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Buelo CD, Pace ML, Carpenter SR, Stanley EH, Ortiz DA, Ha DT. Evaluating the performance of temporal and spatial early warning statistics of algal blooms. Ecol Appl 2022; 32:e2616. [PMID: 35368134 DOI: 10.1002/eap.2616] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Regime shifts have large consequences for ecosystems and the services they provide. However, understanding the potential for, causes of, proximity to, and thresholds for regime shifts in nearly all settings is difficult. Generic statistical indicators of resilience have been proposed and studied in a wide range of ecosystems as a method to detect when regime shifts are becoming more likely without direct knowledge of underlying system dynamics or thresholds. These early warning statistics (EWS) have been studied separately but there have been few examples that directly compare temporal and spatial EWS in ecosystem-scale empirical data. To test these methods, we collected high-frequency time series and high-resolution spatial data during a whole-lake fertilization experiment while also monitoring an adjacent reference lake. We calculated two common EWS, standard deviation and autocorrelation, in both time series and spatial data to evaluate their performance prior to the resulting algal bloom. We also applied the quickest detection method to generate binary alarms of resilience change from temporal EWS. One temporal EWS, rolling window standard deviation, provided advanced warning in most variables prior to the bloom, showing trends and between-lake patterns consistent with theory. In contrast, temporal autocorrelation and both measures of spatial EWS (spatial SD, Moran's I) provided little or no warning. By compiling time series data from this and past experiments with and without nutrient additions, we were able to evaluate temporal EWS performance for both constant and changing resilience conditions. True positive alarm rates were 2.5-8.3 times higher for rolling window standard deviation when a lake was being pushed towards a bloom than the rate of false positives when it was not. For rolling window autocorrelation, alarm rates were much lower and no variable had a higher true positive than false positive alarm rate. Our findings suggest temporal EWS provide advanced warning of algal blooms and that this approach could help managers prepare for and/or minimize negative bloom impacts.
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Affiliation(s)
- C D Buelo
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia, USA
- Center for Limnology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - M L Pace
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - S R Carpenter
- Center for Limnology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - E H Stanley
- Center for Limnology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - D A Ortiz
- Center for Limnology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - D T Ha
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia, USA
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2
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Nguyen MH, Pham TTM, Pham LV, Phan DT, Tran TV, Nguyen HC, Nguyen HC, Ha TH, Dao HK, Nguyen PB, Trinh MV, Do TV, Nguyen HQ, Nguyen TTP, Nguyen NPT, Tran CQ, Tran KV, Duong TT, Nguyen TT, Pham KM, Nguyen LV, Vo TT, Do BN, Dang NH, Le TT, Do NT, Nguyen HTT, Mai TTT, Ha DT, Ngo HTM, Nguyen KT, Bai CH, Duong TV. Associations of Underlying Health Conditions With Anxiety and Depression Among Outpatients: Modification Effects of Suspected COVID-19 Symptoms, Health-Related and Preventive Behaviors. Int J Public Health 2021; 66:634904. [PMID: 34335139 PMCID: PMC8284590 DOI: 10.3389/ijph.2021.634904] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Objectives: We explored the association of underlying health conditions (UHC) with depression and anxiety, and examined the modification effects of suspected COVID-19 symptoms (S-COVID-19-S), health-related behaviors (HB), and preventive behaviors (PB). Methods: A cross-sectional study was conducted on 8,291 outpatients aged 18–85 years, in 18 hospitals and health centers across Vietnam from 14th February to May 31, 2020. We collected the data regarding participant's characteristics, UHC, HB, PB, depression, and anxiety. Results: People with UHC had higher odds of depression (OR = 2.11; p < 0.001) and anxiety (OR = 2.86; p < 0.001) than those without UHC. The odds of depression and anxiety were significantly higher for those with UHC and S-COVID-19-S (p < 0.001); and were significantly lower for those had UHC and interacted with “unchanged/more” physical activity (p < 0.001), or “unchanged/more” drinking (p < 0.001 for only anxiety), or “unchanged/healthier” eating (p < 0.001), and high PB score (p < 0.001), as compared to those without UHC and without S-COVID-19-S, “never/stopped/less” physical activity, drinking, “less healthy” eating, and low PB score, respectively. Conclusion: S-COVID-19-S worsen psychological health in patients with UHC. Physical activity, drinking, healthier eating, and high PB score were protective factors.
