bluuebunny/crossref_metadata_2025_split huggingface dataset:
A rapid PCR‐based test for the endogenous viral element ev3 of chickens
Authors: Benkel B. F. , Perreault J , Gagnon C , Conklin K 
Published: July 2010

SummaryA short fragment of chicken genomic DNA encompassing the insertion site of the endogenous avian leucosis viral element ev3 was isolated using the inverse polymerase chain reaction (inverse PCR) technique. The nucleotide sequence of the unoccupied site was used to design PCR primers that can be used to unambiguously determine the genetic status of any chicken, with respect to ev3. Screening of a small number of individuals from exotic breeds of chickens suggested that the frequency of ev3 is highly variable. The ev3 integration site shows a high degree of sequence homology with the macrophage‐specific tyrosine kinase gene, bmk, in mice.
Two new variants of the bovine PAS‐1 glycoprotein
Authors: Sacchi P , Macchi E , Rasero R , Fiandra P 
Published: July 2010

AbstractTwo new alleles (A and E) of the bovine MUC locus which encodes PAS‐1 protein, a glycoprotein of the milk fat globule membrane, are reported. The A allele was found in Italian Brown while E was present in the Jersey and the Piedmont breeds.
Porcine alpha‐1‐antitrypsin (PI): cDNA sequence, polymorphism and assignment to chromosome 7q2.4‐ > q2.6
Authors: Archibald A. L. , Couperwhite S. , Mellink C. H. M. , Lahbib‐Mansais Y. , Gellin J. 
Published: July 2010

SummaryA cDNA clone encoding the complete coding sequence for porcine alpha‐1‐antitrypsin (or α1‐protease inhibitor, PI) was isolated and its DNA sequence determined. The cDNA is assumed to encode alpha‐1‐antitrypsin on the basis of its sequence similarity to the corresponding cDNAs for human, baboon, rat, mouse, sheep and cow. The porcine cDNA clone was used in conjunction with BamHI, KpnI, MspI, SacI, TuqI and XbaI to develop restriction fragment length polymorphism‐based genetic markers for linkage mapping in pigs. The cDNA has also been used to map the porcine PI locus to chromosome 7q2.4‐ > q2.6 by radioactive in situ hybridization. Thus, the PI locus has been added to the developing physical and genetic maps of the porcine genome.
Sequence comparison of mitochondrial tRNA genes and origin of light strand replication in Bos taurus and Nellore (Bos indicus) breeds
Authors: Pegoraro L. , Yang Z. , Samaké S. , Meirelles F. V. , Bordingnon V. , Moquin L. , Smith L. C. 
Published: July 2010

SummaryAlthough the complete bovine mitochondrial DNA molecule has been previously sequencedand sequence comparisons of the mitochondrial displacement loop have been performed, detailed sequence information is limited on coding regions of mitochondrial DNA within and among breeds of Bos taurus and Bos indicus. This study analysed polymorphism of the mitochondrial DNA transfer RNA genes for trypto‐phan, alanine, asparagine, cysteine, tyrosine and the origin of light strand replication among Ayrshire, Canadian, Belgium Blue, Brown Swiss, Hereford, Jersey, Limousine, Piedmon‐taise, Red Angus, Simmental (Bos taurus) and a Nellore (Bos indicus). Nucleotide sequence analysis of a 420‐bp fragment of mitochondrial DNA comprising the five transfer RNA genes showed 100% homology among single individuals of the Bos taurus breeds. The Nellore breed showed guanine to adenine substitutions in the DHU arm of asparagine tRNA and in the origin of light‐strand replication. This equates to a 0.5% sequence difference between the Nellore andBos taurus breeds and may reflect an independent evolutionary origin of the species.
Unequivocal identification of the equine Dcfmqr phenogroup
Authors: Bell K. , Colling D. T. 
Published: July 2010

SummaryAn alloimmune reagent has been produced that distinguishes the equine factor Df in the D phenogroup, cfmqr, from that occurring in cefmqr and dfklr. Using this reagent it has been possible to correctly genotype Dc, d, f, k, l, m, q and r positive cells without recourse to family data.
Chromosomal assignment of porcine EAD, EAO, LPR and P3 genes by linkage analysis
Authors: čepica S. , Moser G. , Schröffel J. , Knorr C. , Geldermann H. , Stratil A. , Hojný J. 
Published: July 2010

