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Long M, Reid R, Kemper C. Cadmium Accumulation and Toxicity in The Bottlenose Dolphin Tursiops truncatus, The Common Dolphin Delphinus delphis, and Some Dolphin Prey Species in South Australia. AUSTRALIAN MAMMALOGY 1998. [DOI: 10.1071/am97025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Twenty Tursiops truncatus and 20 Delphinus delphis from South Australia were analysed for cadmium levels, as were some fish and squid species which form part of their diet. In the dolphins, cadmium was accumulated mainly in the kidneys (range 0-38 μg/g), with levels in many individuals exceeding 20 μg/g (wet weight). On average, levels in kidney were three-fold higher than in liver and 26-fold higher than in muscle. Cadmium concentrations related to dolphin body length, but the relationship with tooth development class was less clear. 80% of the prey fish species analysed from Spencer Gulf exceeded NH & MRC health recommendations of 0.2 μg/g (wet weight) for human consumption. Sepioteuthis australis from upper Spencer Gulf contained significantly higher cadmium levels than Ceduna samples (0.21 ± 0.01 μg/g versus 0.13 ± 0.01 μg/g, p<0.001) (wet weight). On histological examination, 32% of adult dolphin kidneys showed pathological changes, proteinuria being the most common abnormality. High levels of cadmium were found in dolphins from widely spaced locations in South Australia.
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de Souza SJ, Long M, Schoenbach L, Roy SW, Gilbert W. The correlation between introns and the three-dimensional structure of proteins. Gene X 1997; 205:141-4. [PMID: 9461387 DOI: 10.1016/s0378-1119(97)00401-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We test the hypothesis that introns were used to construct the first genes from small exons, whose protein products represent compact elements of structure. For any three-dimensional structure, a computer program analyzes the structure into a set of modules, segments of the polypeptide chain bounded in space by a maximum diameter, separated by a set of 'boundary regions'. The 'boundary regions' are such that if the gene were divided by an intron in each 'boundary region', the protein would be divided into modules less than the specified diameter. Using a set of 32 ancient proteins, which have no introns in prokaryotes, we examine the intron positions in their eukaryotic homologs and show that the introns are correlated with modules of diameter 21, 28 and 33 A, with P values below 0.001.
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153
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Long M, de Souza SJ, Gilbert W. The yeast splice site revisited: new exon consensus from genomic analysis. Cell 1997; 91:739-40. [PMID: 9413983 DOI: 10.1016/s0092-8674(00)80462-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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154
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Zhou J, Zhu P, Wang Z, Liu D, Wu Z, Song G, Long M. [The effect of hypertonic saline solution on the rheology after burn-blast combined injury]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 1997; 14:338-41. [PMID: 11367623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
To study the effect of hypertonic saline solution on the rheology and putative mechanism, we investigated the changes of plasma viscosity, blood viscosity and reduced viscosity in dogs treated with hypertonic saline solution after burn-blast combined injury and observed the effect of hypertonic saline solution therapy on the viscoelastic property of erythrocyte membranes measured by micropippette aspiration technique in rats with burn. The results showed that the blood viscosity and reduced viscosity increased significantly in dogs after injury, and plasma viscosity also increased significantly at 24 h after injury. Elastic moduli and viscous coefficients of erythrocyte membranes increased obviously in rats after burn. The hypertonic saline solution therapy could significantly improve blood viscosity and reduced viscosity, but it did not significantly improve elastic moduli and viscous coefficients of erythrocyte membranes. These suggested that the hardness of erythrocyte membranes increased, the deform property of erythrocyte membranes decreased, and the blood rheology became worse after burn blast combined injury. Hypertonic saline solution therapy could significantly improve the blood rheology. The effect did not bear a significant relationship with the change of single biomechanics property of erythrocyte membranes. It might be related with other factors.
