bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny of the Brachytheciaceae (Bryophyta) based on morphology and sequence level data
Authors: Huttunen Sanna , Ignatov Michael S. 
Published: May 2004

AbstractBrachytheciaceae is often considered a taxonomically difficult group of mosses. For example, morphological variation has led to difficulty in generic delimitation. We used DNA sequence data (chloroplast psbT‐H and trnL‐F and nuclear ITS2) together with morphology (63 characters) to examine the relationships within this family. The combined unaligned length of the DNA sequences used in the phylogenetic analyses varied between 1277 and 1343 bp. For phylogeny reconstruction we performed direct optimization, as implemented in POY. Analyses were performed with three different gap costs and the morphological data partition was weighted both: (1) equal to gap cost, and (2) with a weight of one. The utility of sensitivity analysis has recently been cast into doubt; hence in this study it was performed only to explore the effects of weighting on homology statements and topologies and to enable more detailed comparisons between earlier studies utilizing the direct optimization method. The wide sequence length variation of non‐coding ITS2 sequences resulted in character optimizations (i.e., “alignments”) of very different lengths when various gap costs were applied. Despite this variation, the topologies of equally parsimonious trees remained fairly stable. The inclusion of several outgroups, instead of only one, was observed to increase the congruence between data sets and to slightly increase the resolution. An inversion event in the 9 bp loop region in the chloroplast psbT‐N spacer in mosses has been postulated to include only uninformative variation, thus possibly negatively impacting the phylogeny reconstruction. Despite this inversion, its variation within Brachytheciaceae was clearly congruent with information from other sources, but inclusion of these 9 bp in the analysis had only a minor effect on the phylogenetic results. In the most parsimonious topology, which was obtained with equal weighting of all data, Meteoriaceae and Brachytheciaceae were resolved as monophyletic sister groups, which had recently been suggested based on a few shared morphological characters. Our study revealed some new generic relationships within the Brachytheciaceae, which are discussed in light of the morphological characters traditionally used for generic delimitation.
Phylogenetic relationships of the genus Cheilosia and the tribe Rhingiini (Diptera, Syrphidae) based on morphological and molecular characters
Authors: Ståhls Gunilla , Stuke Jens‐Hermann , Vujic Ante , Doczkal Dieter , Muona Jyrki 
Published: May 2004

AbstractThe phylogenetic relationships of the tribe Rhingiini and the genus Cheilosia (Diptera, Syrphidae) were investigated using morphological and molecular characters. The genus Cheilosia is one of the most diverse lineages of hoverflies (Syrphidae). The mitochondrial protein coding gene cytochrome c oxidase subunit I (COI), and the D2‐3 region of the nuclear 28S rRNA gene were chosen for sequencing, and morphological characters were scored for both adults and immature stages. The combined dataset included 56 ingroup taxa. The datasets were analyzed separately and in conjunction, using both static and dynamic alignment under the parsimony criterion. The aim of the study was to assess the phylogenetic relationships of the tribe Rhingiini, and to explore if the subgenera of Cheilosia were supported as monophyletic clades. Results showed that the monophyly of subtribes of Rhingiini remained ambiguous, especially due to unstable phylogenetic placements of the genera Portevinia and Rhingia. We recovered most subgenera of Cheilosia as monophyletic clades. Dynamic alignment, using the optimization alignment program POY, always recovered more parsimonious topologies under all parameter weighting schemes, than did parsimony analyses using static alignment and analyzed with NONA.
Close linkage of genes encoding receptors for subgroups A and C of avian sarcoma/leucosis virus on chicken chromosome 28
Authors: Elleder D. , Plachý J. , Hejnar J. , Geryk J. , Svoboda J. 
Published: May 2004

