglobulin gene and milk production traits in dairy cattle
Authors: Khatib H. , Zaitoun I. , Chang Y.M. , Maltecca C. , Boettcher P. 
Published: February 2007

SummaryIn dairy cattle, many studies have reported quantitative trait loci (QTL) on the centromeric end of chromosome 14 that affect milk production traits. One of the candidate genes in this QTL region – thyroglobulin (TG) – was previously found to be significantly associated with marbling in beef cattle. Thus, based on QTL studies in dairy cattle and because of possible effects of this gene on fat metabolism, we investigated the association of TG with milk yield and composition in Holstein dairy cattle. A total of 1279 bulls from the Cooperative Dairy DNA Repository Holstein population were genotyped for a single nucleotide polymorphism in TG used previously in beef cattle studies. Analysis of 29 sire families showed no significant association between TG variants and milk production traits. Within‐sire family analysis suggests that TG is neither the responsible gene nor a genetic marker in association with milk production traits.
Hypotaurine and thiotaurine as indicators of sulfide exposure in bivalves and vestimentiferans from hydrothermal vents and cold seeps
Authors: Brand Garth L. , Horak Robin V. , Bris Nadine Le , Goffredi Shana K. , Carney Susan L. , Govenar Breea , Yancey Paul H. 
Published: February 2007

AbstractVesicomyid clams, vestimentiferans, and some bathymodiolin mussels from hydrothermal vents and cold seeps possess thiotrophic endosymbionts, high levels of hypotaurine and, in tissues with symbionts, thiotaurine. The latter, a product of hypotaurine and sulfide, may store and/or transport sulfide non‐toxically, and the ratio to hypotaurine plus thiotaurine (Th/[H + Th]) may reflect an animal's sulfide exposure. To test this, we analyzed seep and vent animals with in situ sulfide measurements. Calyptogena kilmeri clams occur at high‐sulfide seeps in Monterey Canyon, while C. (Vesicomya) pacifica clams occur at seeps with lower levels but take up and metabolize sulfide more effectively. From one seep where they co‐occur, both had gill thiotaurine contents at 22–25 mmol kg−1 wet mass, and while C. (V.) pacifica had a higher blood sulfide level, it had a lower Th/[H + Th] (0.39) than C. kilmeri (0.63). However, these same species from different seeps with lower sulfide exposures had lower ratios. Bathymodiolus thermophilus [East Pacific Rise (EPR 9°50′ N)] from high‐(84 μm) and a low‐(7 μm) sulfide vents had gill ratios of 0.40 and 0.12, respectively. Trophosomes of Riftia pachyptila (EPR 9°50′ N) from medium‐(33 μm) and low‐(4 μm) sulfide vents had ratios of 0.23 and 0.20, respectively (not significantly different). Ridgeia piscesae vestimentiferans (Juan de Fuca Ridge) have very different phenotypes at high‐ and low‐sulfide sites, and their trophosomes had the greatest differences: 0.81 and 0.04 ratios from high‐ and low‐sulfide sites, respectively. Thus Th/[H + Th] may indicate sulfide exposure levels within species, but not in interspecies comparisons, possibly due to phylogenetic and metabolic differences. Total H + Th was constant within each species (except in R. piscesae); the sum may indicate the maximum potential sulfide load that a species faces.
Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre
Authors: Mincer Tracy J. , Church Matthew J. , Taylor Lance Trent , Preston Christina , Karl David M. , DeLong Edward F. 
Published: February 2007

SummaryThe recent isolation of the ammonia‐oxidizing crenarchaeon Nitrosopumilus maritimus has expanded the known phylogenetic distribution of nitrifying phenotypes beyond the domain Bacteria. To further characterize nitrification in the marine environment and explore the potential crenarchaeal contribution to this process, we quantified putative nitrifying genes and phylotypes in picoplankton genomic libraries and environmental DNA samples from coastal and open ocean habitats. Betaproteobacteria ammonia monooxygenase subunit A (amoA) gene copy numbers were low or undetectable, in stark contrast to crenarchaeal amoA‐like genes that were broadly distributed and reached up to 6 × 104 copies ml−1. Unexpectedly, in the North Pacific Subtropical Gyre, a deeply branching crenarchaeal group related to a hot spring clade (pSL12) was at times abundant below the euphotic zone. Quantitative data suggested that the pSL12 relatives also contain archaeal amoA‐like genes. In both coastal and open ocean habitats, close relatives of known nitrite‐oxidizing Nitrospina species were well represented in genomic DNA libraries and quantitative PCR profiles. Planktonic Nitrospina depth distributions correlated with those of Crenarchaea. Overall, the data suggest that amoA‐containing Crenarchaea are more phylogenetically diverse than previously reported. Additionally, distributional patterns of planktonic Crenarchaea and Nitrospina species suggest potential metabolic interactions between these groups in the ocean's water column.
Selection of nitrogen‐fixing deficient Burkholderia vietnamiensis strains by cystic fibrosis patients: involvement of nif gene deletions and auxotrophic mutations
Authors: Menard Aymeric , Monnez Claire , Estrada de los Santos Paulina , Segonds Christine , Caballero‐Mellado Jesus , LiPuma John J. , Chabanon Gerard , Cournoyer Benoit 
Published: February 2007

