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Abstract
Double-strand breaks and other lesions in DNA can stimulate homologous genetic recombination in two quite different ways: by promoting recombination near the break (roughly within a kb) or far from the break. Recent emphasis on the repair aspect of recombination has focused attention on DNA interactions and recombination near breaks. Here I review evidence for recombination far from DNA breaks in bacteria and fungi and discuss mechanisms by which this can occur. These mechanisms include entry of a traveling entity ("recombination machine") at a break, formation of long heteroduplex DNA, priming of DNA replication by a broken end, and induction of recombination potential in trans. Special emphasis is placed on contrasting views of how the RecBCD enzyme of Escherichia coli promotes recombination far (tens of kb) from a double-strand break. The occurrence of recombination far from DNA breaks and of correlated recombination events far apart suggests that "action at a distance" during recombination is a widespread feature among diverse organisms.
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Mizuno K, Hasemi T, Ubukata T, Yamada T, Lehmann E, Kohli J, Watanabe Y, Iino Y, Yamamoto M, Fox ME, Smith GR, Murofushi H, Shibata T, Ohta K. Counteracting regulation of chromatin remodeling at a fission yeast cAMP response element-related recombination hotspot by stress-activated protein kinase, cAMP-dependent kinase and meiosis regulators. Genetics 2001; 159:1467-78. [PMID: 11779789 PMCID: PMC1461918 DOI: 10.1093/genetics/159.4.1467] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In fission yeast, an ATF/CREB-family transcription factor Atf1-Pcr1 plays important roles in the activation of early meiotic processes via the stress-activated protein kinase (SAPK) and the cAMP-dependent protein kinase (PKA) pathways. In addition, Atf1-Pcr1 binds to a cAMP responsive element (CRE)-like sequence at the site of the ade6-M26 mutation, which results in local enhancement of meiotic recombination and chromatin remodeling. Here we studied the roles of meiosis-inducing signal transduction pathways in M26 chromatin remodeling. Chromatin analysis revealed that persistent activation of PKA in meiosis inhibited M26 chromatin remodeling, suggesting that the PKA pathway represses M26 chromatin remodeling. The SAPK pathway activated M26 chromatin remodeling, since mutants lacking a component of this pathway, the Wis1 or Spc1/Sty1 kinases, had no M26 chromatin remodeling. M26 chromatin remodeling also required the meiosis regulators Mei2 and Mei3 but not the subsequently acting regulators Sme2 and Mei4, suggesting that induction of M26 chromatin remodeling needs meiosis-inducing signals before premeiotic DNA replication. Similar meiotic chromatin remodeling occurred meiotically around natural M26 heptamer sequences. These results demonstrate the coordinated action of genetic and physiological factors required to remodel chromatin in preparation for high levels of meiotic recombination and eukaryotic cellular differentiation.
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Tieleman DP, Biggin PC, Smith GR, Sansom MS. Simulation approaches to ion channel structure-function relationships. Q Rev Biophys 2001; 34:473-561. [PMID: 11852594 DOI: 10.1017/s0033583501003729] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
1. Introduction 4751.1 Ion channels 4751.1.1 Gramicidin 4761.1.2 Helix bundle channels 4771.1.3 K channels 4801.1.4 Porins 4831.1.5 Nicotinic acetylcholine receptor 4831.1.6 Physiological properties 4831.2 Simulations 4841.2.1 Atomistic versus mean-field simulations 4842. Atomistic simulations 4852.1 Modelling of ion-interaction parameters 4852.1.1 Interatomic distances and the problem of ionic radii 4862.1.2 Solvation energy 4872.1.3 Hydration shells and coordination numbers 4892.1.4 Parameters in common use and transferability 4912.1.5 Summary 4912.2 Water in pores versus bulk 4912.2.1 Simple pore models 4942.2.2 gA 4952.2.3 Alm 4962.2.4 LS36 (and LS24) 4962.2.5 Nicotinic receptor M2δ5 4972.2.6 Influenza A M2 4972.2.7 K channels 4972.2.8 nAChR 4982.2.9 Porins 4982.2.10 Relevance 4992.2.11 Problems with simulations 5012.3 Dynamics of ions in pores 5032.3.1 Simple pore models 5032.3.2 Helix bundles 