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Sansom MS, Adcock C, Smith GR. Modelling and simulation of ion channels: applications to the nicotinic acetylcholine receptor. J Struct Biol 1998; 121:246-62. [PMID: 9615441 DOI: 10.1006/jsbi.1997.3950] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular dynamics simulations with experimentally derived restraints have been used to develop atomic models of M2 helix bundles forming the pore-lining domains of the nicotinic acetylcholine receptor and related ligand-gated ion channels. M2 helix bundles have been used in microscopic simulations of the dynamics and energetics of water and ions within an ion channel. Translational and rotational motion of water are restricted within the pore, and water dipoles are aligned relative to the pore axis by the surrounding helix dipoles. Potential energy profiles for translation of a Na+ ion along the pore suggest that the protein and water components of the interaction energy exert an opposing effect on the ion, resulting in a relatively flat profile which favors cation permeation. Empirical conductance calculations based on a pore radius profile suggest that the M2 helix model is consistent with a single channel conductance of ca. 50 pS. Continuum electrostatics calculations indicate that a ring of glutamate residues at the cytoplasmic mouth of the alpha 7 nicotinic receptor M2 helix bundle may not be fully ionized. A simplified model of the remainder of the channel protein when added to the M2 helix bundle plays a significant role in enhancing the ion selectivity of the channel.
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Waters PM, Smith GR, Jaramillo D. Glenohumeral deformity secondary to brachial plexus birth palsy. THE JOURNAL OF BONE AND JOINT SURGERY. AMERICAN VOLUME 1998. [PMID: 9611027 DOI: 10.2106/00004623-199805000-00007.] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Ninety-four patients who had brachial plexus birth palsy were entered into a prospective study to evaluate the association between persistent palsy, age-related musculoskeletal deformity, and functional limitations. Of these patients, forty-two had either computerized tomography or magnetic resonance imaging to assess the presence and degree of incongruity of the glenohumeral joint, deformity of the humeral head, and hypoplasia of the glenoid as part of the preoperative planning for a reconstructive operation. Functional ability was rated with use of the classification of Mallet, on a scale of 1 to 5. The mean glenoscapular angle (the degree of retroversion of the glenoid) on the affected side was -25.7 degrees compared with -5.5 degrees on the unaffected side. Twenty-six (62 per cent) of the forty-two shoulders had evidence of posterior subluxation of the humeral head, with a mean of only 25 per cent (range, 0 to 50 per cent) of the head being intersected by the scapular line. Progressive deformity was found with increasing age (p < 0.001). The natural history of untreated brachial plexus birth palsy with residual weakness is progressive glenohumeral deformity due to persistent muscle imbalance. The status of the glenohumeral joint must be addressed when the choice between tendon transfer and humeral derotation osteotomy for reconstruction of the shoulder is considered for these patients.
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Ding R, Smith GR. Global control of meiotic recombination genes by Schizosaccharomyces pombe rec16 (rep1). MOLECULAR & GENERAL GENETICS : MGG 1998; 258:663-70. [PMID: 9671035 DOI: 10.1007/s004380050780] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Schizosaccharomyces pombe rec16-125 mutation reduces meiotic recombination, delays premeiotic DNA synthesis, and reduces the accumulation of some but not other rec gene transcripts. To elucidate the function of the Rec16 global meiotic regulator, we cloned and sequenced rec16. The data revealed that rec16 is identical to rep1, which was previously shown to encode a protein with a zinc-finger motif required for pre-meiotic DNA synthesis. Transcripts of rec16 (rep1) were strongly induced and subsequently degraded during meiosis. In a rec16 (rep1) deletion mutant, meiotic induction of the seven rec genes tested, which appear to be directly involved in meiotic recombination, was significantly reduced or essentially abolished. Deletion of 80% of the gene essentially abolished meiotic recombination, whereas strains deleted for approximately one-quarter of the gene, from either end, retained partial activity. The rec16-125 mutation strongly reduced recombination in the intervals tested on chromosomes I and III, a phenotype characteristic of mutations in rec genes, such as rec7, whose expression requires Rec16 (Rep1). These results show that Rec16 (Rep1) does not have the regional specificity of Rec10. We infer that Rec16 (Rep1) is a transcriptional activator that is required for meiotic replication and recombination because it plays a role in the transcriptional induction of the rec and other meiosis-specific genes.