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Affiliation(s)
- Minh H Nguyen
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Thu T M Pham
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam.,School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Linh V Pham
- Department of Pulmonary and Cardiovascular Diseases, Hai Phong University of Medicine and Pharmacy Hospital, Hai Phong, Vietnam.,Director Office, Hai Phong University of Medicine and Pharmacy Hospital, Hai Phong, Vietnam
| | - Dung T Phan
- Faculty of Nursing, Hanoi University of Business and Technology, Hanoi, Vietnam.,Nursing Office, Thien an Obstetrics and Gynecology Hospital, Hanoi, Vietnam
| | - Tien V Tran
- Department of Infectious Diseases, Vietnam Military Medical University, Hanoi, Vietnam.,Director Office, Military Hospital 103, Hanoi, Vietnam
| | - Hoang C Nguyen
- Director Office, Thai Nguyen National Hospital, Thai Nguyen, Vietnam.,President Office, Thai Nguyen University of Medicine and Pharmacy, Thai Nguyen, Vietnam
| | - Huu C Nguyen
- Director Office, E Hospital, Hanoi, Vietnam.,Department of Thoracic and Cardiovascular Surgery, E Hospital, Hanoi, Vietnam
| | - Tung H Ha
- Director Office, General Hospital of Agricultural, Hanoi, Vietnam
| | - Hung K Dao
- Director Office, Bac Ninh Obstetrics and Pediatrics Hospital, Bac Ninh, Vietnam
| | | | - Manh V Trinh
- Director Office, Quang Ninh General Hospital, Quang Ninh, Vietnam
| | - Thinh V Do
- Director Office, Bai Chay Hospital, Quang Ninh, Vietnam
| | - Hung Q Nguyen
- Director Office, Quang Ninh Obstetrics and Pediatrics Hospital, Quang Ninh, Vietnam
| | - Thao T P Nguyen
- Health Management Training Institute, Hue University of Medicine and Pharmacy, Thua Thien Hue, Vietnam.,Department of Health Economics, Corvinus University of Budapest, Budapest, Hungary
| | - Nhan P T Nguyen
- General Planning Department, Da Nang Oncology Hospital, Da Nang, Vietnam
| | - Cuong Q Tran
- Director Office, Thu Duc District Health Center, Ho Chi Minh City, Vietnam.,Faculty of Health, Mekong University, Vinh Long, Vietnam
| | - Khanh V Tran
- Director Office, Hospital District 2, Ho Chi Minh City, Vietnam
| | - Trang T Duong
- Nursing Office, Tan Phu District Hospital, Ho Chi Minh City, Vietnam
| | - Tan T Nguyen
- Department of Orthopedics, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam.,Director Office, Can Tho University of Medicine and Pharmacy Hospital, Can Tho, Vietnam
| | - Khue M Pham
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam.,President Office, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam
| | - Lam V Nguyen
- Aesthetic Plastic Surgery & Skin Care Center, Can Tho University of Medicine and Pharmacy Hospital, Can Tho, Vietnam.,President Office, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Tam T Vo
- Director Office, Trieu Phong District Health Center, Quang Tri, Vietnam
| | - Binh N Do
- Department of Infectious Diseases, Vietnam Military Medical University, Hanoi, Vietnam.,Division of Military Science, Military Hospital 103, Hanoi, Vietnam
| | - Nga H Dang
- Training and Direction of Healthcare Activity Center, Thai Nguyen National Hospital, Thai Nguyen, Vietnam.,Department of Quality Control, Thai Nguyen National Hospital, Thai Nguyen, Vietnam
| | - Thuy T Le
- Faculty of Medical Laboratory Science, Da Nang University of Medical Technology and Pharmacy, Da Nang, Vietnam.,President Office, Da Nang University of Medical Technology and Pharmacy, Da Nang, Vietnam
| | - Ngoc T Do
- Nursing Office, E Hospital, Hanoi, Vietnam
| | - Hoai T T Nguyen