SummaryAvian sarcoma and leucosis viruses (ASLV) are classified into six major subgroups (A to E and J) according to the properties of the viral envelope proteins and the usage of cellular receptors for virus entry. Subgroup A and B receptors are identified molecularly and their genomic positions TVA and TVB are mapped. The subgroup C receptor is unknown, its genomic locus TVC is reported to be genetically linked to TVA, which resides on chicken chromosome 28. In this study, we used two chicken inbred lines that carry different alleles coding for resistance (TVCR) and sensitivity (TVCS) to infection by subgroup C viruses. A backross population of these lines was tested for susceptibility to subgroup C infection and genotyped for markers from chicken chromosome 28. We confirmed the close linkage between TVA and TVC loci. Further, we have described the position of TVC on chromosome 28 relative to markers from the consensus map of the chicken genome.
cDNA cloning, genomic structure and polymorphism of the porcine FHL3 gene
Authors: Zuo B. , Xiong Y. Z. , Deng C. Y. , Su Y. H. , Wang J. , Lei M. G. , Li F. E. , Jiang S. W. , Zheng R. 
Published: May 2004

SummaryLIM domain proteins are important regulators of the growth, determination and differentiation of cells. Four‐and‐a‐half LIM‐only protein 3 (FHL3) is a type of LIM‐only protein that contains four tandemly repeated LIM motifs with an N‐terminal single zinc finger (half LIM motif). In this study, we have determined the complete coding sequence of pig FHL3 which encodes a 280 amino acid protein. The coding region of the pig FHL3 gene is organized in five exons and spans an approximately 2.1‐kb genomic region. Comparative sequencing of six pig breeds revealed three single nucleotide polymorphisms (SNPs) within exon 2 of which an A→G substitution at position 313 changes a codon for arginine into a codon for glycine. The substitution was situated within a PstI recognition site and developed as a PCR‐RFLP marker for further use in population variation investigations and association analysis. The A/G polymorphism was segregating only in Landrace pigs. Association studies of the FHL3 polymorphism with carcass traits provided preliminary evidence that the PstI PCR‐restriction fragment length polymorphism (RFLP) genotype may be associated with variation in several carcass traits of interest for pig breeding. Further investigations in more Landrace pigs are needed to confirm this.
Mapping and transcription profiling of CASP1, 3, 6, 7 and 8 in relation to caspase activity in the bovine cumulus–oocyte complex
Authors: Yuan Y. Q. , Peelman L. J. , Williams J. L. , Van Zeveren A. , de Kruif A. , Law A. , Van Soom A. 
Published: May 2004

SummarySo far 12 caspases have been described in mouse and human while only one (CASP13) is known in cattle. The aim of this study was to (1) search for other bovine caspases by reverse transcription and polymerase chain reaction (RT–PCR) and (2) examine the presence of bovine caspase mRNA and active protein in the cumulus–oocyte complex. Five caspases (1, 3, 6, 7 and 8) were identified, partially cloned and sequenced. Four of them were mapped. Differential transcription of the caspase genes was detected, but no active caspase protein was found in diverse bovine oocytes. Cumulus granulosa cells (CGC) contain CASP1, 6, 7 and 8 mRNA and active caspase protein. The presence of caspase mRNA and active caspase proteins in CGCs suggests the occurrence of apoptosis in cumulus–oocyte complex, while caspase activation is blocked in fresh oocytes and therefore caspase transcription cannot be used to predict the oocyte developmental capacity.
The chicken proinflammatory cytokines interleukin‐1β and interleukin‐6: differences in gene structure and genetic location compared with their mammalian orthologues
Authors: Kaiser P. , Rothwell L. , Goodchild M. , Bumstead N. 
Published: May 2004

SummaryThe genes encoding the chicken proinflammatory cytokines interleukin (IL)‐1B and IL‐6 were cloned, sequenced and mapped. The exon:intron structure of the coding region of chicken IL1B corresponds almost exactly to those of mammalian IL1B. As yet, we have no evidence for a 5′‐UTR non‐coding exon equivalent to that found in mammalian IL1B. The exon:intron structure of chicken IL6 differs from those of mammalian IL6, having one exon fewer (the first two exons in mammalian IL6 genes appear to be fused in the chicken gene). We were unable to clone or sequence the promoter of chicken IL1B. The chicken IL6 promoter shares a number of potential regulatory sequences similar to those found in the human IL6 promoter. These putative elements include (5′–3′) a glucocorticoid response element (GRE), an AP‐1 binding site, an NF‐IL‐6 binding site (albeit in the reverse orientation), an NF‐κB binding site, a second AP‐1 binding site and a TATAAA box. A further GRE, a cAMP response element and regions with homology to c‐fos serum responsive elements or retinoblastoma control elements were absent. Promoter sequence polymorphisms were not identified in eight different inbred chicken lines. A restriction single‐stranded conformational polymorphism was identified which enabled chicken IL1B to be genetically mapped to one end of chromosome 2. Chicken IL6 was mapped by fluorescent in situ hybridization also to chromosome 2, at an FLpter of 0.26.
Genetic polymorphisms and antiviral activity in the bovine MX1 gene
Authors: Nakatsu Y. , Yamada K. , Ueda J. , Onogi A. , Ables G. P. , Nishibori M. , Hata H. , Takada A. , Sawai K. , Tanabe Y. , Morita M. , Daikohara M. , Watanabe T. 
Published: May 2004