SummaryA two‐point linkage analysis was performed between blood group (14), allotype (8), polymorphic protein (11), DNA type I (2), and microsatellite (2) loci in Wild Boar x Pietrain and Meishan x Pietrain three‐generation families. The following new pairwise linkages were detected: LPR‐EAN (Zmax= 60.68, Ø= 0.055), EAD‐GH1 (Zmax= 17.43, Ø= 0.246), EAO—P3 (Zmax= 15.81, Ø= 0.239), and P3—S0003 (Zmax= 5.43, Ø= 0.312). This study and published mapping data enabled the localization of LPR (LPR allotype) to chromosome 9, EAD (erythrocyte antigen D) to chromosome 12, and EAO (erythrocyte antigen O) and P3 (P3 allotype) to the q arm of chromosome 6 with gene order SOOO3—P3—EAO, EAO being the most distal.
A parentage evaluation test in North American Elk (Wapiti) using microsatellites of ovine and bovine origin
Authors: Talbot J. , Haigh J. , Plante Y. 
Published: July 2010

SummaryDNA microsatellites originally detected in sheep and cattle are also detectable in North American elk (Wapiti) using polymerase chain reactions. We have developed a parentage test in elk using eleven microsatellite markers that are highly polymorphic and informative.
A MspI polymorphism in the bovine ornithine decarboxylase gene and its possible association with selection for milk production in Holstein bulls
Authors: Yao J. , Zadworny D. , Kuhnlein U. , Aggrey S. E. , Hayes J. F. 
Published: July 2010

SummaryA polymerase chain reaction (PCR)‐based method for detection of a MspI‐restriction fragment length polymorphism (RFLP) in the bovine ornithine decarboxylase gene was developed, and the allele frequencies of the polymorphism in two groups of Holstein bulls representing progeny‐tested bulls during the 1950s‐1960s and 1980s, respectively, were estimated. The frequencies of the MspI(‐) allele were 0.229 and 0.077 and that of MspI(+) were 0.771 and 0–923 in the progeny‐tested bulls of the 1950s‐1960s and 1980s, respectively. The difference in allele frequencies between the two groups was statistically significant (P< 0.005). Genetic drift could be responsible for the changes in allele frequencies; however, it could also be possible that selection for milk production was associated with the changes of the allele frequencies in the two bull populations.
Intra‐ and interbreed genetic variations of mitochondrial DNA major non‐coding regions in Japanese native dog breeds [Canis familiaris)
Authors: Okumura N. , Ishiguro N. , Nakano M. , Matsui A. , Sahara M. 
Published: July 2010

SummaryMitochondrial DNA (mtDNA) major non‐coding regions were amplified from 73 dogs of eight Japanese native dog breeds and from 21 dogs of 16 non‐Japanese dog breeds by the polymerase chain reaction and their DNA sequences were determined. A total of 51 nucleotide positions within the non‐coding region (969–972 base pairs) showed nucleotide variations of which 48 were caused by transition. These nucleotide substitutions were abundant in the region proximate to tRNAPro. In addition to the nucleotide substitutions, the dog mtDNA D‐loop sequences had a heteroplasmic repetitive sequence (TACACGTÀCG) involving size variation. The DNA sequences of the non‐coding region were classified into four different groups by phylogenetic analysis and the deepest branchpoints of this dog phylogeny was calculated to about 100 000 years before the present. Phylogenetic analysis showed that Japanese native dog breeds could not be clearly delimited as distinct breeds. Many haplotypes found in members of some clustering groups were seen in each dog breed, and interbreed nucleotide differences between Japanese dog breeds were almost the same as the intrabreed nucleotide diversities.
The relative abundance of a salivary protein, bSP30, is correlated with susceptibility to bloat in cattle herds selected for high or low bloat susceptibility
Authors: Rajan G H , Morris C A , Carruthers V R , Wilkins R J , Wheeler T T 
Published: July 2010