- Training and Direction of Healthcare Activity Center, Kien an Hospital, Hai Phong, Vietnam
| | - Thuy T T Mai
- Nursing Office, Quang Ninh General Hospital, Quang Ninh, Vietnam
| | - Dung T Ha
- Nursing Office, Bai Chay Hospital, Quang Ninh, Vietnam
| | - Huong T M Ngo
- Nursing Office, Quang Ninh Obstetric and Pediatric Hospital, Quang Ninh, Vietnam
| | - Kien T Nguyen
- Department of Health Education, Faculty of Social Sciences, Behavior and Health Education, Hanoi University of Public Health, Hanoi, Vietnam
| | - Chyi-Huey Bai
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan.,Department of Public Health, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tuyen Van Duong
- School of Nutrition and Health Sciences, Taipei Medical University, Taipei, Taiwan
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3
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Pham KM, Pham LV, Phan DT, Tran TV, Nguyen HC, Nguyen MH, Nguyen HC, Ha TH, Dao HK, Nguyen PB, Trinh MV, Do TV, Nguyen HQ, Nguyen TTP, Nguyen NPT, Tran CQ, Tran KV, Duong TT, Nguyen LV, Do TT, Vo TT, Do BN, Duong TH, Pham TTM, Le TT, Do NT, Nguyen HTT, Mai TTT, Ha DT, Ngo HTM, Nguyen KT, Yang SH, Chao JCJ, Duong TV. Healthy Dietary Intake Behavior Potentially Modifies the Negative Effect of COVID-19 Lockdown on Depression: A Hospital and Health Center Survey. Front Nutr 2020; 7:581043. [PMID: 33304917 PMCID: PMC7701254 DOI: 10.3389/fnut.2020.581043] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/08/2020] [Indexed: 12/13/2022] Open
Abstract
Background: The COVID-19 pandemic causes a huge burden for affected countries. Several public health interventions were applied to contain the infection. However, the pandemic itself and the lockdown measure negatively influence people's lifestyles and psychological health. Purpose: To explore determinants of healthy dietary intake and depression, and examine the interaction between healthy dietary intake and COVID-19 lockdown on depression. Methods: A cross-sectional study was conducted at 18 hospitals and health centers from February 14 to May 31, 2020. Data of 8,291 outpatients were collected including patients' characteristics, clinical parameters, health literacy, healthy dietary intake (using the healthy eating score, HES), other health-related behaviors, and depression (using the patient health questionnaire, PHQ). Depression was defined as PHQ score ≥ 10. Results: Protective factors of healthy dietary intake and depression were higher education, better medication payment ability, higher social status, more physical activity, and higher health literacy, whereas older age, ever married, own business or other types of occupation, lockdown, suspected COVID-19 symptoms, and comorbidity were associated with lower HES scores and a higher depression likelihood. Besides, overweight/obesity and alcohol drinking were associated with lower HES scores. As compared with patients not under lockdown and with lowest HES score, those who were under lockdown and with lowest HES score had 10.6 times higher depression likelihood (odds ratio, OR, 10.60; 95% CI 6.88, 16.32; p < 0.001), whereas people with higher HES score had 15% lower depression likelihood (OR 0.85; 95% CI 0.82, 0.89; p < 0.001). Conclusions: Healthy dietary intake and depression were determined by several sociodemographic, clinical, and behavioral factors. Lockdown measure affects people's dietary intake behavior and depression. Importantly, healthy dietary intake potentially modifies the negative effect of lockdown on depression.