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155
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Xie L, Long M, Liu Y, Wang H, Song G, Wu Z, Wu Y. [Effect of electric field on erythrocyte sedimentation rate. VI--dependence of electric field pattern]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 1997; 14:237-42. [PMID: 11326840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
An automatic analyzer of RBC rheological parameters and a microscopic morphological observation technique were employed to investigate the effect of three electric field patterns on erythrocyte sedimentation and aggregation in a physiological saline solution and in autologous plasma, respectively. Experimental results indicate that in a physiological saline solution: 1) Erythrocytes present a lightly aggregation and settle faster by an alternative current electric field; 2) There exists no erythrocyte aggregation by a direct current electric field of constant current and the enhancement of erythrocyte sedimentation is caused only by the action of electric force; 3) Time courses of erythrocyte sedimentation fit well with an exponential type curve by a direct current electric field of constant voltage, and this exponential type sedimentation curve is not caused by erythrocyte aggregation but caused by the decrease of circuit current with time duration. Also shown by experimental results is that the above three electric field patterns all affect the erythrocyte sedimentation in antologous plasma in different contents, which predicts some change in erythrocyte aggregation behavior in autologous plasma by an external electric field.
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156
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Yang R, Wu Y, Jiang J, Wu Z, Long M, Wu Y. [Experimental study on erythrocyte of obstructive jaundice patient: its changes of membrane protein and mechanical properties]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 1997; 14:274-8. [PMID: 11326849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The component of the erythrocyte membrane protein under three states obstruction, after surgical relief of obstruction, and normal) were analyzed qualitatively by using SDS-PAGE and the method of thin scanning. The result revealed that the membrane protein band 4.2 was absent under the state of obstruction and it recovered after surgical relief of obstruction. Then the mechanical properties of the above three cases of erythrocytes were tested by the micropipette aspiration system and the data were analyzed by Voigt model. The result showed that the elastic modulus and the coefficient of viscosity of the erythrocytes under the state of obstruction were greater than those of the normal; thus the deformability decreased, but "overcorrection" appeared after surgical relief of obstruction. The possible relations between the mechanical properties and the change of membrane protein were discussed.
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Abstract
We discuss two tests of the hypothesis that the first genes were assembled from exons. The hypothesis of exon shuffling in the progenote predicts that intron phases will be correlated so that exons will be an integer number of codons and predicts that the exons will be correlated with compact regions of polypeptide chain. These predictions have been tested on ancient conserved proteins (proteins without introns in prokaryotes but with introns in eukaryotes) and hold with high statistical significance. We conclude that introns are correlated with compact features of proteins 15-, 22-, or 30-amino acid residues long, as was predicted by "The Exon Theory of Genes."
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158
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Wu Z, Zhang G, Wang X, Song G, Wang H, Long M, Cai S, Wu Y. [Investigation on the viscoelastic properties of hepatocytes and their relavances to cytoskeleton structure]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 1997; 14:111-4. [PMID: 9817636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Using micropipette aspiration technique, the authors investigated the viscoelastic properties of human fetal hepatocytes (HFH) and hepatocellular carcinoma (HCC) cells. And further, the effects of two cytoskeleton interferents, cytochalasin D and colchicine on the viscoelastic properties of HFHs were investigated. The results showed: the elastic coefficients K1 and K2 of HCC cells were significantly higher than those of HFHs; the action of cytochalasin D led to an obvious decrease in elastic coefficients K1, K2 as well as the viscous coefficient mu of HFHs; under the action of colchicine, the K1 value of HFHs increased while the K2 and mu values decreased obviously or tended to decrease. A brief discussion was presented about these results.
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159
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Long M, de Souza SJ, Gilbert W. Delta-interacting protein A and the origin of hepatitis delta antigen. Science 1997; 276:824-5. [PMID: 9115212 DOI: 10.1126/science.276.5313.824] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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160
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Sekhar KR, Long M, Long J, Xu ZQ, Summar ML, Freeman ML. Alteration of transcriptional and post-transcriptional expression of gamma-glutamylcysteine synthetase by diethyl maleate. Radiat Res 1997; 147:592-7. [PMID: 9146705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Gamma-glutamylcysteine synthetase (gamma-GCS), also known as glutamate-cysteine ligase (EC 6.3.2.2), is the rate-limiting enzyme in the synthesis of glutathione (GSH). The gene GLCLC encodes the catalytic subunit while GLCLR encodes the regulatory subunit. Although it has been shown that GLCLC can respond to a variety of stresses by increased transcription, it is not known whether a similar response occurs for GLCLR. Nor is it known whether post-transcriptional regulation of either gene product is altered during stress. The present investigation was undertaken to explore transcriptional and post-transcriptional regulation of GLCLC and GLCLR gene products when HepG2 cells were challenged with the radiation sensitizer diethyl maleate (DEM). Expression of steady-state GLCLC and GLCLR mRNA was enhanced 5-20-fold after DEM challenge. Nuclear run-off assays were performed on unstressed and stressed cells to determine whether the increased expression of GLCLC and GLCLR mRNA was due to altered transcriptional activity of these genes. The DEM treatment increased the transcription rates of both genes 2-5-fold. In unstressed HepG2 cells, the half-life of GLCLC mRNA transcripts was approximately 4 h. In contrast, the half-life of GLCLR transcripts was approximately 8 h. In cells treated with DEM, the half-lives of all transcripts were increased, indicating that message stabilization contributed to the increased expression of gene products. Finally, a PEST algorithm has identified a PEST (proline, glutamate, serine, threonine) motif within the catalytic subunit of gamma-GCS, suggesting that this subunit might exhibit conditional proteolytic regulation. These results imply that regulation of the products of the GLCLC and GLCLR genes may be altered at multiple levels during exposure to stress.
