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Ailabouni L, Lewis SE. Laparoscopic Duhamel Procedure: Treatment for Adult Hirschprung's Disease. Dis Colon Rectum 2024:00003453-990000000-00621. [PMID: 38624103 DOI: 10.1097/dcr.0000000000003228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Affiliation(s)
- Luay Ailabouni
- Elson S. Floyd College of Medicine, Kadlec Regional Medical Center, Richland, Washington
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Burrage EN, Coblentz T, Prabhu SS, Childers R, Bryner RW, Lewis SE, DeVallance E, Kelley EE, Chantler PD. Xanthine oxidase mediates chronic stress-induced cerebrovascular dysfunction and cognitive impairment. J Cereb Blood Flow Metab 2023; 43:905-920. [PMID: 36655326 PMCID: PMC10196752 DOI: 10.1177/0271678x231152551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023]
Abstract
Xanthine oxidase (XO) mediates vascular function. Chronic stress impairs cerebrovascular function and increases the risk of stroke and cognitive decline. Our study determined the role of XO on stress-induced cerebrovascular dysfunction and cognitive decline. We measured middle cerebral artery (MCA) function, free radical formation, and working memory in 6-month-old C57BL/6 mice who underwent 8 weeks of control conditions or unpredictable chronic mild stress (UCMS) with or without febuxostat (50 mg/L), a XO inhibitor. UCMS mice had an impaired MCA dilation to acetylcholine vs. controls (p < 0.0001), and increased total free radical formation, XOR protein levels, and hydrogen peroxide production in the liver compared to controls. UCMS increased hydrogen peroxide production in the brain and cerebrovasculature compared to controls. Working memory, using the y-maze test, was impaired (p < 0.05) in UCMS mice compared to control mice. However, blocking XO using febuxostat prevented the UCMS-induced impaired MCA response, while free radical production and hydrogen peroxide levels were similar to controls in the liver and brain of UCMS mice treated with febuxostat. Further, UCMS + Feb mice did not have a significant reduction in working memory. These data suggest that the cerebrovascular dysfunction associated with chronic stress may be driven by XO, which leads to a reduction in working memory.
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Affiliation(s)
- Emily N Burrage
- Department of Neuroscience, West
Virginia University School of Medicine, Morgantown, WV, USA
| | - Tyler Coblentz
- Division of Exercise Physiology,
West Virginia University School of Medicine, Morgantown, WV, USA
| | - Saina S Prabhu
- Department of Pharmaceutical
Sciences, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Ryan Childers
- Division of Exercise Physiology,
West Virginia University School of Medicine, Morgantown, WV, USA
| | - Randy W Bryner
- Division of Exercise Physiology,
West Virginia University School of Medicine, Morgantown, WV, USA
| | - Sarah E Lewis
- Department of Physiology and
Pharmacology, West Virginia University School of Medicine, Morgantown, WV,
USA
| | - Evan DeVallance
- Department of Physiology and
Pharmacology, West Virginia University School of Medicine, Morgantown, WV,
USA
| | - Eric E Kelley
- Department of Physiology and
Pharmacology, West Virginia University School of Medicine, Morgantown, WV,
USA
| | - Paul D Chantler
- Department of Neuroscience, West
Virginia University School of Medicine, Morgantown, WV, USA
- Division of Exercise Physiology,
West Virginia University School of Medicine, Morgantown, WV, USA
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Abstract
OBJECTIVE The objective of this study was to examine the price sensitivity for provider visits among Medicare Advantage beneficiaries. DATA SOURCES We used Medicare Advantage encounter data from 2014 to 2017 accessed as part of an evaluation for the Center for Medicare & Medicaid Innovation. STUDY DESIGN We analyzed the effect of cost-sharing on the utilization of 2 outcome categories: number of visits (specialist and primary care) and the probability of any visit (specialist and primary care). Our main independent variable was the size of the copayment for the visit, which we regressed on the outcomes with several beneficiary-level and plan-level control variables. DATA COLLECTION/EXTRACTION METHODS We included beneficiaries with at least 1 of 4 specific chronic conditions and matched comparison beneficiaries. We did not require beneficiaries to be continuously enrolled from 2014 to 2017, but we required a full year of data for each year they were observed. This resulted in 371,140 beneficiary-year observations. PRINCIPAL FINDINGS Copay reductions were associated with increases in utilization, although the changes were small, with elasticities <-0.2. We also found evidence of substitution effects between primary care provider (PCP) and specialist visits, particularly cardiology and endocrinology. When PCP copays declined, visits to these specialists also declined. CONCLUSIONS We find that individuals with chronic conditions respond to changes in copays, although these responses are small. Reductions in PCP copays lead to reduced use of some specialists, suggesting that lowering PCP copays could be an effective way to reduce the use of specialist care, a desirable outcome if specialists are overused.
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Affiliation(s)
| | | | | | | | - Sarah E Lewis
- Center for Medicare & Medicaid Innovation, Baltimore, MD
| | - Sai Ma
- Clinical Transformation, Humana, Washington, DC
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Quintana DD, Lewis SE, Anantula Y, Garcia JA, Sarkar SN, Cavendish JZ, Brown CM, Simpkins JW. The cerebral angiome: High resolution MicroCT imaging of the whole brain cerebrovasculature in female and male mice. Neuroimage 2019; 202:116109. [PMID: 31446129 DOI: 10.1016/j.neuroimage.2019.116109] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/15/2019] [Accepted: 08/17/2019] [Indexed: 01/09/2023] Open
Abstract
The cerebrovascular system provides crucial functions that maintain metabolic and homeostatic states of the brain. Despite its integral role of supporting cerebral viability, the topological organization of these networks remains largely uncharacterized. This void in our knowledge surmises entirely from current technological limitations that prevent the capturing of data through the entire depth of the brain. We report high-resolution reconstruction and analysis of the complete vascular network of the entire brain at the capillary level in adult female and male mice using a vascular corrosion cast procedure. Vascular network analysis of the whole brain revealed sex-related differences of vessel hierarchy. In addition, region-specific network analysis demonstrated different patterns of angioarchitecture between brain subregions and sex. Furthermore, our group is the first to provide a three-dimensional analysis of the angioarchitecture and network organization in a single reconstructed tomographic data set that encompasses all hierarchy of vessels in the brain of the adult mouse.
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Affiliation(s)
- D D Quintana
- Department of Physiology and Pharmacology, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - S E Lewis
- Department of Physiology and Pharmacology, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - Y Anantula
- Department of Neuroscience, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - J A Garcia
- Department of Neuroscience, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - S N Sarkar
- Department of Physiology and Pharmacology, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - J Z Cavendish
- Department of Physiology and Pharmacology, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - C M Brown
- Department of Neuroscience, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA
| | - J W Simpkins
- Department of Physiology and Pharmacology, Center for Basic Translational and Stroke Research, West Virginia University, Morgantown, WV, 26506, USA.
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Sanchez-Fernandez A, Moody GL, Murfin LC, Arnold T, Jackson AJ, King SM, Lewis SE, Edler KJ. Self-assembly and surface behaviour of pure and mixed zwitterionic amphiphiles in a deep eutectic solvent. Soft Matter 2018; 14:5525-5536. [PMID: 29926037 DOI: 10.1039/c8sm00755a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recent investigations have shown that deep eutectic solvents provide a suitable environment for self-organisation of biomolecules, in particular phospholipids and proteins. However, the solvation of complex lyophilic moieties by deep eutectic solvents still remains unclear. Here we explore the behaviour of zwitterionic surfactants in choline chloride:glycerol eutectic mixture. Dodecyl-2-(trimethylammonio)ethylphosphate and N-alkyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (alkyl = dodecyl, tetradecyl) surfactants were investigated by means of surface tension, X-ray reflectivity and small-angle neutron scattering. These surfactants were found to remain surface active and form globular micelles in deep eutectic solvents. Still, the surface behaviour of these species was found to differ depending on the headgroup and tail structure. The morphology of the micelles also slightly varies between surfactants, demonstrating differences in the packing of individual monomers. The characteristics of mixtures of the dodecyl surfactants is also reported, showing a deviation from ideal mixing associated with attractive interactions between sulfobetaine and phosphocholine headgroups. Such non-ideality results in variation of the surface behaviour and self-assembly of these surfactant mixtures. The results presented here will potentially lead to the development of new alternatives for drug-delivery, protein solubilisation and biosensing through a better fundamental understanding of the behaviour of zwitterionic surfactants in deep eutectic solvents.