5042.3.3 gA and KcsA 5052.4 Energetics of permeation and ion selectivity 5092.4.1 Potential and free energy profiles 5092.4.2 gA 5102.4.3 α-Helix bundles 5112.4.4 KcsA 5122.4.5 Ion selectivity 5142.4.6 Problems of estimating energetic profiles 5152.5 Conformational changes 5162.5.1 gA 5162.5.2 Alm and LS3 5162.5.3 KcsA 5172.6 Protonation states 5233. Coarse-grained simulations 5243.1 Introduction 5243.1.1 Predicting conductance magnitudes 5253.2 Electro-diffusion: the Nernst–Planck approach 5263.2.1 Calculating the potential profile from Poisson and PB theory 5283.2.2 Calculating the potential profile from BD simulations 5303.2.3 Combining Nernst–Planck and Poisson: PNP 5303.3 Beyond PNP 5323.4 BD simulations 5323.4.1 Basic theory in ion channels 5323.4.2 Incorporating the environment 5333.5 Applications 5353.5.1 Model systems 5353.5.1.1 Solving the Poisson and PB equation for channel-like geometries 5353.5.1.2 Comparing PB, PNP and BD 5363.5.2 Applications to known structures 5373.5.2.1 gA 5373.5.2.2 Porin 5393.5.2.3 LS3 5403.5.2.4 Alm 5423.5.2.5 nAChR 5423.5.2.6 KcsA 5433.6 pKa calculations 5433.7 Selectivity 5443.7.1 Anion/cation selectivity 5453.7.2 Monovalent/divalent ion selectivity 5454. Problems 5464.1 Atomistic simulations 5464.1.1 Problems 5464.1.2 Parameters 5484.2 BD 5494.3 Mean-field simulations 5495. Conclusions 5505.1 Progress 5505.2 The future 5506. Acknowledgements 5517. References 551Ion channels are proteins that form ‘holes’ in membranes through which selected ions move
passively down their electrochemical gradients. The ions move quickly, at (nearly) diffusion
limited rates (ca. 107 ions s−1 per channel). Ion channels are central to many properties of cell
membranes. Traditionally they have been the concern of neuroscientists, as they control the
electrical properties of the membranes of excitable cells (neurones, muscle; Hille, 1992).
However, it is evident that ion channels are present in many types of cell, not all of which
are electrically excitable, from diverse organisms, including plants, bacteria and viruses
(where they are involved in functions such as cell homeostasis) in addition to animals. Thus
ion channels are of general cell biological importance. They are also of biomedical interest,
as several dizeases (‘channelopathies’) have been described which are caused by changes in
properties of a specific ion channel (Ashcroft, 2000). Moreover, passive diffusion channels for
substances other than ions are common (porins, aquaporins), as are active membrane
transport processes coupled to ion gradients or ATP hydrolysis. An understanding of ion
channels may also provide a gateway to understanding these processes.
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Smith GR. Effects of acute exposure to a commercial formulation of glyphosate on the tadpoles of two species of anurans. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2001; 67:483-8. [PMID: 11779061 DOI: 10.1007/s001280149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Ranatunga KM, Law RJ, Smith GR, Sansom MS. Electrostatics studies and molecular dynamics simulations of a homology model of the Shaker K+ channel pore. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2001; 30:295-303. [PMID: 11548132 DOI: 10.1007/s002490100134] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A homology model of the pore domain of the Shaker K+ channel has been constructed using a bacterial K+ channel, KcsA, as a template structure. The model is in agreement with mutagenesis and sequence variability data. A number of structural features are conserved between the two channels, including a ring of tryptophan sidechains on the outer surface of the pore domain at the extracellular end of the helix bundle, and rings of acidic sidechains close to the extracellular mouth of the channel. One of these rings, that formed by four Asp447 sidechains at the mouth of the Shaker pore, is shown by pK(A) calculations to be incompletely ionized at neutral pH. The potential energy profile for a K+ ion moved along the central axis of the Shaker pore domain model selectivity filter reveals a shallow well, the depth of which is modulated by the ionization state of the Asp447 ring. This is more consistent with the high cation flux exhibited by the channel in its conductance value of 19 pS.