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Walker AC, Yang TY, Gourlay J, Dines JA, Forbes MG, Prince SM, Baillie DA, Neilson DT, Williams R, Wilkinson LC, Smith GR, Desmulliez MP, Buller GS, Taghizadeh MR, Waddie A, Underwood I, Stanley CR, Pottier F, Vögele B, Sibbett W. Optoelectronic Systems Based on InGaAs- Complementary-Metal-Oxide-Semiconductor Smart-Pixel Arrays and Free-Space Optical Interconnects. APPLIED OPTICS 1998; 37:2822-2830. [PMID: 18273228 DOI: 10.1364/ao.37.002822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Free-space optical interconnects have been identified as a potentially important technology for future massively parallel-computing systems. The development of optoelectronic smart pixels based on InGaAs/AlGaAs multiple-quantum-well modulators and detectors flip-chip solder-bump bonded onto complementary-metal-oxide-semiconductor (CMOS) circuits and the design and construction of an experimental processor in which the devices are linked by free-space optical interconnects are described. For demonstrating the capabilities of the technology, a parallel data-sorting system has been identified as an effective demonstrator. By use of Batcher's bitonic sorting algorithm and exploitation of a perfect-shuffle optical interconnection, the system has the potential to perform a full sort on 1024, 16-bit words in less than 16 mus. We describe the design, testing, and characterization of the smart-pixel devices and free-space optical components. InGaAs-CMOS smart-pixel, chip-to-chip communication has been demonstrated at 50 Mbits/s. It is shown that the initial system specifications can be met by the component technologies.
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Abstract
RecBCD enzyme acts in the major pathway of homologous recombination of linear DNA in Escherichia coli. The enzyme unwinds DNA and is an ATP-dependent double-strand and single-strand exonuclease and a single-strand endonuclease; it acts at Chi recombination hotspots (5'-GCTGGTGG-3') to produce a recombinogenic single-stranded DNA 3'-end. We found that a small RNA with a unique sequence of approximately 24 nt was tightly bound to RecBCD enzyme and co-purified with it. When added to native enzyme this RNA, but not four others, increased DNA unwinding and Chi nicking activities of the enzyme. In seven similarly active enzyme preparations the molar ratio of RNA molecules to RecBCD enzyme molecules ranged from 0.2 to <0.008. These results suggest that, although this unique RNA is not an essential enzyme subunit, it has a biological role in stimulating RecBCD enzyme activity.
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Abstract
Ninety-four patients who had brachial plexus birth palsy were entered into a prospective study to evaluate the association between persistent palsy, age-related musculoskeletal deformity, and functional limitations. Of these patients, forty-two had either computerized tomography or magnetic resonance imaging to assess the presence and degree of incongruity of the glenohumeral joint, deformity of the humeral head, and hypoplasia of the glenoid as part of the preoperative planning for a reconstructive operation. Functional ability was rated with use of the classification of Mallet, on a scale of 1 to 5. The mean glenoscapular angle (the degree of retroversion of the glenoid) on the affected side was -25.7 degrees compared with -5.5 degrees on the unaffected side. Twenty-six (62 per cent) of the forty-two shoulders had evidence of posterior subluxation of the humeral head, with a mean of only 25 per cent (range, 0 to 50 per cent) of the head being intersected by the scapular line. Progressive deformity was found with increasing age (p < 0.001). The natural history of untreated brachial plexus birth palsy with residual weakness is progressive glenohumeral deformity due to persistent muscle imbalance. The status of the glenohumeral joint must be addressed when the choice between tendon transfer and humeral derotation osteotomy for reconstruction of the shoulder is considered for these patients.
