Many quantitative trait loci for feather growth in an F(2) broiler × layer cross collocate with body weight loci.

1. A genome-wide scan of 467 F(2) progeny of a broiler x layer cross was conducted to identify quantitative trait loci (QTL) affecting the rate of growth of the tail, wing and back feathers, and the width of the breast feather tract, at three weeks of age. 2. Correlations between the traits ranged from 0·36 to 0·61. Males had longer tail and wing feathers and shorter back feathers than females. Breast feather tract width was greater in females than males. 3. QTL effects were generally additive and accounted for 11 to 45% of sex average feather lengths of the breeds, and 100% of the breast feather tract width. Positive and negative alleles were inherited from both lines, whereas the layer allele was larger than the broiler allele after adjusting for body weight. 4. A total of 4 genome-significant and 4 suggestive QTL were detected. At three or 6 weeks of age, 5 of the QTL were located in similar regions as QTL for body weight. 5. Analysis of a model with body weight at three weeks as a covariate identified 5 genome significant and 6 suggestive QTL, of which only two were coincident with body weight QTL. One QTL for feather length at 148 cM on GGA1 was identified at a similar location in the unadjusted analysis. 6. The results suggest that the rate of feather growth is largely controlled by body weight QTL, and that QTL specific for feather growth also exist.

Overlap of quantitative trait loci for early growth rate, and for body weight and age at onset of sexual maturity in chickens.

Critical age, weight and body composition have been suggested as necessary correlates of sexual maturity. A genome scan to identify quantitative trait loci (QTL) for age and body weight at first egg (AFE and WFE) was conducted on 912 birds from an F(2) broiler-layer cross using 106 microsatellite markers. Without a covariate, QTL for body WFE were detected on chromosomes 2, 4, 8, 27 and Z and a single QTL for AFE was detected on chromosome 2. With AFE as a covariate, additional QTL for body WFE were found on chromosomes 1 and 13, with abdominal fat pad as covariate a QTL for body WFE was found on chromosome 1. With body WFE as covariate, additional QTL for AFE were found on chromosomes 1, 3, 4, 13 and 27. The QTL generally acted additively and there was no evidence for epistasis. Consistent with the original line differences, broiler alleles had positive effects on body WFE and negative effects on AFE, whereas the phenotypic correlation between the two traits was positive. The mapped QTL for body WFE cumulatively accounted for almost half the body weight difference between the chicken lines at puberty. Overlapping QTL for body WFE and body weight to 9 weeks of age indicate that most QTL affecting growth rate also affect body WFE. The co-localisation of QTL for body weight, growth and sexual maturity suggests that body weight and growth rate are closely related to the attainment of sexual maturity and that the genetic determination of growth rate has correlated effects on puberty.

Quantitative trait loci for bone traits segregating independently of those for growth in an F2 broiler x layer cross.

An F2 broiler-layer cross was phenotyped for 18 skeletal traits at 6, 7 and 9 weeks of age and genotyped with 120 microsatellite markers. Interval mapping identified 61 suggestive and significant QTL on 16 of the 25 linkage groups for 16 traits. Thirty-six additional QTL were identified when the assumption that QTL were fixed in the grandparent lines was relaxed. QTL with large effects on the lengths of the tarsometatarsus, tibia and femur, and the weights of the tibia and femur were identified on GGA4 between 217 and 249 cM. Six QTL for skeletal traits were identified that did not co-locate with genome wide significant QTL for body weight and two body weight QTL did not coincide with skeletal trait QTL. Significant evidence of imprinting was found in ten of the QTL and QTL x sex interactions were identified for 22 traits. Six alleles from the broiler line for weight- and size-related skeletal QTL were positive. Negative alleles for bone quality traits such as tibial dyschondroplasia, leg bowing and tibia twisting generally originated from the layer line suggesting that the allele inherited from the broiler is more protective than the allele originating from the layer.

Predicting severe pain after root canal therapy in the National Dental PBRN.