SummaryPasture bloat is a serious economic and animal welfare problem in cattle grazed on legumes in New Zealand. Analysis of salivary proteins from dairy cattle in herds bred for either low or high susceptibility to bloat has resulted in the identification of a 30 kilodalton protein, which we term bSP30, whose relative abundance is negatively correlated with bloat score (r = ‐0.40 ± 0.12). From 74 animals sampled, relative abundance of bSP30 was 66 ± 15% higher in the low‐susceptibility herd than in the high‐susceptibility herd. Relative abundance of bSP30 also varied significantly within individuals, according to feeding or time of day, and from day to day, A sequence homology search of 38 amino acids derived from three tryptic fragments of the protein suggests that the amino acid sequence of bSP30 has not been described previously. Amino acid analysis indicates that bSP30 is not a member of the proline‐rich family of salivary proteins. The function of bSP30 is unknown but it is conceivable that it plays a role in the aetiology of bloat.
Syntenic assignment of dopamine tautomerase (DCT) to bovine chromosome 12
Authors: Sun H S , Womack J E , Kirkpatrick B W 
Published: July 2010

SummaryHeterologous primers were used to amplify an exon and intron‐containing segment of the bovine homologue of the human dopachrome tautomerase gene. After confirmation of homo‐logy by sequence analysis (exon sequence similarity greater than 90%), bovine‐specific primers were developed for synteny mapping purposes. The dopachrome tautomerase gene was assigned to bovine chromosome 12 (BTA12) with 97% concordance to the coagulation factor 10 locus. Together with previous synteny mapping of bovine chromosome 12 genes, fms‐related tyrosine kinase, esterase D and 5‐hydroxytryptamine receptor 2, this assignment further indicates conservation between human chromosome 13q and bovine chromosome 12.
Optimization of single‐strand conformation polymorphism and sequence analysis of the mitochondrial control region in Pagellus bogaraveo (Sparidae, Teleostei): rationalized tools in fish population biology
Authors: Ostellari L. , Bargelloni L. , Penzo E. , Patarnello P. , Patarnello T. 
Published: July 2010

SummaryWe report the isolation and sequencing of 400–550 base pairs (bp) of the mitochondrial DNA (mtDNA) control region of eight species of Sparidae (Perciformes, Teleostei). This sequence information allowed us to design specific primers to one of these species (Pagellus bogaraveo). The new set of primers was used to test a rationalized approach to study the mtDNA nucleotide variability at the intraspecific level. The single‐strand conformation polymorphism (SSCP) technique was applied to detect sequence variation in two non‐overlapping fragments of the control region of 32 individuals of P. bogaraveo. To assess the sensitivity of the method, the nucleotide sequence of the analysed region was determined for all the specimens. The results showed that, for one of the two fragments, SSCP analysis was able to detect 100% of the underlying genetic variability. In sharp contrast, nucleotide variation of the second DNA fragment was completely unresolved by SSCP under different experimental conditions. This suggests that the resolution power of SSCP is crucially dependent on the nature of the fragment subjected to the analysis; therefore, a preliminary test of the sensitivity of the method should be performed on each specific DNA fragment before starting a large‐scale survey. A rationalized approach, combining the SSCP technique and a simplified sequencing procedure, is proposed for studying intraspecific polymorphism at the mtDNA control region in fish.
Cloning and characterization of 414 polymorphic porcine microsatellites
Authors: Alexander L J , Rohrer G A , Beattie C W 
Published: July 2010

SummaryWe report the sequences, sizes, and number of alleles of 414 new porcine microsatellites that were cloned in our laboratory and 21 micro‐satellites derived from GenBank DNA sequences. We also confirm the usefulness of porcine microsatellite primer pairs derived from short interdispersed elements.
Transfer of bovine microsatellites to the cervine (Cervus elaphus)
Authors: Kühn R , Anastassiadis C , Pirchner F 
Published: July 2010

SummaryBovine microsatellites were used to amplify DNA of red deer (Cervus elaphus). Fourteen of 27 bovine systems (52%) displayed polymorphism, while no (CA)n‐repeat was detected in seven systems and six systems gave no amplificates in red deer. The allele number ranged from 2 to 7, the polymorphism information content between 0.24 and 0.76. The results demonstrate that transfer of microsatellite systems between families of the same order (artiodactyla) is possible. Molecular genetic research will help to clarify the differentiation and ecology of wild animals and will contribute to define criteria needed for the preservation of endangered species.
The porcine TTR locus maps to chromosome 6q
Authors: Archibald A L , Couperwhite S , Jiang Z H 
Published: July 2010

