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Baudains TP, Lloyd P. Habituation and habitat changes can moderate the impacts of human disturbance on shorebird breeding performance. Anim Conserv 2007. [DOI: 10.1111/j.1469-1795.2007.00126.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Derse D, Hill SA, Princler G, Lloyd P, Heidecker G. Resistance of human T cell leukemia virus type 1 to APOBEC3G restriction is mediated by elements in nucleocapsid. Proc Natl Acad Sci U S A 2007; 104:2915-20. [PMID: 17299050 PMCID: PMC1815281 DOI: 10.1073/pnas.0609444104] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human T cell leukemia virus type 1 (HTLV-1) has evolved a remarkable strategy to thwart the antiviral effects of the cellular cytidine deaminase APOBEC3G (hA3G). HTLV-1 infects T lymphocytes in vivo, where, like HIV-1, it is likely to encounter hA3G. HIV-1 counteracts the innate antiviral activity of hA3G by producing an accessory protein, Vif, which hastens the degradation of hA3G. In contrast, HTLV-1 does not encode a Vif homologue; instead, HTLV-1 has evolved a cis-acting mechanism to prevent hA3G restriction. We demonstrate here that a peptide motif in the C terminus of the HTLV-1 nucleocapsid (NC) domain inhibits hA3G packaging into nascent virions. Mutation of amino acids within this region resulted in increased levels of hA3G incorporation into virions and increased susceptibility to hA3G restriction. Elements within the C-terminal extension of the NC domain are highly conserved among the primate T cell leukemia viruses, but this extension is absent in all other retroviral NC proteins.
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Mitchell MS, Bodine ET, Hill S, Princler G, Lloyd P, Mitsuya H, Matsuoka M, Derse D. Phenotypic and genotypic comparisons of human T-cell leukemia virus type 1 reverse transcriptases from infected T-cell lines and patient samples. J Virol 2007; 81:4422-8. [PMID: 17287279 PMCID: PMC1900182 DOI: 10.1128/jvi.02660-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is well established that cell-free infection with human T-cell leukemia virus type 1 (HTLV-1) is less efficient than that with other retroviruses, though the specific infectivities of only a limited number of HTLV-1 isolates have been quantified. Earlier work indicated that a post-entry step in the infectious cycle accounted for the poor cell-free infectivity of HTLV-1. To determine whether variations in the pol gene sequence correlated with virus infectivity, we sequenced and phenotypically tested pol genes from a variety of HTLV-1 isolates derived from primary sources, transformed cell lines, and molecular clones. The pol genes and deduced amino acid sequences from 23 proviruses were sequenced and compared with 14 previously published sequences, revealing a limited number of amino acid variations among isolates. The variations appeared to be randomly dispersed among primary isolates and proviruses from cell lines and molecular clones. In addition, there was no correlation between reverse transcriptase sequence and the disease phenotype of the original source of the virus isolate. HTLV-1 pol gene fragments encoding reverse transcriptase were amplified from a variety of isolates and were subcloned into HTLV-1 vectors for both single-cycle infection and spreading-infection assays. Vectors carrying pol genes that matched the consensus sequence had the highest titers, and those with the largest number of variations from the consensus had the lowest titers. The molecular clone from CS-1 cells had four amino acid differences from the consensus sequence and yielded infectious titers that were approximately eight times lower than those of vectors encoding a consensus reverse transcriptase.
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Lloyd P, Freebairn R. Using quantitative acid-base analysis in the ICU. CRIT CARE RESUSC 2006; 8:19-30. [PMID: 16536715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Accepted: 11/09/2005] [Indexed: 05/07/2023]
Abstract
The quantitative acid-base 'Strong Ion' calculator is a practical application of quantitative acid-base chemistry, as developed by Peter Stewart and Peter Constable. It quantifies the three independent factors that control acidity, calculates the concentration and charge of unmeasured ions, produces a report based on these calculations and displays a Gamblegram depicting measured ionic species. Used together with the medical history, quantitative acid-base analysis has advantages over traditional approaches.
