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Parajulee P, Lee JS, Abbas K, Cannon J, Excler JL, Kim JH, Mogasale V. State transitions across the Strep A disease spectrum: scoping review and evidence gaps. BMC Infect Dis 2024; 24:108. [PMID: 38243271 PMCID: PMC10799450 DOI: 10.1186/s12879-023-08888-4] [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] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 12/11/2023] [Indexed: 01/21/2024] Open
Abstract
The spectrum of diseases caused by Streptococcus pyogenes (Strep A) ranges from superficial to serious life-threatening invasive infections. We conducted a scoping review of published articles between 1980 and 2021 to synthesize evidence of state transitions across the Strep A disease spectrum. We identified 175 articles reporting 262 distinct observations of Strep A disease state transitions. Among the included articles, the transition from an invasive or toxin-mediated disease state to another disease state (i.e., to recurrent ARF, RHD or death) was described 115 times (43.9% of all included transition pairs) while the transition to and from locally invasive category was the lowest (n = 7; 0.02%). Transitions from well to any other state was most frequently reported (49%) whereas a relatively higher number of studies (n = 71) reported transition from invasive disease to death. Transitions from any disease state to locally invasive, Strep A pharyngitis to invasive disease, and chronic kidney disease to death were lacking. Transitions related to severe invasive diseases were more frequently reported than superficial ones. Most evidence originated from high-income countries and there is a critical need for new studies in low- and middle-income countries to infer the state transitions across the Strep A disease spectrum in these high-burden settings.
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Affiliation(s)
| | - Jung-Seok Lee
- International Vaccine Institute, Seoul, Republic of Korea
| | - Kaja Abbas
- London School of Hygiene and Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki, Japan
| | - Jeffrey Cannon
- Telethon Kids Institute, University of Western Australia, Perth, Australia
- Harvard T.H. Chan School of Public Health, Boston, USA
| | | | - Jerome H Kim
- International Vaccine Institute, Seoul, Republic of Korea
- College of Natural Sciences, Seoul National University, Seoul, Republic of Korea
| | - Vittal Mogasale
- International Vaccine Institute, Seoul, Republic of Korea
- World Health Organization, Geneva, Switzerland
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2
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Wu J, Zhao R, Sun J. State transition of carbon emission efficiency in China: empirical analysis based on three-stage SBM and Markov chain models. Environ Sci Pollut Res Int 2023; 30:117050-117060. [PMID: 36598727 DOI: 10.1007/s11356-022-24885-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/03/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Assessing China's carbon emission efficiency (CEE) and analyzing efficiency state transition trends are necessary to accelerate the promotion of carbon emission reduction and achieve low carbon goals. This study evaluates China's economic and social environments by using the entropy weight method. The CEE of 30 Chinese provinces from 2006 to 2020 is measured using the three-stage slack-based model with an undesirable output. Then, this study introduces a Markov chain to explore the state transition trend of China's CEE. The research conclusions are as follows. First, compared with the social environment, the economic environment has a more significant impact on CEE. Second, the CEE of the eastern region is the highest, followed by that of the central region and the western region, which has the worst CEE. Third, the inefficiency of the central and western regions pulls down the overall CEE of China. Fourth, the state of China's CEE is gradually shifting to a high level; however, achieving a leapfrog shift is difficult.
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Affiliation(s)
- Jie Wu
- School of Management, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
| | - Ruizeng Zhao
- School of Management, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
- School of Economics and Management, Southwest University of Science and Technology, Mianyang, 621000, Sichuan, China
| | - Jiasen Sun
- School of Business and Dongwu Think Tank, Soochow University, Suzhou, 215012, Jiangsu, China.