SummaryThe sequence of a cDNA clone encoding porcine transthyretin (prealbumin) was used to develop polymorphic markers for the TTR locus. The single‐strand conformation polymorphism (SSCP) detected is caused by a silent AIT mutation in the penultimate coding codon and can also be revealed as a SacI restriction fragment length polymorphism (RFLP). The TTR locus was mapped to chromosome 6q by segregation and linkage analysis with these polymorphisms. This assignment confirms the predictions of homology between human chromosome 18 and pig chromosome 6q2.5‐2.6.
Alignment of the PiGMaP and USDA linkage maps of porcine chromosomes 3 and 9
Authors: Groenen M A M , de Vries B J , van der Poel J J 
Published: July 2010

SummaryThe European Pig Gene Mapping Project (PiGMaP) and United States Department of Agriculture (USDA) porcine linkage maps for chromosomes 3 and 9 have been aligned by typing three USDA microsatellites from chromosome 3 and five from chromosome 9 on the PiGMaP reference families. Using the crimap linkage analysis package, revised multipoint linkage maps were constructed for chromosome 3 and 9. Inclusion of these USDA markers in the multipoint analysis resulted in an increase in length of 47% and 33% respectively for these two PiGMaP linkage groups. This increase in size is mainly the result of extension of the ends of both linkage groups.
Variation in the control region sequence of the sheep mitochondrial genome
Authors: Wood N. J. , Phua S. H. 
Published: July 2010

SummaryThe DNA sequences of the control region of the mitochondrial genome of fifty unrelated sheep were determined in order to ascertain the extent and distribution of its variability. A consensus sequence was derived, and 1081 differences from it were observed amongst the fifty animals. Some constant groups of differences were observed that were held in common by a number of animals, which thus fell into two main groups, although neither group was typical of anyof the breeds sampled. The consensus sequence also allowed comparison between the control region sequences of sheep and other mammals. The sequence contains four tandem repeats of a 75 base‐pair motif that accounts for the difference in its size from the cattle control region, to which it is otherwise very similar. Comparison with the cattle sequence allowed the determination of the homologues of various functionally important sites. The homologues of the transcription promoters, the origin of replication and the central conserved sequence block were all identified by this method.
Chicken red blood cells as a substrate for direct polymerase chain reaction
Authors: Khatib H. , Gruenbaum Y. 
Published: July 2010

SummaryA protocol is presented for direct polymerase chain reaction (PCR) amplification of DNA from chicken nucleated red blood cells. Chicken blood in EDTA was found to have a strong inhibitory effect on the PCR. Consequently, PCR using this protocol should be performed only on a narrow range of blood volumes, from 0125 to 025 |ll.
Cytogenetic mapping of immunity‐related genes in the domestic horse
Authors: Musilova P. , Kubickova S. , Vychodilova‐Krenkova L. , Kralik P. , Matiasovic J. , Hubertova D. , Rubes J. , Horin P. 
Published: July 2010

SummaryChromosomal locations of 19 horse immunity‐related loci (CASP1, CD14, EIF5A, FCER1A, IFNG, IL12A, IL12B, IL12RB2, IL1A, IL23A, IL4, IL6, MMP7, MS4A2, MYD88, NOS2A, PTGS2, TFRC and TLR2) were determined by fluorescence in situ hybridization. For IFNG and PTGS2, this study is a confirmation of their previously reported position. In addition, microsatellite (HMBr1) was localized in the same region as IFNG. All genes were assigned to regions of conserved synteny and the data obtained in this study enhance the comparative human–horse map. Cytogenetic localization of IL6 to ECA4q14–q21.1 suggested a new breakage point that changes the order of loci compared with HSA7. The map assignments of these loci serve as anchors for other loci and will aid in the search for candidate genes associated with traits in the horse.
Application of bovine microsatellite markers for genetic diversity analysis of Swiss yak (Poephagus grunniens)
Authors: Nguyen T. T. , Genini S. , Ménétrey F. , Malek M. , Vögeli P. , Goe M. R. , Stranzinger G. 
Published: July 2010

