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Phillips RB, Ventura AB, Dekoning JJ, Nichols KM. Mapping rainbow trout immune genes involved in inflammation reveals conserved blocks of immune genes in teleosts. Anim Genet 2012; 44:107-13. [PMID: 23013476 DOI: 10.1111/j.1365-2052.2011.02314.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2011] [Indexed: 02/03/2023]
Abstract
We report the genetic map location of 14 genes involved in the inflammatory response to salmonid bacterial and viral pathogens, which brings the total number of immune genes mapped in rainbow trout (RT, Oncorhynchus mykiss) to 61. These genes were mapped as candidate genes that may be involved in resistance to bacterial kidney disease, as well as candidates for known QTL for resistance to infectious hematopoietic necrosis virus, infectious pancreatic necrosis virus and Ceratomyxa shasta. These QTL map to one or more of the linkage groups containing immune genes. The combined analysis of these linkage results and those of previously mapped immune genes in RT shows that many immune genes are found in syntenic blocks of genes that have been retained in teleosts despite species divergence and genome duplication events.
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Affiliation(s)
- R B Phillips
- Washington State University-Vancouver, 14204 NE Salmon Creek Avenue, Vancouver, WA 98686, USA.
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Li J, Phillips RB, Harwood AS, Koop BF, Davidson WS. Identification of the sex chromosomes of brown trout (Salmo trutta) and their comparison with the corresponding chromosomes in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Cytogenet Genome Res 2011; 133:25-33. [PMID: 21252487 DOI: 10.1159/000323410] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2010] [Indexed: 12/26/2022] Open
Abstract
Males are the heterogametic sex in salmonid fishes. In brown trout (Salmo trutta) the sex-determining locus, SEX, has been mapped to the end of linkage group BT-28, which corresponds to linkage group AS-8 and chromosome SSA15 in Atlantic salmon (Salmo salar). We set out to identify the sex chromosomes in brown trout. We isolated Atlantic salmon BAC clones containing microsatellite markers that are on BT-28 and also on AS-8, and used these BACs as probes for fluorescent in situ hybridization (FISH) analysis. SEX is located on the short arm of a small subtelocentric/acrocentric chromosome in brown trout, which is consistent with linkage analysis. The acrocentric chromosome SSA15 in Atlantic salmon appears to have arisen by a centric fusion of 2 small acrocentric chromosomes in the common ancestor of Salmo sp. We speculate that the fusion process that produced Atlantic salmon chromosome SSA15 disrupted the ancestral sex-determining locus in the Atlantic salmon lineage, providing the impetus either for the relocation of SEX or selection pressure for a novel sex-determining gene to arise in this species. Thus, the sex-determining genes may differ in Atlantic salmon and brown trout.
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Affiliation(s)
- J Li
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C., Canada
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Phillips RB, DeKoning JJ, Ventura AB, Nichols KM, Drew RE, Chaves LD, Reed KM, Felip A, Thorgaard GH. Recombination is suppressed over a large region of the rainbow trout Y chromosome. Anim Genet 2009; 40:925-32. [PMID: 19744144 DOI: 10.1111/j.1365-2052.2009.01944.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The previous genetic mapping data have suggested that most of the rainbow trout sex chromosome pair is pseudoautosomal, with very small X-specific and Y-specific regions. We have prepared an updated genetic and cytogenetic map of the male rainbow trout sex linkage group. Selected sex-linked markers spanning the X chromosome of the female genetic map have been mapped cytogenetically in normal males and genetically in crosses between the OSU female clonal line and four different male clonal lines as well as in outcrosses involving outbred OSU and hybrids between the OSU line and the male clonal lines. The cytogenetic maps of the X and Y chromosomes were very similar to the female genetic map for the X chromosome. Five markers on the male maps are genetically very close to the sex determination locus (SEX), but more widely spaced on the female genetic map and on the cytogenetic map, indicating a large region of suppressed recombination on the Y chromosome surrounding the SEX locus. The male map is greatly extended at the telomere. A BAC clone containing the SCAR (sequence characterized amplified region) Omy-163 marker, which maps close to SEX, was subjected to shotgun sequencing. Two carbonyl reductase genes and a gene homologous to the vertebrate skeletal ryanodine receptor were identified. Carbonyl reductase is a key enzyme involved in production of trout ovarian maturation hormone. This brings the number of type I genes mapped to the sex chromosome to six and has allowed us to identify a region on zebrafish chromosome 10 and medaka chromosome 13 which may be homologous to the distal portion of the long arm of the rainbow trout Y chromosome.
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Affiliation(s)
- R B Phillips
- School of Biological Sciences, Washington State University, Vancouver, WA 98686-9600, USA.
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Alfaqih MA, Phillips RB, Wheeler PA, Thorgaard GH. The cutthroat trout Y chromosome is conserved with that of rainbow trout. Cytogenet Genome Res 2008; 121:255-9. [PMID: 18758167 DOI: 10.1159/000138893] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2008] [Indexed: 11/19/2022] Open
Abstract
Five genetic markers previously shown to be located on the sex chromosomes of rainbow trout (Oncorhynchus mykiss) were tested for linkage with the sex locus of Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri) in a genetic cross created from a rainbow x cutthroat male hybrid. We show that the sex locus of both rainbow and cutthroat trout is on the same homologous linkage group. Fluorescence in situ hybridization (FISH) using a probe for the microsatellite marker Omm1665, which maps close to the sex locus of Yellowstone cutthroat trout, was used to identify the Y chromosome of cutthroat trout in the hybrid. The Y chromosome of cutthroat trout is sub-telocentric and lacks a DAPI band found on the short arm of the Y chromosome of some rainbow trout males.
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Affiliation(s)
- M A Alfaqih
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4236, USA
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Phillips RB, DeKoning J, Morasch MR, Park LK, Devlin RH. Identification of the sex chromosome pair in chum salmon (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha). Cytogenet Genome Res 2007; 116:298-304. [PMID: 17431328 DOI: 10.1159/000100414] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Accepted: 12/22/2006] [Indexed: 11/19/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) using a probe to the male-specific GH-Y (growth hormone pseudogene) was used to identify the Y chromosome in the karyotypes of chum salmon (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha). The sex chromosome pair is a small acrocentric chromosome pair in chum salmon and the smallest metacentric chromosome pair in pink salmon. Both of these chromosome pairs are morphologically different from the sex chromosome pairs in chinook salmon (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch). The 5S rRNA genes are on multiple chromosome pairs including the sex chromosome pair in chum salmon, but at the centromeres of two autosomal metacentric pairs in pink salmon. The sex chromosome pairs and the chromosomal locations of the 5S rDNA appear to be different in all five of the North American Pacific salmon species and rainbow trout. The implications of these results for evolution of sex chromosomes in salmonids are discussed.
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Affiliation(s)
- R B Phillips
- Department of Biological Sciences, Washington State University, Vancouver, WA 98686-9600, USA.