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Kramer TL, Evans RB, Landes R, Mancino M, Booth BM, Smith GR. Comparing outcomes of routine care for depression: the dilemma of case-mix adjustment. J Behav Health Serv Res 2001; 28:287-300. [PMID: 11497024 DOI: 10.1007/bf02287245] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The purpose of this study was to formulate and test two case-mix models for depression treatment that permit comparisons of patient outcomes across diverse clinical settings. It assessed demographics; eight, diagnostic-specific, case-mix variables; and clinical status at baseline and follow-up for 187 patients. Regressions were performed to test two models for four dependent variables including depression severity and diagnosis. Individual treatment settings were then ranked based on a comparison of actual versus predicted outcomes using regression coefficients and predictor variables. A model inclusive of baseline physical health status and depression severity predicted depression severity, mental health, and physical health functioning at follow-up. A simpler model performed well in predicting depression remission. This study identifies variables to be included in case-mix adjustment models and demonstrates statistical methods to control for differences across settings when comparing depression outcomes.
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82
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Davis L, Smith GR. Meiotic recombination and chromosome segregation in Schizosaccharomyces pombe. Proc Natl Acad Sci U S A 2001; 98:8395-402. [PMID: 11459981 PMCID: PMC37449 DOI: 10.1073/pnas.121005598] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In most organisms homologous recombination is vital for the proper segregation of chromosomes during meiosis, the formation of haploid sex cells from diploid precursors. This review compares meiotic recombination and chromosome segregation in the fission yeast Schizosaccharomyces pombe and the distantly related budding yeast Saccharomyces cerevisiae, two especially tractable microorganisms. Certain features, such as the occurrence of DNA breaks associated with recombination, appear similar, suggesting that these features may be common in eukaryotes. Other features, such as the role of these breaks and the ability of chromosomes to segregate faithfully in the absence of recombination, appear different, suggesting multiple solutions to the problems faced in meiosis.
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Rost K, Williams C, Wherry J, Smith GR. The process and outcomes of care for major depression in rural family practice settings. J Rural Health 2001; 11:114-21. [PMID: 10143272 DOI: 10.1111/j.1748-0361.1995.tb00404.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although primary care physicians provide the majority of care for rural residents with major depression, little is known about the quality of the care they provide. The aim of this study was to characterize the process and outcomes of care for rural patients with major depression, and to examine the relationship between the process and outcomes of care in this population. Six hundred and thirty-one patients in 21 primary care practices in small towns were screened; 47 patients (7.4% of patients screened) meeting DSM-III-R criteria for current major depression were recruited into the study, and 38 (81.0% of patients recruited) were followed an average of five months later using the Depression Outcomes Module (Rost, Smith, Burnam, & Burns, 1992). While 24 (63.1%) of the 38 depressed subjects received a prescription for one or more antidepressants between the index visit and follow-up, only 11 (28.9%) received pharmacologic treatment in concordance with the new Agency for Health Care Policy and Research (AHCPR) guidelines; 26 (68.4%) of 38 depressed patients continued to meet criteria for major depression at five months. Those who received pharmacologic treatment concordant with AHCPR guidelines showed more improvement at follow-up. The findings suggest that outcomes for major depression may be worse in rural family practice settings than in urban settings. The study also demonstrates that AHCPR guidelines define effective treatment for major depression in the study sample. The Depression Outcomes Module appears to be a reliable and valid instrument for monitoring the outcomes of care for major depression in family practice settings.