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Affiliation(s)
- Khue M. Pham
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam
- President Office, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam
| | - Linh V. Pham
- Department of Pulmonary and Cardiovascular Diseases, Hai Phong University of Medicine and Pharmacy Hospital, Hai Phong, Vietnam
- Director Office, Hai Phong University of Medicine and Pharmacy Hospital, Hai Phong, Vietnam
| | - Dung T. Phan
- Faculty of Nursing, Hanoi University of Business and Technology, Hanoi, Vietnam
- Nursing Office, Viet Duc University Hospital, Hanoi, Vietnam
| | - Tien V. Tran
- Department of Infectious Diseases, Vietnam Military Medical University, Hanoi, Vietnam
- Director Office, Military Hospital 103, Hanoi, Vietnam
| | - Hoang C. Nguyen
- Director Office, Thai Nguyen National Hospital, Thai Nguyen, Vietnam
- President Office, Thai Nguyen University of Medicine and Pharmacy, Thai Nguyen, Vietnam
| | - Minh H. Nguyen
- International Master/Ph.D. Program in Medicine, Taipei Medical University, Taipei, Taiwan
| | - Huu C. Nguyen
- Director Office, E Hospital, Hanoi, Vietnam
- Department of Thoracic and Cardiovascular Surgery, E Hospital, Hanoi, Vietnam
| | - Tung H. Ha
- Director Office, General Hospital of Agricultural, Hanoi, Vietnam
| | - Hung K. Dao
- Director Office, Bac Ninh Obstetrics and Pediatrics Hospital, Bac Ninh, Vietnam
| | | | - Manh V. Trinh
- Director Office, Quang Ninh General Hospital, Quang Ninh, Vietnam
| | - Thinh V. Do
- Director Office, Bai Chay Hospital, Quang Ninh, Vietnam
| | - Hung Q. Nguyen
- Director Office, Quang Ninh Obstetrics and Pediatrics Hospital, Quang Ninh, Vietnam
| | - Thao T. P. Nguyen
- Health Management Training Institute, Hue University of Medicine and Pharmacy, Hue, Vietnam
- Department of Health Economics, Corvinus University of Budapest, Budapest, Hungary
| | - Nhan P. T. Nguyen
- General Planning Department, Da Nang Oncology Hospital, Da Nang, Vietnam
| | - Cuong Q. Tran
- Director Office, Thu Duc District Health Center, Ho Chi Minh City, Vietnam
- Faculty of Health, Mekong University, Vinh Long, Vietnam
| | - Khanh V. Tran
- Director Office, Hospital District 2, Ho Chi Minh City, Vietnam
| | - Trang T. Duong
- Nursing Office, Tan Phu District Hospital, Ho Chi Minh City, Vietnam
| | - Lam V. Nguyen
- President Office, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
- Aesthetic Plastic Surgery & Skin Care Center, Can Tho University of Medicine and Pharmacy Hospital, Can Tho, Vietnam
| | - Thao T. Do
- Department of Oral Pathology and Periodontology, Faculty of Odonto-Stomatology, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Tam T. Vo
- Director Office, Trieu Phong District Health Center, Quang Tri, Vietnam
| | - Binh N. Do
- Department of Infectious Diseases, Vietnam Military Medical University, Hanoi, Vietnam
- Division of Military Science, Military Hospital 103, Hanoi, Vietnam
| | - Thai H. Duong
- Director Office, Thai Nguyen National Hospital, Thai Nguyen, Vietnam
- Department of Internal Medicine, Thai Nguyen University of Medicine and Pharmacy, Thai Nguyen, Vietnam
| | - Thu T. M. Pham
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam
- International Master/Ph.D. Program in Medicine, Taipei Medical University, Taipei, Taiwan
| | - Thuy T. Le
- Faculty of Medical Laboratory Science, Da Nang University of Medical Technology and Pharmacy, Da Nang, Vietnam
- President Office, Da Nang University of Medical Technology and Pharmacy, Da Nang, Vietnam
| | - Ngoc T. Do
- Nursing Office, E Hospital, Hanoi, Vietnam
| | - Hoai T. T. Nguyen
- Training and Direction of Healthcare Activity Center, Kien an Hospital, Hai Phong, Vietnam
| | - Thuy T. T. Mai
- Nursing Office, Quang Ninh General Hospital, Quang Ninh, Vietnam
| | - Dung T. Ha
- Nursing Office, Bai Chay Hospital, Quang Ninh, Vietnam
| | - Huong T. M. Ngo
- Nursing Office, Quang Ninh Obstetric and Pediatric Hospital, Quang Ninh, Vietnam
| | - Kien T. Nguyen
- Department of Health Education, Faculty of Social Sciences, Behavior and Health Education, Hanoi University of Public Health, Hanoi, Vietnam
| | - Shwu-Huey Yang
- School of Nutrition and Health Sciences, Taipei Medical University, Taipei, Taiwan
- Nutrition Research Center, Taipei Medical University Hospital, Taipei, Taiwan
- Research Center of Geriatric Nutrition, Taipei Medical University, Taipei, Taiwan
| | - Jane C.-J. Chao
- School of Nutrition and Health Sciences, Taipei Medical University, Taipei, Taiwan
- Nutrition Research Center, Taipei Medical University Hospital, Taipei, Taiwan
- Master Program in Global Health and Development, College of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Tuyen Van Duong
- School of Nutrition and Health Sciences, Taipei Medical University, Taipei, Taiwan
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4
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Laksman J, Kooser K, Levola H, Itälä E, Ha DT, Rachlew E, Kukk E. Dissociation pathways in the cysteine dication after site-selective core ionization. J Phys Chem B 2014; 118:11688-95. [PMID: 25233490 DOI: 10.1021/jp508161s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A photoelectron-ion-ion coincidence experiment has been carried out on the amino acid molecule cysteine after core-ionization of the O 1s, N 1s, C 1s, and S 2p orbitals. A number of different dissociation channels have been identified. Some of them show strong site-selective dependence that can be attributed to a combination of nuclear motion in the core-ionized state and Auger processes that populate different final electronic states in the dication.