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Affiliation(s)
- P. C. Gibbons
- a Department of Physics , Washington University , St. Louis , Missouri , 63130 , U.S.A
| | - K. F. Kelton
- a Department of Physics , Washington University , St. Louis , Missouri , 63130 , U.S.A
| | - L. E. Levine
- a Department of Physics , Washington University , St. Louis , Missouri , 63130 , U.S.A
| | - R. B. Phillips
- a Department of Physics , Washington University , St. Louis , Missouri , 63130 , U.S.A
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Phillips RB, Amores A, Morasch MR, Wilson C, Postlethwait JH. Assignment of zebrafish genetic linkage groups to chromosomes. Cytogenet Genome Res 2006; 114:155-62. [PMID: 16825768 DOI: 10.1159/000093332] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 01/25/2006] [Indexed: 01/23/2023] Open
Abstract
In this report the zebrafish genetic linkage groups are assigned to specific chromosomes using fluorescence in situ hybridization (FISH) with BAC probes containing genes mapped to each linkage group (LG). Chromosomes were identified using a combination of relative size and arm ratios. The largest genetic maps generally corresponded to the largest chromosomes, but genetic recombination tended to be elevated in the smaller chromosomes and near telomeres. Large insert clones containing genes near telomeres often hybridized to telomeres of multiple chromosome pairs, suggesting the presence of shared subtelomeric repetitive DNAs near telomeres. Evidence from comparative gene mapping in medaka, zebrafish, pufferfish, and humans suggests that the linkage groups of these species have the content of duplicate proto-chromosomes. However, these duplicate linkage groups are not associated with chromosomes of similar size or morphology. This suggests that considerable chromosome restructuring occurred subsequent to the genome duplication in teleosts.
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Affiliation(s)
- R B Phillips
- Department of Biological Sciences, Washington State University, Vancouver 98686-9600, USA.
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Artieri CG, Mitchell LA, Ng SHS, Parisotto SE, Danzmann RG, Hoyheim B, Phillips RB, Morasch M, Koop BF, Davidson WS. Identification of the sex-determining locus of Atlantic salmon (Salmo salar) on chromosome 2. Cytogenet Genome Res 2006; 112:152-9. [PMID: 16276105 DOI: 10.1159/000087528] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2005] [Accepted: 04/27/2005] [Indexed: 11/19/2022] Open
Abstract
We have integrated data from linkage mapping, physical mapping and karyotyping to gain a better understanding of the sex-determining locus, SEX, in Atlantic salmon (Salmo salar). SEX has been mapped to Atlantic salmon linkage group 1 (ASL1) and is associated with several microsatellite markers. We have used probes designed from the flanking regions of these sex-linked microsatellite markers to screen a bacterial artificial chromosome (BAC) library, representing an 11.7x coverage of the Atlantic salmon genome, which has been HindIII fingerprinted and assembled into contigs. BACs containing sex-linked microsatellites and their related contigs have been identified and representative BACs have been placed on the Atlantic salmon chromosomes by fluorescent in situ hybridization (FISH). This identified chromosome 2, a large metacentric, as the sex chromosome. By positioning several BACs on this chromosome by FISH, it was possible to orient ASL1 with respect to chromosome 2. The region containing SEX appears to lie on the long arm between marker Ssa202DU and a region of heterochromatin identified by DAPI staining. BAC end-sequencing of clones within sex-linked contigs revealed five hitherto unmapped genes along the sex chromosome. We are using an in silico approach coupled with physical probing of the BAC library to extend the BAC contigs to provide a physical map of ASL1, with a view to sequencing chromosome 2 and, in the process, identifying the sex-determining gene.
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Affiliation(s)
- C G Artieri
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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Phillips RB, Morasch MR, Park LK, Naish KA, Devlin RH. Identification of the sex chromosome pair in coho salmon (Oncorhynchus kisutch): lack of conservation of the sex linkage group with chinook salmon (Oncorhynchus tshawytscha). Cytogenet Genome Res 2006; 111:166-70. [PMID: 16103659 DOI: 10.1159/000086387] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2004] [Accepted: 01/11/2005] [Indexed: 11/19/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) using a probe to the male-specific GH-Y (growth hormone pseudogene) was used to identify the Y chromosome in coho salmon (Oncorhynchus kisutch). The sex chromosome pair is morphologically similar to chinook salmon (Oncorhynchus tshawytscha) with the GH-Y localized to the small short arm of the largest subtelocentric chromosome pair. FISH experiments with probes containing sex-linked genes in rainbow trout (Oncorhynchus mykiss) (SCAR163) and chinook salmon (Omy7INRA) showed that the coho sex linkage group is different from chinook and rainbow trout and this was confirmed by segregation analysis for the Omy7INRA locus. The telomeric location of the SEX locus, the presence of shared male-specific markers in coho and chinook salmon, and the lack of conservation of sex-linkage groups suggest that transposition of a small male-specific region may have occurred repeatedly in salmonid fishes of the genus Oncorhynchus.
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Affiliation(s)
- R B Phillips
- Department of Biological Sciences, Washington State University, Vancouver, WA, USA.
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10
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Affiliation(s)
- R B Phillips
- Department of Biological Sciences, Washington State University, Vancouver, WA 98686-9600, USA.
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B. Phillips R, D. Cooke B, Campbell K, Carrion V, Marouez C, L. Snell H. Eradicating Feral Cats to protect Galapagos Land Iguanas: methods and strategies. ACTA ACUST UNITED AC 2005. [DOI: 10.1071/pc050257] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A three-year programme to eradicate Feral Cats Felis catus from the island of Baltra in the Galapagos archipelago achieved good results by initially poisoning with sodium monofluoroacetate (compound 1080) then trapping or shooting the remaining cats. The poisoning campaign removed 90% of the cats, its success being attributable to pre-baiting with unpolsoned baits to accustom cats to eating baits and placing enough baits to ensure that all cats encountered several baits within their home range. This, together with the use of metaclopromide (Pileran) as an anti-emetic, overcame a problem associated with poor retention of 1080 in thawed fish baits that limited the dose available to 1 mg 1080/bait, a quality insufficient to kill large cats. Removal of the remaining cats was delayed by a weather-induced irruption of Black Rats Rattus rattus and House Mice Mus musculus that enabled recruitment of kittens in 2002, but made cats more susceptible to trapping and shooting in 2003 when rodent populations collapsed. Since July 2003 no sign of a cat has been detected on Baltra despite extensive searching and monitoring throughout 2004. As cat abundance has decreased there have been more locally-bred Juvenile iguanas (Conolophus subcristatus) seen during annual censuses. However, such recruitment may reflect the increasing maturity and higher fecundity of iguanas repatriated from 1991 onwards rather than being a direct result of reduced cat predation alone. More time is necessary to determine the benefits of reduced cat predation on the Iguana population.
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Phillips RB, Noakes MA, Morasch M, Felip A, Thorgaard GH. Does differential selection on the 5S rDNA explain why the rainbow trout sex chromosome heteromorphism is not linked to the SEX locus? Cytogenet Genome Res 2004; 105:122-5. [PMID: 15218267 DOI: 10.1159/000078018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Accepted: 12/08/2003] [Indexed: 11/19/2022] Open
Abstract
Many but not all rainbow trout strains have morphologically distinguishable sex chromosomes. In these strains, the short arm of the X has multiple copies of 5S rDNA and a bright DAPI band near the centromere, both of which are missing from the Y chromosome, which has a very small short arm. We examined the presence of these markers using fluorescence in situ hybridization (FISH) in four different YY clonal lines derived from different strains and compared the results with sexed fish of the Donaldson strain with the normal X/Y heteromorphism. The Y chromosome in two of the YY clonal lines (Arlee and Swanson) is indistinguishable from the X chromosome and it is positive for 5S rDNA and the DAPI bright band. On the other hand, both 5S rDNA sequences and the DAPI band were not found on the Y chromosome in Hot Creek and Clearwater which have the normal Y. Thus the presence of these two cytogenetic markers may account for the size difference between the short arm of the X and Y chromosome found in most rainbow trout strains. In fishes the expression of one type of 5S rRNA is restricted to oocytes and previous work suggests that although XX males are fairly common, XY females are rare, implying a selective disadvantage for XY females. A hypothesis is presented to explain why this sex chromosome heteromorphism is not closely linked to the SEX locus, which is found on the long arm of the Y chromosome in rainbow trout.
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Affiliation(s)
- R B Phillips
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA.