SummaryBovine MX1 cDNAs consisting of 2280 bp from 11 animals of five breeds and from a cultured cell line were sequenced and compared with previously reported data. Ten nucleotide substitutions were synonymous mutations, and a single nucleotide substitution at 458 resulted in an amino acid exchange of Ile (ATT) and Met (ATG). A 13‐bp deletion–insertion mutation was also found in the 3′‐UTR. Based on the nucleotide substitutions found in this study, bovine MX1 cDNA was classified into 11 genotypes. A phylogenetic tree of the 11 genotypes suggested that the genotypes observed in Brahman were a great genetic distance from other genotypes. An 18‐bp deletion–insertion variation at position 171 was found to be the result of alternative splicing. The 18‐bp deletion–insertion is located at the boundary between exon 3 and intron 3. Permanently transfected 3T3 cell lines expressing bovine MX1 mRNA were established to analyse the antiviral potential against VSVΔG*‐G infection. Transfected cell clones expressing bovine MX1 mRNA showed a significantly smaller number of cells infected with VSVΔG*‐G compared with the control cells. These results indicate that the bovine MX1 protein has potent antiviral activity.
Radiation hybrid map assignments of 11 ESTs obtained from a 28‐day‐old swine embryo cDNA library to the IMpRH map
Authors: Sarker N. , Kiuchi S. , Yasue H. , Mitsuhashi T. 
Published: May 2004

SummaryIn order to improve the map resolution and to locate more genes on the porcine radiation hybrid map, expressed sequence tags (ESTs) were isolated from a 28‐day‐old normal pig embryo cDNA library. The ESTs were sequenced from the 5′‐end and similarities were checked with sequences registered in the NCBI DNA database (http://www.ncbi.nlm.nih.gov/blast/). The ESTs sequences which have high identity scores (>80%) against human genes or ESTs were further sequenced from the 3′ untranslated region. The ESTs which were sequenced successfully were used to design primers for PCR analysis of the radiation hybrid panel. Eleven ESTs were physically mapped to porcine chromosomes 2, 4, 8, 10, 13, 14 and X. The localizations are in agreement with the comparative mapping data between human and pig. The results will provide unique information to the comparative map of human and pig.
Genetic mapping of quantitative trait loci affecting body weight, egg character and egg production in F2 intercross chickens
Authors: Sasaki O. , Odawara S. , Takahashi H. , Nirasawa K. , Oyamada Y. , Yamamoto R. , Ishii K. , Nagamine Y. , Takeda H. , Kobayashi E. , Furukawa T. 
Published: May 2004

SummaryPhenotypic measurements of chicken egg character and production traits are restricted to mature females only. Marker assisted selection of immature chickens using quantitative trait loci (QTL) has the potential to accelerate the genetic improvement of these traits in the chicken population. The QTL for 12 traits (i.e. body weight (BW), six for egg character, three for egg shell colour and two for egg production) of chickens were identified. An F2 population comprising 265 female chickens obtained by crossing White Leghorn and Rhode Island Red breeds and genotyped for 123 microsatellite markers was used for detecting QTL. Ninety‐six markers were mapped on 25 autosomal linkage groups, and 13 markers were mapped on one Z chromosomal linkage group. Eight previous unmapped markers were assigned to their respective chromosomes in this study. Significant QTL were detected for BW on chromosomes 4 and 27, egg weight on chromosome 4, the short length of egg on chromosome 4, and redness of egg shell colour (using the L*a*b* colour system) on chromosome 11. A significant QTL on the Z chromosome was linked with age at first egg. Significant QTL could account for 6–19% of the phenotypic variance in the F2 population.
A first‐generation microsatellite linkage map of the Japanese quail
Authors: Kayang B. B. , Vignal A. , Inoue‐Murayama M. , Miwa M. , Monvoisin J. L. , Ito S. , Minvielle F. 
Published: May 2004

