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E J Smith

Publications and source records attributed to E J Smith.

At least 37 records · Page 2Linked to original sources
PubMed2002

Expressed sequence tags for the chicken genome from a normalized 10-day-old white leghorn whole-embryo cDNA library. 3. DNA sequence analysis of genetic variation in commercial chicken populations.

Single nucleotide polymorphisms (SNPs) have emerged as a major class of DNA markers with the advantage of permitting the development of high-density genetic maps adequate for quantitative trait loci (QTL) identification by linkage-disequilibrium analysis. Here we describe results of a relatively high-depth survey of chicken broiler and layer populations for SNPs in targeted genomic regions of chicken expressed sequence tag (EST) sites. The sequences scanned, representing the composite sequence of 12 amplified fragments for a total of 6489 bp, were randomly distributed, occurring on six different chromosomes or linkage groups in the chicken genome. Although one of the genomic DNA sequences did not match the reference cDNA sequence, another contained an intron that separated two putative exons. The number of SNPs observed within each of the 12 EST-targeted genomic regions ranged from 0 to 10 for a total of 44 and a frequency of 0.7%. About 70% of the polymorphisms were shared between layer and broiler populations. The average heterozygosity within the populations ranged from 0.15 to 0.48, with the layer populations showing the higher heterozygosity. SNPs and oligonucleotides described will provide a resource for genetic analysis in commercial chicken populations. The data appear to indicate that the relative frequency of SNPs in the targeted regions scanned is higher than the frequency reported for any of the other regions scanned to date in other eukaryotic genomes. Additionally, the results suggest that the use of DNA pools may offer an efficient approach to SNP detection in chickens, as has been shown in other vertebrates.

Animals↗
PubMed2001

Frequency and distribution in three ethnic populations of single nucleotide polymorphisms in the MICA gene.

The Homo sapiens major histocompatibility complex (MHC) class 1 chain related gene A (MICA) was scanned for novel single nucleotide polymorphisms (SNPs) using a panel of DNA samples from African-, Japanese- and Mexican-Americans. Overlapping primer-pairs were used to amplify products in the size range of 300 to 400 bp that were sequenced and scanned for SNPs using Phred, Phrap, Polyphred and Consed sequence analysis programs. A total of 16 SNPs were detected, six of which represent new variant nucleotides in the Homo sapiens MICA gene. Three of the variants also represent amino acid changes in the MICA protein. Differences among the three ethnic panels in the frequency of the variant nucleotides observed were inconsistent, but significant for seven of the SNPs detected. Though a small sample size, this study represents the first multi-population based analysis of the frequency and distribution of SNPs in the MICA gene, a locus that may be essential in the antigenic recognition by gammadelta T cells.

Alleles↗
PubMed2001

Expressed sequence tags for the chicken genome from a normalized, ten-day-old white leghorn whole embryo cDNA library. 2. Comparative DNA sequence analysis of guinea fowl, quail, and turkey genomes.

Accelerated efforts to develop a high-utility chicken genome map have resulted in the development of resources that may be useful for genetic analysis in other economically important poultry species. Here we describe a total of 26 comparative genomic DNA sequences (CGS) for the guinea fowl, Japanese quail, and domestic turkey developed using 10 primer pairs specific for 10 previously reported, unique, chicken expressed sequence tags (EST). The total length of CGS developed for each of the three species was 4,193, 4,597, and 6,057 bp in quail, turkey, and guinea fowl, respectively. About 70% of the CGS showed significant sequence similarity to reference database sequences, including the reference chicken EST and other avian and nonavian genes. A majority of the between-species comparisons of the CGS from all but two primer pairs were significant and ranged from 81 to 99%. The percentage similarity of the CGS appears to be a function of phylogenetic relatedness and was generally higher for comparisons between the chicken, quail, and turkey and lower between the guinea fowl and chicken, quail, or turkey. Maximum likelihood estimation of the phylogenetic relationships using CGS from two primer pairs also showed a closer relationship, as expected, among chicken, quail, and turkey than between guinea fowl and either chicken, quail, or turkey. Within the guinea fowl, quail, and turkey CGS developed, the total number of single nucleotide polymorphisms detected was 28, 17, and 14, respectively. Together, these resources represent tools that will facilitate genetic analysis of species that have been studied very little and our understanding of their genomes and genome evolution.

Animals↗
PubMed2000

IRF3 and IRF7 phosphorylation in virus-infected cells does not require double-stranded RNA-dependent protein kinase R or Ikappa B kinase but is blocked by Vaccinia virus E3L protein.