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84
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Buckley SL, Smith GR, Sponseller PD, Thompson JD, Robertson WW, Griffin PP. Severe (type III) open fractures of the tibia in children. J Pediatr Orthop 2001; 16:627-34. [PMID: 8865049 DOI: 10.1097/00004694-199609000-00015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Twenty children with acute type III open fractures of the tibial metaphyses or diaphysis were retrospectively studied. The average age was 9 years, 1 month (range, 2 years, 11 months to 16 years, 2 months). There were seven type IIIA fractures, 10 type IIIB fractures, and 3 type IIIC fractures. All fractures were irrigated and debrided, and prophylactic antibiotics were given for a minimum of 48 h. Fifteen fractures were initially treated with external fixation, three with casts, one with internal fixation, and one with a combination of external fixation and limited internal fixation. Free muscle flaps were used for soft-tissue coverage in six patients, and a local muscle flap in one patient. The average time to fracture healing was 29 weeks, and the median time to fracture healing was 20 weeks (range, 8-104). Four patients had delayed union, and two additional patients had nonunion. Both patients with nonunion were successfully treated with autologous bone grafting. The time to fracture union was related to the severity of soft-tissue injury, fracture configuration, segmental bone loss, and infection. Osteomyelitis developed in three patients. All were successfully treated. Two patients treated with external fixation had leg-length discrepancies of > 1 cm, with the injured extremity longer in both cases. There were no late amputations. Children with severe open fractures of the tibia have a good prognosis for limb salvage with aggressive wound care and fracture management.
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85
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Robbins JM, Taylor JL, Rost KM, Burns BJ, Phillips SD, Burnam MA, Smith GR. Measuring outcomes of care for adolescents with emotional and behavioral problems. J Am Acad Child Adolesc Psychiatry 2001; 40:315-24. [PMID: 11288773 DOI: 10.1097/00004583-200103000-00011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OBJECTIVES To validate the prototype Adolescent Treatment Outcomes Module (ATOM), examine its sensitivity to clinical change, and determine its feasibility for administration in routine clinical settings. METHOD A sample of 67 adolescents, aged 11 through 18, was selected from new patients at two inpatient and two outpatient mental health programs. Adolescents and parents completed the ATOM and validating instruments at intake, 1 week postintake, and again at 6 months. RESULTS Nine self-report symptoms predicted positive diagnoses of oppositional defiant, conduct, anxiety, and depressive disorders on the basis of structured diagnoses, with sensitivities of 0.7 to 0.8. Test-retest correlations for outcome scales were largely excellent (>0.70). Scales that measured functioning at home, in school, and in the community were moderately correlated in the expected direction with global functioning. Decreases in symptom severity and functional impairment were generally associated with decreases in validating instruments. Administration time averaged 25 minutes for adolescents and 28 minutes for parents. CONCLUSIONS Both parents and adolescents readily completed the ATOM. Module scales demonstrated excellent reliability and good to fair concurrent validity. The ATOM was able to detect change and its absence.
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86
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Ranatunga KM, Shrivastava IH, Smith GR, Sansom MS. Side-chain ionization states in a potassium channel. Biophys J 2001; 80:1210-9. [PMID: 11222285 PMCID: PMC1301316 DOI: 10.1016/s0006-3495(01)76097-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
KcsA is a bacterial K+ channel that is gated by pH. Continuum dielectric calculations on the crystal structure of the channel protein embedded in a low dielectric slab suggest that side chains E71 and D80 of each subunit, which lie adjacent to the selectivity filter region of the channel, form a proton-sharing pair in which E71 is neutral (protonated) and D80 is negatively charged at pH 7. When K+ ions are introduced into the system at their crystallographic positions the pattern of proton sharing is altered. The largest perturbation is for a K+ ion at site S3, i.e., interacting with the carbonyls of T75 and V76. The presence of multiple K+ ions in the filter increases the probability of E71 being ionized and of D80 remaining neutral (i.e., protonated). The ionization states of the protein side chains influence the potential energy profile experienced by a K+ ion as it is translated along the pore axis. In particular, the ionization state of the E71-D80 proton-sharing pair modulates the shape of the potential profile in the vicinity of the selectivity filter. Such reciprocal effects of ion occupancy on side-chain ionization states, and of side-chain ionization states on ion potential energy profiles will complicate molecular dynamics simulations and related studies designed to calculate ion permeation energetics.