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161
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Richter B, Long M, Lewontin RC, Nitasaka E. Nucleotide variation and conservation at the dpp locus, a gene controlling early development in Drosophila. Genetics 1997; 145:311-23. [PMID: 9071586 PMCID: PMC1207797 DOI: 10.1093/genetics/145.2.311] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A study of polymorphism and species divergence of the dpp gene of Drosophila has been made. Eighteen lines from a population of D. melanogaster were sequenced for 5200 bp of the Hin region of the gene, coding for the dpp polypeptide. A comparison was made with sequence from D. simulans. Ninety-six silent polymorphisms and three amino acid replacement polymorphisms were found. The overall silent polymorphism (0.0247) is low, but haplotype diversity (0.0066 for effectively silent sites and 0.0054 for all sites) is in the range found for enzyme loci. Amino acid variation is absent in the N-terminal signal peptide, the C-terminal TGF-beta peptide and in the N-terminal half of the pro-protein region. At the nucleotide level there is strong conservation in the middle half of the large-intron and in the 3' untranslated sequence of the last exon. The 3' untranslated conservation, which is perfect for 110 bp among all the divergent species, is unexplained. There is strong positive linkage disequilibrium among polymorphic sites, with stretches of apparent gene conversion among originally divergent sequences. The population apparently is a migration mixture of divergent clades.
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de Souza SJ, Long M, Schoenbach L, Roy SW, Gilbert W. Intron positions correlate with module boundaries in ancient proteins. Proc Natl Acad Sci U S A 1996; 93:14632-6. [PMID: 8962105 PMCID: PMC26186 DOI: 10.1073/pnas.93.25.14632] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We analyze the three-dimensional structure of proteins by a computer program that finds regions of sequence that contain module boundaries, defining a module as a segment of polypeptide chain bounded in space by a specific given distance. The program defines a set of "linker regions" that have the property that if an intron were to be placed into each linker region, the protein would be dissected into a set of modules all less than the specified diameter. We test a set of 32 proteins, all of ancient origin, and a corresponding set of 570 intron positions, to ask if there is a statistically significant excess of intron positions within the linker regions. For 28-A modules, a standard size used historically, we find such an excess, with P < 0.003. This correlation is neither due to a compositional or sequence bias in the linker regions nor to a surface bias in intron positions. Furthermore, a subset of 20 introns, which can be putatively identified as old, lies even more explicitly within the linker regions, with P < 0.0003. Thus, there is a strong correlation between intron positions and three-dimensional structural elements of ancient proteins as expected by the introns-early approach. We then study a range of module diameters and show that, as the diameter varies, significant peaks of correlation appear for module diameters centered at 21.7, 27.6, and 32.9 A. These preferred module diameters roughly correspond to predicted exon sizes of 15, 22, and 30 residues. Thus, there are significant correlations between introns, modules, and a quantized pattern of the lengths of polypeptide chains, which is the prediction of the "Exon Theory of Genes."