Induction of interferon-alpha (IFNalpha) gene expression in virus-infected cells requires phosphorylation-induced activation of the transcription factors IRF3 and IRF7. However, the kinase(s) that targets these proteins has not been identified. Using a combined pharmacological and genetic approach, we found that none of the kinases tested was responsible for IRF phosphorylation in cells infected with Newcastle disease virus (NDV). Although the broad-spectrum kinase inhibitor staurosporine potently blocked IRF3 and -7 phosphorylation, inhibitors for protein kinase C, protein kinase A, MEK, SAPK, IKK, and protein kinase R (PKR) were without effect. Both IkappaB kinase and PKR have been implicated in IFN induction, but cells genetically deficient in IkappaB kinase, PKR, or the PKR-related genes PERK, IRE1, or GCN2 retained the ability to phosphorylate IRF7 and induce IFNalpha. Interestingly, PKR mutant cells were defective for response to double-stranded (ds) RNA but not to virus infection, suggesting that dsRNA is not the only activating viral component. Consistent with this notion, protein synthesis was required for IRF7 phosphorylation in virus-infected cells, and the kinetics of phosphorylation and viral protein production were similar. Despite evidence for a lack of involvement of dsRNA and PKR, vaccinia virus E3L protein, a dsRNA-binding protein capable of inhibiting PKR, was an effective IRF3 and -7 phosphorylation inhibitor. These results suggest that a novel cellular protein that is activated by viral products in addition to dsRNA and is sensitive to E3L inhibition is responsible for IRF activation and reveal a novel mechanism for the anti-IFN effect of E3L distinct from its inhibition of PKR.

Animals↗
PubMed2000

Reversal of acidification in tributaries of the River Duddon (English Lake District) between 1970 and 1998.

Long-term changes in stream water chemistry in the upper Duddon catchment (southwest Lake District, UK) were investigated. Ten streams were sampled and analysed weekly during 1998, and the results compared with data for the early 1970s and 1986. The waters exhibited a range of pH, average values for 1998 being 5.04-7.04. For all the streams, the average pH in 1998 was greater than that during 1971-73. Statistical analysis was carried out, using the 1970s data to estimate the magnitude of inter-annual variation, and taking discharge into account on the basis of antecedent rainfall. The results showed that for two of the streams the pH increase was significant at the 2.5% level, while for a further three it was significant at the 10% level. Comparison of the 1998 concentrations of nitrate and non-marine sulphate with data obtained for five streams in 1973-74 showed that average nitrate concentration had increased from 11 to 20 microeq dm(-3) while that of non-marine sulphate had decreased from 94 to 50 microeq dm(-3). For four of the streams, comparisons were also made between the 1998 data and those for 1986. In three cases, pH in 1998 was generally higher, and Al generally lower, than the values for 1986, but in the fourth case little difference was evident. The present results support observations for five nearby standing waters, strengthening the evidence for a general reversal of acidification in the southwest part of Lake District, due to a decline in the deposition of pollutant sulphur.

Journal Article↗
PubMed2000

Comparative DNA sequence analysis of genetic variation in the African grey parrot, Psittacus erythacus.

Comparative genome analysis promises to provide an insight into avian species that have been very little studied. To test the feasibility of this approach, we investigated the use of heterologous primers to generate single nucleotide polymorphisms (SNP) in the African grey parrot, Psittacus erythacus, using primers specific for chicken and turkey DNA fragments. Three of the primers were specific for three expressed sequence tagged sites in the turkey and the fourth for a chicken proteoglycan core protein-like DNA sequence. A total of about 2200 bp of the parrot genome was evaluated for DNA sequence variation. Seven SNPs were identified and confirmed by Mendelian segregation. The frequency distribution of the most common nucleotide at each SNP locus in an unrelated group of parrots ranged from 0.84 to 0.97. The percent similarity of each parrot sequence to the reference sequence was inconsistent and ranged from zero to 100%. The primers as well as the nucleotide variants described represent valuable resources for genetic analysis in the parrot.

Animals↗
PubMed2000

Amplification of sequence tagged sites in five avian species using heterologous oligonucleotides.

Short of a complete genomic DNA sequence, sequence tagged sites (STSs) have emerged as major genomic reagents for the genetic analysis of little-studied ecologically and agriculturally important organisms. Here, we report STS developed for the turkey (Meleagris gallopavo), guinea fowl (Numidea meleagris), Japanese quail (Coturnix coturnix) and pigeon using primers specific for reference DNA sequences of two chicken (Gallus gallus) genes, aggrecan (agc1) and type X collagen (col10). Additional STSs were also developed for turkey, quail and chicken using primers specific for the human apobec-1 gene. The total length of the STSs developed was 5990, 2522, 4127, 1539 and 6600 bp for the turkey, guinea fowl, Japanese quail, pigeon and chicken, respectively. Based on splice site consensus GT and AG sequences, four of the seven agc1-based chicken STS appear to contain introns. The human gene-based STSs showed no significant sequence identity with the reference GenBank sequences. Maximum likelihood, maximum parsimony and neighbour-joining analysis of an agc1-based STS that was common to all five species showed phylogenetic relationships consistent with those previously defined using mitochondria DNA sequences and nuclear gene restriction maps. Additionally, several putative single nucleotide polymorphisms (SNPs) were detected within the STSs, including eight in the turkey, two in the quail, and two in the chicken when multiple sequences were evaluated from each species. This report describes new STSs that are resources for genetic and physical mapping and genome analysis within and among avian species. These resources should further aid in our understanding of the biology of agriculturally important but little-studied guinea fowl and turkey.