Some patients experience severe pain following root canal therapy (RCT) despite advancements in care. We sought to identify factors, which can be measured preoperatively, that predict this negative outcome so that future research may focus on preemptive steps to reduce postoperative pain intensity. Sixty-two practitioners (46 general dentists and 16 endodontists) who are members of the National Dental Practice-Based Research Network enrolled patients receiving RCT for this prospective observational study. Baseline data collected from patients and dentists were obtained before treatment. Severe postoperative pain was defined based on a rating of ≥7 on a scale from 0 (no pain) to 10 (pain as bad as can be) for the worst pain intensity experienced during the preceding week, and this was collected 1 wk after treatment. Multiple logistic regression analyses were used to develop and validate the model. A total of 708 patients were enrolled during a 6-m period. Pain intensity data were collected 1 wk postoperatively from 652 patients (92.1%), with 19.5% (n = 127) reporting severe pain. In multivariable modeling, baseline factors predicting severe postoperative pain included current pain intensity (odds ratio [OR], 1.15; 95% confidence interval [CI], 1.07 to 1.25; P = 0.0003), number of days in the past week that the subject was kept from their usual activities due to pain (OR, 1.32; 95% CI, 1.13 to 1.55; P = 0.0005), pain made worse by stress (OR, 2.55; 95% CI, 1.22 to 5.35; P = 0.0130), and a diagnosis of symptomatic apical periodontitis (OR, 1.63; 95% CI, 1.01 to 2.64; P = 0.0452). Among the factors that did not contribute to predicting severe postoperative pain were the dentist's specialty training, the patient's age and sex, the type of tooth, the presence of swelling, or other pulpal and apical endodontic diagnoses. Factors measured preoperatively were found to predict severe postoperative pain following RCT. Practitioners could use this information to better inform patients about RCT outcomes and possibly use different treatment strategies to manage their patients (Clinicaltrials.gov NCT01201681).

The expression of transforming growth factor-beta by cultured chick growth plate chondrocytes: differential regulation by 1,25-dihydroxyvitamin D3.

1,25-Dihydroxyvitamin D3 (1,25(OH)2D3) and transforming growth factor-beta (TGF-beta) are both important regulators of chondrocyte growth and differentiation. We report here that 1,25(OH)2D3 differentially regulates the expression of the genes for TGF-beta 1 to -beta 3 and the secretion of the corresponding proteins in cultured chick chondrocytes. Confluent growth plate chondrocytes were serum-deprived and cultured in varying concentrations of 1,25(OH)2D3. Cells were assayed for TGF-beta mRNA and conditioned medium was assayed for TGF-beta activity and isoform composition. Active TGF-beta was only detected in 10(-8) M 1,25(OH)2D3-treated cultures (8.37 ng active TGF-beta/mg protein). There was a significant decrease in total (latent-active) TGF-beta activity in conditioned medium of 10(-12) M (23.4%; P < 0.05) and 10(-10) M (20.7%; P < 0.05) 1,25(OH)2D3-treated cultures but 10(-8) M 1,25(OH)2D3 significantly increased (30.9%; P < 0.01) TGF-beta activity. The amounts of TGF-beta 1, -beta 2 and -beta 3 isoforms produced were similar in control, 10(-10) or 10(-12) M 1,25(OH)2D3-treated cultures but the conditioned medium of 10(-8) M 1,25(OH)2D3-treated cultures contained significantly higher amounts of all three isoforms. Quantification of TGF-beta mRNA demonstrated differential control of TGF-beta gene expression with TGF-beta 1 and -beta 3 mRNA levels reduced by all concentrations of 1,25(OH)2D3 examined (10(-8), 10(-10) and 10(-12) M) whilst TGF-beta 2 mRNA concentrations were elevated. Our results indicated that 1,25(OH)2D3 regulates chick growth plate chondrocyte TGF-beta secretion and mRNA expression in a concentration-dependent and isoform-specific manner. This interaction may be important in the regulation of chondrocyte metabolism and endochondral bone growth.

The chicken transforming growth factor-beta 3 gene: genomic structure, transcriptional analysis, and chromosomal location.

In this paper, we report the isolation, characterization, and mapping of the chicken transforming growth factor-beta 3 (TGF-beta 3) gene. The gene contains seven exons and six introns spanning 16-kb of the chicken genome. A comparison of the 5'-flanking regions of human and chicken TGF-beta 3 genes reveals two regions of sequence conservation. The first contains ATF/CRE and TBP/TATA sequence motifs within an 87-bp region. The second is a 162-bp region with no known sequence motifs. Identification of transcription start sites using chicken RNA isolated from various embryonic and adult tissues reveals two sites of initiation, P1 and P2, which map to these two conserved regions. Comparison of 3'-flanking regions of chicken and mammalian TGF-beta 3 genes also revealed conserved sequences. The most significant homologies were found in the 3'-most end of the transcribed region. DNA sequence analysis of chicken TGF-beta 3 cDNAs isolated by 3'-RACE revealed multiple polyadenylation sites unusually distant from a poly(A) signal motif. A Msc I restriction fragment length polymorphism (RFLP) marker was used to map the TGFB3 locus to linkage group E7 on the East Lansing reference backcross. Linkage to the TH locus showed that the TGFB3 locus was physically located on chicken chromosome 5.