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Affiliation(s)
- A Sanchez-Fernandez
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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Witt KD, Beresford L, Bhattacharya S, Brian K, Coomarasamy A, Cutting R, Hooper R, Kirkman-Brown J, Khalaf Y, Lewis SE, Pacey A, Pavitt S, West R, Miller D, Cutting R. Hyaluronic Acid Binding Sperm Selection for assisted reproduction treatment (HABSelect): study protocol for a multicentre randomised controlled trial. BMJ Open 2016; 6:e012609. [PMID: 27855103 PMCID: PMC5073628 DOI: 10.1136/bmjopen-2016-012609] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION The selection of a sperm with good genomic integrity is an important consideration for improving intracytoplasmic sperm injection (ICSI) outcome. Current convention selects sperm by vigour and morphology, but preliminary evidence suggests selection based on hyaluronic acid binding may be beneficial. The aim of the Hyaluronic Acid Binding Sperm Selection (HABSelect) trial is to determine the efficacy of hyaluronic acid (HA)-selection of sperm versus conventionally selected sperm prior to ICSI on live birth rate (LBR). The mechanistic aim is to assess whether and how the chromatin state of HA-selected sperm corresponds with clinical outcomes-clinical pregnancy rate (CPR), LBR and pregnancy loss (PL). METHODS AND ANALYSIS Couples attending UK Centres will be approached, eligibility screening performed and informed consent sought. Randomisation will occur within 24 hours prior to ICSI treatment. Participants will be randomly allocated 1:1 to the intervention arm (physiological intracytoplasmic sperm injection, PICSI) versus the control arm using conventional methods (ICSI). The primary clinical outcome is LBR ≥37 weeks' gestation with the mechanistic study determining LBR's relationship with sperm DNA integrity. Secondary outcomes will determine this for CPR and PL. Only embryologists performing the procedure will be aware of the treatment allocation. Steps will be taken to militate against biases arising from embryologists being non-blinded. Randomisation will use a minimisation algorithm to balance for key prognostic variables. The trial is powered to detect a 5% difference (24-29%: p=0.05) in LBR ≥37 weeks' gestation. Selected residual sperm samples will be tested by one or more assays of DNA integrity. ETHICS AND DISSEMINATION HABSelect is a UK NIHR-EME funded study (reg no 11/14/34; IRAS REF. 13/YH/0162). The trial was designed in partnership with patient and public involvement to help maximise patient benefits. Trial findings will be reported as per CONSORT guidelines and will be made available in lay language via the trial web site (http://www.habselect.org.uk/). TRIAL REGISTRATION NUMBER ISRCTN99214271; Pre-results.
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Affiliation(s)
- K D Witt
- Department: Centre for Primary Care & Public Health, Queen Mary University of London, London, UK
| | - L Beresford
- Department: Centre for Primary Care & Public Health, Queen Mary University of London, London, UK
| | - S Bhattacharya
- School of Medicine and Dentistry, University of Aberdeen, Aberdeen, UK
| | - K Brian
- Charity Registration No. 1099960 (InfertilityNetworkUK), London, UK
| | - A Coomarasamy
- Centre for Human Reproductive Science, University of Birmingham, Birmingham Women's Fertility Centre, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Rachel Cutting
- Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM), University of Leeds, Leeds, UK
| | - R Hooper
- Department: Centre for Primary Care & Public Health, Queen Mary University of London, London, UK
| | - J Kirkman-Brown
- Centre for Human Reproductive Science, University of Birmingham, Birmingham Women's Fertility Centre, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Y Khalaf
- Assisted Conception Unit, Guy's and St Thomas's Hospital, London, UK
| | - S E Lewis
- Queen's University Belfast, Institute of Pathology, Belfast, UK
| | - A Pacey
- Department of Human Metabolism, University of Sheffield, Sheffield, UK
| | - S Pavitt
- Dental Translational and Clinical Research Unit, School of Dentistry, University of Leeds, Leeds, UK
| | - R West
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - D Miller
- Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM), University of Leeds, Leeds, UK
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Lewis SE, Rice A, Hurst GDD, Baylis M. First detection of endosymbiotic bacteria in biting midges Culicoides pulicaris and Culicoides punctatus, important Palaearctic vectors of bluetongue virus. Med Vet Entomol 2014; 28:453-456. [PMID: 24612104 DOI: 10.1111/mve.12055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 12/07/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
Heritable bacteria have been highlighted as important components of vector biology, acting as required symbionts with an anabolic role, altering competence for disease transmission, and affecting patterns of gene flow by altering cross compatibility. In this paper, we tested eight U.K. species of Culicoides (Diptera: Ceratopogonidae) midge for the presence of five genera of endosymbiotic bacteria: Cardinium (Bacteroidales: Bacteroidaceae); Wolbachia (Rickettsiales: Rickettsiaceae); Spiroplasma (Entomoplasmatales: Spiroplasmataceae); Arsenophonus (Enterobacteriales: Enterobacteriaceae), and Rickettsia (Rickettsiales: Rickettsiaceae). Cardinium spp. were detected in both sexes of Culicoides pulicaris and Culicoides punctatus, two known vectors of bluetongue virus. Cardinium spp. were not detected in any other species, including the Culicoides obsoletus group, the main vector of bluetongue and Schmallenberg viruses in northern Europe. The other endosymbionts were not detected in any Culicoides species. The Cardinium strain detected in U.K. Culicoides species is very closely related to the Candidatus Cardinium hertigii group C, previously identified in Culicoides species in Asia. Further, we infer that the symbiont is not a sex ratio distorter and shows geographic variation in prevalence within a species. Despite its detection in several species of Culicoides that vector arboviruses worldwide, the absence of Cardinium in the C. obsoletus group suggests that infections of these symbionts may not be necessary to the arboviral vector competence of biting midges.
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Affiliation(s)
- S E Lewis
- School of Veterinary Science, University of Liverpool, Liverpool, U.K
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Jones CD, Holmes GM, Lewis SE, Thompson KW, Cykert S, DeWalt DA. Satisfaction with electronic health records is associated with job satisfaction among primary care physicians. Inform Prim Care 2014; 21:18-20. [PMID: 24629652 DOI: 10.14236/jhi.v21i1.27] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To evaluate the association between electronic health record (EHR) satisfaction and job satisfaction in primary care physicians (PCPs). METHOD Cross-sectional survey of PCPs at 825 primary care practices in North Carolina. RESULTS Surveys were returned from 283 individuals across 214 practices (26% response rate for practices), of whom 122 were physicians with EHRs and no missing information. We found that for each point increase in EHR satisfaction, job satisfaction increased by ∼0.36 points both in an unadjusted and an adjusted model (β 0.359 unadjusted, 0.361 adjusted; p < 0.001 for both models). CONCLUSION We found that EHR satisfaction was associated with job satisfaction in a cross-sectional survey of PCPs. Our conclusions are limited by suboptimum survey response rate, but if confirmed may have substantial implications for how EHR vendors develop their product to support the needs of PCPs.
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Affiliation(s)
- Christine D Jones
- Assistant Professor Hospital Medicine Group, Division of General Internal Medicine University of Colorado F782, 12401 E 17th Avenue, Aurora Denver, CO 80045, USA.
| | - George M Holmes
- The Cecil G. Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Sarah E Lewis
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Kristie W Thompson
- The Cecil G. Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Samuel Cykert
- Division of General Internal Medicine and Clinical Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Darren A DeWalt
- The Cecil G. Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Division of General Internal Medicine and Clinical Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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Davis AM, Lewis SE, Brodie JE, Benson A. The potential benefits of herbicide regulation: a cautionary note for the Great Barrier Reef catchment area. Sci Total Environ 2014; 490:81-92. [PMID: 24840283 DOI: 10.1016/j.scitotenv.2014.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 03/17/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
Industry transitions away from traditional photosystem II inhibiting (PSII) herbicides towards an 'alternative' herbicide suite are now widely advocated as a key component of improved environmental outcomes for Australia's Great Barrier Reef and improved environmental stewardship on the part of the Queensland sugar industry. A systematic desktop risk analysis found that based on current farming practices, traditional PSII herbicides can pose significant environmental risks. Several of the 'alternatives' that can directly fill a specific pre-emergent ('soil residual') weed control function similar to regulated PSII herbicides also, however, presented a similar environmental risk profile, regardless of farming systems and bio-climatic zones being considered. Several alternatives with a pre-emergent residual function as well as alternative post-emergent (contact or 'knockdown') herbicides were, predicted to pose lower environmental risks than the regulated PSII herbicides to most trophic levels, although environmental risks could still be present. While several herbicides may well be viable alternatives in terms of weed control, they can still present equal or possibly higher risks to the environment. Imposing additional regulations (or even de-registrations) on particular herbicides could result in marginal, and possibly perverse environmental impacts in the long term, if usage shifts to alternative herbicides with similar risk profiles. Regardless of any regulatory efforts, improved environmental sustainability outcomes in pesticide practices within the Great Barrier Reef catchment area will hinge primarily on the continuing adoption of integrated, strategic pest management systems and technologies applied to both traditional and 'alternative' herbicides. One of the emerging policy challenges is ensuring the requisite technical and extension support for cane growers to ensure effective adoption of rapidly evolving farming system technologies, in a very dynamic and scrutinised herbicide management environment.
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Affiliation(s)
- A M Davis
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), James Cook University, Townsville, Australia.
| | - S E Lewis
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), James Cook University, Townsville, Australia
| | - J E Brodie
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), James Cook University, Townsville, Australia
| | - Ash Benson
- Herbert Cane Productivity Services Limited, 181 Fairford Road , Ingham, Qld 4850, Australia.