SummaryA linkage map of the Japanese quail (Coturnix japonica) genome was constructed based upon segregation analysis of 72 microsatellite loci in 433 F2 progeny of 10 half‐sib families obtained from a cross between two quail lines of different genetic origins. One line was selected for long duration of tonic immobility, a behavioural trait related to fearfulness, while the other was selected based on early egg production. Fifty‐eight of the markers were resolved into 12 autosomal linkage groups and a Z chromosome‐specific linkage group, while the remaining 14 markers were unlinked. The linkage groups range from 8 cM (two markers) to 206 cM (16 markers) and cover a total map distance of 576 cM with an average spacing of 10 cM between loci. Through comparative mapping with chicken (Gallus gallus) using orthologous markers, we were able to assign linkage groups CJA01, CJA02, CJA05, CJA06, CJA14 and CJA27 to chromosomes. This map, which is the first in quail based solely on microsatellites, is a major step towards the development of a quality molecular genetic map for this valuable species. It will provide an important framework for further genetic mapping and the identification of quantitative trait loci controlling egg production and fear‐related behavioural traits in quail.
Verification of selective DNA pooling methodology through identification and estimation of the DGAT1 effect
Authors: Fisher P. J. , Spelman R. J. 
Published: May 2004

SummaryThe discovery of markers linked to genes that are responsible for traits of interest to the dairy industry might prove useful because they could aid in selection and breeding decisions. We have developed a selective DNA pooling methodology to allow us to efficiently screen the bovine genome in order to find genes responsible for production traits. Using markers on chromosome 14 as a test case, we identified a gene (DGAT1) previously known to affect three traits (fat yield, protein yield and total milk yield). Furthermore, we predicted similar effects to those previously shown for DGAT1 in a New Zealand Holstein‐Friesian herd. Additionally, we showed a low error rate (1.6%) for the pooling procedure. Hence we are confident that we can apply this procedure to an entire genome scan in the search for quantitative trait loci (QTL).
Evidence for quantitative trait loci affecting twinning rate in North American Holstein cattle
Authors: Cruickshank J. , Dentine M. R. , Berger P. J. , Kirkpatrick B. W. 
Published: May 2004

SummaryTwinning in dairy cattle has been associated with many negative health and reproductive events that cause economic loss to the producer. Reports have suggested that twinning rates are increasing and that there may be a positive relationship between milk production and twinning frequency. Putative quantitative trait loci (QTL) for twinning and ovulation rate on bovine chromosomes 5, 7, 19 and 23 have been previously identified in other populations. The objective of this study was to detect and possibly confirm the existence and effects of these QTL in the North American Holstein population. Half‐sib families of 20 North American Holstein sires with above average twinning rate predicted transmitting abilities (PTA) comprised the sample population under investigation. Twinning rate PTA values had been estimated from calving data. DNA extracted from semen samples was analysed using 45–61 microsatellite markers across the four chromosomes. Marker heterozygosity of the patriarchs averaged 62%. Evidence of twinning QTL was found in multiple families on chromosomes 5, 7 and 23 and in one family on chromosome 19. Four of the sires formed one three‐generation family: one sire and three half‐sib sons with sons of their own. This extended family was analysed with additional markers confirming a twinning QTL of significant size on chromosome 5.
Mapping of the porcine oestrogen receptor 2 gene and association study with litter size in Iberian pigs
Authors: Muñoz G. , Óvilo C. , Amills M. , Rodríguez C. 
Published: May 2004