Summary Burkholderia vietnamiensis is the third most prevalent species of the Burkholderia cepacia complex (Bcc) found in cystic fibrosis (CF) patients. Its ability at fixing nitrogen makes it one of the main Bcc species showing strong filiations with environmental reservoirs. In this study, 83% (29 over 35) of the B. vietnamiensis CF isolates and 100% of the environmental ones (over 29) were found expressing the dinitrogenase complex (encoded by the nif cluster) which is essential in N2 fixation. Among the deficient strains, two were found growing with ammonium chloride suggesting that they were defective in N2 fixation, and four with amino acids supplements suggesting that they were harbouring auxotrophic mutations. To get insights about the genetic events that led to the emergence of the N2‐fixing defective strains, a genetic analysis of B. vietnamiensis nitrogen‐fixing property was undertaken. A 40‐kb‐long nif cluster and nif regulatory genes were identified within the B. vietnamiensis strain G4 genome sequence, and analysed. Transposon mutagenesis and nifH genetic marker exchanges showed the nif cluster and several other genes like gltB (encoding a subunit of the glutamate synthase) to play a key role in B. vietnamiensis ability at growing in nitrogen‐free media. nif cluster DNA probings of restricted genomic DNA blots showed a full deletion of the nif cluster for one of the N2‐fixing defective strain while the other one showed a genetic organization similar to the one of the G4 strain. For 17% of B. vietnamiensis clinical strains, CF lungs appeared to have favoured the selection of mutations or deletions leading to N2‐fixing deficiencies.
Microbial CO2 fixation and sulfur cycling associated with low‐temperature emissions at the Lilliput hydrothermal field, southern Mid‐Atlantic Ridge (9°S)
Authors: Perner Mirjam , Seifert Richard , Weber Stefan , Koschinsky Andrea , Schmidt Katja , Strauss Harald , Peters Marc , Haase Karsten , Imhoff Johannes F. 
Published: February 2007

SummaryLilliput was discovered in 2005 as the southernmost known hydrothermal field along the Mid‐Atlantic Ridge. It is exceptional in that it lacks high‐temperature venting probably because of a thickened crust. The absence of thermophilic and hyperthermophilic prokaryotes in emissions supports the argument against the presence of a hot subsurface at Lilliput, as is typically suggested for diffuse emissions from areas of high‐temperature venting. The high phylogenetic diversity and novelty of bacteria observed could be because of the low‐temperature influence, the distinct location of the hydrothermal field or the Bathymodiolus assemblages covering the sites of discharge. The low‐temperature fluids at the Lilliput are characterized by lowered pH and slightly elevated hydrogen (16 nM) and methane (∼2.6 μM) contents compared with ambient seawater. No typical hydrogen and methane oxidizing prokaryotes were detected. The higher diversity of reverse tricarboxylic acid genes and the form II RubisCO genes of the Calvin Benson‐Bassham (CBB) cycle compared with the form I RubisCO genes of the CBB cycle suggests that the chemoautotrophic community is better adapted to low oxygen concentrations. Thiomicrospira spp. and Epsilonproteobacteria dominated the autotrophic community. Sulfide is the most abundant inorganic energy source (0.5 mM). Diverse bacteria were associated with sulfur cycling, including Gamma‐, Delta‐ and Epsilonproteobacteria, with the latter being the most abundant bacteria according to fluorescence in situ hybridization. With members of various Candidate Divisions constituting for 25% of clone library sequences we suggest that their role in vent ecosystems might be more important than previously assumed and propose potential mechanisms they might be involved in at the Lilliput hydrothermal field.
Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples
Authors: Witzig Robert , Aly Hamdy A. H. , Strömpl Carsten , Wray Victor , Junca Howard , Pieper Dietmar H. 
Published: February 2007