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87
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Biggin PC, Smith GR, Shrivastava I, Choe S, Sansom MS. Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1510:1-9. [PMID: 11342142 DOI: 10.1016/s0005-2736(00)00345-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have performed simulations of both a single potassium ion and a single sodium ion within the pore of the bacterial potassium channel KcsA. For both ions there is a dehydration energy barrier at the cytoplasmic mouth suggesting that the crystal structure is a closed conformation of the channel. There is a potential energy barrier for a sodium ion in the selectivity filter that is not seen for potassium. Radial distribution functions for both ions with the carbonyl oxygens of the selectivity filter indicate that sodium may interact more tightly with the filter than does potassium. This suggests that the key to the ion selectivity of KcsA is the greater dehydration energy of Na(+) ions, and helps to explain the block of KcsA by internal Na(+) ions.
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88
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Fischer WB, Pitkeathly M, Wallace BA, Forrest LR, Smith GR, Sansom MS. Transmembrane peptide NB of influenza B: a simulation, structure, and conductance study. Biochemistry 2000; 39:12708-16. [PMID: 11027151 DOI: 10.1021/bi001000e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The putative transmembrane segment of the ion channel forming peptide NB from influenza B was synthesized by standard solid-phase peptide synthesis. Insertion into the planar lipid bilayer revealed ion channel activity with conductance levels of 20, 61, 107, and 142 pS in a 0.5 M KCl buffer solution. In addition, levels at -100 mV show conductances of 251 and 413 pS. A linear current-voltage relation reveals a voltage-independent channel formation. In methanol and in vesicles the peptide appears to adopt an alpha-helical-like structure. Computational models of alpha-helix bundles using N = 4, 5, and 6 NB peptides per bundle revealed water-filled pores after 1 ns of MD simulation in a solvated lipid bilayer. Calculated conductance values [using HOLE (Smart et al. (1997) Biophys. J. 72, 1109-1126)] of ca. 20, 60, and 90 pS, respectively, suggested that the multiple conductance levels seen experimentally must correspond to different degrees of oligomerization of the peptide to form channels.
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Fox ME, Yamada T, Ohta K, Smith GR. A family of cAMP-response-element-related DNA sequences with meiotic recombination hotspot activity in Schizosaccharomyces pombe. Genetics 2000; 156:59-68. [PMID: 10978275 PMCID: PMC1461235 DOI: 10.1093/genetics/156.1.59] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The heptamer sequence ATGACGT is essential for activity of the M26 meiotic recombination hotspot in the ade6 gene of Schizosaccharomyces pombe. Hotspot activity is associated with binding of the heterodimeric transcription factor Atf1.Pcr1 to M26. We have found that the sequences (C/T/G) TGACGT also bound Atf1.Pcr1 and acted as meiotic hotspots, but unlike M26 they must be followed by A or C for Atf1.Pcr1 binding and hotspot activity. The basis of the hotspot activity of CTGACGTA (ade6-3013) appears to be identical to that of M26: hotspot activity of both sequences was abolished in cells mutant for atf1, pcr1, spc1, or wis1 and was undetectable in mitotic recombination and in meiotic recombination when located on a plasmid. Both hotspot sequences were sites of micrococcal nuclease hypersensitivity in meiotic chromatin, suggesting that they create an open chromatin structure during meiosis at the site of the hotspots. The newly identified hotspot sequences (C/T/G)TGACGT(A/C) and M26 are closely related to the cAMP response element (CRE) consensus sequence for binding of cAMP-responsive transcription factors such as Atf1.Pcr1, suggesting a link between transcription and meiotic recombination. These results significantly expand the list of identified sequences with meiotic recombination hotspot activity in S. pombe from a single sequence to a family of CRE-related sequences.
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90
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Sansom MS, Shrivastava IH, Ranatunga KM, Smith GR. Simulations of ion channels--watching ions and water move. Trends Biochem Sci 2000; 25:368-74. [PMID: 10916155 DOI: 10.1016/s0968-0004(00)01613-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ion channels mediate electrical excitability in neurons and muscle. Three-dimensional structures for model peptide channels and for a potassium (K+) channel have been combined with computer simulations to permit rigorous exploration of structure-function relations of channels. Water molecules and ions within transbilayer pores tend to diffuse more slowly than in bulk solutions. In the narrow selectivity filter of the bacterial K+ channel (i.e. the region of the channel that discriminates between different species of ions) a column of water molecules and K+ ions moves in a concerted fashion. By combining atomistic simulations (in which all atoms of the channel molecule, water and ions are treated explicitly) with continuum methods (in which the description of the channel system is considerably simplified) it is possible to simulate some of the physiological properties of channels.