SummaryGenes encoding the oestrogen receptors (ESR) are considered candidate genes for prolificacy traits due to the key role these molecules play in the regulation of reproductive physiology. In this paper, we report the assignment of the pig ESR2 gene to porcine chromosome 1 by radiation hybrid mapping. Most of the ESR2 cDNA was sequenced from Iberian pig ovarian RNA samples and one A/G single nucleotide polymorphism (SNP) was found at exon 5, being associated with a Met/Val substitution at position 949. This SNP was genotyped using a PCR‐RFLP (Hsp92II) protocol and its potential effect on litter size was evaluated in two Iberian pig populations. However, no statistically significant association between the ESR2 polymorphism and litter size was found.
Impact of candidate sire number and sire relatedness on DNA polymorphism‐based measures of exclusion probability and probability of unambiguous parentage
Authors: Sherman G. B. , Kachman S. D. , Hungerford L. L. , Rupp G. P. , Fox C. P. , Brown M. D. , Feuz B. M. , Holm T. R. 
Published: May 2004

SummaryGenetic paternity testing can provide sire identity data for offspring when females have been exposed to multiple males. However, correct paternity assignment can be influenced by factors determined in the laboratory and by size and genetic composition of breeding groups. In the present study, DNA samples from 26 commingled beef bulls and their calves from the Nebraska Reference Herd‐1 (NRH1), along with previously reported Illinois Reference/Resource Families data, were used to estimate the impact of sire number and sire relatedness on microsatellite‐based paternity testing. Assay performance was measured by exclusion probabilities and probabilities of unambiguous parentage (PUP) were derived. Proportion of calves with unambiguous parentage (PCUP) was also calculated to provide a readily understandable whole‐herd measure of unambiguous paternity assignment. For NRH1, theoretical and observed PCUP values were in close agreement (85.3 and 85.8%, respectively) indicating good predictive value. While the qualitative effects on PUP values of altering sire number and sire relatedness were generally predictable, we demonstrate that the impacts of these variables, and their interaction effects, can be large, are non‐linear, and are quantitatively distinct for different combinations of sire number and degree of sire relatedness. In view of the potentially complex dynamics and practical consequences of these relationships in both research and animal production settings, we suggest that a priori estimation of the quantitative impact of a given set of interacting breeding group‐specific and assay‐specific parameters on PUP may be indicated, particularly when candidate sire pools are large, sire relatedness may be high, and/or loci numbers or heterozygosity values may be limiting.
Subclinical alteration of taste sensitivity induced by candesartan in healthy subjects
Authors: Tsuruoka Shuichi , Wakaumi Michi , Nishiki Kenta , Araki Nobutaka , Harada Kenichi , Sugimoto Koichi , Fujimura Akio 
Published: May 2004

AimsThere have been case reports of taste disturbance for the angiotensin II receptor blockers losartan and valsartan, but not for candesartan. This study was undertaken to examine whether candesartan causes taste disturbance.MethodsCandesartan cilexetil (4 mg day−1) or vehicle was given to healthy volunteers (n = 8) for 7 days in a randomized, double‐blind, placebo‐controlled, cross‐over design with a 2‐week washout period. Clinical gustometry using the filter‐paper disc test and electrogustometry were sequentially performed before and at the end of each trial. Serum and salivary zinc concentrations were also measured.ResultsDetection thresholds of four basic tastes (sweet, salty, sour and bitter) determined by the paper disc test were significantly (P < 0.05 in all tests) worsened (i.e. score of test increased) after repeated dosing of the drug, although the subjects did not notice such changes. The mean ± SEM (and 95% CI) scores of the four tastes at just before the seventh dosing of candesartan or vehicle was 3.38 ± 0.32 (3.02, 3.74) and 2.63 ± 0.18 (2.18, 3.08) for sweetness, 3.63 ± 0.38 (4.49, 2.77) and 2.63 ± 0.26 (3.27, 1.98) for salt, 4.01 ± 0.42 (3.04, 4.98) and 2.61 ± 0.32 (3.35, 1.87) for sourness, 4.01 ± 0.38 (3.22, 4.80) and 2.99 ± 0.33 (2.24, 3.74) for bitterness, for candesartan and placebo, respectively. Electrogustometry confirmed the candesartan‐related taste disturbance. Serum and salivary zinc concentrations were not influenced by candesartan.ConclusionsThese data suggest that candesartan subclinically reduces taste sensitivity after repeated dosing in healthy subjects. Because similar events are reported for losartan and valsartan in case reports, this adverse effect might be a class effect of angiotensin‐II receptor blockers (ARBs).