Localization and changes in NADPH-diaphorase reactivity and nitric oxide synthase immunoreactivity in rat pulp following tooth preparation.

Inflammatory changes in the dental pulp are accompanied by release of a wide variety of chemical mediators. Nitric oxide, an oxidative free radical produced by the enzyme nitric oxide synthase (NOS), has been implicated in multiple inflammatory processes, which makes it a suitable marker for changes which likely occur following tooth pulp insult. Since limited information on nitric oxide in the pulp is available, it is necessary first to examine relative distributions of NOS in uninflamed and inflamed rat pulp. We accomplished this by characterizing regions of nicotinamide adenine dinucleotide phosphate diaphorase (NADPH-d) activity and the distribution of both macrophage NOS (macNOS) and neuronal NOS (nNOS) immunoreactivity in normal and inflamed rat molar pulp at multiple time points. The results showed that: (1) deep cavity preparation on the mesial surface of the molar produced a time-dependent inflammation, with acute inflammation early progressing to chronic, granulomatous inflammation with necrosis later that spread preferentially down the mesial root; (2) control (non-prepared) teeth showed a relatively faint and homogeneous distribution of NADPH-d and macNOS reactivity but no discernible nNOS reactivity; (3) inflamed teeth displayed localized increased intensity of NADPH-d and macNOS reactivity surrounding the inflamed area of pulp, but no increased nNOS activity; (4) pulp vessels supplying the inflamed area showed increased NADPH-d reactivity, but no increased macNOS or nNOS reactivity; and (5) neither NADPH-d, macNOS, nor nNOS reactivity was observed in pulpal nerves. Therefore, nitric oxide may mediate the pulpal inflammatory response through its effects on the paralesional pulp tissue and surrounding endothelial/vascular structures.

Atypical odontalgia misdiagnosed as odontogenic pain: a case report and discussion of treatment.

Atypical odontalgia is characterized by prolonged periods of throbbing or burning pain in the teeth or alveolar process, which occurs in the absence of any identifiable odontogenic etiology. The pain may be bilateral and change in location. This article presents two cases of atypical odontalgia that were misdiagnosed and initially treated as pain of odontogenic origin. A therapeutic regimen of tricyclic antidepressants alleviated the pain in one patient and was unsuccessful in the second. These two cases demonstrate the importance of having a thorough knowledge of both odontogenic and nonodontogenic causes of orofacial pain as well as the need for careful diagnosis before undertaking any treatment.

Trigeminal neuralgia mimicking odontogenic pain. A report of two cases.

Trigeminal neuralgia or tic douloureux is characterized by paroxysmal episodes of facial pain in the distribution of the trigeminal nerve, although patients may have a variety of symptoms that mimic odontogenic pain. This article presents two cases of trigeminal neuralgia that were misdiagnosed and initially treated endodontically as pain of odontogenic origin. A therapeutic regimen of carbamazepine alleviated the pain in both patients. These two cases demonstrate the importance of having a thorough knowledge of both odontogenic and nonodontogenic causes of orofacial pain, as well as the need for careful diagnosis before undertaking any treatment.

Expression of the gene for transforming growth factor-beta in avian dyschondroplasia.