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Quinn MT, Gunter KE, Nocon RS, Lewis SE, Vable AM, Tang H, Park SY, Casalino LP, Huang ES, Birnberg J, Burnet DL, Summerfelt WT, Chin MH. Undergoing transformation to the patient centered medical home in safety net health centers: perspectives from the front lines. Ethn Dis 2013; 23:356-362. [PMID: 23914423 PMCID: PMC3740439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
OBJECTIVES Safety net health centers (SNHCs), which include federally qualified health centers (FQHCs) provide primary care for underserved, minority and low income patients. SNHCs across the country are in the process of adopting the patient centered medical home (PCMH) model, based on promising early implementation data from demonstration projects. However, previous demonstration projects have not focused on the safety net and we know little about PCMH transformation in SNHCs. DESIGN This qualitative study characterizes early PCMH adoption experiences at SNHCs. SETTING AND PARTICIPANTS We interviewed 98 staff (administrators, providers, and clinical staff) at 20 of 65 SNHCs, from five states, who were participating in the first of a five-year PCMH collaborative, the Safety Net Medical Home Initiative. MAIN MEASURES We conducted 30-45 minute, semi-structured telephone interviews. Interview questions addressed benefits anticipated, obstacles encountered, and lessons learned in transition to PCMH. RESULTS Anticipated benefits for participating in the PCMH included improved staff satisfaction and patient care and outcomes. Obstacles included staff resistance and lack of financial support for PCMH functions. Lessons learned included involving a range of staff, anticipating resistance, and using data as frequent feedback. CONCLUSIONS SNHCs encounter unique challenges to PCMH implementation, including staff turnover and providing care for patients with complex needs. Staff resistance and turnover may be ameliorated through improved health care delivery strategies associated with the PCMH. Creating predictable and continuous funding streams may be more fundamental challenges to PCMH transformation.
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Affiliation(s)
- Michael T Quinn
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
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Lewis SE, Nocon RS, Tang H, Park SY, Vable AM, Casalino LP, Huang ES, Quinn MT, Burnet DL, Summerfelt WT, Birnberg JM, Chin MH. Patient-centered medical home characteristics and staff morale in safety net clinics. ACTA ACUST UNITED AC 2012; 172:23-31. [PMID: 22232143 DOI: 10.1001/archinternmed.2011.580] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
BACKGROUND We sought to determine whether perceived patient-centered medical home (PCMH) characteristics are associated with staff morale, job satisfaction, and burnout in safety net clinics. METHODS Self-administered survey among 391 providers and 382 clinical staff across 65 safety net clinics in 5 states in 2010. The following 5 subscales measured respondents' perceptions of PCMH characteristics on a scale of 0 to 100 (0 indicates worst and 100 indicates best): access to care and communication with patients, communication with other providers, tracking data, care management, and quality improvement. The PCMH subscale scores were averaged to create a total PCMH score. RESULTS Six hundred three persons (78.0%) responded. In multivariate generalized estimating equation models, a 10% increase in the quality improvement subscale score was associated with higher morale (provider odds ratio [OR], 2.64; 95% CI, 1.47-4.75; staff OR, 3.62; 95% CI, 1.84-7.09), greater job satisfaction (provider OR, 2.45; 95% CI, 1.42-4.23; staff OR, 2.55; 95% CI 1.42-4.57), and freedom from burnout (staff OR, 2.32; 95% CI, 1.31-4.12). The total PCMH score was associated with higher staff morale (OR, 2.63; 95% CI, 1.47-4.71) and with lower provider freedom from burnout (OR, 0.48; 95% CI, 0.30-0.77). A separate work environment covariate correlated highly with the quality improvement subscale score and the total PCMH score, and PCMH characteristics had attenuated associations with morale and job satisfaction when included in models. CONCLUSIONS Providers and staff who perceived more PCMH characteristics in their clinics were more likely to have higher morale, but the providers had less freedom from burnout. Among the PCMH subscales, the quality improvement subscale score particularly correlated with higher morale, greater job satisfaction, and freedom from burnout.
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Affiliation(s)
- Sarah E Lewis
- Department of Medicine, University of Chicago, Chicago, Illinois, USA.
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13
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Brodie JE, Kroon FJ, Schaffelke B, Wolanski EC, Lewis SE, Devlin MJ, Bohnet IC, Bainbridge ZT, Waterhouse J, Davis AM. Terrestrial pollutant runoff to the Great Barrier Reef: An update of issues, priorities and management responses. Mar Pollut Bull 2012; 65:81-100. [PMID: 22257553 DOI: 10.1016/j.marpolbul.2011.12.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 05/07/2023]
Abstract
The Great Barrier Reef (GBR) is a World Heritage Area and contains extensive areas of coral reef, seagrass meadows and fisheries resources. From adjacent catchments, numerous rivers discharge pollutants from agricultural, urban, mining and industrial activity. Pollutant sources have been identified and include suspended sediment from erosion in cattle grazing areas; nitrate from fertiliser application on crop lands; and herbicides from various land uses. The fate and effects of these pollutants in the receiving marine environment are relatively well understood. The Australian and Queensland Governments responded to the concerns of pollution of the GBR from catchment runoff with a plan to address this issue in 2003 (Reef Plan; updated 2009), incentive-based voluntary management initiatives in 2007 (Reef Rescue) and a State regulatory approach in 2009, the Reef Protection Package. This paper reviews new research relevant to the catchment to GBR continuum and evaluates the appropriateness of current management responses.
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Affiliation(s)
- J E Brodie
- Catchment to Reef Research Group, Australian Centre for Tropical Freshwater Research, James Cook University, Townsville, Qld 4811, Australia.
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Birnberg JM, Drum ML, Huang ES, Casalino LP, Lewis SE, Vable AM, Tang H, Quinn MT, Burnet DL, Summerfelt T, Chin MH. Development of a safety net medical home scale for clinics. J Gen Intern Med 2011; 26:1418-25. [PMID: 21837377 PMCID: PMC3235610 DOI: 10.1007/s11606-011-1767-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 05/24/2011] [Accepted: 06/08/2011] [Indexed: 11/28/2022]
Abstract
BACKGROUND Existing tools to measure patient-centered medical home (PCMH) adoption are not designed for research evaluation in safety-net clinics. OBJECTIVE Develop a scale to measure PCMH adoption in safety-net clinics. RESEARCH DESIGN Cross-sectional survey. SUBJECTS Sixty-five clinics in five states. MAIN MEASURES Fifty-two-item Safety Net Medical Home Scale (SNMHS). The total score ranges from 0 (worst) to 100 (best) and is an average of multiple subscales (0-100): Access and Communication, Patient Tracking and Registry, Care Management, Test and Referral Tracking, Quality Improvement, and External Coordination. The scale was tested for internal consistency reliability and tested for convergent validity using The Assessment of Chronic Illness Care (ACIC) and the Patient-Centered Medical Home Assessment (PCMH-A). The scale was applied to centers in the sample. In addition, linear regression models were used to measure the association between clinic characteristics and medical home adoption. RESULTS The SNMHS had high internal consistency reliability (Cronbach's alpha = 0.84). The SNMHS score correlated moderately with the ACIC score (r = 0.64, p < 0.0001) and the PCMH-A (r = 0.56, p < 0.001). The mean SNMHS score was 61 ± SD 13. Among the subscales, External Coordination (66 ± 16) and Access and Communication (65 ± 14) had the highest mean scores, while Quality Improvement (55 ± 17) and Care Management (55 ± 16) had lower mean scores. Clinic characteristics positively associated with total SNMHS score were having more providers (β 15.8 95% CI 8.1-23.4 >8 provider FTEs compared to <4 FTEs) and participation in financial incentive programs (β 8.4 95% 1.6-15.3). CONCLUSION The SNMHS demonstrated reliability and convergent validity for measuring PCMH adoption in safety-net clinics. Some clinics have significant PCMH adoption. However, room for improvement exists in most domains, especially for clinics with fewer providers.
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Affiliation(s)
- Jonathan M Birnberg
- Section of General Internal Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
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15
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Lewis SE, Brodie JE, McCulloch MT, Mallela J, Jupiter SD, Williams HS, Lough JM, Matson EG. An assessment of an environmental gradient using coral geochemical records, Whitsunday Islands, Great Barrier Reef, Australia. Mar Pollut Bull 2011; 65:306-319. [PMID: 22030106 DOI: 10.1016/j.marpolbul.2011.09.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 09/15/2011] [Accepted: 09/26/2011] [Indexed: 05/31/2023]
Abstract
Coral cores were collected along an environmental and water quality gradient through the Whitsunday Island group, Great Barrier Reef (Australia), for trace element and stable isotope analysis. The primary aim of the study was to examine if this gradient could be detected in coral records and, if so, whether the gradient has changed over time with changing land use in the adjacent river catchments. Y/Ca was the trace element ratio which varied spatially across the gradient, with concentrations progressively decreasing away from the river mouths. The Ba/Ca and Y/Ca ratios were the only indicators of change in the gradient through time, increasing shortly after European settlement. The Mn/Ca ratio responded to local disturbance related to the construction of tourism infrastructure. Nitrogen isotope ratios showed no apparent trend over time. This study highlights the importance of site selection when using coral records to record regional environmental signals.
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Affiliation(s)
- S E Lewis
- Catchment to Reef Research Group, Australian Centre for Tropical Freshwater Research, James Cook University, Townsville, QLD 4811, Australia.