SummaryIn order to assess the applicability of bovine microsatellite markers for population genetic studies in Swiss yak, 131 bovine microsatellite markers were tested on a panel of 10 animals. Efficient amplification was observed for 124 markers (94.6%) with a total of 476 alleles, of which 117 markers (94.3%) were polymorphic. The number of alleles per locus among the polymorphic markers ranged from two to nine. Seven loci (ILSTS005, BMS424B, BMS1825, BMS672, BM1314, ETH123 and BM6017) failed to amplify yak genomic DNA. Two cattle Y‐chromosome specific microsatellite markers (INRA126 and BM861) amplified genomic DNA from both male and female yaks. However, two additional markers on cattle Y‐chromosome (INRA124 and INRA189) amplified DNA from only males. Of the polymorphic markers, 24 microsatellites proposed by CaDBase for within‐ and cross‐species comparisons and two additional highly polymorphic markers (MHCII and TGLA73) were used to investigate the genetic variability and the population structure of a Swiss yak herd that included 51 additional animals. The polymorphic information content ranged from 0.355 to 0.752, while observed heterozygosity (HO) ranged from 0.348 to 0.823. Furthermore, a set of 13 markers, organized into three multiplex polymerase chain reactions, was evaluated for routine parentage testing. This set provided an exclusion probability in a family of four yaks (both parents and two offspring) of 0.995. These microsatellites serve as useful tools for genetic characterization of the yak, which continues to be an important domestic livestock species.
Diverse products of near‐surface sediment mobilization in an ancient eolianite: outcrop features of the early Jurassic Navajo Sandstone
Authors: Bryant Gerald , Miall Andrew 
Published: July 2010

ABSTRACTThe Navajo Sandstone of the Colorado Plateau, USA, displays a wide range of soft‐sediment deformation (SSD) features, including decametre‐scale features that have not been found in any modern desert environment. Laboratory simulations and partial analogues from other depositional environments suggest that these features derived from episodic liquefaction and fluidization of unconsolidated dune deposits. Outcrop details at many locations preserve the effects of fluid‐escape dynamics through porous, permeable, well‐sorted sand, which was partitioned by subtle textural changes at depositional boundaries between successive dune deposits and, less commonly, by distinct lithofacies changes marking the interface between wet and dry depositional environments. Extreme deformation and turbulent sediment flow have effaced primary structures in some zones of deformation; but other sites preserve the ductile modification of primary structures. Some outcrops preserve evidence of dramatic alterations in topography and sedimentation patterns due to localized compaction and large, subsurface, sediment displacements. Particularly notable among these extraordinary features are those representing the foundering of active dunes, sediment eruptions, and the subsidence of interdune surfaces in the ancient erg. The distinctive patterns of deformation in the Navajo Sandstone, interpreted in the context of its primary sedimentary architecture, provide unique insights into environmental conditions in the region during the Early Jurassic. Widespread ductile deformation in the Navajo indicates extraordinarily wet conditions for an active dune environment. The truncation of successive deformation features by deflation surfaces establishes the episodic nature of deformation in the unit and also suggests climatic variability. The widespread, episodic occurrence of SSD features, viewed within the seismic context provided by palaeotectonic reconstructions, strongly suggests that earthquake triggering of localized liquefaction controlled the distribution of deformation in this unit.
Three‐dimensional seismic analysis of the morphology and spatial distribution of chimneys beneath the Nyegga pockmark field, offshore mid‐Norway
Authors: Hustoft Steinar , Bünz Stefan , Mienert Jürgen 
Published: July 2010

ABSTRACTThree‐dimensional (3D) seismic data analysis has identified 415 seismic chimneys in the Nyegga area, on the mid‐Norwegian continental margin. The majority of the seismic chimneys connect with pockmarks at the modern seafloor, suggesting that the seismic chimneys represent the acoustic imprint of highly focused, cross‐stratal fluid flow. A semi‐quantitative spatial analysis of the seismic chimney complex, measuring parameters describing the dimension, geometry and root zone, provides constraints on the geological controls on chimney formation. Most of the seismic chimneys in the Nyegga region descriptively fall into the categories of ‘blowout chimneys’, because they diagnostically link to topography‐controlled leakage locations within strata showing acoustic indications of free gas. We find that approximately 60% of the fluid‐escape chimneys emanate from free gas layers below the gas hydrate stability zone. The timing of highly focused fluid expulsion through chimneys and the formation of the Nyegga pockmark field postdate the last glacial maximum at 25 000 years before present.