Previous immunolocalisation studies of dyschondroplasia have indicated that there is a reduction in the number of growth plate chondrocytes containing the protein transforming growth factor beta 3 (TGF-beta 3). The reduction in TGF-beta 3 in dyschondroplasia is likely to be a direct result of a reduction in the expression of the TGF-beta 3 gene. mRNA was extracted from small (0.09 g) samples of growth cartilage from the proximal tibiotarsus of three-week-old broiler chicks. The cartilage samples contained cells from all three zones of the growth plate (proliferative, transitional and upper hypertrophic) and were collected from normal and dyschondroplastic growth plates. The dyschondroplastic growth plates were identified by an accumulation of transitional chondrocytes which were considered to be a result of a failure to differentiate to the hypertrophic phenotype. A semi-quantitative polymerase chain reaction (PCR) was used to estimate the quantity of mRNA specific for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and for each of the three isoforms of TGF beta (TGF-beta 1, TGF-beta 2 and TGF-beta 3) in each of the cartilage samples. The levels of expression of mRNA for GAPDH, TGF-beta 1 and TGF-beta 2 were similar in the two groups, but the expression of TGF-beta 3 mRNA was significantly reduced in the samples from the dyschondroplastic growth plates. The reduction in TGF-beta 3 levels is thought to be associated with the failure of chondrocyte hypertrophy in dyschondroplasia, and provides in vivo evidence that TGF-beta 3 is part of the cascade of events associated with the differentiation of chondrocytes during endochondral ossification in the chick.

Retreatment versus initial root canal treatment: factors affecting posttreatment pain.

OBJECTIVE: The purpose of this study was to determine the factors associated with posttreatment pain in patients receiving root canal retreatment (RCR) and in those receiving initial root canal treatment (IRCT). STUDY DESIGN: Eighty four patients scheduled for RCR or IRCT completed questionnaires on pretreatment pain levels (Visual Analogue Scale, 0-100) and demographic data. Diagnosis and original obturating material, if applicable, were also recorded, and treatment was initiated. At 4, 8, 12, 24, 48, 72, 96, and 120 hours, patients recorded posttreatment pain levels. Seventy one patients returned completed questionnaires. RESULTS: There was no significant difference in posttreatment pain with respect to patients undergoing RCR and patients undergoing IRCT, type of original obturating material, or pretreatment diagnosis. Posttreatment pain levels were significantly increased at 4, 8, and 12 hours after treatment. Patients reporting higher levels of pretreatment pain (Visual Analogue Scale > 20) had significantly increased posttreatment pain (P <.05) up to 24 hours after the procedure. CONCLUSIONS: Pretreatment pain level influenced posttreatment pain more than RCR or IRCT, the type of original obturating material, or the pretreatment diagnosis.

Localization and changes in superoxide dismutase immunoreactivity in rat pulp after tooth preparation.

OBJECTIVE: To examine the distribution of superoxide in the uninflamed and inflamed dental pulp by characterizing the immunoreactivity of the detoxifying antioxidant enzymes, manganese and copper-zinc superoxide dismutases (MnSOD and CuZnSOD, respectively). STUDY DESIGN: In 12 rats, mesial cavity preparations were made on the maxillary right first molar; left molars were unoperated controls. After 5 days, the rats were killed, and histologic sections were processed by using MnSOD and CuZnSOD immunoreactivity, and the extent of inflammation was evaluated on alternate sections stained with hematoxylin and eosin. RESULTS: In the hematoxylin and eosin-stained sections, inflammation was consistent with round-cells: macrophages, lymphocytes, and plasma cells that coalesced into a distinct leukocytic "lesion", which obliterated portions of the underlying pulp. Both MnSOD and CuZnSOD immunoreactivity increased dramatically in inflammatory cells within the leukocytic lesion and in the tissue surrounding the lesion. CONCLUSIONS: The findings suggest that the protective role of SOD increases within pulp cells that are undergoing inflammatory stimulation. SOD immunoreactivity may be an early indicator of stress in pulp.

Detection of quantitative trait loci for androstenone, skatole and boar taint in a cross between Large White and Meishan pigs.

'Boar taint' is a strong perspiration-like, urine-like unpleasant odour given off upon heating or cooking of meat from some intact (uncastrated) male pigs. Data from the F(2) generation of a Large White (LW) x Meishan (MS) crossbred population were analysed to detect quantitative trait loci (QTL) for traits associated with boar taint. Fat samples from 178 intact male pigs slaughtered at 85 +/- 5 kg were analysed for the major contributors to boar taint (androstenone, indole and skatole). Fat and lean samples from cooked meat were scored for boar, abnormal and pork flavour and odour by a trained sensory panel (SP). A scan with 117 markers covering the whole genome was performed in the F(2) individuals, together with their F(1) parents and purebred grandparents. At the 5% chromosomal significance threshold (approximately equal to the genome-wide suggestive significance threshold), QTL were detected for the laboratory estimate of androstenone on chromosomes 2, 4, 6, 7 and 9. However, only on chromosome 6 were there QTL for boar flavour (BF) traits in the same or adjacent marker intervals as a QTL for the laboratory estimate of androstenone. On chromosome 14, QTL were detected for the laboratory estimates of indole and skatole, the SP score for skatole and the scores for BF in lean and BF in fat. In all five cases, the MS allele generally increased the estimate or score, compared with the LW allele, but it appeared that desirable and undesirable alleles were present in both breeds. This locus on chromosome 14 has considerable potential for use to reduce the incidence of boar taint, especially if further research can identify the causative polymorphism or strongly associated markers.