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Affiliation(s)
- J Laksman
- Department of Physics, University of Oulu , P.O. Box 3000, FIN-90014 Oulu, Finland
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5
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Murphy BF, Osipov T, Jurek Z, Fang L, Son SK, Mucke M, Eland JHD, Zhaunerchyk V, Feifel R, Avaldi L, Bolognesi P, Bostedt C, Bozek JD, Grilj J, Guehr M, Frasinski LJ, Glownia J, Ha DT, Hoffmann K, Kukk E, McFarland BK, Miron C, Sistrunk E, Squibb RJ, Ueda K, Santra R, Berrah N. Femtosecond X-ray-induced explosion of C60 at extreme intensity. Nat Commun 2014; 5:4281. [PMID: 24969734 DOI: 10.1038/ncomms5281] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 06/02/2014] [Indexed: 11/09/2022] Open
Abstract
Understanding molecular femtosecond dynamics under intense X-ray exposure is critical to progress in biomolecular imaging and matter under extreme conditions. Imaging viruses and proteins at an atomic spatial scale and on the time scale of atomic motion requires rigorous, quantitative understanding of dynamical effects of intense X-ray exposure. Here we present an experimental and theoretical study of C60 molecules interacting with intense X-ray pulses from a free-electron laser, revealing the influence of processes not previously reported. Our work illustrates the successful use of classical mechanics to describe all moving particles in C60, an approach that scales well to larger systems, for example, biomolecules. Comparisons of the model with experimental data on C60 ion fragmentation show excellent agreement under a variety of laser conditions. The results indicate that this modelling is applicable for X-ray interactions with any extended system, even at higher X-ray dose rates expected with future light sources.
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Affiliation(s)
- B F Murphy
- 1] Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008, USA [2]
| | - T Osipov
- 1] Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008, USA [2]
| | - Z Jurek
- 1] Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany [2] The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany [3]
| | - L Fang
- Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - S-K Son
- 1] Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany [2] The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
| | - M Mucke
- Gothenburg University, Department of Physics Origovägen 6, SE-412 96 Gothenburg, Sweden
| | - J H D Eland
- 1] Gothenburg University, Department of Physics Origovägen 6, SE-412 96 Gothenburg, Sweden [2] Department of Chemistry, Oxford University, Oxford OX1 3QZ, UK
| | - V Zhaunerchyk
- Gothenburg University, Department of Physics Origovägen 6, SE-412 96 Gothenburg, Sweden
| | - R Feifel
- Gothenburg University, Department of Physics Origovägen 6, SE-412 96 Gothenburg, Sweden
| | - L Avaldi
- Instituto di Metodologie Inorganiche e dei Plasmi, C.N.R., Rome 00133, Italy
| | - P Bolognesi
- Instituto di Metodologie Inorganiche e dei Plasmi, C.N.R., Rome 00133, Italy
| | - C Bostedt
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - J D Bozek
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - J Grilj
- PULSE, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - M Guehr
- PULSE, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - L J Frasinski
- Blackett Laboratory, Imperial College London, London SW7 2AZ, UK
| | - J Glownia
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - D T Ha
- Department of Physics, University of Turku, FIN-20014 Turku, Finland
| | - K Hoffmann
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, USA
| | - E Kukk
- Department of Physics, University of Turku, FIN-20014 Turku, Finland
| | - B K McFarland
- PULSE, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - C Miron
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - E Sistrunk
- PULSE, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - R J Squibb
- 1] Gothenburg University, Department of Physics Origovägen 6, SE-412 96 Gothenburg, Sweden [2] Blackett Laboratory, Imperial College London, London SW7 2AZ, UK