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Jessen JR, Meng A, McFarlane RJ, Paw BH, Zon LI, Smith GR, Lin S. Modification of bacterial artificial chromosomes through chi-stimulated homologous recombination and its application in zebrafish transgenesis. Proc Natl Acad Sci U S A 1998; 95:5121-6. [PMID: 9560239 PMCID: PMC20224 DOI: 10.1073/pnas.95.9.5121] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/1997] [Accepted: 02/24/1998] [Indexed: 02/07/2023] Open
Abstract
The modification of yeast artificial chromosomes through homologous recombination has become a useful genetic tool for studying gene function and enhancer/promoter activity. However, it is difficult to purify intact yeast artificial chromosome DNA at a concentration sufficient for many applications. Bacterial artificial chromosomes (BACs) are vectors that can accommodate large DNA fragments and can easily be purified as plasmid DNA. We report herein a simple procedure for modifying BACs through homologous recombination using a targeting construct containing properly situated Chi sites. To demonstrate a usage for this technique, we modified BAC clones containing the zebrafish GATA-2 genomic locus by replacing the first coding exon with the green fluorescent protein (GFP) reporter gene. Molecular analyses confirmed that the modification occurred without additional deletions or rearrangements of the BACs. Microinjection demonstrated that GATA-2 expression patterns can be recapitulated in living zebrafish embryos by using these GFP-modified GATA-2 BACs. Embryos microinjected with the modified BAC clones were less mosaic and had improved GFP expression in hematopoietic progenitor cells compared with smaller plasmid constructs. The precise modification of BACs through Chi-stimulated homologous recombination should be useful for studying gene function and regulation in cultured cells or organisms where gene transfer is applicable.
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Handley JA, Smith GR, Dale JL, Harding RM. Sequence diversity in the NIb coding region of eight sugarcane mosaic potyvirus isolates infecting sugarcane in Australia. Arch Virol 1998; 141:2289-300. [PMID: 9526537 DOI: 10.1007/bf01718631] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have sequenced the NIb coding region of sugarcane mosaic potyvirus strain SC (SCMV-SC) and eight field isolates of SCMV from Australia. This region comprised 1563 nucleotides and encoded a putative protein of 521 amino acids containing the consensus motif GDD. The protease cleavage sites between the NIa/NIb and the NIb/coat protein were found to be Q/C and Q/A, respectively. The SCMV sequences were most similar to sorghum mosaic potyvirus with identities of 70% and 78% at the nucleotide and amino acid levels, respectively. When the sequences were compared to each other, there was a maximum of 3.3% variation between isolates at the nucleotide level and a maximum of 0.8% at the amino acid level. Phylogenetic analysis of the sequences indicated the field isolates were grouped according to their geographical location. The SCMV sequence with most homology to all other isolates has been selected to generate constructs for replicase-mediated resistance.
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Booth BM, Zhang M, Rost KM, Clardy JA, Smith LG, Smith GR. Measuring outcomes and costs for major depression. PSYCHOPHARMACOLOGY BULLETIN 1998; 33:653-8. [PMID: 9493475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This article addresses briefly the measurement of multidimensional outcomes and costs for major depression. We emphasize the importance of measuring outcomes in a variety of domains, including the broader issues of improvement or decline in functioning and impairment based on domains known to be affected by major depression. We emphasize the importance of measuring the economic costs of illness, both the direct total health care costs and indirect costs. Direct costs include mental health treatment costs and all other health care costs. Indirect costs include such varied factors as lost wages for the depressed individual and caregiver burden. We demonstrate the usefulness and importance of using these measures with several examples from our own research.
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135
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Ranatunga KM, Kerr ID, Adcock C, Smith GR, Sansom MS. Protein-water-ion interactions in a model of the pore domain of a potassium channel: a simulation study. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1370:1-7. [PMID: 9518528 DOI: 10.1016/s0005-2736(97)00271-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A model of the selectivity filter of a voltage-gated K+ (Kv) channel formed by an eight-stranded beta-barrel is compared with physiological properties of the channel. Continuum electrostatic calculations suggest that only two of the eight Asp sidechains at the extracellular mouth of the pore will ionise. A ring of four Tyr sidechains forms the narrowest region of the pore. Molecular dynamic simulations of the potential energy of a K+ ion as translated along the model pore indicate that the two ionised Asp sidechains and the hydroxyl groups of the Tyr sidechains stabilise the partially desolvated ion as it passes through the narrowest region.