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Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA, Thorgaard GH. A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim Genet 2003; 34:102-15. [PMID: 12648093 DOI: 10.1046/j.1365-2052.2003.00957.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Androgenetic doubled haploid progeny produced from a cross between the Oregon State University and Arlee clonal rainbow trout (Oncorhynchus mykiss) lines, used for a previous published rainbow trout map, were used to update the map with the addition of more amplified fragment length polymorphic (AFLP) markers, microsatellites, type I and allozyme markers. We have added more than 900 markers, bringing the total number to 1359 genetic markers and the sex phenotype including 799 EcoRI AFLPs, 174 PstI AFLPs, 226 microsatellites, 72 VNTR, 38 SINE markers, 29 known genes, 12 minisatellites, five RAPDs, and four allozymes. Thirty major linkage groups were identified. Synteny of linkage groups in our map with the outcrossed microsatellite map has been established for all except one linkage group in this doubled haploid cross. Putative homeologous relationships among linkage groups, resulting from the autotetraploid nature of the salmonid genome, have been revealed based on the placement of duplicated microsatellites and type I loci.
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Affiliation(s)
- K M Nichols
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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Affiliation(s)
- M A Noakes
- School of Biological Science, Washington State University Vancouver, Vancouver, WA, USA
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Abstract
The various applications of the technique of fluorescence in situ hybridization (FISH) to fish genetics will be reviewed for fishes being used as model organisms to study human disease, including those species for which major genome projects have been initiated. "FISH on fish" has been used to map highly repetitive sequences including centromere-specific sequences and sex-specific sequences, moderately repetitive sequences such as rRNAs and histones, and single-copy sequences. Paint probes specific for whole genomes, whole chromosomes, and chromosome subregions have been prepared for several species. The potential future applications of FISH to fish genetics and genome mapping will be discussed.
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Affiliation(s)
- R B Phillips
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Box 413, Milwaukee, WI 53201, USA.
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Abstract
The Y chromosome in chinook salmon, Oncorhynchus tshawytscha, was identified using fluorescence in situ hybridization (FISH) with a probe to a male-specific repetitive sequence isolated from this species. The probe highlights the distal end of the short arm of an acrocentric chromosome with a DAPI-bright interstitial band of variable size. The proximal portion of the short arm of the Y chromosome contains 5S rDNA sequences, which are also found on the short arms of six other acrocentric chromosomes in this species.
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Affiliation(s)
- J Stein
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI 53201, USA
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Abstract
Sequence variation in a 216 bp portion of the major histocompatibility complex (MHC) II B1 domain was examined in 74 individual lake trout (Salvelinus namaycush) from different locations in Lake Superior. Forty-three alleles were obtained which encoded 71-72 amino acids of the mature protein. These sequences were compared with previous data obtained from five Pacific salmon species and Atlantic salmon using the same primers. Although all of the lake trout alleles clustered together in the neighbor-joining analysis of amino acid sequences, one amino acid allelic lineage was shared with Atlantic salmon (Salmo salar), a species in another genus which probably diverged from Salvelinus more than 10-20 million years ago. As shown previously in other salmonids, the level of nonsynonymous nucleotide substitution (dN) exceeded the level of synonymous substitution (dS). The level of nucleotide diversity at the MHC class II B1 locus was considerably higher in lake trout than in the Pacific salmon (genus Oncorhynchus). These results are consistent with the hypothesis that lake trout colonized Lake Superior from more than one refuge following the Wisconsin glaciation. Recent population bottlenecks may have reduced nucleotide diversity in Pacific salmon populations.
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Affiliation(s)
- M O Dorschner
- Department of Biological Sciences, University of Wisconsin-Milwaukee 53201, USA
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Dasmahapatra AK, Wimpee BA, Budsberg KJ, Dorschner MO, Phillips RB, Hutz RJ. Lack of effect of beta-naphthoflavone on induction of Nramp genes in adult rainbow trout Oncorhynchus mykiss. Mar Environ Res 2000; 50:147-151. [PMID: 11460681 DOI: 10.1016/s0141-1136(00)00113-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Natural resistance-associated macrophage protein (Nramp) genes in rainbow trout, Oncorhynchus mykiss, were identified and characterized. The greatest mRNA level encoding these genes was in the developing ovary of rainbow trout. We evaluated the response of these genes to a certain aromatic hydrocarbon receptor (AHR) agonist. Adult rainbow trout were treated with beta-naphthoflavone (BNF) (50 and 100 mg/kg) for 48 h. Using reverse-transcriptase polymerase chain reaction with ovary and head kidney RNA and specific alpha and beta Nramp primers, a 400 bp Nramp-alpha- and a 400 bp Nramp-beta-specific cDNA were obtained. There were no changes in the alpha and beta Nramp mRNA levels in the ovary following BNF administration. CYP1A1 mRNA was increased in the ovary and kidney, suggesting the presence of AHR in rainbow trout ovary, while the AHR agonist produced no effect on Nramp mRNAs.
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Affiliation(s)
- A K Dasmahapatra
- NIEHS Marine and Freshwater Biomedical Sciences Center, University of Wisconsin-Milwaukee, Milwaukee, WI 53204, USA
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Abstract
This study examines sequence divergence in three spacer regions of the ribosomal DNA (rDNA) cistron, to test the hypothesis of unequal mutation rates. Portions of two transcribed spacers (ITS-1 and 5' ETS) and the non-transcribed spacer (NTS) or intergenic spacer (IGS) formed the basis of comparative analyses. Sequence divergence was measured both within an individual lake trout (Salvelinus namaycush) and among several related salmonid species (lake trout; brook trout, Salvelinus fontinalis; Arctic char, Salvelinus alpinus; Atlantic salmon, Salmo salar; and brown trout, Salmo trutta). Despite major differences in the length of the rDNA cistron within individual lake trout, minimal sequence difference was detected among cistrons. Interspecies comparisons found that molecular variation in the rDNA spacers did not conform to the predicted pattern of evolution (ITS spacers<ETS spacers<IGS). Specifically, the IGS contains a region that appears to be as highly, or more conserved than the ITS-1.
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Affiliation(s)
- K M Reed
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 53211, USA.
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20
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Abstract
A total-genomic cosmid library was created to isolate complete copies of the rDNA cistron of lake trout (Salvelinus namaycush) in order to study the structure and organization of the intergenic spacer (IGS) in this species. A total of 60 rDNA-positive clones (average inserts > 25 kb) was recovered by screening the library with a rDNA-specific probe. Positive clones were assayed for the presence of the two internal rDNA spacers (ITS-1 and ITS-2) and the entire IGS fragment was successfully amplified from 42 clones by PCR. Length of the IGS fragments ranged from 9.4 to 17.8 kb. Comparative restriction mapping of the IGS-PCR products of several clones indicated two regions of extensive length variation surrounding a central region with sequence conservation. DNA sequence analysis was used to investigate the molecular basis of the IGS length variation and focused on identifying the region responsible for this variation. Over 9 kb of DNA sequence was obtained for one clone (A1) with a total IGS length of approximately 12.4 kb. Sequence of a conserved central region contained two open reading frames and a number of short direct repeats. Length variation in the IGS was determined by RFLP to result from differences in the number of copies of repetitive DNA sequences. These included an 89-bp tandem repeat (alpha repeats), an 82-bp element (beta repeats), a 168-177-bp element (chi repeats), and a 179-201-bp element (delta repeats). Overall nucleotide composition of the IGS was biased towards A and T (%GC = 47.4). Maintenance of discrete rDNA-length variants in lake trout suggests that the rate of gene conversion is insufficient to produce homogeneous copies across the genome.
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Affiliation(s)
- K M Reed
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 53211, USA.