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163
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Means LW, Long M, Jones TA, Curtis WC. Rats perform better on spatial than brightness delayed matching-to-sample water-escape due to an unlearned bias to use spatial cues. Physiol Behav 1996; 60:1239-45. [PMID: 8916177 DOI: 10.1016/s0031-9384(96)00129-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Rats readily acquire water-escape spatial delayed matching-to-sample (DMTS) tasks and show excellent performance with retention intervals as long as 120 m (17). They also acquire the task more readily with a 5-min retention interval (RI) than with a 1-min RI (16). To determine if these observations are unique to spatial DMTS, or are also true of nonspatial water-escape DMTS, 75-day-old rats were compared on acquisition and subsequent retention of spatial and brightness DMTS. A larger proportion of the rats tested on the spatial problem were able to acquire the task, made fewer acquisition errors, and demonstrated better retention when tested at RIs of 1, 5, 15, 30, 60, and 120 min than did the rats tested on the brightness problem. Acquisition RI did not affect the rate of acquisition on either task. Examination of perserveration errors, the occurrence of intrusions, and position-congruent performance (escape platform in the same physical location on both runs of a trial) revealed that the choices of brightness-trained rats were often more influenced by spatial than brightness cues, suggesting that rats have an unlearned bias to use spatial cues in water-escape DMTS tasks.
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164
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Means LW, Holsten RD, Long M, High KM. Scopolamine- and morphine-induced deficits in water maze alternation: failure to attenuate with glucose. Neurobiol Learn Mem 1996; 66:167-75. [PMID: 8946409 DOI: 10.1006/nlme.1996.0057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Glucose has previously been shown to improve performance on memory tasks and to ameliorate performance deficits induced by scopolamine or morphine. To test the generality of these observations, Sprague-Dawley rats were trained to alternate choices to reach an escape platform in a two-choice circular water maze. The rats attained a high level of alternation, alternating on a mean of 9 of 10 daily trials. Daily glucose injections (100 and 250 mg/ kg) failed to facilitate acquisition of the alternation. Single injections of scopolamine (0.5, 1.0, and 2.0 mg/kg), but not methylscopolamine (0.5 mg/kg), and daily injections of scopolamine (0.5 mg/kg) or morphine (5.0 mg/kg) impaired alternation performance. The scopolamine- and morphine-induced deficits in alternation behavior were not ameliorated by pretrial glucose injections at doses which have previously been found to be effective (100 and 250 mg/kg). The mechanism of glucose facilitation of memory is currently unknown. The present results show that glucose given at previously established effective doses does not activate the mechanism or produces too weak an effect to be observed in water maze alternation.
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165
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Long M, de Souza SJ, Rosenberg C, Gilbert W. Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor. Proc Natl Acad Sci U S A 1996; 93:7727-31. [PMID: 8755543 PMCID: PMC38815 DOI: 10.1073/pnas.93.15.7727] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Since most of the examples of "exon shuffling" are between vertebrate genes, the view is often expressed that exon shuffling is limited to the evolutionarily recent lineage of vertebrates. Although exon shuffling in plants has been inferred from the analysis of intron phases of plant genes [Long, M., Rosenberg, C. & Gilbert, W. (1995) Proc. Natl. Acad. Sci. USA 92, 12495-12499] and from the comparison of two functionally unknown sunflower genes [Domon, C. & Steinmetz, A. (1994) Mol. Gen. Genet. 244, 312-317], clear cases of exon shuffling in plant genes remain to be uncovered. Here, we report an example of exon shuffling in two important nucleus-encoded plant genes: cytosolic glyceraldehyde-3-phosphate dehydrogenase (cytosolic GAPDH or GapC) and cytochrome c1 precursor. The intron-exon structures of the shuffled region indicate that the shuffling event took place at the DNA sequence level. In this case, we can establish a donor-recipient relationship for the exon shuffling. Three amino terminal exons of GapC have been donated to cytochrome c1, where, in a new protein environment, they serve as a source of the mitochondrial targeting function. This finding throws light upon an old important but unsolved question in gene evolution: the origin of presequences or transit peptides that generally exist in nucleus-encoded organelle genes.