APOBEC-1 Deaminase↗
PubMed2000

Detection of fungi in sinus fluid of patients with allergic fungal rhinosinusitis.

We aim to develop a rapid, accurate and sensitive diagnostic assay with which to detect the surface antigens of fungi thought to be involved in allergic fungal rhinosinusitis (AFRS), by assessing the usefulness of immunofluorescence microscopy (IMF) and enzyme linked immuno-absorbent assays (ELISA). The age, sex, clinical symptoms and signs, imaging (CT and/or MRI), microbiological subculture data, sinus contents, blood eosinophilia, aspergillosis precipitins, radioallergoabsorbent technology (RAST) for fungal allergens and histopathology were performed on individuals undergoing endoscopic sinus surgery for suspected AFRS. Thirteen patients were examined, and five monoclonal antibodies raised to the surface washings of various fungi were found to recognize and differentiate between fungal species implicated in sinus disease, i.e. Aspergillus niger, Alternaria alternata, Cochliobolus lunata, Penicillium expansum and Cladosporium species. The IMF microscopy proved to be a useful assay to distinguish visually between the cultured fungi, but was less useful for visualization of fungi in the patient samples. However, ELISA assays with 5 monoclonal antibodies gave clear and unambiguous data as to the presence of certain fungi within the patient samples. There is good correlation between the ELISA data and the pathology findings. This preliminary study suggests that both IMF and ELISA techniques may offer an important advance in this area.

Adolescent↗
PubMed2000

Cementless acetabular replacement in the young. A 5- to 10-year prospective study.

This article presents a prospective clinical and radiologic review of 55 total hip replacements in 50 patients in which the cementless Harris-Galante porous-coated acetabular component was used. All patients were 50 years of age or younger. The cups were inserted by 15 different surgeons. The minimum followup was 5 years, with a mean of 7 years. No acetabular component has been revised for loosening, and none have migrated. Three (5.5%) cups have progressive bone-component radiolucent lines, two (3.6%) of which are complete. Six (10.9%) acetabular liners have been replaced for excessive polyethylene wear, and an additional four (7.3%) show sufficient wear to produce obvious radiographic eccentricity of the femoral head. All of the revised liners had 32-mm femoral heads and an initial polyethylene thickness of less than 6 mm. Although the results reflect excellent fixation of this component in the medium term, the incidence of exchange of the polyethylene liner for excessive wear is unacceptably high. The reduction in polyethylene thickness associated with the use of a metal-backed component and a 32-mm articulation was one of the factors contributing to the accelerated wear patterns seen in this series.

Acetabulum↗
PubMed1999

A mechanism for Rb/p130-mediated transcription repression involving recruitment of the CtBP corepressor.

Previous work has demonstrated the critical role for transcription repression in quiescent cells through the action of E2F-Rb or E2F-p130 complexes. Recent studies have shown that at least one mechanism for this repression involves the recruitment of histone deacetylase. Nevertheless, these studies also suggest that other events likely contribute to E2F/Rb-mediated repression. Using a yeast two-hybrid screen to identify proteins that specifically interact with the Rb-related p130 protein, we demonstrate that p130, as well as Rb, interacts with a protein known as CtIP. This interaction depends on the p130 pocket domain, which is important for repression activity, as well as an LXCXE sequence within CtIP, a motif previously shown to mediate interactions of viral proteins with Rb. CtIP interacts with CtBP, a protein named for its ability to interact with the C-terminal sequences of adenovirus E1A. Recent work has demonstrated that the Drosophila homologue of CtBP is a transcriptional corepressor for Hairy, Knirps, and Snail. We now show that both CtIP and CtBP can efficiently repress transcription when recruited to a promoter by the Gal4 DNA binding domain, thereby identifying them as corepressor proteins. Moreover, the full repression activity of CtIP requires a PLDLS domain that is also necessary for the interaction with CtBP. We propose that E2F-mediated repression involves at least two events, either the recruitment of a histone deacetylase or the recruitment of the CtIP/CtBP corepressor complex.

Alcohol Oxidoreductases↗
PubMed1999

Turkey sperm mobility influences paternity in the context of competitive fertilization.