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21
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Abstract
The genome of the zebrafish, Danio rerio, contains two major classes of tandem repetitive elements (AT-rich and GC-rich). The AT-rich repeats can be further subdivided into two subgroups which differ by about 10% of 185 bp in the repeating unit. The chromosomal location of these sequences and the moderately repetitive 5S rDNA sequences was determined in two diploid zebrafish cell lines using in-situ hybridization with fluorochrome-labeled probes. The AT-rich sequences were found at the centromeres of all chromosome pairs and the GC-rich sequences were found in paracentromeric location on over half of the chromosomal pairs. Different patterns of hybridization were found for the two subgroups of the AT-rich family. One type hybridized primarily to centromeres of one half to two thirds of the chromosomal pairs and the other type to centromeres of about three fourths of the chromosomal pairs. The pattern of hybridization with the GC-rich sequences varied somewhat between the cell lines consistent with interindividual variation in the location of paracentromeric heterochromatin. The 5S rRNA genes are found on the long arm of chromosome 3. Most of this chromosome arm is late replicating, but apparently does not contain either the AT-rich or GC-rich repetitive sequences.
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Affiliation(s)
- R B Phillips
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 53201, USA.
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Reinartz GE, Karron JD, Phillips RB, Weber JL. Patterns of microsatellite polymorphism in the range-restricted bonobo (Pan paniscus): considerations for interspecific comparison with chimpanzees (P. troglodytes). Mol Ecol 2000; 9:315-28. [PMID: 10736029 DOI: 10.1046/j.1365-294x.2000.00852.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The endangered great ape, Pan paniscus (bonobo) has the smallest range of the African apes. Virtually nothing is known about the genetic diversity or genetic structure of this species, while substantial amounts of polymorphism have been reported for the bonobo's widespread congener, the chimpanzee (P. troglodytes). Given its restricted range, what is the extent of genetic variation in the bonobo relative to the chimpanzee, and is the bonobo genetically depauperate? To investigate patterns of genetic polymorphism, bonobos of wild origin were genotyped for 28 microsatellite loci. The mean number of alleles per locus (5.2) and the mean observed heterozygosity (0.52) in bonobos were similar to variation observed in a wild chimpanzee community (P. t. schweinfurthii). The rarer bonobo is not genetically depauperate and may have genetic diversity comparable to the eastern chimpanzee subspecies. Bonobos have approximately 55% of the allelic diversity and 66% of the observed heterozygosity exhibited by all three chimpanzee subspecies sampled across equatorial Africa. Resampling techniques were used to quantify the effects of sample size differences and number and choice of loci between bonobos and chimpanzees. The examination of these variables underscores their importance in accurately interpreting interspecific comparisons of diversity estimates.
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Affiliation(s)
- G E Reinartz
- Department of Biological Sciences, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201, USA.
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Phillips RB. Letters: Industry not rattled. Environ Sci Technol 1999; 33:481A. [PMID: 21657504 DOI: 10.1021/es9931168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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24
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Ráb P, Rábová M, Reed KM, Phillips RB. Chromosomal characteristics of ribosomal DNA in the primitive semionotiform fish, longnose gar Lepisosteus osseus. Chromosome Res 1999; 7:475-80. [PMID: 10560970 DOI: 10.1023/a:1009202030456] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromosomes of longnose gar, Lepisosteus osseus, an extant representative of early radiation of actinopterygian fishes, were studied using conventional Giemsa-staining, Ag-staining, CMA3-fluorescence and fluorescence in-situ hybridization (FISH). The diploid chromosome number was 2n = 56 and the karyotype contained 11 pairs of metacentric, 6 pairs of submetacentric, 3 pairs of subtelocentric macrochromosomes and 16 microchromosomes. Nearly all macrochromosomes showed large CMA3-positive regions resembling the R-bands of higher vertebrates, indicating extensive distribution of GC-rich DNA along chromosomes. The nucleolar organizer regions (NORs) were located on the end of the short arm of a single small metacentric macrochromosomal pair. These sites were strongly CMA3-positive, suggesting that ribosomal sites are associated with GC-rich DNA. In-situ hybridization (FISH) with a rDNA probe gave consistently positive signals in the same regions detected by Ag-staining and CMA3-fluorescence. The evolutionary conservation of positive CMA3-fluorescence of ribosomal sites in 'holostean' and teleostean fishes is discussed.
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Affiliation(s)
- P Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republich.
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25
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Phillips RB, Matsuoka MP, Smoker WW, Gharrett AJ. Inheritance of a chromosomal polymorphism in odd-year pink salmon from southeastern Alaska. Genome 1999. [DOI: 10.1139/g99-010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In previous work we found a high frequency of heterozygotes for a fission translocation involving the seventh chromosome pair in odd-year populations of pink salmon (Oncorhynchus gorbuscha) sampled from Washington State to south central Alaska. The populations from southeastern Alaska and northern British Columbia had high frequencies of heterozygotes for a second rearrangement of this same chromosome pair. In these fish one fission product, the larger acrocentric chromosome bearing the nucleolar organizer region (NOR), has undergone an inversion to produce a submetacentric chromosome. In this paper, we present inheritance data on pink salmon from the Gastineau hatchery stock in Juneau, Alaska, where individuals with the two rearrangements are found. Although most of the fish were either homozygous for the normal cytotype or heterozygous for the inversion cytotype, a few individuals heterozygous for the fission cytotype were found. Ten males and ten females were karyotyped, and crosses were set up in all combinations. Individuals with both rearrangements were found in crosses between the two types of heterozygotes, and the ratios of cytotypes in the progeny did not deviate significantly from the expected values. No significant difference in viability of offspring from crosses between individuals with different cytotypes was found up to the age of hatching.Key words: salmon, chromosomal polymorphism, translocation, inversion, cytotype.
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26
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Abstract
Innate resistance to intracellular parasites is controlled in part by Nramp1 (Natural resistance-associated macrophage protein 1) in mammals and birds. To isolate Nramp homologs from rainbow trout, a combination of library screening and rapid amplification of cDNA ends was performed. Two closely related Nramp loci, designated OmNramp alpha and OmNramp beta, were cloned and characterized. OmNramp alpha and OmNramp beta encode two highly conserved proteins of 585 and 558 amino acids, respectively. Deduced amino acid seqences showed that the OmNramp alpha and OmNramp beta proteins share 90% of their residues and contain all of the signature features of the Nramp family of proteins: 12 transmembrane domains, two N-linked glycosylation sites, and a conserved transport motif. Phylogenetic analysis supported a close relation to Nramp2 proteins, a related member of the Nramp family. Despite this relation, juvenile trout expressed OmNramp alpha in a manner consistent with an Nramp1 homolog and OmNramp beta similar to an Nramp2 locus. Both trout loci were expressed at relatively high amounts in the ovaries of juveniles, a finding not reported in the investigations of previously characterized mammalian and avian homologs. These results suggest a role for Nramp loci in the follicular development of teleost fishes, as well as in mammals. Because salmonid fishes are ancestral tetraploids, fragments of OmNramp alpha and OmNramp beta were isolated from smelt, a diploid relative, to determine whether the trout loci represent duplicates of a single gene. Homologous sequences for both loci were found in smelt, supporting the hypothesis that OmNramp alpha and OmNramp beta are indeed independent loci that were present before the chromosomal duplication of salmonids. The isolation of Nramp loci from rainbow trout may eventually produce a genetic tool for the control of disease in aquaculture operations. Determining the involvement of trout homologs in innate immunity may also provide insight regarding the evolution of host resistance to pathogens.
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Affiliation(s)
- M O Dorschner
- Department of Biological Sciences and NIEHS Marine and Freshwater Biomedical Research Facility, University of Wisconsin-Milwaukee, 53204, USA.