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16
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Kristinsson R, Lewis SE, Danielson PB. Comparative analysis of the HV1 and HV2 regions of human mitochondrial DNA by denaturing high-performance liquid chromatography. J Forensic Sci 2009; 54:28-36. [PMID: 19120825 DOI: 10.1111/j.1556-4029.2008.00940.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Denaturing high-performance liquid chromatography (DHPLC) was evaluated as a sequencing-independent means of detecting the presence of sequence differences in pair-wise mixtures of nonconcordant amplicons of human mitochondrial DNA (mtDNA). A total of 920 pair-wise combinations of HV1 and HV2 mtDNA amplicons from 95 individuals were assayed by DHPLC for sequence concordance/nonconcordance. For the 72 combinations of amplicons from different individuals who shared identical DNA sequences, DHPLC assays consistently indicated sequence concordance between the samples. This was in 100% agreement with sequencing data. For the 849 combinations of amplicons which differed in sequence, DHPLC detected the presence of sequence nonconcordance in all but 13 assays to yield 98.5% concordance with sequencing. Thus, DHPLC can be used to detect a diversity of sequence differences (transitions, transversions, insertions, and deletions) in the mtDNA D-loop. Accordingly, DHPLC may have utility as a presumptive indicator of mtDNA sequence concordance samples, as a screen for heteroplasmy/situational mixtures, and as a means for the physical fractionation of the individual contributors to an mtDNA mixture prior to sequencing.
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Affiliation(s)
- Richard Kristinsson
- Department of Biological Sciences, University of Denver, 2190 E. Iliff Avenue, Denver, Colorado 80208, USA.
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17
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Bennetts LE, De Iuliis GN, Nixon B, Kime M, Zelski K, McVicar CM, Lewis SE, Aitken RJ. Impact of estrogenic compounds on DNA integrity in human spermatozoa: evidence for cross-linking and redox cycling activities. Mutat Res 2008; 641:1-11. [PMID: 18342339 DOI: 10.1016/j.mrfmmm.2008.02.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 02/02/2008] [Indexed: 05/26/2023]
Abstract
A great deal of circumstantial evidence has linked DNA damage in human spermatozoa with adverse reproductive outcomes including reduced fertility and high rates of miscarriage. Although oxidative stress is thought to make a significant contribution to DNA damage in the male germ line, the factors responsible for creating this stress have not been elucidated. One group of compounds that are thought to be active in this context are the estrogens, either generated as a result of the endogenous metabolism of androgens within the male reproductive tract or gaining access to the latter as a consequence of environmental exposure. In this study, a wide variety of estrogenic compounds were assessed for their direct effects on human spermatozoa in vitro. DNA integrity was assessed using the Comet and TUNEL assays, lesion frequencies were quantified by QPCR using targets within the mitochondrial and nuclear (beta-globin) genomes, DNA adducts were characterized by mass spectrometry and redox activity was monitored using dihydroethidium (DHE) as the probe. Of the estrogenic and estrogen analogue compounds evaluated, catechol estrogens, quercetin, diethylstilbestrol and pyrocatechol stimulated intense redox activity while genistein was only active at the highest doses tested. Other estrogens and estrogen analogues, such as 17beta-estradiol, nonylphenol, bisphenol A and 2,3-dihydroxynaphthalene were inactive. Estrogen-induced redox activity was associated with a dramatic loss of motility and, in the case of 2-hydroxyestradiol, the induction of significant DNA fragmentation. Mass spectrometry also indicated that catechol estrogens were capable of forming dimers that can cross-link the densely packed DNA strands in sperm chromatin, impairing nuclear decondensation. These results highlight the potential importance of estrogenic compounds in creating oxidative stress and DNA damage in the male germ line and suggest that further exploration of these compounds in the aetiology of male infertility is warranted.
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Affiliation(s)
- L E Bennetts
- ARC Centre of Excellence in Biotechnology and Development and Discipline of Biological Sciences, University of Newcastle, NSW, Australia
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18
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Newman HA, Romeo MJ, Lewis SE, Yan BC, Orlean P, Levin DE. Gpi19, the Saccharomyces cerevisiae homologue of mammalian PIG-P, is a subunit of the initial enzyme for glycosylphosphatidylinositol anchor biosynthesis. Eukaryot Cell 2006; 4:1801-7. [PMID: 16278447 PMCID: PMC1287868 DOI: 10.1128/ec.4.11.1801-1807.2005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Glycosylphosphatidylinositols (GPIs) are attached to the C termini of some glycosylated secretory proteins, serving as membrane anchors for many of those on the cell surface. Biosynthesis of GPIs is initiated by the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol. This reaction is carried out at the endoplasmic reticulum (ER) by an enzyme complex called GPI-N-acetylglucosaminyltransferase (GPI-GlcNAc transferase). The human enzyme has six known subunits, at least four of which, GPI1, PIG-A, PIG-C, and PIG-H, have functional homologs in the budding yeast Saccharomyces cerevisiae. The uncharacterized yeast gene YDR437w encodes a protein with some sequence similarity to human PIG-P, a fifth subunit of the GPI-GlcNAc transferase. Here we show that Ydr437w is a small but essential subunit of the yeast GPI-GlcNAc transferase, and we designate its gene GPI19. Similar to other mutants in the yeast enzyme, temperature-sensitive gpi19 mutants display cell wall defects and hyperactive Ras phenotypes. The Gpi19 protein associates with the yeast GPI-GlcNAc transferase in vivo, as judged by coimmuneprecipitation with the Gpi2 subunit. Moreover, conditional gpi19 mutants are defective for GPI-GlcNAc transferase activity in vitro. Finally, we present evidence for the topology of Gpi19 within the ER membrane.
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Affiliation(s)
- Heather A Newman
- Department of Biochemistry & Molecular Biology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21205-2179, USA
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19
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Ashburner M, Mungall CJ, Lewis SE. Ontologies for biologists: a community model for the annotation of genomic data. Cold Spring Harb Symp Quant Biol 2004; 68:227-35. [PMID: 15338622 DOI: 10.1101/sqb.2003.68.227] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- M Ashburner
- Department of Genetics, University of Cambridge & EMBL-EBI, Hinxton, Cambridge, United Kingdom
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20
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Bell IR, Lewis DA, Brooks AJ, Schwartz GE, Lewis SE, Walsh BT, Baldwin CM. Improved clinical status in fibromyalgia patients treated with individualized homeopathic remedies versus placebo. Rheumatology (Oxford) 2004; 43:577-82. [PMID: 14734789 DOI: 10.1093/rheumatology/keh111] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE To assess the efficacy of individualized classical homeopathy in the treatment of fibromyalgia. METHODS This study was a double-blind, randomized, parallel-group, placebo-controlled trial of homeopathy. Community-recruited persons (N = 62) with physician-confirmed fibromyalgia (mean age 49 yr, s.d. 10 yr, 94% women) were treated in a homeopathic private practice setting. Participants were randomized to receive oral daily liquid LM (1/50,000) potencies with an individually chosen homeopathic remedy or an indistinguishable placebo. Homeopathic visits involved joint interviews and concurrence on remedy selection by two experienced homeopaths, at baseline, 2 months and 4 months (prior to a subsequent optional crossover phase of the study which is reported elsewhere). Tender point count and tender point pain on examination by a medical assessor uninvolved in providing care, self-rating scales on fibromyalgia-related quality of life, pain, mood and global health at baseline and 3 months, were the primary clinical outcome measures for this report. RESULTS Fifty-three people completed the treatment protocol. Participants on active treatment showed significantly greater improvements in tender point count and tender point pain, quality of life, global health and a trend toward less depression compared with those on placebo. CONCLUSIONS This study replicates and extends a previous 1-month placebo-controlled crossover study in fibromyalgia that pre-screened for only one homeopathic remedy. Using a broad selection of remedies and the flexible LM dose (1/50,000 dilution factor) series, the present study demonstrated that individualized homeopathy is significantly better than placebo in lessening tender point pain and improving the quality of life and global health of persons with fibromyalgia.
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Affiliation(s)
- I R Bell
- Department of Psychiatry, Mel and Enid Zuckerman Arizona College of Public Health at the University of Arizona, Tucson, USA.
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21
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Abstract
The 63-kDa murine fatty acid transport protein 1 (FATP1) was cloned on the basis of its ability to augment fatty acid import when overexpressed in mammalian cells. The membrane topology of this integral plasma membrane protein does not resemble that of polytopic membrane transporters for other substrates. Western blot analysis of 3T3-L1 adipocytes that natively express FATP1 demonstrate a prominent 130-kDa species as well as the expected 63-kDa FATP1, suggesting that this protein may participate in a cell surface transport protein complex. To test whether FATP1 is capable of oligomerization, we expressed functional FATP1 molecules with different amino- or carboxyl-terminal epitope tags in fibroblasts. These epitope-tagged proteins also form apparent higher molecular weight species. We show that, when expressed in the same cells, differentially tagged FATP1 proteins co-immunoprecipitate. The region between amino acid residues 191 and 475 is sufficient for association of differentially tagged truncated FATP1 constructs. When wild type FATP1 and the non-functional s250a FATP1 mutant are co-expressed in COS7 cells, mutant FATP1 has dominant inhibitory function in fatty acid uptake assays. Taken together, these results are consistent with a model in which FATP1 homodimeric complexes play an important role in cellular fatty acid import.