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Kirchner JE, Booth BM, Owen RR, Lancaster AE, Smith GR. Predictors of patient entry into alcohol treatment after initial diagnosis. J Behav Health Serv Res 2000; 27:339-46. [PMID: 10932447 DOI: 10.1007/bf02291745] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To improve the quality of care for alcohol-related disorders, key transitions in the continuum of care, including treatment entry, must be fully understood. The purpose of this study was to investigate identifiable predictors of patient entry into a substance-use treatment program following the initial diagnosis of an alcohol-related disorder on a medical or surgical inpatient unit. An administrative computerized database was used to identify the sample for this study. Inpatient and outpatient records were obtained from the Little Rock VAMC/DHCP. Predictors of patient entry into treatment within six months of the initial diagnosis of an alcohol related disorder included age younger than than 60 (odds ratio [OR] = 4.6), not married (OR = 1.7), primary diagnosis of an alcohol-related disorder (OR = 7.7), diagnosis of a comorbid drug (OR = 4.3) or psychiatric disorder (OR = 3.6), diagnosis by a medical as opposed to a surgical specialty (OR = 6.0), and African American (OR = 1.7).
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Adcock C, Smith GR, Sansom MS. The nicotinic acetylcholine receptor: from molecular model to single-channel conductance. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2000; 29:29-37. [PMID: 10826776 DOI: 10.1007/s002490050248] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nicotinic acetylcholine receptor (nAChR) is the archetypal ligand-gated ion channel. A model of the alpha7 homopentameric nAChR is described in which the pore-lining M2 helix bundle is treated atomistically and the remainder of the molecule is treated as a "low resolution" cylinder. The surface charge on the cylinder is derived from the distribution of charged amino acids in the amino acid sequence (excluding the M2 segments). This model is explored in terms of its predicted single-channel properties. Based on electrostatic potential profiles derived from the model, the one-dimensional Poisson-Nernst-Planck equation is used to calculate single-channel current/voltage curves. The predicted single-channel conductance is three times higher (ca. 150 pS) than that measured experimentally, and the predicted ion selectivity agrees with the observed cation selectivity of nAChR. Molecular dynamics (MD) simulations are used to estimate the self-diffusion coefficients (D) of water molecules within the channel. In the narrowest region of the pore, D is reduced ca. threefold relative to that of bulk water. Assuming that the diffusion of ions scales with that of water, this yields a revised prediction of the single-channel conductance (ca. 50 pS) in good agreement with the experimental value. We conclude that combining atomistic (MD) and continuum electrostatics calculations is a promising approach to bridging the gap between structure and physiology of ion channels.
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Smith GR, Borg Z, Lockhart BE, Braithwaite KS, Gibbs MJ. Sugarcane yellow leaf virus: a novel member of the Luteoviridae that probably arose by inter-species recombination. J Gen Virol 2000; 81:1865-9. [PMID: 10859394 DOI: 10.1099/0022-1317-81-7-1865] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 5895 nucleotide long single-stranded RNA genome of Sugarcane yellow leaf virus Florida isolate (SCYLV-F) includes six major ORFs. All but the first of these are homologous to genes of known function encoded by viruses of the three newly defined genera in the LUTEOVIRIDAE: ('luteovirids'), i.e. poleroviruses, luccccteoviruses and the enamoviruses. SCYLV-F ORFs 1 and 2 are most closely related to their polerovirus counterparts, whereas SCYLV-F ORFs 3 and 4 are most closely related to counterparts in luteovirus genomes, and SCYLV-F ORF5 is most closely related to the read-through protein gene of the only known enamovirus. These differences in affinity result from inter-species recombination. Two recombination sites in the genome of SCYLV-F map to the same genomic locations as previously described recombinations involving other luteovirids. A fourth type of luteovirid, Soybean dwarf virus, has already been described. Our analyses indicate that SCYLV-F represents a distinct fifth type.