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Oakley TH, Phillips RB. Phylogeny of salmonine fishes based on growth hormone introns: Atlantic (Salmo) and Pacific (Oncorhynchus) salmon are not sister taxa. Mol Phylogenet Evol 1999; 11:381-93. [PMID: 10196079 DOI: 10.1006/mpev.1998.0599] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Though salmonid fishes are a well-studied group, phylogenetic questions remain, especially with respect to genus-level relationships. These questions were addressed with duplicate growth hormone (GH) introns. Intron sequences from each duplicate gene yielded phylogenetic trees that were not significantly different from each other in topology. Statistical tests supported validity of the controversial monotypic genus Parahucho, monophyly of Oncorhynchus, and inclusion of Acantholingua ohridana within Salmo. Suprisingly, GH1 intron C (GH1C) did not support the widely accepted hypothesis that Oncorhynchus (Pacific salmon and trout) and Salmo (Atlantic salmon and trout) are sibling genera; GH2C was ambiguous at this node. Previously published data were also examined for support of Salmo and Oncorhynchus as sister taxa and only morphology showed significant support. If not sister taxa, the independent evolution of anadromy-the migration to sea and return to freshwater for spawning-is most parsimonious. While there was incongruence with and among published data sets, the GH1C intron phylogeny was the best hypothesis, based on currently available molecular data.
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Affiliation(s)
- T H Oakley
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 53201, USA.
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28
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Reed KM, Dorschner MO, Todd TN, Phillips RB. Sequence analysis of the mitochondrial DNA control region of ciscoes (genus Coregonus): taxonomic implications for the Great Lakes species flock. Mol Ecol 1998; 7:1091-6. [PMID: 9734069 DOI: 10.1046/j.1365-294x.1998.00419.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sequence variation in the control region (D-loop) of the mitochondrial DNA (mtDNA) was examined to assess the genetic distinctiveness of the shortjaw cisco (Coregonus zenithicus). Individuals from within the Great Lakes Basin as well as inland lakes outside the basin were sampled. DNA fragments containing the entire D-loop were amplified by PCR from specimens of C. zenithicus and the related species C. artedi, C. hoyi, C. kiyi, and C. clupeaformis. DNA sequence analysis revealed high similarity within and among species and shared polymorphism for length variants. Based on this analysis, the shortjaw cisco is not genetically distinct from other cisco species.
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Affiliation(s)
- K M Reed
- Department of Biological Sciences, University of Wisconsin-Milwaukee 53201, USA.
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29
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Abstract
This study was designed to characterize further the nontranscribed intergenic spacers (NTSs) of the 5S rRNA genes of fish and evaluate this marker as a tool for comparative studies. Two members of the closely related North American Great Lakes cisco species complex (Coregonus artedi and C. zenithicus) were chosen for comparison. Fluorescence in situ hybridization found the ciscoes to have a single multicopy 5S locus located in a C band-positive region of the largest submetacentric chromosome. The entire NTS was amplified from the two species by polymerase chain reaction with oligonucleotide primers anchored in the conserved 5S coding region. Complete sequences were determined for 25 clones from four individuals representing two discrete NTS length variants. Sequence analysis found the length variants to result from presence of a 130-bp direct repeat. No two sequences from a single fish were identical. Examination of sequence from the coding region revealed two types of 5S genes in addition to pseudogenes. This suggests the presence of both somatic and germline (oocyte) forms of the 5S gene in the genome of Coregonus. The amount of variation present among NTS sequences indicates that accumulation of variation (mutation) is greater in this multicopy gene than is gene conversion (homogenization). The high level of sequence variation makes the 5S NTS an inappropriate DNA sequence for comparisons of closely related taxa.
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Affiliation(s)
- S L Sajdak
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
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Reed KM, Dorschner MO, Phillips RB. Characteristics of two salmonid repetitive DNA families in rainbow trout, Oncorhynchus mykiss. Cytogenet Cell Genet 1998; 79:184-7. [PMID: 9605846 DOI: 10.1159/000134716] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
DNA sequence and genomic location of two repetitive DNA families in rainbow trout (Oncorhynchus mykiss) were investigated to develop molecular markers for chromosome identification. DNA fragments with sequences similar to the tandem and interspersed elements described in other salmonids were isolated. One clone showed differential hybridization to 12 pairs of chromosomes and should be a useful marker for physical mapping.
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Affiliation(s)
- K M Reed
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 53201, USA.
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Moran P, Reed KM, Oakley TH, Phillips RB, Garcia-Vazquez E, Pendas AM. Physical localization and characterization of the BglI element in the genomes of Atlantic salmon (Salmo salar L.) and brown trout (S. trutta L.). Gene 1997; 194:9-18. [PMID: 9266667 DOI: 10.1016/s0378-1119(97)00093-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This work describes chromosomal localization, fine physical mapping, and population variation of the BglI element in the genome of Atlantic salmon (Salmo salar L.) and a similar sequence in the genome of brown trout (S. trutta L.). Results from a variety of complementary approaches, clearly demonstrate that the BglI element does not occur as a satellite-like repetitive DNA in these species but is part of the rDNA cistron as suggested by Goodier and Davidson (1993). Coincident hybridization of BglI clones with rDNA loci in both single and double-probe fluorescence in situ hybridization (FISH) experiments demonstrated physical linkage between the BglI element and rDNA loci. Fine physical mapping by Southern analysis and PCR amplification showed the BglI element to be located approximately 1.6 kb upstream of the 18S gene. The BglI element was used to screen for population-specific markers by Southern analysis. Population-specific banding patterns were only observed in brown trout, allowing identification of individual populations of this species. Sequence comparisons revealed sequences similar to the BglI element present in the rDNA cistron of other salmonids. This result suggests the presence of this sequence in the genome of the salmonid tetraploid ancestor.
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Affiliation(s)
- P Moran
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo Julían Claveria, Spain
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32
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Jarvis KB, Phillips RB, Danielson C. Managed care preapproval and its effect on the cost of Utah worker compensation claims. J Manipulative Physiol Ther 1997; 20:372-6. [PMID: 9272469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To determine the effect of preauthorization of chiropractic services costs in non-surgical back injury cases in a managed care environment. The program was implemented in the chiropractic provider group by the Worker Compensation Fund of Utah. The results were compared with those of similar injury claims in a separate provider group in which there was no preauthorization program. DESIGN The study was a retrospective review of approximately 5000 claims from 1986 and 5000 claims from 1989 of injured workers in the Utah Worker Compensation Fund. We extracted approximately 1000 nonsurgical back-related injury claims from each year. MAIN OUTCOME MEASURE Cost comparisons between medical and chiropractic provider groups in the management of nonsurgical compensable back pain in both 1986 and 1989. RESULTS Treatment costs in cases managed by chiropractic physicians increased 12% between 1986 and 1989. Treatment cost in cases managed by medical physicians increased 71% in the same time period. Compensation (wage replacement) costs increased 21% for the chiropractic group and 114% for the medical group. CONCLUSION Retrospective analysis of worker compensation databases continue to struggle with issues related to measurement of severity, appropriate condition identification, adequate inclusion of all related costs and unbiased case selection. Treatment costs appeared to be controlled under the auspices of a preapproval program required of the chiropractic physician whereas medical costs escalated in the absence of price controls.