| | - K Ueda
- Department of Physics, Tohoku University, Sendai 980-8577, Japan
| | - R Santra
- 1] Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany [2] The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany [3] Department of Physics, University of Hamburg, 20355 Hamburg, Germany
| | - N Berrah
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA
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6
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Huu NB, Denner EB, Ha DT, Wanner G, Stan-Lotter H. Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oil-producing well. Int J Syst Bacteriol 1999; 49 Pt 2:367-75. [PMID: 10319457 DOI: 10.1099/00207713-49-2-367] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Several strains of moderately halophilic and mesophilic bacteria were isolated at the head of an oil-producing well on an offshore platform in southern Vietnam. Cells were Gram-negative, non-spore-forming, rod-shaped and motile by means of a polar flagellum. Growth occurred at NaCl concentrations between 0 and 20%; the optimum was 5% NaCl. One strain, which was designated VT8T, could degrade n-hexadecane, pristane and some crude oil components. It grew anaerobically in the presence of nitrate on succinate, citrate or acetate, but not on glucose. Several organic acids and amino acids were utilized as sole carbon and energy sources. The major components of its cellular fatty acids were C12:0 3-OH, C16:1, omega 9c, C16:0 and C18:1 omega 9c. The DNA G + C content was 55.7 mol%. 16S rDNA sequence analysis indicated that strain VT8T was closely related to Marinobacter sp. strain CAB (99.8% similarity) and Marinobaster hydrocarbonoclasticus (99.4% similarity). Its antibiotic resistance, isoprenoid quinones and fatty acids were similar to those of Marinobacter hydrocarbonoclasticus and Pseudomonas nautica. However, the whole-cell protein pattern of VT8T differed from that of other halophilic marine isolates, including P. nautica. DNA-DNA hybridization indicated that the level of relatedness to Marinobacter hydrocarbonoclasticus was 65% and that to P. nautica was 75%. Further differences were apparent in Fourier-transformed IR spectra of cells and lipopolysaccharide composition. It is proposed that VT8T should be the type strain of a new species and should be named Marinobacter aquaeolei. P. nautica may have been misclassified, as suggested previously, and may also belong to the genus Marinobacter.
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Affiliation(s)
- N B Huu
- Institute of Biotechnology, National Center for Natural Science and Technology, Tu liem, Hanoi, Vietnam
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7
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Huy NQ, Jin S, Amada K, Haruki M, Huu NB, Hang DT, Ha DT, Imanaka T, Morikawa M, Kanaya S. Characterization of petroleum-degrading bacteria from oil-contaminated sites in Vietnam. J Biosci Bioeng 1999; 88:100-2. [PMID: 16232582 DOI: 10.1016/s1389-1723(99)80184-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/1999] [Accepted: 04/14/1999] [Indexed: 11/17/2022]
Abstract
Four petroleum-degrading bacterial strains, 2TN-NB, 6TBX-CL, MVK2-5, and XCK, were isolated from various oil-contaminated sites in Vietnam. Determination of the nucleotide sequence of the gene encoding 16S rRNA allowed 2TN-NB to be identified as Acinetobacter sp. and the other three stains as Pseudomonas sp. Among the four isolates, 2TN-NB was most effective in degrading crude oil: in 1 d, it degraded 95% of the crude oil in the culture medium (5%, v/v). The isolated strains could also degrade a sulfur-containing aromatic hydrocarbon, dibenzothiophene (DBT), with low efficiency. Except for MVK2-5, which degraded crude oil least efficiently, the isolates produced biosurfactants in amounts sufficient for structural analysis. FT-IR measurement suggested that strains 6TBX-CL and XCK produced glycolipid-type biosurfactants while that produced by 2TN-NB was of the polysaccharide type.