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Amundsen SK, Taylor AF, Smith GR. The RecD subunit of the Escherichia coli RecBCD enzyme inhibits RecA loading, homologous recombination, and DNA repair. Proc Natl Acad Sci U S A 2000; 97:7399-404. [PMID: 10840065 PMCID: PMC16557 DOI: 10.1073/pnas.130192397] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The RecBCD enzyme is required for homologous recombination and DNA repair in Escherichia coli. The structure and function of RecBCD enzyme is altered on its interaction with the recombination hotspot Chi (5'-GCTGGTGG-3'). It has been hypothesized that the RecD subunit plays a role in Chi-dependent regulation of enzyme activity [Thaler, D. S., Sampson, E., Siddiqi, I., Rosenberg, S. M., Stahl, F. W. & Stahl, M. (1988) in Mechanisms and Consequences of DNA Damage Processing, eds. Friedberg, E. & Hanawalt, P. (Liss, New York), pp. 413-422; Churchill, J. J., Anderson, D. G. & Kowalczykowski, S. C. (1999) Genes Dev. 13, 901-911]. We tested the hypothesis that the RecD subunit inhibits recombination by deleting recD from the nuclease- and recombination-deficient mutant recB(D1080A)CD. We report here that the resulting strain, recB(D1080A)C, was proficient for recombination and DNA repair. Recombination proficiency was accompanied by a change in enzyme activity: RecB(D1080A)C enzyme loaded RecA protein onto DNA during DNA unwinding whereas RecB(D1080A)CD enzyme did not. Together, these genetic and biochemical results demonstrate that RecA loading by RecBCD enzyme is required for recombination in E. coli cells and suggest that RecD interferes with the enzyme domain required for its loading. A nuclease-dependent signal appears to be required for a change in RecD that allows RecA loading. Because RecA loading is not observed with wild-type RecBCD enzyme until it acts at a Chi site, our observations support the view that RecD inhibits recombination until the enzyme acts at Chi.
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Capener CE, Shrivastava IH, Ranatunga KM, Forrest LR, Smith GR, Sansom MS. Homology modeling and molecular dynamics simulation studies of an inward rectifier potassium channel. Biophys J 2000; 78:2929-42. [PMID: 10827973 PMCID: PMC1300878 DOI: 10.1016/s0006-3495(00)76833-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A homology model has been generated for the pore-forming domain of Kir6.2, a component of an ATP-sensitive K channel, based on the x-ray structure of the bacterial channel KcsA. Analysis of the lipid-exposed and pore-lining surfaces of the model reveals them to be compatible with the known features of membrane proteins and Kir channels, respectively. The Kir6.2 homology model was used as the starting point for nanosecond-duration molecular dynamics simulations in a solvated phospholipid bilayer. The overall drift from the model structure was comparable to that seen for KcsA in previous similar simulations. Preliminary analysis of the interactions of the Kir6.2 channel model with K(+) ions and water molecules during these simulations suggests that concerted single-file motion of K(+) ions and water through the selectivity filter occurs. This is similar to such motion observed in simulations of KcsA. This suggests that a single-filing mechanism is conserved between different K channel structures and may be robust to changes in simulation details. Comparison of Kir6.2 and KcsA suggests some degree of flexibility in the filter, thus complicating models of ion selectivity based upon a rigid filter.