We have devised a novel means of investigating competitive fertilization in turkeys, using microsatellite genotyping to identify male parentage. Our results demonstrate that sperm mobility is a mechanism responsible in part for paternity efficiency in turkeys. Sperm mobility is composed of several parameters in which sperm motility is a component. Differences between ejaculates in the number of sperm penetrating into a dense, insert, nontoxic solution were measured and used to classify males into high, average, or low sperm mobility phenotypes. Microsatellite genotyping was used to determine parentage of poults after equal numbers of sperm from 10 males (either high or average phenotype, n = 5, mixed with low phenotype, n = 5) were inseminated simultaneously. In a separate study, the numbers of sperm hydrolyzing the perivitelline layer of eggs were compared between hens inseminated with sperm from high-, average-, or low-phenotype males. Overall, heterospermic inseminations resulted in consistently fewer offspring produced by low-mobility phenotype males. This correlated with physiological data in which semen from the low-mobility males had reduced numbers of sperm at the fertilization site as determined by sperm hole counts in the perivitelline layer of eggs. This is the first illustration of a measurable sperm trait predictive of paternity success in a competitive fertilization trial in turkeys, a species that is predominately reproduced by artificial insemination of multiple-sire pools.

Animals↗
PubMed1998

Mapping chicken genes using preferential amplification of specific alleles.

To map the chicken genome, an international reference population was developed at our laboratory (East Lansing, MI) using an F2 backcross between inbred jungle fowl (JF) and inbred white leghorns (WL). To augment the number of type I genes on the East Lansing (E) map, segregation of the JF-specific allele was followed using preferential amplification of specific alleles (PASA) in polymerase chain reactions (PCR). Among 15 functional genes that were added to the E map, agrin and mannose-6-phosphate receptor genes were found to occur in conserved syntenic groups. Using this PCR-based approach, six conserved groups spanning more than 243 centimorgans (cM) in the chicken were syntenic with human and mouse.

Alleles↗
PubMed1998

The CAR1 gene encoding a cellular receptor specific for subgroup B and D avian leukosis viruses maps to the chicken tvb locus.

Host susceptibility to subgroup B, D, and E avian leukosis viruses (ALV) is determined by specific alleles of the chicken tvb locus. Recently, a chicken gene that encodes a cellular receptor, designated CAR1, specific for subgroups B and D ALV was cloned, and it was proposed that this gene was the s3 allele of tvb (J. Brojatsch, J. Naughton, M. M. Rolls, K. Zingler, and J. A. T. Young, Cell 87:845-855, 1996). We now report that in a backcross derived from an F1 (Jungle Fowl x White Leghorn [WL]) male mated with inbred WL females, the cloned ALV receptor gene cosegregated with two markers linked to tvb. The two markers used were a tvb(s1)-specific antigen recognized by the chicken R2 alloantiserum and restriction fragment length polymorphisms associated with the expressed sequence tag com152e. With all three markers, no crossovers were observed among 52 backcross progeny tested and LOD linkage scores of 15.7 were obtained. These data demonstrate that CAR1 is the subgroup B and D ALV susceptibility gene located at tvb(s3).

Animals↗
PubMed1998

Entrainment of the circadian system of mammals by nonphotic cues.

Although light is the principal zeitgeber to the mammalian circadian system, other cues can be shown to have a potent resetting effect on the clock of both adult and perinatal mammals. Nonphotic entrainment may have both biological and therapeutic significance. This review focuses on the effect of behavioral arousal as a nonphotic cue and the neurochemical circuitry that mediates arousal-induced entrainment in the adult rodent. In addition, it considers the role of nonphotic entrainment of the developing circadian system in perinatal life prior to the establishment of retinal input to the clock.

Animals↗
PubMed1998

Distinct mechanisms control the accumulation of the Rb-related p107 and p130 proteins during cell growth.

A variety of studies have demonstrated the critical role of the Rb/E2F pathway in the control of cell growth and have highlighted a complexity in the accumulation of both the E2F family proteins and the Rb family of proteins. Whereas the Rb protein is found in both growing and quiescent cells, the accumulation of p130 and p107 is tightly regulated with respect to the growth state of the cell. The p130 protein is found in quiescent cells but not in growing cells, whereas the inverse is true for the p107 protein. Control of p130 accumulation is posttranscriptional, because p130 RNA is relatively constant in growing and quiescent cells. The disappearance of the p130 protein after stimulation of cell growth coincides with cyclin-dependent kinase-mediated phosphorylation and is blocked by inhibitors of the 26S proteasome. In contrast, the cell growth-dependent regulation of p107 expression reflects the transcriptional regulation of the p107 gene. Similar to several other growth-regulated genes, the control of p107 expression is largely the result of E2F-dependent repression in quiescent cells. These experiments thus demonstrate a control of Rb family member expression mediated through distinct mechanisms of both transcriptional and posttranslational control and also suggest an intimate relationship in which p130 controls the expression of p107.

Adenoviridae↗