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136
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Zhang M, Booth BM, Smith GR. Services utilization before and after the prospective payment system by patients with somatization disorder. J Behav Health Serv Res 1998; 25:76-82. [PMID: 9516296 DOI: 10.1007/bf02287502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This study analyzed services utilization before and after the implementation of Medicare's Prospective Payment System (PPS) in psychiatric patients with somatization disorder in two samples: one recruited before the PPS and the other after the PPS. Individuals with this psychiatric disorder present with multiple unexplained medical complaints and consume a great number of health resources. The results from this study indicated that Medicare PPS was associated with fewer hospital admissions and fewer hospital days, with a greater number of physician visits (for Medicare patients) and emergency room visits (for non-Medicare patients) and with lower overall health expenditures. However, there were no significant changes in the average length of stay after PPS. In contrast to previous studies, Medicare PPS was significantly associated with changes in service utilization by non-Medicare patients as well, a possible "spillover effect." This study confirms the results from other research indicating that higher levels of efficiency may be achieved for certain psychiatric disorders through prospective payment mechanisms.
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Smith GR, Thomas PR, Ritchey M, Norkool P. Long-term renal function in patients with irradiated bilateral Wilms tumor. National Wilms' Tumor Study Group. Am J Clin Oncol 1998; 21:58-63. [PMID: 9499259 DOI: 10.1097/00000421-199802000-00013] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The treatment of bilateral Wilms tumor (BWT) involves a multidisciplinary approach including surgery, chemotherapy, and radiation therapy. The long-term renal function in patients receiving all three treatment modalities has not been evaluated. Long-term renal function was evaluated in 81 children with synchronous BWT who received radiation therapy as part of their treatment. Renal function was assessed by measuring blood urea nitrogen (BUN) and serum creatinine (Cr). The normal range for the BUN was defined as 10-24 mg/dl, and the Cr was considered normal at levels of <1.5 mg/dl. Moderate elevations were defined as a BUN of 25-50 mg/dl and/or a Cr of 1.6-2.5 mg/dl and marked elevations as a BUN of >50 mg/dl and/or a Cr of >2.5 mg/dl. BUN and Cr levels were measured prior to treatment and at the following intervals: 6 months after treatment, 1 year after treatment, 2 years after treatment, and at last follow-up. Any elevation during the posttreatment follow-up period was considered abnormal. A total of 28 children (34.6%) had elevated BUN and/or Cr levels, and 18 had moderate and 10 had marked renal insufficiency. No dose-response relationship was established when comparing the radiation doses of those with elevated values to those with normal values. The renal complication rate was moderate, and other factors including surgery, extent and nature of chemotherapy, and recurrent tumor must also be taken into account. The elevations present in several children could be attributed to tumor recurrence and in one case to gentamicin toxicity. The management of children with BWT should consider all of these risks, and attempts to preserve renal parenchyma are warranted.
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Clardy JA, Booth BM, Smith LG, Nordquist CR, Smith GR. Implementing a statewide outcomes management system for consumers of public mental health services. Psychiatr Serv 1998; 49:191-5. [PMID: 9575003 DOI: 10.1176/ps.49.2.191] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The authors describe the development and implementation of an outcomes management system designed to measure outcomes and processes of care for public mental health consumers in Arkansas. The public-academic project was implemented in 1995 and is based on the Shewhart-Deming model of continuous quality improvement. All 15 community mental health centers (CMHCs) in the state participate in the project, which prospectively measures longitudinal outcomes of care for the tracer conditions of major depression and schizophrenia. Multiperspective measurement tools are used to measure patients' psychiatric status and general health status at periodic intervals; information is gathered on functioning, symptoms, severity of illness, social factors, demographic characteristics, and quality of life. A problem encountered during implementation was the relatively low rate of referral of patients with the tracer conditions for monitoring. Voluntary rather than mandatory participation in the outcomes management system by the CMHCs as well as clinicians' misperceptions about the system's purpose and concerns about confidentiality may have partly accounted for the low rate.