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166
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Mescall FM, Kane MT, Keyes WM, Quinlan LR, Hynes AC, Kane MT, Jordan FM, Hynes AC, McGarvey C, Kelly JP, O’Donnell JM, Kelliher P, O’Donnell JM, Cotton KD, Hollywood MA, Thornbury KD, McHale NG, Curran AK, O’Halloran KD, Bradford A, O’Rourke M, Docherty JR, Brady G, Lyall P, Felle P, Fanning P, O’Boyle KM, Cummins M, Naughton Y, Ryan MP, Clarke H, O’Connell C, McNamara B, Cuffe J, O’Sullivan G, Harvey B, Urbach V, Leguen I, Butt G, MacDonncha C, Watson AWS, Aherne AM, Vaughan CJ, Murphy MB, O’Connell DP, Walsh DE, Harvey BJ, Connor TJ, Kelly JP, Leonard BE, Wrynn AS, Earley B, Harkin AJ, Cassidy EM, O’Connor JJ, Brayden DJ, Dunne JF, Baird AW, McCole DF, Newsholme PN, Love GP, Keenan AK, Doolan CM, Higgins MA, Higgins T, Horwitz E, Reidy D, Redmond AM, McNamara MG, Maginn M, Tamate K, Charleton M, Leavy J, Nolan A, Egan D, Gosling JP, Fottrell PF, Kane M, Murphy N, Long M, Fitzgerald D, O’Fegan P, O’Doherty A, Forde T, Molloy G, Dawson MA, Maher M, Houghton JA, Mccole JC, Moran AP, O/rsmalley DT, Helander IM, Lindner B, Callaghan GA, Mcclorey MB, Hannigan BM, Gilmore WS, Allen JM, Whelton HJ, Dowdall D, Dawson M, Smith T, Whelton H, O≿doherty A, Mccusker J, Joyce KM, Mlay P, Leek BF, Clements BA, Grimes F, Walsh DM, Baxter GD, Toussi H, Lagan KM, Ashford R. Royal academy of medicine in ireland section of biomedical sciences. Ir J Med Sci 1996. [DOI: 10.1007/bf02940256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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167
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Zhou X, Yang Z, Long M. [Monocellular quantitative study on the adhesive ability of eosinophils in the course of eosinophils activation]. ZHONGHUA JIE HE HE HU XI ZA ZHI = ZHONGHUA JIEHE HE HUXI ZAZHI = CHINESE JOURNAL OF TUBERCULOSIS AND RESPIRATORY DISEASES 1996; 19:147-8. [PMID: 9387483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To observe the dynamic changes of eosinophils (EOS) adhesive ability in the course of eosinophils activation. METHODS The adhesive ability EOS to vascular endothelial cell (EC) was measured by the use of a microminpulation technique. RESULTS The critical separation stress (Sc) between rest EOS and EC was 0.61 +/- 0.07kPa. Treatment of EOS with platelet activaty factor (PAF) caused a significant increase in Sc. The Sc was 4.1 +/- 0.6kPa within 30 minutes of EOS exposure to PAF, and had no tendency to increase continuously by exposure time prolonged. CONCLUSIONS The increase of EOS adhesive ability belongs to a kind of rapid response while EOS is activated. The increase could be an important basis of EOS adhesion to EC and EOS entry into bronchial mucosa.
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Abstract
In one scenario of gene evolution, exon shuffling has a fundamental role in increasing gene diversity. As DNA sequences accumulate in the databases, the picture of the intron/exon structures of genes becomes more and more clear. We discuss in this review some features of this picture that suggest that introns have been present since the early stages of evolution, and that exon shuffling was a fundamental process in the construction of ancient as well as modern genes.
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169
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Long M, Rosenberg C, Gilbert W. Intron phase correlations and the evolution of the intron/exon structure of genes. Proc Natl Acad Sci U S A 1995; 92:12495-9. [PMID: 8618928 PMCID: PMC40384 DOI: 10.1073/pnas.92.26.12495] [Citation(s) in RCA: 186] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Two issues in the evolution of the intron/exon structure of genes are the role of exon shuffling and the origin of introns. Using a large data base of eukaryotic intron-containing genes, we have found that there are correlations between intron phases leading to an excess of symmetric exons and symmetric exon sets. We interpret these excesses as manifestations of exon shuffling and make a conservative estimate that at least 19% of the exons in the data base were involved in exon shuffling, suggesting an important role for exon shuffling in evolution. Furthermore, these excesses of symmetric exons appear also in those regions of eukaryotic genes that are homologous to prokaryotic genes: the ancient conserved regions. This last fact cannot be explained in terms of the insertional theory of introns but rather supports the concept that some of the introns were ancient, the exon theory of genes.