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Affiliation(s)
- K B Jarvis
- Los Angeles College of Chiropractic, Whittier, CA 90609-1166, USA
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33
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Reed KM, Phillips RB. Polymorphism of the nucleolus organizer region (NOR) on the putative sex chromosomes of Arctic char (Salvelinus alpinus) is not sex related. Chromosome Res 1997; 5:221-7. [PMID: 9244448 DOI: 10.1023/a:1018411417816] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Polymorphism of the nucleolus organizer region (NOR) on the putative sex chromosomes of Arctic char (Salvelinus alpinus) was examined using conventional cytogenetic and molecular techniques. Variation was observed in the number, size and position of rDNA loci on the sex pair. Fluorescence in situ hybridization (FISH) analyses showed that the sex chromosomes of Arctic char lack the repetitive DNA sequences (Mbol/BglII family) that are a prominent feature of the sex chromosomes of lake trout (S. namaycush). Southern analyses of genomic DNAs using an rDNA fragment as probe revealed extensive restriction fragment length polymorphism (RFLP) variation among individuals. Despite the presence of variation in all aspects of this rDNA locus, no sex-specific differences were detected. Repetitive DNAs (multicopy rDNA as in Arctic char or tandem repetitive DNA as in lake trout) appear to play important but different roles in the evolution of the sex chromosomes in these species.
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Affiliation(s)
- K M Reed
- Department of Biological Sciences, University of Wisconsin-Milwaukee 53201, USA.
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34
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Abstract
The relationship between a 217-bp AluI fragment (SnAluI-33c) from lake trout (Salvelinus namaycush) which hybridizes to the nucleolar organizer regions (NORs) and the ribosomal RNA genes was examined by Southern analysis and comparative hybridization. Restriction enzymes with recognition sites mapped in the lake trout rDNA cistron were used to digest genomic DNA into fragments of predetermined size. Comparison of the hybridization pattern of SnAluI-33c with those of two rDNA-specific probes placed this fragment within the intergenic spacer region of the rDNA cistron, approximately 3 kb upstream (5') of the 18S gene. This finding is consistent with in situ hybridization experiments showing hybridization of this fragment to sites of rDNA [Reed, K.M. and Phillips, R.B., Cytogenet. Cell Genet. 70 (1995) 104-107]. Based on cross hybridization and sequence comparisons, homologous sequences are present in other salmonid species.
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Affiliation(s)
- K M Reed
- Department of Biological Sciences, University of Wisconsin-Milwaukee 53201, USA.
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35
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Doxey TT, Phillips RB. Comparison of entrance requirements for health care professions. J Manipulative Physiol Ther 1997; 20:86-91. [PMID: 9046456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To compare U.S. chiropractic college admissions requirements with those of allopathy, osteopathy, optometry, podiatry and dentistry. DESIGN Survey. PARTICIPANTS The schools that participated in the comparison were selected based on their geographic location within the United States. The number of schools selected were 16 chiropractic college, 17 allopathic colleges, 16 osteopathic colleges, 16 optometric colleges, 7 podiatric colleges and 15 dental colleges. MAIN OUTCOME MEASURES Information collected from the individual schools included: (a) minimum number of undergraduate semester hours (toward a bachelor's degree) that are required on entrance; (b) actual percentage of applicants with a 4-yr bachelor's degree on entrance; (c) minimum GPA required on entrance and (d) actual average GPA of applicants on entrance. RESULTS Averages were computed for each outcome. Overall, allopathic averages were highest and chiropractic averages were lowest for each of the four outcome measures, with the other programs scoring at varying points in between. CONCLUSION Successful completion of preprofessional requirements may be an indicator for success within a rigorous professional curriculum. These data reflect overall differences between health-care professions on a very few entrance criteria. Further investigation is needed to understand the long-term impact of these differences as well as the possible economic or political factors that may be influencing these results.
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Affiliation(s)
- T T Doxey
- Los Angeles College of Chiropractic, Whittier, California 90609-1166, USA
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Rab P, Reed KM, Ponce de León FA, Phillips RB. A new method for detecting nucleolus organizer regions in fish chromosomes using denaturation and propidium iodide staining. Biotech Histochem 1996; 71:157-62. [PMID: 8724442 DOI: 10.3109/10520299609117153] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A rapid method for detecting nucleolus organizer regions (NORs) in fish chromosomes based on thermal denaturation and staining with propidium iodide is described. Under epifluorescence, the NORs of 15 fish species from six families could be detected. This protocol differentiates constitutive heterochromatin in mammalian and avian chromosomes, and in some cases, heterochromatic blocks in fish chromosomes. The staining of NORs of fish chromosomes with propidium iodide following denaturation with formalin is likely the result of differential denaturation of the rDNA due to the thermal characteristics of AT- and GC-rich domains of the rDNA cistron. This technique provides a new useful marker for descriptive fish cytogenetic studies.
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Affiliation(s)
- P Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic
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37
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Abstract
The chromosomes of lake trout (Salvelinus namaycush) contain a considerable amount of heterochromatin located at the centromeres and/or telomeres of several chromosomes, including a sex-specific block located distally on the X chromosome. In order to investigate further the repetitive DNAs of lake trout, genomic DNA from a female was size fractionated (<600 bp) with the restriction endonuclease AluI and fragments were cloned into the bacteriophage M13. A total of 42 clones were isolated. Relative copy number of individual inserts within the lake trout genome was estimated by Southern analysis. Twelve clones were determined to be highly repetitive and were chosen for further investigation. Inserts of these clones contained sequences similar to the AluI/RsaI, EcoRI/DraI, DraI/BstEII, and MboI/BglII families reported from Arctic char (Salvelinus alpinus). The chromosomal location of several of these fragments was determined in lake trout by fluorescence in situ hybridization (FISH). Two related AluI/RsaI sequences (Type A, approximately 140 bp, and Type B,approximately 120 bp) showed differential hybridization. Type A hybridized to the centromeres of all metacentric as well as several acrocentric chromosomes. Type B hybridized to the centromeres of most acrocentric chromosomes. A sequence with homology to the EcoRI/DraI family hybridized to the centromeres of several acrocentric chromosomes. Sequences with partial similarity to the DraI/BstEII family hybridized to the major rDNA sites (nucleolar organizer regions, NORs) and several minor telomeric sites. The interstitial and telomeric heterochromatin of lake trout, including that of the X chromosome, appears to comprise sequences belonging to the MboI/BglII family.
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Affiliation(s)
- K M Reed
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
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Abstract
Previous phylogenetic analyses of the fishes belonging to the genus Oncorhynchus based on mitochondrial DNA data have produced conflicting trees. This is especially true with respect to the relationships among the three most derived Pacific salmon species, the pink salmon (Oncorhynchus gorbuscha), sockeye salmon (Oncorhynchus nerka), and chum salmon (Oncorhynchus keta). Smith (Syst. Biol. 41(1): 41-57, 1992) suggested that introgression in opposite directions on either side of the Pacific ocean may account for some of the conflicting data. The ATPase 6 and ND3 mitochondrial genes were sequenced from Asian and North American representatives of several species of Pacific salmon and the aligned sequences were analyzed along with other data on these genes. Analysis of the ATPase 6 and ND3 sequence data and RFLP data gives strong support for a sister relationship between pink salmon and chum salmon.
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Affiliation(s)
- M J Domanico
- Department of Biological Sciences, University of Wisconsin-milwaukee 53201, USA
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39
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Abstract
Variation in the intergenic spacer (IGS) of the ribosomal DNA (rDNA) of lake trout (Salvelinus namaycush) was examined. Digestion of genomic DNA with restriction enzymes showed that almost every individual had a unique combination of length variants with most of this variation occurring within rather than between populations. Sequence analysis of a 2.3 kilobase (kb) EcoRI-DraI fragment spanning the 3' end of the 28S coding region and approximately 1.8 kb of the IGS revealed two blocks of repetitive DNA. Putative transcriptional termination sites were found approximately 220 bases (b) downstream from the end of the 28S coding region. Comparison of the 2.3-kb fragments with two longer (3.1 kb) fragments showed that the major difference in length resulted from variation in the number of short (89 b) repeats located 3' to the putative terminator. Repeat units within a single nucleolus organizer region (NOR) appeared relatively homogeneous and genetic analysis found variants to be stably inherited. A comparison of the number of spacer-length variants with the number of NORs found that the number of length variants per individual was always less than the number of NORs. Examination of spacer variants in five populations showed that populations with more NORs had more spacer variants, indicating that variants are present at different rDNA sites on nonhomologous chromosomes.