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Pemberton IJ, Smith GR, Philley GL, Rouquette FM, Yuen GY. First Report of Pythium ultimum, P. irregulare, Rhizoctonia solani AG4, and Fusarium proliferatum from Arrowleaf Clover (Trifolium vesiculosum): A Disease Complex. PLANT DISEASE 1998; 82:128. [PMID: 30857054 DOI: 10.1094/pdis.1998.82.1.128b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Poor stand establishment, failure to recover after grazing, and premature plant death have reduced the utilization of arrowleaf clover (Trifolium vesiculosum Savi) as a forage crop in the southeastern United States in recent years. Clover plants collected from poor stands in east Texas pastures during the 1995 to 1996 and 1996 to 1997 seasons first exhibited root disease symptoms as young seedlings in the fall. Symptoms consisted of one or more of the following: tan discoloration of lateral roots and taproot; root pruning; and small, tan, sunken lesions on the taproot and crown. Many Rhizobium nodules were brown and dead. Toward spring, symptoms increased in severity. Root lesions became larger and darker, and internal crown discoloration was observed. Disease incidence reached 100% in both growing seasons. Premature death of plants also was observed, especially in pastures where plants had been grazed. Most of the fungi isolated from diseased roots were Pythium, multi- and binucleate Rhizoctonia, and Fusarium spp. Many plants were infected with two or three pathogens simultaneously. Two Rhizoctonia isolates (AR96-17 and -26) were identified as R. solani anastomosis group 4 (AG4; D. R. Sumner, University of Georgia). AR96-8 was identified as Fusarium proliferatum (T. Matsushima) Nirenberg (Fusarium Research Center, Penn State University; deposited as isolate M-8382). Three Pythium isolates (AR96-7, -11 and -39) were identified as P. irregulare Buisman, based on oogonial and sporangial characteristics. Eight other Pythium isolates were not identified. Pythium isolate AR97-1, found in 1997, was identified as P. ultimum Trow. Greenhouse studies to confirm pathogenicity of these isolates were conducted by sowing cv. Yuchi arrowleaf clover seed into artificially infested soilless medium. In pathogenicity tests for P. ultimum, seedling emergence for controls was 69% after 8 days, but no seedlings emerged from P. ultimum-infested media. Several seeds showed imbibition and emerging radicles but were symptomatic. The pathogen was reisolated from necrotic radicles. After 19 weeks, survival and root disease symptoms were recorded for plants infected by the other isolates. Pathogens were reisolated from diseased plants. Disease symptoms were similar to those observed on plants collected in the field, and differed among pathogens. The Pythium isolates and P. irregulare caused tan discoloration and pruning of the entire root system, sometimes leaving only stubs along the taproot. Survival of clover plants infected by Pythium spp. and P. irregulare isolates averaged 79 and 83%, respectively. R. solani AG4 isolates caused internal crown discoloration, root lesions, and severe root rot, and plant survival was only 31%. F. proliferatum caused hyperelongation of the hypocotyl and stem, mild chlorosis, tan discoloration of roots, and 94% plant survival. Survival was 86% for control plants. P. ultimum, P. irregulare, R. solani AG4, and F. proliferatum are part of a larger disease complex occurring on arrowleaf clover in east Texas that also includes bean yellow mosaic virus (1) and possibly other root and crown rot diseases. This report is the first to identify some of the components of this disease complex impacting arrowleaf clover in Texas, and to demonstrate pathogenicity of each fungal pathogen individually. There are no arrowleaf clover cultivars currently known to have resistance to any of these pathogens. Reference: (1) I. J. Pemberton et al. Phytopathology 81:1001, 1991.