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Martin TE, Bassar RD, Bassar SK, Fontaine JJ, Lloyd P, Mathewson HA, Niklison AM, Chalfoun A. Life-history and ecological correlates of geographic variation in egg and clutch mass among passerine species. Evolution 2006; 60:390-8. [PMID: 16610329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Broad geographic patterns in egg and clutch mass are poorly described, and potential causes of variation remain largely unexamined. We describe interspecific variation in avian egg and clutch mass within and among diverse geographic regions and explore hypotheses related to allometry, clutch size, nest predation, adult mortality, and parental care as correlates and possible explanations of variation. We studied 74 species of Passeriformes at four latitudes on three continents: the north temperate United States, tropical Venezuela, subtropical Argentina, and south temperate South Africa. Egg and clutch mass increased with adult body mass in all locations, but differed among locations for the same body mass, demonstrating that egg and clutch mass have evolved to some extent independent of body mass among regions. A major portion of egg mass variation was explained by an inverse relationship with clutch size within and among regions, as predicted by life-history theory. However, clutch size did not explain all geographic differences in egg mass; eggs were smallest in South Africa despite small clutch sizes. These small eggs might be explained by high nest predation rates in South Africa; life-history theory predicts reduced reproductive effort under high risk of offspring mortality. This prediction was supported for clutch mass, which was inversely related to nest predation but not for egg mass. Nevertheless, clutch mass variation was not fully explained by nest predation, possibly reflecting interacting effects of adult mortality. Tests of the possible effects of nest predation on egg mass were compromised by limited power and by counterposing direct and indirect effects. Finally, components of parental investment, defined as effort per offspring, might be expected to positively coevolve. Indeed, egg mass, but not clutch mass, was greater in species that shared incubation by males and females compared with species in which only females incubate eggs. However, egg and clutch mass were not related to effort of parental care as measured by incubation attentiveness. Ecological and life-history correlates of egg and clutch mass variation found here follow from theory, but possible evolutionary causes deserve further study.
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Martin TE, Bassar RD, Bassar SK, Fontaine JJ, Lloyd P, Mathewson HA, Niklison AM, Chalfoun A. LIFE-HISTORY AND ECOLOGICAL CORRELATES OF GEOGRAPHIC VARIATION IN EGG AND CLUTCH MASS AMONG PASSERINE SPECIES. Evolution 2006. [DOI: 10.1111/j.0014-3820.2006.tb01115.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Martin TE, Bassar RD, Bassar SK, Fontaine JJ, Lloyd P, Mathewson HA, Niklison AM, Chalfoun A. LIFE-HISTORY AND ECOLOGICAL CORRELATES OF GEOGRAPHIC VARIATION IN EGG AND CLUTCH MASS AMONG PASSERINE SPECIES. Evolution 2006. [DOI: 10.1554/05-429.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lloyd P. Strong ion gap or net unmeasured ions? CRIT CARE RESUSC 2005; 7:64. [PMID: 16548825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
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Yuen CT, Storring PL, Tiplady RJ, Izquierdo M, Wait R, Gee CK, Gerson P, Lloyd P, Cremata JA. Relationships Between the N-Glycan Structures and Biological Activities Of Recombinant Human Erythropoietins Produced Using Different Culture Conditions and Purification Procedures. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2005; 564:141-2. [PMID: 16400821 DOI: 10.1007/0-387-25515-x_25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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Lloyd P. Strong ion calculator--a practical bedside application of modern quantitative acid-base physiology. CRIT CARE RESUSC 2004; 6:285-94. [PMID: 16556109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2004] [Accepted: 07/19/2004] [Indexed: 05/08/2023]
Abstract
OBJECTIVE To review acid-base balance by considering the physical effects of ions in solution and describe the use of a calculator to derive the strong ion difference and Atot and strong ion gap. DATA SOURCES A review of articles reporting on the use of strong ion difference and Atot in the interpretation of acid base balance. SUMMARY OF REVIEW Tremendous progress has been made in the last decade in our understanding of acid-base physiology. We now have a quantitative understanding of the mechanisms underlying the acidity of an aqueous solution. We can now predict the acidity given information about the concentration of the various ion-forming species within it. We can predict changes in acid-base status caused by disturbance of these factors, and finally, we can detect unmeasured anions with greater sensitivity than was previously possible with the anion gap, using either arterial or venous blood sampling. Acid-base interpretation has ceased to be an intuitive and arcane art. Much of it is now an exact computation that can be automated and incorporated into an online hospital laboratory information system. CONCLUSIONS All diseases and all therapies can affect a patient's acid-base status only through the final common pathway of one or more of the three independent factors. With Constable's equations we can now accurately predict the acidity of plasma. When there is a discrepancy between the observed and predicted acidity we can deduce the net concentration of unmeasured ions to account for the difference.