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Affiliation(s)
- L Zhuo
- Department of Biological Sciences, University of Wisconsin-Milwaukee 53201, USA
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40
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Reed KM, Bohlander SK, Phillips RB. Microdissection of the Y chromosome and fluorescence in situ hybridization analysis of the sex chromosomes of lake trout, Salvelinus namaycush. Chromosome Res 1995; 3:221-6. [PMID: 7606359 DOI: 10.1007/bf00713046] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Lake trout, Salvelinus namaycush, is one of the few salmonids with morphologically differentiated sex chromosomes. Genetic analysis suggested that the sex-determining region of this species lies on the short arm of the Y chromosome. The differential arm of the Y chromosome was microdissected and the resulting DNA amplified in a sequence-independent manner. Amplified DNA was biotin labeled as a probe for fluorescence in situ hybridization (FISH). Strong hybridization signals were seen covering defined regions of both the Y and X chromosomes. Homeologous chromosomes of the ancestrally tetraploid genome were not identified by FISH with the Y probe, indicating diploidization of this region of the genome.
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Affiliation(s)
- K M Reed
- Department of Biological Sciences, University of Wisconsin-Milwaukee 53201, USA
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41
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Reed KM, Phillips RB. Molecular cytogenetic analysis of the double-CMA3 chromosome of lake trout, Salvelinus namaycush. Cytogenet Cell Genet 1995; 70:104-7. [PMID: 7537646 DOI: 10.1159/000134002] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The chromosome possessing two chromomycin A3 (CMA3) staining sites in lake trout (Salvelinus namaycush) was examined using FISH. All CMA3-bands in the karyotype contained ribosomal DNA (rDNA), including both sites on the double-CMA3 chromosome. One rDNA site on this chromosome was bordered by telomeric repeats, implicating a rearrangement in the origin of the second NOR.
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Affiliation(s)
- K M Reed
- Department of Biological Sciences, University of Wisconsin-Milwaukee 53201, USA
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42
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Pope MH, Phillips RB, Haugh LD, Hsieh CY, MacDonald L, Haldeman S. A prospective randomized three-week trial of spinal manipulation, transcutaneous muscle stimulation, massage and corset in the treatment of subacute low back pain. Spine (Phila Pa 1976) 1994; 19:2571-7. [PMID: 7855683 DOI: 10.1097/00007632-199411001-00013] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
STUDY DESIGN A randomized prospective trial of manipulation, massage, corset and transcutaneous muscle stimulation (TMS) was conducted in patients with subacute low back pain. OBJECTIVES The authors determined the relative efficacy of chiropractic treatment to massage, corset, and TMS. SUMMARY OF BACKGROUND DATA Although all of these treatments are used for subacute low back pain treatment, there have been few comparative trials using objective outcome criteria. Patients were enrolled for a period of 3 weeks. They were evaluated once a week by questionnaires, visual analog scale, range of motion, maximum voluntary extension effort, straight leg raising and Biering-Sorensen fatigue test. The dropout rate was highest in the muscle stimulation and corset groups and lowest in the manipulation group. Rates of full compliance did not differ significantly across treatments. A measure of patient confidence was greatest in the manipulation group. RESULTS After 3 weeks, the manipulation group scored the greatest improvements in flexion and pain while the massage group had the best extension effort and fatigue time, and the muscle stimulation group the best extension. CONCLUSION None of the changes in physical outcome measures (range of motion, fatigue, strength or pain) were significantly different between any of the groups.
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Affiliation(s)
- M H Pope
- Iowa Spine Research Center, University of Iowa, Iowa City
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Zhuo L, Sajdak SL, Phillips RB. Minimal intraspecific variation in the sequence of the transcribed spacer regions of the ribosomal DNA of lake trout (Salvelinus namaycush). Genome 1994; 37:664-71. [PMID: 7545959 DOI: 10.1139/g94-094] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Intraspecific variation in the sequence of the transcribed spacer regions of the ribosomal DNA (rDNA) in lake trout was examined by restriction mapping and sequencing of these regions amplified by the polymerase chain reaction. The length of the first internal transcribed spacer region (ITS-1) was 566 bases and the second internal transcribed spacer region (ITS-2) was 368 bases in lake trout. When the 1.4-kb region including the ITS-1, the 5.8S coding region, and the ITS-2 was amplified from 12 individuals from four populations and digested with eight different enzymes only one intraindividual polymorphism was found that occurred in each population. When the amplified ITS-1 region was sequenced from an additional 10 individuals from five populations, no interindividual variation was found in the sequence. A 6-kb portion of the rDNA repeat unit including 1.6 kb of the 18S coding region, the 5' external spacer region (5' ETS), and part of the adjacent intergenic spacer was cloned and a restriction map was prepared for these regions in lake trout. No intraspecific variation was found in the region adjacent to the 18S rDNA, which includes the 5' ETS, although intraspecific and intraindividual length variation was found in the intergenic spacer region 3-6 kb from the 18S. Sequencing of a 609-b segment of the 5' ETS adjacent to the 18S coding region revealed the presence of two 41-b repeats. The 198-b sequence between the repeats had some similarity to the 18S coding region of other fishes. Primers were designed for amplification of 559 b of the 5' ETS using the polymerase chain reaction.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- L Zhuo
- Department of Biological Sciences, University of Wisconsin-Milwaukee 53201
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Keating JC, Jackson RB, Oliva M, Phillips RB. Origins of the LACC, 1901-1922. J Manipulative Physiol Ther 1994; 17:93-106. [PMID: 8169549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The Los Angeles College of Chiropractic (LACC) can trace its history from D. D. Palmer through Thomas H. Storey, D.C. to Charles A. Cale, D.C., N.D., the LACC's founder. The formation and early history of the College is intimately intertwined with the naturopathic movement and to a lesser extent the osteopathic profession in southern California during the first two decades of this century. Although the school would eventually become the largest producer of chiropractors in the densest chiropractic jurisdiction in the world, its early survival was not always certain, and its later status as a bellwether for the rest of the profession was not yet in evidence. Organized by Charles Cale in 1910 and chartered in 1911, the school would suspend operations for several years (1914-6) while Charles and Linnie Cale acquired osteopathic credentials. The school's rebirth in 1916 marked the beginning of the final push for the initiative act of 1922 that licensed chiropractors and ended some of the most intensive legal persecutions by organized medicine that chiropractors would ever experience. This initial phase of LACC's history (through 1922) set the stage for at least 12 subsequent mergers and reorganizations to form today's LACC. The College would later lead the state's and the profession's efforts to broaden and deepen the chiropractic curriculum during the middle ages of chiropractic.
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Affiliation(s)
- J C Keating
- Western States Chiropractic College, Portland, OR 97230
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Phillips RB, Mootz RD, Nyiendo J, Cooperstein R, Konsler J, Mennon M. The descriptive profile of low back pain patients of field practicing chiropractors contrasted with those treated in the clinics of west coast chiropractic colleges. J Manipulative Physiol Ther 1992; 15:512-7. [PMID: 1402411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE To compare the demographic and clinical characteristics of low back pain patients from chiropractic college clinics and private practice settings on the west coast of the United States. DESIGN AND SETTING A survey analysis of consecutive new patients in a specified time frame from multiple private office settings contrasted with a previous survey of consecutive new patients in a similar time frame from chiropractic college clinics. PATIENTS In the private practice setting, new patients were selected on a consecutive basis as subjects for the study. Selection was limited to low back pain patients. INTERVENTIONS None. This was a self-report survey only. MAIN OUTCOME There is a strong similarity of the two low back pain patient groups, with the exception of higher levels of income, work time loss, severity and functional disability reported in the private practice setting. RESULTS Similarities between the two low back pain patient groups were found in the distribution of gender, age, job description and education. Statistical significances were not determined due to variations in data collection. CONCLUSIONS The two patient populations are reasonably comparable in sociodemographic variables, but clinical variation does exist. These results suggest the need to consider clinical findings when extrapolating research findings in a college clinic setting to the chiropractic profession in general.