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Rost K, Zhang M, Fortney J, Smith J, Coyne J, Smith GR. Persistently poor outcomes of undetected major depression in primary care. Gen Hosp Psychiatry 1998; 20:12-20. [PMID: 9506250 DOI: 10.1016/s0163-8343(97)00095-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite its relevance for quality care initiatives, the field of psychiatry has little scientific knowledge regarding the course of current major depression when primary care patients with the disorder remain undetected. Using statewide telephone screening, we identified and followed 98 adults with current major depression who made one or more visits to a primary care physician during the 6 months following baseline. Thirty-two percent of primary care patients with current major depression remained undetected for up to 1 year. Almost half of undetected patients developed suicidal ideation. Less than one-third of undetected patients made a visit during the month they reported their worst symptoms. Fifty-three percent of undetected patients reported five or more current symptoms at 1 year follow-up. Primary care patients with undetected major depression report persistently poor outcomes. Comparison of outcomes with detected patients suggests that quality improvement efforts directed at improving detection without improving management of detected patients may not improve outcomes.
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Kon N, Krawchuk MD, Warren BG, Smith GR, Wahls WP. Transcription factor Mts1/Mts2 (Atf1/Pcr1, Gad7/Pcr1) activates the M26 meiotic recombination hotspot in Schizosaccharomyces pombe. Proc Natl Acad Sci U S A 1997; 94:13765-70. [PMID: 9391101 PMCID: PMC28381 DOI: 10.1073/pnas.94.25.13765] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/1997] [Accepted: 10/13/1997] [Indexed: 02/05/2023] Open
Abstract
Homologous recombination hotspots increase the frequency of recombination in nearby DNA. The M26 hotspot in the ade6 gene of Schizosaccharomyces pombe is a meiotic hotspot with a discrete, cis-acting nucleotide sequence (5'-ATGACGT-3') defined by extensive mutagenesis. A heterodimeric M26 DNA binding protein, composed of subunits Mts1 and Mts2, has been identified and purified 40,000-fold. Cloning, disruption, and genetic analyses of the mts genes demonstrate that the Mts1/Mts2 heterodimer is essential for hotspot activity. This provides direct evidence that a specific trans-acting factor, binding to a cis-acting site with a unique nucleotide sequence, is required to activate this meiotic hotspot. Intriguingly, the Mts1/Mts2 protein subunits are identical to the recently described transcription factors Atf1 (Gad7) and Pcr1, which are required for a variety of stress responses. However, we report differential dependence on the Mts proteins for hotspot activation and stress response, suggesting that these proteins are multifunctional and have distinct activities. Furthermore, ade6 mRNA levels are equivalent in hotspot and nonhotspot meioses and do not change in mts mutants, indicating that hotspot activation is not a consequence of elevated transcription levels. These findings suggest an intimate but separable link between the regulation of transcription and meiotic recombination. Other studies have recently shown that the Mts1/Mts2 protein and M26 sites are involved in meiotic recombination elsewhere in the S. pombe genome, suggesting that these factors help regulate the timing and distribution of homologous recombination.
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142
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Sansom MS, Smith GR, Smart OS, Smith SO. Channels formed by the transmembrane helix of phospholamban: a simulation study. Biophys Chem 1997; 69:269-81. [PMID: 9474759 DOI: 10.1016/s0301-4622(97)00109-9] [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]
Abstract
Phospholamban is a small membrane protein which can form cation selective ion channels in lipid bilayers. Each subunit contains a single, largely hydrophobic transmembrane helix. The helices are thought to assemble as a pentameric and approximately parallel bundle surrounding a central pore. A model of this assembly (PDB code IPSL) has been used as the starting point for molecular dynamics (MD) simulations of a system consisting of the pentameric helix bundle, plus 217 water molecules located within and at either mouth of the pore. Interhelix distance restraints were employed to maintain the integrity of the helix bundle during a 500 ps MD simulation. Water molecules within the pore exhibited reduced diffusional and rotational mobility. Interactions between the alpha-helix dipoles and the water dipoles, the latter aligned anti-parallel to the former, contribute to the stability of the system. Analysis of the potential energy of interaction of a K+ ion as it was moved through the pore suggested that unfavourable interactions of the cation with the aligned helix dipoles at the N-terminal mouth were overcome by favourable ion-water interactions. Comparable analysis for a Cl ion revealed that the ion-(pore + water) interactions were unfavourable along the whole of the pore, increasingly so from the N- to the C-terminal mouth. Overall, the interaction energy profiles were consistent with a pore selective for cations over anions. Pore radius profiles were used to predict a channel conductance of 50 to 70 ps in 0.2 M KCl, which compares well with an experimental value of 100 ps.