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Affiliation(s)
- N Q Huy
- Institute of Biotechnology, Nghia Do, Cau Giay-Hanoi, Vietnam
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8
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Bögre L, Jonak C, Mink M, Meskiene I, Traas J, Ha DT, Swoboda I, Plank C, Wagner E, Heberle-Bors E, Hirt H. Developmental and cell cycle regulation of alfalfa nucMs1, a plant homolog of the yeast Nsr1 and mammalian nucleolin. Plant Cell 1996; 8:417-28. [PMID: 8721748 PMCID: PMC161110] [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] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We report here the isolation and characterization of the nucMs1 alfalfa cDNA, whose predicted amino acid sequence structurally resembles the yeast Nsr1 protein and animal nucleolins. These proteins consist of an N-terminal acidic domain, centrally located RNA recognition motifs (RRMs), and a C-terminal glycine- and arginine-rich domain. In comparison with animal nucleolins that contain four RRMs, NucMs1 more closely resembles the yeast Nsr1 protein, which contains only two RRMs. A NucMs1 C-terminal peptide antibody specifically recognized a 95-kD nucleolar protein in alfalfa cells that changed its localization in a cell cycle-dependent manner. The nucMs1 transcript and p95nucMs1 protein levels correlated with cell proliferation, and nucMs1 gene expression was found to be induced in the G1 phase upon mitogenic stimulation of G0-arrested leaf cells. In situ hybridization analysis of different alfalfa organs during various developmental stages showed that nucMs1 gene expression is highest in root meristematic cells, but it is also found in other meristematic cells of the plant body. nucMs1 expression is tightly linked to cell proliferation but does not depend on a particular cell cycle phase. No nucMs1 expression was observed in cells that had exited the cell cycle and were undergoing differentiation or polar growth, indicating that nucMs1 may not be necessary for processes other than cell proliferation.
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Affiliation(s)
- L Bögre
- Institute of Microbiology and Genetics, University of Vienna, Austria
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Dahl M, Meskiene I, Bögre L, Ha DT, Swoboda I, Hubmann R, Hirt H, Heberle-Bors E. The D-type alfalfa cyclin gene cycMs4 complements G1 cyclin-deficient yeast and is induced in the G1 phase of the cell cycle. Plant Cell 1995; 7:1847-57. [PMID: 8535138 PMCID: PMC161043 DOI: 10.1105/tpc.7.11.1847] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cyclins are key regulators of the cell cycle in all eukaryotes. In alfalfa, we have previously isolated three B-type cyclins. The closely related cycMs1 and cycMs2 genes are expressed primarily during the G2 and M phases and are most likely mitotic cyclins; expression of the cycMs3 gene is induced in the G0-to-G1 transition, when cells reenter the cell cycle. By complementation of G1 cyclin-deficient yeast cells, a novel alfalfa cyclin, designated cycMs4, was isolated. The predicted amino acid sequence of the cycMs4 gene is most similar to that of the Arabidopsis cyclin delta 3 gene. CycMs4 and cyclin delta 3 belong to the class of D-type cyclins and contain PEST-rich regions and a retinoblastoma binding motif. When comparing expression levels in different organs, cycMs4 transcripts were present predominantly in roots. Whereas expression of the cycMs4 gene was cell cycle-regulated in suspension-cultured cells, transcription in roots was observed to depend also on the positional context of the cell. When differentiated G0-arrested leaf cells were induced to resume cell division by treatment with plant hormones, cycMs4 transcription was induced before the onset of DNA synthesis. Whereas this induction was preceded by that of the cycMs3 gene, cycMs2 expression occurred later and at the same time as mitotic activity. These data suggest that cycMs4 plays a role in the G1-to-S transition and provide a model to investigate the plant cell cycle at the molecular level.