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Affiliation(s)
- M Rachel Richards
- Center for Cardiovascular Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110-1010, USA
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22
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Listenberger LL, Han X, Lewis SE, Cases S, Farese RV, Ory DS, Schaffer JE. Triglyceride accumulation protects against fatty acid-induced lipotoxicity. Proc Natl Acad Sci U S A 2003; 100:3077-82. [PMID: 12629214 PMCID: PMC152249 DOI: 10.1073/pnas.0630588100] [Citation(s) in RCA: 1408] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Excess lipid accumulation in non-adipose tissues is associated with insulin resistance, pancreatic beta-cell apoptosis and heart failure. Here, we demonstrate in cultured cells that the relative toxicity of two common dietary long chain fatty acids is related to channeling of these lipids to distinct cellular metabolic fates. Oleic acid supplementation leads to triglyceride accumulation and is well tolerated, whereas excess palmitic acid is poorly incorporated into triglyceride and causes apoptosis. Unsaturated fatty acids rescue palmitate-induced apoptosis by channeling palmitate into triglyceride pools and away from pathways leading to apoptosis. Moreover, in the setting of impaired triglyceride synthesis, oleate induces lipotoxicity. Our findings support a model of cellular lipid metabolism in which unsaturated fatty acids serve a protective function against lipotoxicity though promotion of triglyceride accumulation.
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Affiliation(s)
- Laura L Listenberger
- Center for Cardiovascular Research, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110-1010, USA
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23
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Meloni I, Muscettola M, Raynaud M, Longo I, Bruttini M, Moizard MP, Gomot M, Chelly J, des Portes V, Fryns JP, Ropers HH, Magi B, Bellan C, Volpi N, Yntema HG, Lewis SE, Schaffer JE, Renieri A. FACL4, encoding fatty acid-CoA ligase 4, is mutated in nonspecific X-linked mental retardation. Nat Genet 2002; 30:436-40. [PMID: 11889465 DOI: 10.1038/ng857] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
X-linked mental retardation (XLMR) is an inherited condition that causes failure to develop cognitive abilities, owing to mutations in a gene on the X chromosome. The latest XLMR update lists up to 136 conditions leading to 'syndromic', or 'specific', mental retardation (MRXS) and 66 entries leading to 'nonspecific' mental retardation (MRX). For 9 of the 66 MRX entries, the causative gene has been identified. Our recent discovery of the contiguous gene deletion syndrome ATS-MR (previously known as Alport syndrome, mental retardation, midface hypoplasia, elliptocytosis, OMIM #300194), characterized by Alport syndrome (ATS) and mental retardation (MR), indicated Xq22.3 as a region containing one mental retardation gene. Comparing the extent of deletion between individuals with ATS-MR and individuals with ATS alone allowed us to define a critical region for mental retardation of approximately 380 kb, containing four genes. Here we report the identification of two point mutations, one missense and one splice-site change, in the gene FACL4 in two families with nonspecific mental retardation. Analysis of enzymatic activity in lymphoblastoid cell lines from affected individuals of both families revealed low levels compared with normal cells, indicating that both mutations are null mutations. All carrier females with either point mutations or genomic deletions in FACL4 showed a completely skewed X-inactivation, suggesting that the gene influences survival advantage. FACL4 is the first gene shown to be involved in nonspecific mental retardation and fatty-acid metabolism.
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Affiliation(s)
- Ilaria Meloni
- Medical Genetics, Department of Molecular Biology, University of Siena, Italy
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24
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Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM, Lewis SE. An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol 2002; 3:RESEARCH0081. [PMID: 12537570 PMCID: PMC151183 DOI: 10.1186/gb-2002-3-12-research0081] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Accepted: 11/28/2002] [Indexed: 01/02/2023] Open
Abstract
We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome annotation. The key contributions to overall annotation quality are the marshalling of high-quality sequences for alignments and the design of a system with an adaptable and expandable flexible architecture.
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Affiliation(s)
- C J Mungall
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.
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25
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Lewis SE, Searle SMJ, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME. Apollo: a sequence annotation editor. Genome Biol 2002; 3:RESEARCH0082. [PMID: 12537571 PMCID: PMC151184 DOI: 10.1186/gb-2002-3-12-research0082] [Citation(s) in RCA: 311] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2002] [Revised: 11/13/2002] [Accepted: 11/23/2002] [Indexed: 11/10/2022] Open
Abstract
The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects.
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Affiliation(s)
- S E Lewis
- Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94720-3200, USA.
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26
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Abstract
OBJECTIVE To investigate effects of cryopreservation on sperm motility and DNA integrity. DESIGN Pre-cryopreservation and post-cryopreservation analysis of motility and DNA integrity of semen and prepared sperm samples. SETTING A hospital andrology laboratory. PATIENT(S) Forty men attending the Regional Fertility Centre, Belfast, Northern Ireland. INTERVENTION(S) Each sample was divided, and an aliquot was frozen unprepared. Remaining aliquots were prepared by Percoll density centrifugation (95.0:47.5) or direct swim-up procedure and divided into aliquots to allow direct comparison of fresh and frozen semen and prepared sperm (frozen with or without the addition of seminal plasma) from the same ejaculate. Samples were frozen by static-phase vapor cooling and being plunged into liquid nitrogen. Thawing was carried out at room temperature. MAIN OUTCOME MEASURE(S) Sperm DNA integrity was determined using a modified alkaline single cell gel electrophoresis (comet) assay, and motility was determined using computer-assisted semen analysis. RESULT(S) Sperm frozen unprepared in seminal fluid appeared more resistant to freezing damage than frozen prepared sperm. Further improvements can be achieved by selecting out the subpopulation of sperm with best motility and DNA integrity and freezing these sperm in seminal plasma, making this the optimal procedure. CONCLUSION(S) Freezing sperm in seminal plasma improves postthaw motility and DNA integrity.
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Affiliation(s)
- E T Donnelly
- Department of Obstetrics and Gynaecology, The Queen's University of Belfast, Northern Ireland.
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27
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Abstract
The murine fatty acid transport protein (FATP1) was identified in an expression cloning screen for proteins that facilitate transport of fatty acids across the plasma membranes of mammalian cells. Hydropathy analysis of this protein suggests a model in which FATP1 has multiple membrane-spanning domains. To test this model, we inserted a hemagglutinin epitope tag at the amino terminus or a FLAG tag at the carboxyl terminus of the FATP1 cDNA and expressed these constructs in NIH 3T3 cells. Both tagged constructs produce proteins of the expected molecular masses and are functional in fatty acid import assays. Indirect immunofluorescence studies with selective permeabilization conditions and protease protection studies of sealed membrane vesicles from cells expressing epitope-tagged FATP1 were performed. These experiments show that the extreme amino terminus of tagged FATP1 is oriented toward the extracellular space, whereas the carboxyl terminus faces the cytosol. Additionally, enhanced green fluorescent protein fusion constructs containing predicted membrane-associated or soluble portions of FATP1 were expressed in Cos7 cells and analyzed by immunofluorescence and subcellular fractionation. These experiments demonstrate that amino acids 1-51, 52-100, and 101-190 contain signals for integral association with the membrane, whereas residues 258-313 and 314-475 are only peripherally membrane-associated. Amino acid residues 191-257 and 476-646 do not direct membrane association and likely face the cytosol. Taken together, these data support a model of FATP1 as a polytopic membrane protein with at least one transmembrane and multiple membrane-associated domains. This study provides the first experimental evidence for topology of a member of the family of plasma membrane fatty acid transport proteins.
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Affiliation(s)
- S E Lewis
- Center for Cardiovascular Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110-1010, USA
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28
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Donnelly ET, Steele EK, McClure N, Lewis SE. Assessment of DNA integrity and morphology of ejaculated spermatozoa from fertile and infertile men before and after cryopreservation. Hum Reprod 2001; 16:1191-9. [PMID: 11387291 DOI: 10.1093/humrep/16.6.1191] [Citation(s) in RCA: 189] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cryopreservation of human spermatozoa is extensively used in artificial insemination and IVF programmes. Despite various advances in cryopreservation methodology, the recovery rate of functional post-thaw spermatozoa remains mediocre, with sperm motility being significantly decreased after freezing. This aim of this study was to investigate the effects of cryopreservation on both DNA integrity and morphology of spermatozoa from fertile and infertile men. Semen samples were obtained from 17 fertile and 40 infertile men. All samples were prepared by discontinuous Percoll density centrifugation (95.0:47.5). Samples were divided into aliquots to allow direct comparison of fresh and frozen spermatozoa from the same ejaculate. Aliquots for cryopreservation were mixed with a commercial cryoprotectant and frozen by static phase vapour cooling before plunging into liquid nitrogen. Thawing was carried out slowly at room temperature. Sperm DNA integrity was determined using a modified alkaline single cell gel electrophoresis (comet) assay and sperm morphology analysed using the Tygerberg criteria. DNA of semen and prepared spermatozoa from fertile men was found to be unaffected by cryopreservation. In marked contrast, spermatozoa from infertile men were significantly damaged by freeze-thawing. Cryopreservation had a detrimental effect on morphology of semen and prepared samples from fertile and infertile men.