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Selnick HG, Liverton NJ, Baldwin JJ, Butcher JW, Claremon DA, Elliott JM, Freidinger RM, King SA, Libby BE, McIntyre CJ, Pribush DA, Remy DC, Smith GR, Tebben AJ, Jurkiewicz NK, Lynch JJ, Salata JJ, Sanguinetti MC, Siegl PK, Slaughter DE, Vyas K. Class III antiarrhythmic activity in vivo by selective blockade of the slowly activating cardiac delayed rectifier potassium current IKs by (R)-2-(2,4-trifluoromethyl)-N-[2-oxo-5-phenyl-1-(2,2,2-trifluoroethyl)- 2, 3-dihydro-1H-benzo[e][1,4]diazepin-3-yl]acetamide. J Med Chem 1997; 40:3865-8. [PMID: 9397166 DOI: 10.1021/jm970517u] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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145
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Sansom MS, Smith GR, Adcock C, Biggin PC. The dielectric properties of water within model transbilayer pores. Biophys J 1997; 73:2404-15. [PMID: 9370434 PMCID: PMC1181142 DOI: 10.1016/s0006-3495(97)78269-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Ion channels contain extended columns of water molecules within their transbilayer pores. The dynamic properties of such intrapore water have been shown to differ from those of water in its bulk state. In previous molecular dynamics simulations of two classes of model pore (parallel bundles of Ala20 alpha-helices and antiparallel barrels of Ala10 beta-strands), a substantially reduced translational and rotational mobility of waters was observed within the pore relative to bulk water. Molecular dynamics simulations in the presence of a transpore electrostatic field (i.e., a voltage drop along the pore axis) have been used to estimate the resultant polarization (due to reorientation) of the intrapore water, and hence to determine the local dielectric behavior within the pore. It is shown that the local dielectric constant of water within a pore is reduced for models formed by parallel alpha-helix bundles, but not by those formed by beta-barrels. This result is discussed in the context of electrostatics calculations of ion permeation through channels, and the effect of the local dielectric of water within a helix bundle pore is illustrated with a simple Poisson-Boltzmann calculation.
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146
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Farah JA, Smith GR. The RecBCD enzyme initiation complex for DNA unwinding: enzyme positioning and DNA opening. J Mol Biol 1997; 272:699-715. [PMID: 9368652 DOI: 10.1006/jmbi.1997.1259] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The Escherichia coli RecBCD enzyme unwinds DNA from a free double-stranded DNA end to produce single-stranded DNA intermediates of homologous recombination. In the absence of ATP RecBCD binds to a free DNA end to form an initiation complex for DNA unwinding. We studied the structure of these complexes formed with blunt-ended, 5'-extended, and 3'-extended DNA. Reactivity to the single-stranded DNA-specific reagents KMnO4 and dimethyl sulfate indicated that RecBCD opened, in a Mg(2+)-dependent manner, the terminal five or six base-pairs in each substrate. Thymine residues located four to six nucleotides from the 5' end were only partially reactive to KMnO4, suggesting that part of the 5'-terminated strand was partially shielded by the enzyme. DNase I footprinting indicated that the enzyme positions itself relative to the end of the longer of the two strands, although an exception was noted. These results imply flexibility in the ability of RecBCD to open the DNA and position itself for unwinding on DNA with different types of ends. They also imply conformational differences of RecBCD enzyme bound to different types of ends; these conformational differences may be related to those occurring during the unwinding cycle.