SummaryResin acids are tricyclic diterpenoids naturally synthesized by trees that are released from wood during pulping processes. Using a newly designed primer set, genes similar to that encoding the DitA1 catalytic α‐subunit of the diterpenoid dioxygenase, a key enzyme in abietane resin acid degradation by Pseudomonas abietaniphila BKME‐9, could be amplified from different Pseudomonas strains, whereas ditA1 gene sequence types representing distinct branches in the evolutionary tree were amplified from Burkholderia and Cupriavidus isolates. All isolates harbouring a ditA1‐homologue were capable of growth on dehydroabietic acid as the sole source of carbon and energy and reverse transcription polymerase chain reaction analysis in three strains confirmed that ditA1 was expressed constitutively or in response to DhA, demonstrating its involvement in DhA‐degradation. Evolutionary analyses indicate that gyrB (as a phylogenetic marker) and ditA1 genes have coevolved under purifying selection from their ancestral variants present in the most recent common ancestor of the genera Pseudomonas, Cupriavidus and Burkholderia. A polymerase chain reaction‐single‐strand conformation poylmorphism fingerprinting method was established to monitor the diversity of ditA1 genes in environmental samples. The molecular fingerprints indicated the presence ofa broad, previously unrecognized diversity of diterpenoid dioxygenase genes in soils, and suggest that other bacterial phyla may also harbour the genetic potential for DhA‐degradation.
Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream)
Authors: Countway Peter D. , Gast Rebecca J. , Dennett Mark R. , Savai Pratik , Rose Julie M. , Caron David A. 
Published: February 2007

SummaryProtistan diversity was characterized at three locations in the western North Atlantic (Sargasso Sea and Gulf Stream) by sequencing 18S rRNA genes in samples from euphotic (≤ 125 m) and bathypelagic depths (2500 m). A total of 923 partial‐length protistan sequences were analysed, revealing 324 distinct operational taxonomic units (OTUs) determined by an automated OTU‐calling program set to 95% sequence similarity. Most OTUs were comprised of only one or two sequences suggesting a large but rare pool of protistan diversity. Many OTUs from both depth strata were associated with recently described novel alveolate and stramenopile lineages while many OTUs from the bathypelagic were affiliated with Acantharea, Polycystinea and Euglenozoa and were not observed in euphotic zone libraries. Protistan assemblages from the euphotic zone and the deep sea were largely composed of distinct OTUs; only 28 of the 324 protistan OTUs were detected in both shallow and deep sea clone libraries. The diversity of protistan assemblages in the deep sea was distinctly lower than the diversity of euphotic zone assemblages. Protistan assemblages from the Gulf Stream were the most diverse for either depth strata. Overall, protistan assemblages from different stations but comparable depths were more similar than the assemblages from different depths at the same station. These data suggest that particular groups of protistan OTUs formed distinct ‘shallow’ and ‘deep‐sea’ assemblages across widely spaced oceanic locales.
Variation of patients’ views on Type 2 diabetes management over time
Authors: Vég A. , Rosenqvist U. , Sarkadi A. 
Published: February 2007

AbstractAims  The aim of the study was to examine the relationship between participants’ views about their role in diabetes treatment and their glycaemic control 3–7 years after having entered an educational intervention, and to investigate whether people's attitudes towards diabetes management change over an extended period of time.Methods  The present study is a long‐term follow‐up analysis of data collected from 193 persons with Type 2 diabetes. A qualitative content analysis of three open‐ended questions about participants’ self‐perceived role in diabetes treatment was used. The related outcome measure was haemoglobin A1c (HbA1c).Results  The way people viewed their role in diabetes management affected glycaemic control. Individuals in the Disease Manager or Compliant categories had significantly lower HbA1c compared with those in the Disheartened category. Furthermore, in people whose attitudes towards diabetes treatment was variable, weight and age influenced why participants changed their views and thus switched categories. Paradoxically, when people changed their views, this change did not produce a change in blood glucose control, which would have been expected.Conclusions  From the health‐care provider's perspective, it is important to know how the person with diabetes perceives his/her role in disease management and to determine if a change in perception would be followed by intervention to adjust glycaemic control. Consequently, individuals’ perception of disease management should be incorporated in patient education programmes and routine diabetes care to enable customized care and prevent stagnation in negative roles.