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Affiliation(s)
- E T Donnelly
- Department of Obstetrics & Gynaecology, The Queen's University of Belfast, Northern Ireland, UK.
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29
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Abstract
OBJECTIVE To assess the effect of Trucut needle biopsy on the ultrasound appearances of the testis in obstructive and nonobstructive azoospermia to test serum samples for antisperm antibodies and gonadotropin and testosterone levels. DESIGN Prospective case analysis. SETTING IVF unit. PATIENT(S) Sixteen subjects with obstructive azoospermia had postbiopsy ultrasound scans, 18 had assessment of hormone profiles, and 20 had evaluation of antisperm antibodies. INTERVENTION(S) Trucut needle testicular biopsies under local anesthetic. MAIN OUTCOME MEASURE(S) Postbiopsy testicular ultrasound, the presence of serum antisperm antibodies, and follicle stimulating and luteinizing hormone and testosterone levels. RESULT(S) There were no postbiopsy hematomas or scars, antisperm antibodies did not develop, and pituitary gonadotropins did not rise nor testosterone levels fall. CONCLUSION(S) Trucut needle testicular biopsy in men with obstructive azoospermia is not associated with defects of parenchymal structure or function.
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Affiliation(s)
- E K Steele
- School of Medicine, Department of Obstetrics and Gynecology, The Queen's University of Belfast, Grosvenor Road, Belfast BT12 6BJ, Northern Ireland, United Kingdom
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30
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Steele EK, McNally JA, Lewis SE, McClure N. The delivery of the first babies conceived using testicular sperm in Northern Ireland. Ulster Med J 2000; 69:165-7. [PMID: 11196731 PMCID: PMC2449185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- E K Steele
- Department of Obstetrics and Gynaecology, Queen's University of Belfast, Institute of Clinical Science, Grosvenor Road, Belfast BT12 6BJ
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31
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Abstract
OBJECTIVE To assess the effects of two methods of freezing on testicular sperm DNA from subjects with obstructive azoospermia and to compare these with samples of fresh and freeze-thawed testicular sperm from fertile men. DESIGN The Comet assay was used to determine the percentage of undamaged DNA in fresh testicular sperm, testicular sperm freeze-thawed in suspension and in a biopsy sample (men with obstructive azoospermia), and in fresh and freeze-thawed testicular sperm (fertile men). SETTING The Regional Fertility Center, Royal Maternity Hospital, Belfast, Northern Ireland, United Kingdom. PATIENT(S) Twelve males with obstructive azoospermia (normal testicular volume and hormone profiles) and nine fertile control subjects. INTERVENTION(S) Trucut needle testicular biopsy under local anesthetic. MAIN OUTCOME MEASURE(S) Measurement of the percentage of undamaged DNA in fresh and freeze-thawed testicular sperm using the Comet assay. RESULT(S) No significant difference was found between the percentage of undamaged DNA of fresh testicular sperm and of both types of freeze-thawed testicular sperm. There was also no significant difference between the percentage of undamaged DNA in fresh or freeze-thawed testicular sperm from controls. Control ejaculated sperm DNA was significantly more damaged than testicular sperm DNA from control men. CONCLUSION(S) Cryopreservation of testicular sperm does not increase baseline levels of DNA damage.
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Affiliation(s)
- E K Steele
- Department of Obstetrics and Gynecology, The Queen's University of Belfast, Institute of Clinical Science, Northern, Belfast, Ireland
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Steele EK, Kelly JD, Lewis SE, McNally JA, Sloan JM, McClure N. Testicular sperm extraction by Trucut needle and milking of seminiferous tubules: a technique with high yield and patient acceptability. Fertil Steril 2000; 74:380-3. [PMID: 10927063 DOI: 10.1016/s0015-0282(00)00655-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVE To assess the sperm yield and patient acceptability of Trucut needle testicular biopsy followed by seminiferous tubule milking. DESIGN Prospective case analysis. SETTING The Regional Fertility Center, Royal Maternity Hospital, Belfast, Northern Ireland, United Kingdom. PATIENT(S) Forty-one males with obstructive azoospermia (normal testicular volume and FSH and LH levels). INTERVENTION(S) Trucut needle testicular biopsies under local anesthetic with milking of the seminiferous tubules. MAIN OUTCOME MEASURE(S) Quantitation of sperm retrieved per biopsy core and patient follow-up by questionnaire. RESULT(S) A mean of 105,634 sperm (range, 5,000-427,800) were retrieved, and the mean biopsy weight was 9.17 mg. Twenty-six subjects found the biopsy painless and 15 were pain-free after biopsy. CONCLUSION(S) The Trucut needle can be used in combination with seminiferous tubule milking to obtain large numbers of sperm in men with obstructive azoospermia.
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Affiliation(s)
- E K Steele
- Department of Obstetrics and Gynecology, The Queen's University of Belfast, Institute of Clinical Science, Belfast, Northern Ireland, UK.
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Donnelly ET, O'Connell M, McClure N, Lewis SE. Differences in nuclear DNA fragmentation and mitochondrial integrity of semen and prepared human spermatozoa. Hum Reprod 2000; 15:1552-61. [PMID: 10875865 DOI: 10.1093/humrep/15.7.1552] [Citation(s) in RCA: 170] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sperm DNA integrity is essential for accurate transmission of genetic material to offspring. Fragmentation of genomic DNA is an initial hallmark of apoptosis (programmed cell death). The aim of this study was to determine sperm nuclear DNA integrity and mitochondrial function, to quantify possible apoptosis and to investigate any relationship between these parameters. Semen samples (n = 25) were prepared by discontinuous Percoll density centrifugation (95.0:47.5). DNA integrity was determined using a modified alkaline single cell gel electrophoresis (Comet) assay. DNA fragmentation, possibly indicative of apoptosis, was detected by terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling (TUNEL). Mitochondrial transmembrane potential was determined using the mitochondrial probe 5,5',6,6'-tetrachloro-1,1', 3,3'-tetraethylbenzimidazolyl carbocyanine iodide (JC-1). The DNA integrity of prepared spermatozoa was significantly greater than that of semen (P < 0.005). Further, the percentage of spermatozoa with fragmented DNA and the degree of fragmentation within these cells in prepared spermatozoa is significantly less than in semen (P < 0.005). There is a significant correlation between DNA damage quantified using the Comet assay and DNA fragmentation determined using TUNEL (R = 0.562, P < 0.01). The percentage of spermatozoa with dysfunctional, possibly apoptotic, mitochondria was significantly lower in prepared spermatozoa than in neat semen samples (P < 0.001). There was a negative correlation between the percentage of spermatozoa with dysfunctional mitochondria and the percentage of progressively motile spermatozoa (R = -0.67, P < 0.01).
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Affiliation(s)
- E T Donnelly
- Department of Obstetrics & Gynaecology, The Queen's University of Belfast, Northern Ireland, UK.
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Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE. Genome annotation assessment in Drosophila melanogaster. Genome Res 2000; 10:483-501. [PMID: 10779488 PMCID: PMC310877 DOI: 10.1101/gr.10.4.483] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2000] [Accepted: 02/29/2000] [Indexed: 11/24/2022]
Abstract
Computational methods for automated genome annotation are critical to our community's ability to make full use of the large volume of genomic sequence being generated and released. To explore the accuracy of these automated feature prediction tools in the genomes of higher organisms, we evaluated their performance on a large, well-characterized sequence contig from the Adh region of Drosophila melanogaster. This experiment, known as the Genome Annotation Assessment Project (GASP), was launched in May 1999. Twelve groups, applying state-of-the-art tools, contributed predictions for features including gene structure, protein homologies, promoter sites, and repeat elements. We evaluated these predictions using two standards, one based on previously unreleased high-quality full-length cDNA sequences and a second based on the set of annotations generated as part of an in-depth study of the region by a group of Drosophila experts. Although these standard sets only approximate the unknown distribution of features in this region, we believe that when taken in context the results of an evaluation based on them are meaningful. The results were presented as a tutorial at the conference on Intelligent Systems in Molecular Biology (ISMB-99) in August 1999. Over 95% of the coding nucleotides in the region were correctly identified by the majority of the gene finders, and the correct intron/exon structures were predicted for >40% of the genes. Homology-based annotation techniques recognized and associated functions with almost half of the genes in the region; the remainder were only identified by the ab initio techniques. This experiment also presents the first assessment of promoter prediction techniques for a significant number of genes in a large contiguous region. We discovered that the promoter predictors' high false-positive rates make their predictions difficult to use. Integrating gene finding and cDNA/EST alignments with promoter predictions decreases the number of false-positive classifications but discovers less than one-third of the promoters in the region. We believe that by establishing standards for evaluating genomic annotations and by assessing the performance of existing automated genome annotation tools, this experiment establishes a baseline that contributes to the value of ongoing large-scale annotation projects and should guide further research in genome informatics.