Two applications to facilitate the viewing of database search result files on the Macintosh.

MOTIVATION: MacBOB (Macintosh BLAST Output Browser) and MacBOB Filter are two Macintosh-based applications that greatly simplify the viewing of BLAST and FASTA search results files. AVAILABILITY: The programs can be obtained via anonymous ftp from ftp.ri.bbsrc.ac.uk from the directory/pub/software/MacBOB, or via WWW from the Roslin Institute Home Page (http://www.ri.bbsrc.ac.uk/).

qValue--a program to calculate comparative measures of genomic reorganisation from cytogenetic and/or linkage information.

A program qValue, which calculates a measure of the genomic reorganisation that has occurred between pairs of species since their divergence from a common ancestor, is described. The program takes a tab-delimited text file containing data describing the location of various genetic loci in multiple species and generates an output text file, also in tab-delimited format, that lists various parameters of genomic reorganisation between all possible pairs of species considered. This provides a useful tool for the developing field of comparative genome mapping, particularly in the study of the evolution of the vertebrate genome.

Evolution of the transforming growth factor-beta superfamily.

Transforming growth factor beta 1 (TGF-beta 1) is the prototype of an increasingly complex superfamily of growth and differentiation factors. To date, a total of 74 TGF-beta-like sequences have been published, probably representing 23 distinct genes. These sequences were obtained from mammalian, avian, amphibian and insect species, thus emphasising the ancient nature of the TGF-beta superfamily peptides. This article summarises current hypotheses concerning the evolutionary history of this protein superfamily, based on the molecular phylogeny of the published sequences. Comparison of the deduced amino acid sequences leads to the definition of five main groups within the superfamily (TGF-beta, Bone Morphogenetic Proteins [BMP], Anti-Müllerian Hormone [AMH], Inhibin alpha [INH alpha] and GDF-9) and six subgroups within the BMPs (60A, Decapentaplegic [dpp], Vg1, BMP-3, Inhibin beta [INH beta A/B] and nodal). This classification predicts possible phylogenetic and functional relationships among these proteins.

Farm animal genome databases.

The requirements for bioinformatics resources to support genome research in farm animals is reviewed. The resources developed to meet these needs are described. Resource databases and associated tools have been developed to handle experimental data. Several of these systems serve the needs of multinational collaborations. Genome databases have been established to provide contemporary summaries of the status of genome maps in a range of farm and domestic animals along with experimental details and citations. New resources and tools will be required to address the informatics needs of emerging technologies such as microarrays. However, continued investment is also required to maintain the currency and utility of the current systems, especially the genome databases.

Establishment of a sequence-based typing system for BoLA-DRB3 exon 2.

A rapid, high-resolution sequence-based typing (SBT) system for BoLA-DRB3 exon 2 was developed. Amplification of the entire exon was achieved by a fully nested PCR with locus-specific primers and sequencing was performed directly on the PCR product. Heterozygous sequence data were obtained by automated sequence analysis of both alleles. Forward and reverse sequence data were assembled to improve identification of all heterozygous positions. Specific software (Haplofinder, Roslin Institute Software, Roslin, UK) was designed for allele assignment. Fifty-four females from a Holstein-Charolais resource herd cross, their 12 sires and five unrelated Holstein animals were used to establish the method. In parallel, these animals were typed by DRB3 polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) to confirm the results. Polymerase chain reaction-RFLP analysis defined 15 known types in the 71 animals, while SBT of the same animals showed 19 known alleles. Subsequently, 72 more animals from the same resource herd were typed by the established SBT method without PCR-RFLP typing. This SBT strategy and the Haplofinder software can be applied to the analysis of any polymorphic locus for which suitable locus-specific primers and allelic sequences are available.