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Derse D, Heidecker G, Mitchell M, Hill S, Lloyd P, Princler G. Infectious transmission and replication of human T-cell leukemia virus type 1. FRONT BIOSCI-LANDMRK 2004; 9:2495-9. [PMID: 15353302 DOI: 10.2741/1411] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Retrovirus infection proceeds by attachment of the envelope glycoprotein to a cell surface receptor, followed by fusion of the viral and cellular membranes. Once in the cell, the viral enzymes and structural proteins form a replication complex that converts the single-stranded viral genomic RNA into a double-stranded DNA, which is then integrated into the host cell chromosome. For HTLV-1, these events are not well characterized. We have developed cell culture systems, infectious molecular clones, and viral vectors that can be used to characterize the mechanisms of HTLV-1 infection and replication. Infection with cell-free HTLV-1 virions is orders of magnitude less efficient compared with other retroviruses. This inefficiency is the result of a block in the replication process after the virion is bound to the cell surface. We are determining whether this block is conferred by the viral replication enzymes, results from the actions of cellular restriction factors, reflects the need for cell-cell contact, or is caused by a combination of these factors.
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Lloyd P. Wave propagation through an assembly of spheres: III. The density of states in a liquid. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0370-1328/90/1/324] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lloyd P, Berry MV. Wave propagation through an assembly of spheres: IV. Relations between different multiple scattering theories. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0370-1328/91/3/321] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lloyd P. Wave propagation through an assembly of spheres: II. The density of single-particle eigenstates. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0370-1328/90/1/323] [Citation(s) in RCA: 277] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Barclay JA, Don CG, Lloyd P, Osborne CF, Wilson GVH. Single and multiple passage resonance studies of 60Co nuclei oriented in iron. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0305-4608/1/6/330] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Lloyd P. The x ray spectra and the response of conduction electrons to a potential change: The phase-shift operator approach. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0305-4608/1/5/326] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Lloyd P, Sholl CA. A structural expansion of the cohesive energy of simple metals in an effective Hamiltonian approximation. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0022-3719/1/6/319] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lloyd P. Exactly solvable model of electronic states in a three-dimensional disordered Hamiltonian: non-existence of localized states. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0022-3719/2/10/303] [Citation(s) in RCA: 276] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Cox BN, Coulthard MA, Lloyd P. A calculation of the Coulomb correlation energy, U, for transition metals in Hubbard's model. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0305-4608/4/6/009] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Lloyd P, Oglesby J. The asymptotically exact form of the multi-ion interaction in metals. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0305-4608/3/9/010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Oglesby J, Lloyd P. Some single-site structure-independent approximations in condensed materials. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0022-3719/9/15/010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Cragg DM, Lloyd P. Universality and the renormalisability of rotationally invariant Kondo Hamiltonians. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0022-3719/12/16/018] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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