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Smith GR, Thornton EA. Classification of human and animal strains of Fusobacterium necrophorum by their pathogenic effects in mice. J Med Microbiol 1997; 46:879-82. [PMID: 9364145 DOI: 10.1099/00222615-46-10-879] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Forty-six strains of Fusobacterium necrophorum, 24 from animals and 22 of human origin, were examined by pathogenicity tests in mice, while the same strains were being examined in laboratories elsewhere by other methods. The pathogenicity tests consisted of (1) subcutaneous inoculation with a large dose of a pure culture, (2) subcutaneous inoculation with a small dose of F. necrophorum mixed with a large but relatively harmless dose of Staphylococcus aureus, and (3) intravenous inoculation with a large dose of a pure culture. Fourteen strains, all of animal origin, showed the characteristic behaviour of biotype A. Twenty-eight strains, 10 of animal origin and 18 from man, were classified as biotype B. The remaining four strains, all from man, produced a distinct type of infection in mice; these strains were referred to as 'A2433-like' because of their resemblance to a strain described in an earlier study. It would appear that biotype A strains, responsible for classical necrobacillosis in animals, do not infect man; that biotype B strains occur in both man and animals; and that 'A2433-like' strains are probably confined to man.
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148
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Smith GR, Sansom MS. Molecular dynamics study of water and Na+ ions in models of the pore region of the nicotinic acetylcholine receptor. Biophys J 1997; 73:1364-81. [PMID: 9284304 PMCID: PMC1181036 DOI: 10.1016/s0006-3495(97)78169-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The nicotinic acetylcholine receptor (nAChR) is an integral membrane protein that forms ligand-gated and cation-selective channels. The central pore is lined by a bundle of five approximately parallel M2 helices, one from each subunit. Candidate model structures of the solvated pore region of a homopentameric (alpha7)5 nAChR channel in the open state, and in two possible forms of the closed state, have been studied using molecular dynamics simulations with restraining potentials. It is found that the mobility of the water is substantially lower within the pore than in bulk, and the water molecules become aligned with the M2 helix dipoles. Hydrogen-bonding patterns in the pore, especially around pore-lining charged and hydrophilic residues, and around exposed regions of the helix backbone, have been determined. Initial studies of systems containing both water and sodium ions together within the pore region have also been conducted. A sodium ion has been introduced into the solvated models at various points along the pore axis and its energy profile evaluated. It is found that the ion causes only a local perturbation of the water structure. The results of these calculations have been used to examine the effectiveness of the central ring of leucines as a component of a gate in the closed-channel model.
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149
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Evans DH, Li YF, Fox ME, Smith GR. A WD repeat protein, Rec14, essential for meiotic recombination in Schizosaccharomyces pombe. Genetics 1997; 146:1253-64. [PMID: 9258671 PMCID: PMC1208072 DOI: 10.1093/genetics/146.4.1253] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Mutations in the Schizosaccharomyces pombe rec14 gene reduce meiotic recombination by as much as a factor of 1000 in the three intervals tested on chromosomes I and III. A DNA clone complementing the rec14 mutation was shown by genetic and physical analysis to contain the rec14 gene, which was functional in plasmid-borne inserts as small as 1.4 kb. The rec14 gene contains two exons separated by a 53-bp intron, which was confirmed by analysis of rec14 transcripts. The spliced transcript encodes a protein product of 302 amino acids, which contains six WD repeat motifs found in the G-beta transducin family of proteins and other proteins, including the Saccharomyces cerevisiae Ski8 (Rec103) protein. Although the rec14 transcripts were present in mitotically dividing cells, rec14 mutations had no detectable effect on mitotic recombination. The pattern of expression of rec14 differes from that of previously analyzed S. pombe rec genes. Based upon mutant phenotypes and amino acid sequence similarities, we propose that S. pombe Rec14 is a functional homologue of S. cerevisiae Rec103.
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150
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Adcock C, Smith GR, Sansom MS. Molecular modelling and electrostatic properties of the pore domain of ligand-gated receptors. Biochem Soc Trans 1997; 25:549S. [PMID: 9388763 DOI: 10.1042/bst025549s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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