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Affiliation(s)
- M G Reese
- Berkeley Drosophila Genome Project, Department of Molecular and Cell Biology, University of California, Berkeley 94720-3200, USA.
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Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC. The genome sequence of Drosophila melanogaster. Science 2000; 287:2185-95. [PMID: 10731132 DOI: 10.1126/science.287.5461.2185] [Citation(s) in RCA: 3976] [Impact Index Per Article: 165.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.
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Affiliation(s)
- M D Adams
- Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
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Donnelly ET, McClure N, Lewis SE. Glutathione and hypotaurine in vitro: effects on human sperm motility, DNA integrity and production of reactive oxygen species. Mutagenesis 2000; 15:61-8. [PMID: 10640532 DOI: 10.1093/mutage/15.1.61] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sperm DNA integrity is of paramount importance for the accurate conveyance of genetic material. DNA damage may be a major contributory factor in male infertility as DNA from sperm of infertile men has been found to be more susceptible to induced DNA damage in vitro than DNA from fertile men. Reactive oxygen species (ROS) are a significant source of DNA damage and human sperm are extremely sensitive to ROS attack due to their high content of polyunsaturated fatty acids and lack of capacity for DNA repair. Seminal plasma, which contains a wealth of antioxidants, provides sperm with crucial protection against oxidative insult. However, during preparation for use in assisted conception techniques, sperm are separated from seminal plasma and deprived of that essential protection. The aim of this study was to determine the effects of supplementation with glutathione and hypotaurine during sperm preparation on subsequent sperm motility, DNA integrity, induced DNA damage and ROS generation. Semen samples (n = 45) were divided into aliquots and prepared by Percoll density centrifugation (95.0-47.5%) using medium which had been supplemented with these antioxidants to a number of different concentrations all within physiological levels. Control aliquots were included which had no glutathione or hypotaurine added. Sperm motility was determined using computer-assisted semen analysis. DNA damage was induced using H(2)O(2) and DNA integrity was determined using a modified alkaline single cell gel electrophoresis (Comet) assay, while ROS generation was measured using chemiluminescence. Addition of glutathione and hypotaurine, either singly or in combination, to sperm preparation medium had no significant effect on sperm progressive motility or baseline DNA integrity. Despite this, sperm were still afforded significant protection against H(2)O(2)-induced damage and ROS generation.
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Affiliation(s)
- E T Donnelly
- Department of Obstetrics and Gynaecology, The Queen's University of Belfast, Institute of Clinical Science, Grosvenor Road, Belfast BT12 6BJ, UK.
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Lewis SE, Mannion RJ, White FA, Coggeshall RE, Beggs S, Costigan M, Martin JL, Dillmann WH, Woolf CJ. A role for HSP27 in sensory neuron survival. J Neurosci 1999; 19:8945-53. [PMID: 10516313 PMCID: PMC6782783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/1999] [Accepted: 08/06/1999] [Indexed: 02/14/2023] Open
Abstract
Peripheral nerve injury in neonatal rats results in the death of the majority of the axotomized sensory neurons by 7 d after injury. In adult animals, however, all sensory neurons survive for at least 4 months after axotomy. How sensory neurons acquire the capacity to survive axonal injury is not known. Here we describe how the expression of the small heat shock protein 27 (HSP27) is correlated with neuronal survival after axotomy in vivo and after NGF withdrawal in vitro. The number of HSP27-immunoreactive neurons in the L4 DRG is low at birth and does not change significantly for 21 d after postnatal day 0 (P0) sciatic nerve axotomy. In contrast, in the adult all axotomized neurons begin to express HSP27. One week after P0 sciatic nerve section the total number of neurons in the L4 DRG is dramatically reduced, but all surviving axotomized neurons, as identified by c-jun immunoreactivity, are immunoreactive for HSP27. In addition, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling reveals that very few HSP27-expressing neurons are dying 48 hr after neonatal axotomy. In vitro, a similar correlation exists between HSP27 expression and survival; in P0 DRG cultures, neurons that express HSP27 preferentially survive NGF withdrawal. Finally, overexpression of human HSP27 in neonatal rat sensory and sympathetic neurons significantly increases survival after NGF withdrawal, with nearly twice as many neurons surviving at 48 hr. Together these results suggest that HSP27 in sensory neurons plays a role in promoting survival after axotomy or neurotrophin withdrawal.
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Affiliation(s)
- S E Lewis
- Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02129, USA
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Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, Hartzell G, Harvey D, Hong L, Houston K, Hoskins R, Johnson G, Martin C, Moshrefi A, Palazzolo M, Reese MG, Spradling A, Tsang G, Wan K, Whitelaw K, Celniker S. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region. Genetics 1999; 153:179-219. [PMID: 10471707 PMCID: PMC1460734 DOI: 10.1093/genetics/153.1.179] [Citation(s) in RCA: 191] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized "Adh region." A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species. Before beginning a Hunt, it is wise to ask someone what you are looking for before you begin looking for it. Milne 1926
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Affiliation(s)
- M Ashburner
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, England.
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Steele EK, McClure N, Maxwell RJ, Lewis SE. A comparison of DNA damage in testicular and proximal epididymal spermatozoa in obstructive azoospermia. Mol Hum Reprod 1999; 5:831-5. [PMID: 10460221 DOI: 10.1093/molehr/5.9.831] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Testicular and epididymal spermatozoa are used routinely for intracytoplasmic sperm injection (ICSI) to treat men with obstructive azoospermia. Little is known of the effects of obstruction and stasis on the DNA of these spermatozoa, particularly in the epididymis where spermatozoa have been retained for long periods. Surgical epididymal aspiration for ICSI could provide spermatozoa that are senescent or dying. Using the Comet assay, the percentage of undamaged DNA of testicular spermatozoa from 20 men with obstructive azoospermia was significantly better (83.0 +/- 1. 2%) than from proximal epididymal spermatozoa (75.4 +/- 2.3%; P < 0. 05). There was no difference between the percentage of undamaged DNA of testicular spermatozoa from 39 men with obstructive azoospermia (84.0 +/- 0.9) or from 10 fertile men at vasectomy (86.8 +/- 1.8) or from ejaculated spermatozoa from five of the controls (78.9 +/- 3.9; P > 0.05). In nine subjects, a second biopsy was carried out 6 months later. There was no significant difference in undamaged DNA on these two occasions (83.5 +/- 5.6 and 84.1 +/- 4.2; P > 0.05). This confirms the reproducibility of the Comet assay for non-ejaculated spermatozoa. Our data suggest that testicular sperm DNA appears to be significantly less damaged than epididymal sperm DNA, and so testicular spermatozoa should be used in preference for ICSI to treat men with obstructive azoospermia.
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Affiliation(s)
- E K Steele
- Department of Obstetrics & Gynaecology, The Queen's University of Belfast, Institute of Clinical Science, Grosvenor Road, Belfast BT12 6BJ, UK
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Donnelly ET, McClure N, Lewis SE. The effect of ascorbate and alpha-tocopherol supplementation in vitro on DNA integrity and hydrogen peroxide-induced DNA damage in human spermatozoa. Mutagenesis 1999; 14:505-12. [PMID: 10473655 DOI: 10.1093/mutage/14.5.505] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aim of this study was to determine the effects of supplementation with ascorbate and alpha-tocopherol, both singly and in combination, during sperm preparation on subsequent sperm DNA integrity, induced DNA damage and reactive oxygen species (ROS) generation. Semen samples with normozoospermic and asthenozoospermic profiles (n = 15 for each control and antioxidant group) were prepared by Percoll density centrifugation (95.0-47.5%) where the medium had been supplemented with these antioxidants to a number of different concentrations, all within physiological levels. Controls were included which had no ascorbate or alpha-tocopherol added. DNA damage was induced using hydrogen peroxide (H(2)O(2)) and DNA integrity was determined using a modified alkaline single cell gel electrophoresis (Comet) assay, while ROS generation was measured using chemiluminescence. Addition of ascorbate to sperm preparation medium did not affect baseline DNA integrity but did provide sperm with complete protection against H(2)O(2)-induced DNA damage. Generation of H(2)O(2)-induced ROS was also significantly reduced after treatment with ascorbate, although baseline levels were unaffected by this antioxidant. Supplementation of sperm preparation medium with alpha-tocopherol did not influence baseline DNA integrity but provided sperm with dose-dependent protection against H(2)O(2)-induced DNA damage. Generation of H(2)O(2)-induced ROS was significantly reduced after treatment with alpha-tocopherol, although baseline ROS levels were unaffected by this antioxidant. Addition of both ascorbate and alpha-tocopherol in combination to sperm preparation medium actually induced DNA damage and intensified the damage induced by H(2)O(2), however, H(2)O(2)-induced ROS production was significantly reduced in a dose-dependent manner by supplementation with both vitamins.
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Affiliation(s)
- E T Donnelly
- Department of Obstetrics and Gynaecology, The Queen's University of Belfast, Institute of Clinical Science, Grosvenor Road, Belfast BT12 6BJ, UK.