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Abstract
The origin and evolution of intron-exon structures continue to be controversial topics. Two alternative theories, the 'exon theory of genes' and the 'insertional theory of introns', debate the presence or absence of introns in primordial genes. Both sides of the argument have focused on the positions of introns with respect to protein and gene structures. A new approach has emerged in the study of the evolution of intron-exon structures: a population analysis of genes. One example is the statistical analysis of intron phases--the position of introns within or between codons. This analysis detected a significant signal of exon shuffling in the DNA sequence database containing both ancient and modern exon sequences: intron phase correlations, that is, the association together within genes of introns of the same phase. The results of this analysis suggest that exon shuffling played an important role in the origin of both ancient and modern genes.
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171
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Lee MH, Long M. Off-diagonal long-range order, pair distribution function, and structure factor of the ideal Fermi gas in D dimensions and Price's inequality. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 52:189-195. [PMID: 9963419 DOI: 10.1103/physreve.52.189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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172
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Meert KL, Long M, Kaplan J, Sarnaik AP. Alterations in immune function following head injury in children. Crit Care Med 1995; 23:822-8. [PMID: 7736738 DOI: 10.1097/00003246-199505000-00008] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE To investigate cellular and humoral immunity in children immediately after severe head injury and during the early recovery period. DESIGN Prospective, observational study with factorial design. SETTING Pediatric ICU of a university teaching hospital. PATIENTS Fifteen children (median age 9.6 yrs, range 1.7 to 18) with head injury and Glasgow Coma Score of < or = 7. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Skin testing with seven standard antigens was performed and blood samples were obtained for the following measurements: total lymphocyte count and subsets; proliferative response to phytohemagglutinin, concanavalin A, and pokeweed mitogen; and immunoglobulin concentrations on days 1, 7, and 14 and 3 months after injury. The effect of patient plasma on phytohemagglutinin-induced proliferative responses of normal donor lymphocytes was also assessed at these times. Anergy was present in 71% of patients on day 1, 54% of patients on day 7, 31% of patients on day 14, and 18% of patients at 3 months. Total, helper, and suppressor T-cell counts were decreased on day 1, and the T-cell response to phytohemagglutinin was decreased on days 1, 7, and 14 compared with values at 3 months. B-cell counts were increased on day 1, followed by an increase in serum immunoglobulin concentrations 1 to 2 wks later. The B-cell response to pokeweed mitogen was unchanged over the 3-month study period. The phytohemagglutinin responses of normal donor lymphocytes were decreased when incubated with patient plasma obtained on day 7 after injury. CONCLUSIONS Severe head injury in children is associated with depressed cell-mediated immunity. Plasma immunosuppressive factors may contribute to T-cell dysfunction.
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Feeney T, O’Muire O, Gilmartin JJ, Manning P, Sinclair H, Clancy L, O’Connell F, Springall DR, Polak JM, Thomas VE, Fuller RW, Pride NB, Lyons RA, Leonard C, Faul J, Tormey VJ, Poulter LW, Burke CM, Pathmakanthan S, Barry MC, Wang JH, Kelly CJ, Burke PE, Sheehan SJ, Redmond HP, Bouchier-Hayes D, Abdih H, Watson RWG, Burke P, Egan JJ, Barber L, Lomax J, Fox A, Craske J, Yonan N, Rahman AN, Deiraniya AK, Carroll KB, Turner A, Woodcock AA, McNeill K, Bookless B, Gould K, Corris P, Higgenbottam T, Webb A, Woodcock A, McManus K, Miller D, Allen M, Ilstrup D, Deschamps C, Trastek V, Pairolero P, Cotter TP, Vaughan C, Kealy WP, Duggan PF, Curtain A, Bredin CP, Waite A, Maguire CP, Ryan J, O’Neill D, Coakley D, Walsh JB, Kilgallen I, O’Neill S, Ryan M, O’Connor CM, McDonnell T, Lowry RC, Buick JB, Magee TRA, O’Riordan D, Hayes J, O’Connor C, FitzGerald MX, Cosgrave C, Costello C, Deegan