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Affiliation(s)
- R B Phillips
- Los Angeles College of Chiropractic, Whittier, CA 90609
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Hansen DT, Adams AH, Meeker WC, Phillips RB. Proposal for establishing structure and process in the development of implicit chiropractic standards of care and practice guidelines. J Manipulative Physiol Ther 1992; 15:430-8. [PMID: 1431630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
With the advent of health care's "era of accountability", the chiropractic profession is now faced with generating implicit standards and guidelines for care or having it done for us by outside agencies. Already we see chiropractic groups in individual states and provinces being pressured into naive efforts of guideline development. Current knowledge and experience are available through recent health care literature that clearly defines the structure and process of guideline development and offers suggestions on how to measure outcomes of those processes. In addition, the United States Congress has directed a new federal agency to oversee this activity and monitor outcomes of quality improvement programs. The time has come for the chiropractic profession to define its exact role in health care delivery and develop implicit standards of care and practice guidelines. This sentinel effort should be managed by a commissioned body of empaneled experts that generally represent the academic and clinical chiropractic profession. A protocol for selection of these panelists and the panel chairperson needs to be developed and memorialized. Appropriate methodology (with definitions) needs to be developed for the process of standards/guideline development. Adherence to the accepted structure and process of guideline development will ensure the continuity of this dynamic process in the coming generations. This proposal offers a preliminary definition of the structure and process, including a "seed" policy statement and decision flow chart, specific to guideline development. Once the structure and process of guideline development for chiropractic are defined, the profession can then present this product to federal and state agencies, private sector health care purchasers, patient advocacy groups and other stakeholders of chiropractic care.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- D T Hansen
- Los Angeles College of Chiropractic, Whittier, CA
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Pleyte KA, Duncan SD, Phillips RB. Evolutionary relationships of the salmonid fish genus Salvelinus inferred from DNA sequences of the first internal transcribed spacer (ITS 1) of ribosomal DNA. Mol Phylogenet Evol 1992; 1:223-30. [PMID: 1342939 DOI: 10.1016/1055-7903(92)90019-d] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DNA sequences of the ribosomal DNA (rDNA) first internal transcribed spacer region (ITS 1) of six species of the salmonid fish genus Salvelinus (alpinus, malma, confluentus, leucomaenis, fontinalis, and namaycush) and the closely related species Hucho perryi were determined. Phylogenetic analysis of the aligned sequences by both phenetic and cladistic methods with H. perryi as an outgroup generated one best topology which pairs S. alpinus with S. malma as the most recently derived species, and pairs S. confluentus with S. leucomaenis. Three other possible topologies favor the pairing of S. namaycush and S. fontinalis, with one tree placing them on separate branches, and vary the branching order of the interior groups. These results agree with previous studies based on comparisons of morphologies, isozymes, karyotypes, and restriction sites showing a close genetic relationship and possible hybridization between the members of this genus.
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Affiliation(s)
- K A Pleyte
- Department of Biological Sciences, University of Wisconsin-Milwaukee 53201
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Phillips RB. Plain film radiology in chiropractic. J Manipulative Physiol Ther 1992; 15:47-50. [PMID: 1531491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The use of plain film radiography in the early stages of acute low back pain has been challenged. Health care providers who maintain their own radiological services tend to charge more and take more X-rays than those who refer patients out for such services. Chiropractic physicians generally own their own X-ray equipment and see a predominance of low back pain in practice. There is a basis for unjustified utilization of X-ray. The chiropractic physician justifies the use of X-ray in the management of low back pain to a) rule out pathology, b) perform a biomechanical evaluation, c) protect against medicolegal action, d) obtain financial gain and e) out of habit. The literature fails to support or justify the use of X-ray in the management of acute low back pain for any of the above listed reasons. Arguments to this effect are presented. A guidelines is provided as a suggestion for improved decision making regarding the use of X-ray in the low back patient. A challenge is issued to the practitioners who treat low back pain to seek better justification for their current practice patterns.
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Affiliation(s)
- R B Phillips
- Los Angeles College of Chiropractic, Whittier, CA 90609-1166
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Hsieh CY, Phillips RB, Adams AH, Pope MH. Functional outcomes of low back pain: comparison of four treatment groups in a randomized controlled trial. J Manipulative Physiol Ther 1992; 15:4-9. [PMID: 1531488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The revised Oswestry Low Back Pain Questionnaire (ROLBPQ) and Roland-Morris Activity Scale (RMAS) were compared in a randomized controlled trial of chiropractic manipulation, stroking massage, corset and transcutaneous muscular stimulation (TMS). This trial employed specific inclusion and exclusion criteria, including nonspecific low back pain for a duration of 3 wk to 6 months and ages between 18 and 55. We had the opportunity to ask 85 patients to answer the questionnaires. Sixty-three patients, who completed the initial and final evaluations, were used for data analysis. Both ROLBPQ and RMAS showed good internal consistency with alpha coefficients ranging from .77 to .93. Both instruments showed a significant difference between the chiropractic manipulation and massage groups (p less than .05). RMAS was able to further show significant differences between the chiropractic manipulation and TMS groups, and between the corset and massage groups, but the ROLBPQ failed to do so. RMAS also showed that chiropractic manipulation had a better but nonsignificant result than corset, possibly due to insufficient sample size and/or duration of treatment. We conclude that both instruments are reliable for measuring low back pain disability, and chiropractic manipulation has a superior short-term benefit when compared to stroking massage and TMS in subacute low back pain patients. In addition, it appears that RMAS is preferable in a clinical trial situation for subacute low back pain because it is more sensitive than ROLBPQ to detect changes.
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Affiliation(s)
- C Y Hsieh
- Research Division, Los Angeles College of Chiropractic, Whittier, CA 90609
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McNamee KP, Magarian K, Phillips RB, Greenman PE. Osteopathic vs. chiropractic education: a student perspective. J Manipulative Physiol Ther 1991; 14:422-7. [PMID: 1940675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
This study compares nationwide survey results from 506 second year students of 11 osteopathic schools and 881 students from the first and second academic year (third term/fourth quarter) of eight chiropractic colleges. Each student was given a questionnaire regarding his/her perspective on the education he/she was receiving. Both populations were questioned about whether or not they came from an osteopathic/chiropractic family, their application process, the efficacy of osteopathic manipulative therapy (OMT)/chiropractic adjustments, their first year attitude concerning the efficacy of OMT/chiropractic adjustments, the integration of osteopathic/chiropractic principles into the curriculum and the justification for separate health care professions. Osteopathic and chiropractic students entered their respective professions from nonosteopathic/non-chiropractic families. Although both populations selected their profession as a first and primary choice, chiropractic students were more substantially represented. Upon entering their program, osteopathic students were not convinced, but had an open mind concerning the effectiveness of osteopathic manipulative therapy (OMT), and were divided as to whether there is enough of a distinction between DOs and MDs to justify separate professions. Chiropractic students, on the other hand, entered their program convinced that chiropractic adjustments are effective, and saw a clear distinction between the roles of chiropractic physicians and medical doctors.
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Affiliation(s)
- K P McNamee
- Los Angeles College of Chiropractic, Research Division, Whittier, CA 90609-1166
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