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Abstract
OBJECTIVE To determine the effects of supplementation of preparation media with ascorbate and alpha-tocopherol on subsequent sperm motility and reactive oxygen species production. DESIGN Prospective study to analyze postpreparation human sperm motility parameters and reactive oxygen species production following antioxidant supplementation. SETTING Andrology Laboratory, Royal Maternity Hospital, Belfast, Northern Ireland. PATIENT(S) Sixty patients attending the Andrology Laboratory for semen analysis. INTERVENTION(S) Normozoospermic and asthenozoospermic semen samples (n = 10 for each control and antioxidant group) were prepared by Percoll density centrifugation (95%-47.5%) in media supplemented with ascorbate or alpha-tocopherol to different concentrations within physiologic levels. Controls were included that were not exposed to antioxidant. MAIN OUTCOME MEASURE(S) Sperm motility parameters were assessed using computer-assisted semen analysis. The generation of reactive oxygen species was determined using luminol-dependent chemiluminescence. RESULT(S) The production of reactive oxygen species by sperm was reduced by supplementation in vitro with ascorbate and alpha-tocopherol. However, progressive motility, average path velocity, curvilinear velocity, straight-line velocity, and linearity were decreased significantly, with the greatest inhibition observed with the highest concentrations of antioxidants. CONCLUSION(S) Supplementation of preparation media with ascorbate and alpha-tocopherol, either singly or in combination, is not beneficial to sperm motility.
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Affiliation(s)
- E T Donnelly
- Department of Obstetrics and Gynaecology, The Queen's University of Belfast, Northern Ireland.
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Rajadhyaksha A, Barczak A, Macías W, Leveque JC, Lewis SE, Konradi C. L-Type Ca(2+) channels are essential for glutamate-mediated CREB phosphorylation and c-fos gene expression in striatal neurons. J Neurosci 1999; 19:6348-59. [PMID: 10414964 PMCID: PMC4204489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023] Open
Abstract
The second messenger pathways linking receptor activation at the membrane to changes in the nucleus are just beginning to be unraveled in neurons. The work presented here attempts to identify in striatal neurons the pathways that mediate cAMP response element-binding protein (CREB) phosphorylation and gene expression in response to NMDA receptor activation. We investigated the phosphorylation of the transcription factor CREB, the expression of the immediate early gene c-fos, and the induction of a transfected reporter gene under the transcriptional control of CREB after stimulation of ionotropic glutamate receptors. We found that neither AMPA/kainate receptors nor NMDA receptors were able to stimulate independently a second messenger pathway that led to CREB phosphorylation or c-fos gene expression. Instead, we saw a consecutive pathway from AMPA/kainate receptors to NMDA receptors and from NMDA receptors to L-type Ca(2+) channels. AMPA/kainate receptors were involved in relieving the Mg(2+) block of NMDA receptors, and NMDA receptors triggered the opening of L-type Ca(2+) channels. The second messenger pathway that activates CREB phosphorylation and c-fos gene expression is likely activated by Ca(2+) entry through L-type Ca(2+) channels. We conclude that in primary striatal neurons glutamate-mediated signal transduction is dependent on functional L-type Ca(2+) channels.
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Affiliation(s)
- A Rajadhyaksha
- Molecular and Developmental Neuroscience Laboratory and Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, USA
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Abstract
To examine whether there is a tendency for individuals to be multiply addicted, overlapping addictions to common substances (alcohol, caffeine, chocolate, cigarettes) and activities (exercise, gambling, Internet use, television, video games) were studied in 129 college men and women. Contrary to previous research, moderate to large correlations were found, both within and between substances and activities. Self-esteem was positively related to exercise but unrelated to the remaining addictions. Several gender differences in addictive tendencies were also revealed: Men scored higher than women on addiction to alcohol, cigarettes, gambling, television, and Internet use, but women scored higher on caffeine and chocolate. The results have implications for theories of addiction and suggest new directions for the study of addiction among normally functioning young adults.
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Byrne PA, Lewis SE, Traub AI, McClure N. Why the NHS should fund infertility services. Ulster Med J 1999; 68:2-3. [PMID: 10489804 PMCID: PMC2449150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Affiliation(s)
- S E Lewis
- Department of Anesthesiology, University of Alabama at Birmingham School of Medicine, Veterans Affairs Medical Center 35233, USA.
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Abstract
A brief history of the developmental life cycle of the mammalian germ cell, from fertilization to gametogenesis in the mature gonad, is presented. The differences between gametogenesis in the mature gonad of males and females are also described with regard to properties that may affect their susceptibilities to mutation. It is emphasized that any historical control background rate of necessity will include mutations that occur in germinal tissue at all stages of development and differentiation, although it is not always possible to determine at what stage of germline development a spontaneous mutation has occurred. Studies of induced mutations suggest that the impact on the molecular level and the distribution of mutations among the F1 and F2 progeny may be partly determined by the stage and sex of germ cells in which spontaneous mutations occur. In summary, historical control rates should only be considered the sum total of mutations that occur during the entire life of the individual and cannot represent the control values of any individual germ cell stage. Nonetheless, it is certainly important and valid to use historical control data for calculating human risk, because the primary use of the estimation of mutant frequencies is to access the potential impact of agents in increasing the genetic load in the human population.
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Affiliation(s)
- S E Lewis
- Research Triangle Institute, Research Triangle Park, North Carolina 27709-2194, USA
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47
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Affiliation(s)
- E K Steele
- Department of Obstetrics and Gynaecology, Queen's University of Belfast, Institute of Clinical Science, UK
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48
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Donnelly GP, McClure N, Kennedy MS, Lewis SE. Direct effect of alcohol on the motility and morphology of human spermatozoa. Andrologia 1999; 31:43-7. [PMID: 9949888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
Excessive alcohol consumption has been associated with impaired reproductive function by causing the inhibition of penile tumescence and ejaculatory capability. Alcohol intoxication has also been implicated in impaired spermatogenesis and an increase in sperm structural anomalies. The aim of this study was to determine the direct effects of alcohol on sperm motility and morphology in vitro. Semen samples from 67 subjects were prepared using density centrifugation. Ethanol was added, at concentrations in serum equivalent to social, moderate and heavy drinking, to the medium in which the spermatozoa were cultured. Sperm motility was assessed using computer assisted semen analysis and morphology was assessed by Tygerberg strict criteria after 0, 15, 30, 60, 120, 180 and 240 min exposure. Each concentration of ethanol produced significant decreases in the percentage progressive motility, straight line velocity and curvilinear velocity. The amplitude of lateral head displacement was also depressed by 300 and 500 mg dL-1 of ethanol. A significant decrease in the number of spermatozoa with normal morphology and an increase in irreversible tail defects were observed after exposure to 300 mg dL-1 ethanol. When alcohol is added directly to sperm, at concentrations equivalent to those in serum after moderate and heavy drinking, damaging effects are observed in both sperm motility and morphology.
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Affiliation(s)
- G P Donnelly
- Department of Obstetrics and Gynaecology, Queen's University of Belfast, UK
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49
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Abstract
DNA integrity in sperm is essential for the accurate transmission of genetic information and therefore the maintenance of good health in future generations. The ELISA and Comet assays, two techniques that detect DNA damage in cells, are compared in this study of DNA integrity in human sperm. Both techniques rely on alkaline unwinding for the release of single strands of DNA from the nucleus. The ELISA detects single strands immunochemically whereas the Comet assay measures single strands drawn out by electrophoresis, stained with ethidium bromide and quantified by image analysis. The two techniques, both modified for use with sperm, detect similar levels of baseline DNA damage along with similar dose-dependent patterns of induced damage by X-ray irradiation at 10 and 30 Gy (P < 0.05). The assays are also comparable in the detection of a significant protective effect by ascorbic acid (300 and 600 microM) and alpha-tocopherol (30 and 60 microM) on DNA integrity, both at baseline levels and following X-ray irradiation (p < 0.01). The advantages and disadvantages of each technique are discussed.
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Affiliation(s)
- C M Hughes
- Department of Obstetrics and Gynaecology, Queens University of Belfast, UK
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50
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Abstract
Infertility affects approximately 15% of couples, and in about one-third the primary cause is a male factor. Patients undergoing infertility investigations frequently experience sexual dysfunction, which often is due to inadequate vaginal lubrication. This can lead to increased use of coital lubricants. The effects of such lubricants on sperm motility have not been widely studied, although sperm motility is one of the best prognostic indicators of fertilization. Using a prospective longitudinal control-based study, we analysed the effect of adding four lubricants: KY jelly, baby oil, olive oil and saliva on sperm motion in 16 samples from patients undergoing infertility investigations. Sperm samples were prepared by density gradient centrifugation prior to mixing with lubricants. Motility parameters were determined using computer-assisted semen analysis after 5, 15 and 30 min. All lubricants except baby oil significantly decreased percentage progressive motility, progressive velocity, curvilinear velocity and lateral head displacement at 12.5% concentration. At a lower concentration of 6.25%, both olive oil and saliva still significantly reduced progressive motility parameters, while KY jelly diminished head movement parameters. Hence, even at these very low concentrations, coital lubricants impair sperm motility and thus may adversely affect fertility.
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Affiliation(s)
- L Anderson
- Department of Obstetrics and Gynaecology, The Queen's University of Belfast, Institute of Clinical Science, UK
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