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96
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Fischer WB, Forrest LR, Smith GR, Sansom MS. Transmembrane domains of viral ion channel proteins: a molecular dynamics simulation study. Biopolymers 2000; 53:529-38. [PMID: 10766949 DOI: 10.1002/(sici)1097-0282(200006)53:7<529::aid-bip1>3.0.co;2-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanosecond molecular dynamics simulations in a fully solvated phospholipid bilayer have been performed on single transmembrane alpha-helices from three putative ion channel proteins encoded by viruses: NB (from influenza B), CM2 (from influenza C), and Vpu (from HIV-1). alpha-Helix stability is maintained within a core region of ca. 28 residues for each protein. Helix perturbations are due either to unfavorable interactions of hydrophobic residues with the lipid headgroups or to the need of the termini of short helices to extend into the surrounding interfacial environment in order to form H-bonds. The requirement of both ends of a helix to form favorable interactions with lipid headgroups and/or water may also lead to tilting and/or kinking of a transmembrane alpha-helix. Residues that are generally viewed as poor helix formers in aqueous solution (e.g., Gly, Ile, Val) do not destabilize helices, if located within a helix that spans a lipid bilayer. However, helix/bilayer mismatch such that a helix ends abruptly within the bilayer core destabilizes the end of the helix, especially in the presence of Gly and Ala residues. Hydrogen bonding of polar side-chains with the peptide backbone and with one another occurs when such residues are present within the bilayer core, thus minimizing the energetic cost of burying such side-chains.
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97
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Fischer EP, Marder SR, Smith GR, Owen RR, Rubenstein L, Hedrick SC, Curran GM. Quality Enhancement Research Initiative in Mental Health. Med Care 2000; 38:I70-81. [PMID: 10843272 DOI: 10.1097/00005650-200006001-00008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Veterans Administration (VA) recently introduced its Quality Enhancement Research Initiative (QUERI) to facilitate the translation of best practices into usual clinical care. The Mental Health QUERI (MHQ) was charged with developing strategic plans for major depressive disorder (MDD) and schizophrenia. Twenty percent or more of VA service users are affected by 1 of these 2 disorders, disorders that often have a devastating impact on affected individuals. Despite the increasing availability of efficacious treatments for each disorder, substantial gaps remain between best practices and routine care. In this context, the MHQ identified steps critical to the success of a sustained process of rapid-cycle health care improvement for MDD and schizophrenia, including research initiatives to close gaps in knowledge of best treatment practices, demonstration projects to close gaps in practice and to expand understanding of effective strategies for implementing clinical guidelines, targeted enhancements of the VA information system, and research and dissemination initiatives to increase the availability of resources to support the accelerated incorporation of best practices into routine care. This article presents an overview of the elements in the initial MHQ strategic plans and the rationale behind them.
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98
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Budil DE, Ding Z, Smith GR, Earle KA. Jones matrix formalism for quasioptical EPR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 144:20-34. [PMID: 10783270 DOI: 10.1006/jmre.2000.2024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The Jones matrix formalism that has been used to analyze quasioptical millimeter-wave circuits is extended for specific application to high-frequency electron paramagnetic resonance (EPR). A survey of general expressions for Jones matrices of elements commonly used in quasioptical EPR spectrometers is given. The Jones matrix representations of quasioptical transmission and reflection cavities are derived, and their relationship to the equivalent circuit and transmission line representations used for conventional EPR cavities is demonstrated. The formalism is applied to selected quasioptical EPR spectrometer designs and experimental tests of the formalism are presented for two configurations of a quasioptical spectrometer operating at 220 GHz.
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Abstract
In the fission yeast Schizosaccharomyces pombe, we have detected prominent DNA breaks that appeared shortly after premeiotic DNA replication. These breaks, like meiotic recombination, required the products of the six rec genes tested. Prominent breaks were detected at widely separated sites, about 100-300 kb apart, equivalent to about 50-150 sites per genome or approximately the number of meiotic recombination events. Certain features of these breaks are similar to those in the distantly related yeast Saccharomyces cerevisiae, the only other organism in which meiotic DNA breaks have been reported. Other features, however, appear to be different. These results suggest that, although DNA breaks may be a general feature of meiotic recombination, the breaks in S. pombe may play a role different from those in S. cerevisiae.
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100
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Smith GR. Devices for blood pressure measurement. PROFESSIONAL NURSE (LONDON, ENGLAND) 2000; 15:337-40. [PMID: 10986960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Blood pressure may be recorded by manual or automatic methods. Manual techniques are susceptible to operator bias. Automatic devices are prone to unreliable readings in patients with certain conditions. Staff need training in the use of blood pressure monitoring devices.
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