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Affiliation(s)
- M Dahl
- Institute of Microbiology and Genetics, Vienna Biocenter, Austria
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Meskiene I, Bögre L, Dahl M, Pirck M, Ha DT, Swoboda I, Heberle-Bors E, Ammerer G, Hirt H. cycMs3, a novel B-type alfalfa cyclin gene, is induced in the G0-to-G1 transition of the cell cycle. Plant Cell 1995; 7:759-71. [PMID: 7647566 PMCID: PMC160829 DOI: 10.1105/tpc.7.6.759] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cyclins are key regulators of the cell cycle in all eukaryotes. We have previously isolated two B-type cyclin genes, cycMs1 and cycMs2, from alfalfa that are primarily expressed during the G2-to-M phase transition and are most likely mitotic cyclin genes. Here, we report the isolation of a novel alfalfa cyclin gene, termed cycMs3 (for cyclin Medicago sativa), by selecting for mating type alpha-pheromone-induced cell cycle arrest suppression in yeast. The central region of the predicted amino acid sequence of the cycMs3 gene is most similar to the cyclin box of yeast B-type and mammalian A- and B-type cyclins. In situ hybridization showed that cycMs3 mRNA can be detected only in proliferating cells and not in differentiated alfalfa cells. When differentiated G0-arrested cells were induced to reenter the cell cycle in the G1 phase and resume cell division by treatment with plant hormones, cycMs3 transcript levels increased long before the onset of DNA synthesis. In contrast, histone H3-1 mRNA and cycMs2 transcripts were not observed before DNA replication and mitosis, respectively. In addition, cycMs3 mRNA was found in all stages of the cell cycle in synchronously dividing cells, whereas the cycMs2 and histone H3-1 genes showed a G2-to-M phase- or S phase-specific transcription pattern, respectively. These data suggest that the role of cyclin CycMs3 differs from that of CycMs1 and CycMs2. We propose that CycMs3 helps control reentry of quiescent G0-arrested cells into the G1 phase of the cell cycle.
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Affiliation(s)
- I Meskiene
- Vienna Biocenter, Institute of Microbiology and Genetics, Austria
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Putnoky P, Petrovics G, Kereszt A, Grosskopf E, Ha DT, Bánfalvi Z, Kondorosi A. Rhizobium meliloti lipopolysaccharide and exopolysaccharide can have the same function in the plant-bacterium interaction. J Bacteriol 1990; 172:5450-8. [PMID: 2168384 PMCID: PMC213212 DOI: 10.1128/jb.172.9.5450-5458.1990] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [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: 12/30/2022] Open
Abstract
A fix region of Rhizobium meliloti 41 involved both in symbiotic nodule development and in the adsorption of bacteriophage 16-3 was delimited by directed Tn5 mutagenesis. Mutations in this DNA region were assigned to four complementation units and were mapped close to the pyr-2 and pyr-29 chromosomal markers. Phage inactivation studies with bacterial cell envelope preparations and crude lipopolysaccharides (LPS) as well as preliminary characterization of LPS in the mutants indicated that these genes are involved in the synthesis of a strain-specific LPS. Mutations in this DNA region resulted in a Fix- phenotype in AK631, an exopolysaccharide (EPS)-deficient derivative of R. meliloti 41; however, they did not influence the symbiotic efficiency of the parent strain. An exo region able to restore the EPS production of AK631 was isolated and shown to be homologous to the exoB region of R. meliloti SU47. By generating double mutants, we demonstrated that exo and lps genes determine similar functions in the course of nodule development, suggesting that EPS and LPS may provide equivalent information for the host plant.
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Affiliation(s)
- P Putnoky
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged
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Abstract
To identify bacterial genes involved in symbiotic nodule development, ineffective nodules of alfalfa (Medicago sativa) induced by 64 different Fix-mutants of Rhizobium meliloti were characterized by assaying for symbiotic gene expression and by morphological studies. The expression of leghemoglobin and nodulin-25 genes from alfalfa and of the nifHD genes from R. meliloti were monitored by hybridizing the appropriate DNA probes to RNA samples prepared from nodules. The mutants were accordingly divided into three groups. In group I none of the genes were expressed, in group II only the plant genes were expressed and in group III all three genes were transcribed. Light and electron microscopical analysis of nodules revealed that nodule development was halted at different stages in nodules induced by different group I mutants. In most cases nodules were empty lacking infection threads and bacteroids or nodules contained infection threads and a few released bacteroids. In nodules induced by a third mutant class bacteria were released into the host cells, however the formation of the peribacteroid membrane was not normal. On this basis we suggest that peribacteroid membrane formation precedes leghemoglobin and nodulin-25 induction, moreover, after induction of nodulation by the nod genes at least two communication steps between the bacteria and the host plants are necessary for the development of the mature nodule. By complementing each mutant of group I with a genomic R. meliloti library made in pLAFRl, four new fix loci were identified, indicating that several bacterial genes are involved in late nodule development.
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Affiliation(s)
- P Putnoky
- Institute of Genetics, Hungarian Academy of Sciences, Szeged
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