PC, McNicholas WT, Nugent AM, Lyons J, Gleadhill I, MacMahon J, Stevenson EC, Heaney LG, Shields MD, Cadden IS, Taylor R, Ennis M, Kharitonov SA, O’Connor J, Owens WA, O’Kane H, Cleland J, Gladstone DJ, Sarsam M, Graham ANJ, Anikin V, McGuigan JA, Curry RC, Varghese G, Keelan P, Rutherford R, O’Keeffe D, McCarthy P, Gilmartin JJ, Moore H, Balbernie E, Gilmartin JJ, Coakley R, Keane M, Costello R, Byrne P, McKeogh D, McLoughlin P, Finlay G, Concannon D, McKeown D, Kelly P, Tanner WA, Bouchier-Hayes DJ, Arumugasamy M, Yacoub K, O’Leary G, Stokes K, Geraghty J, Osborne H, O’Dwyer R, Gilliland R, Saleem SM, Aherne T, Power CK, Burke CH, Byrne A, Murphy JFA, Sharkey R, Mulloy E, Sharkey K, Long M, Birchall MA, Moorat A, Henderson J, Jacques L, Cahill P, Condron C, Royston D, Murphy J, Neill SO. Irish Thoracic Society. Ir J Med Sci 1995. [DOI: 10.1007/bf02973289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
BACKGROUND Colonization of patients' mechanical ventilation bags was examined to evaluate two criteria (days in use and appearance) for replacing the disposable adapter that interfaces with the patient. METHODS Adapters used 1 to 2, 3 to 4 and 6 to 7 days formed groups I, II, and III, respectively (n = 29 to 67 per group). Another group (IA) contained 33 adapters used 1 to 2 days from patients intubated at least 7 days. Appearance of adapters was noted and adapters were swab cultured on nonselective medium. RESULTS Analysis of variance indicated a difference in log colony-forming units per adapter between groups I and II (p = 0.032), but colony-forming units per adapter varied widely. Group III had a lower mean colony-forming unit count than group II. Groups I and II differed in variables other than days of use, but these confounding variables were eliminated by substituting group IA for group I. When adapter appearance versus colonization was examined by chi 2 test, a significant difference was found between adapters that looked "clean" and those with precipitate or with mucus or blood. CONCLUSIONS For the subjects studied, colonization of adapters increased significantly between 1 to 2 and 3 to 4 days of use but varied widely. Appearance may be more useful than days in use as a criterion for changing adapters.
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Gerety MB, Williams JW, Mulrow CD, Cornell JE, Kadri AA, Rosenberg J, Chiodo LK, Long M. Performance of case-finding tools for depression in the nursing home: influence of clinical and functional characteristics and selection of optimal threshold scores. J Am Geriatr Soc 1994; 42:1103-9. [PMID: 7930337 DOI: 10.1111/j.1532-5415.1994.tb06217.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVE To compare case-finding tools for depression in the nursing home setting and to evaluate effects of subject function, cognition, and disease number on test performance. DESIGN Cross-sectional survey. SETTING One academic and four community homes. SUBJECTS One hundred thirty-four randomly selected, mildly cognitively impaired, functionally dependent residents. METHODS AND MEASURES The Geriatric Depression Scale (GDS), Short Geriatric Depression Scale (SGDS), Center for Epidemiologic Studies Depression Scale (CES-D), and Brief Carrol Depression Rating Scale (BCDRS) were administered. The Structured Clinical Interview for DSM-III-R diagnoses was administered independently,. Operating characteristics and the effects of subject characteristics on test performance were evaluated using McNemar's test and logistic regression. Selection of "optimal" threshold scores was guided by Kraemer's quality indices and clinical judgment. RESULTS Thirty-five subjects (26%) had major depression. No differences were found among the instruments in sensitivity (range 0.74-0.89), specificity (range 0.62-0.77), or area under the receiver operating curve (ROC) (range 0.85-0.91). Resident characteristics did not affect test performance. Quality indices showed the GDS and BCDRS met criteria for moderate to substantial agreement with the criterion standard, whereas the SGDS and the CES-D achieved only fair agreement. No change in threshold scores was warranted. CONCLUSIONS The GDS and BCDRS performed well in the nursing home. As the GDS can serve as a both a case-finding and severity instrument, it is preferred. Use of brief, interviewer-administered tools may improve detection of depression in the nursing home.
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