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3
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Fujita Y, Zhang X, Mohamed A, Ye S, Shibata Y. Accumulation of quenched LHCII around PSI in Chlamydomonas cells in state2 revealed by cryo-fluorescence lifetime imaging. J Photochem Photobiol B 2022; 236:112584. [PMID: 36272337 DOI: 10.1016/j.jphotobiol.2022.112584] [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: 07/07/2022] [Revised: 09/20/2022] [Accepted: 10/02/2022] [Indexed: 02/17/2023]
Abstract
Fluorescence-spectral microscope observations of photosynthetic organisms at cryogenic temperatures have the ability to spectrally resolve the two photosystems (PSs) and thus provide a powerful tool to elucidate the functional analysis of photosynthesis in vivo. In the present study, a measurement channel of the fluorescence lifetime at 680 nm was added to the cryo-microscope system previously developed by the authors. This provides access to information on the functional state of the light-harvesting system in living cells during regulation by a mechanism called state transitions. The observations of state1-locked and state2-locked Chlamydomonas cells at 80 K enabled us to identify a component showing rapidly decaying fluorescence with a lifetime of ca. 3 ps and emitting at around 676 nm. The component was assigned to the light-harvesting complex II (LHCII) that is isolated from both PSs and in a quenched state, probably due to the formation of aggregates. Simultaneous spectral observations revealed the accumulation of this free LHCII in the photosystem I (PSI)-enriched region within each state2-locked cell. To the best of our knowledge, this is the first in-vivo observation which suggests the localization of the quenched LHCII aggregates.
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Affiliation(s)
- Yuki Fujita
- Department of Chemistry, Graduate School of Sciences, Tohoku University, 980-8578 Sendai, Japan
| | - XianJun Zhang
- Department of Chemistry, Graduate School of Sciences, Tohoku University, 980-8578 Sendai, Japan; Division for Interdisciplinary Advanced Research and Education, Tohoku University, 980-8578 Sendai, Japan
| | - Ahmed Mohamed
- Department of Chemistry, Graduate School of Sciences, Tohoku University, 980-8578 Sendai, Japan
| | - Shen Ye
- Department of Chemistry, Graduate School of Sciences, Tohoku University, 980-8578 Sendai, Japan
| | - Yutaka Shibata
- Department of Chemistry, Graduate School of Sciences, Tohoku University, 980-8578 Sendai, Japan.
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Matsumoto S, Taniguchi-Tamura H, Araki M, Kawamura T, Miyamoto R, Tsuda C, Shima F, Kumasaka T, Okuno Y, Kataoka T. Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein. Biochem Biophys Res Commun 2021; 565:85-90. [PMID: 34102474 DOI: 10.1016/j.bbrc.2021.05.084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/23/2021] [Indexed: 11/24/2022]
Abstract
GTP-bound forms of Ras proteins (Ras•GTP) assume two interconverting conformations, "inactive" state 1 and "active" state 2. Our previous study on the crystal structure of the state 1 conformation of H-Ras in complex with guanosine 5'-(β, γ-imido)triphosphate (GppNHp) indicated that state 1 is stabilized by intramolecular hydrogen-bonding interactions formed by Gln61. Since Ras are constitutively activated by substitution mutations of Gln61, here we determine crystal structures of the state 1 conformation of H-Ras•GppNHp carrying representative mutations Q61L and Q61H to observe the effect of the mutations. The results show that these mutations alter the mode of hydrogen-bonding interactions of the residue 61 with Switch II residues and induce conformational destabilization of the neighboring regions. In particular, Q61L mutation results in acquirement of state 2-like structural features. Moreover, the mutations are likely to impair an intramolecular structural communication between Switch I and Switch II. Molecular dynamics simulations starting from these structures support the above observations. These findings may give a new insight into the molecular mechanism underlying the aberrant activation of the Gln61 mutants.
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Berry H, Genet S. A model of on/off transitions in neurons of the deep cerebellar nuclei: deciphering the underlying ionic mechanisms. J Math Neurosci 2021; 11:7. [PMID: 33796951 PMCID: PMC8017079 DOI: 10.1186/s13408-021-00105-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
The neurons of the deep cerebellar nuclei (DCNn) represent the main functional link between the cerebellar cortex and the rest of the central nervous system. Therefore, understanding the electrophysiological properties of DCNn is of fundamental importance to understand the overall functioning of the cerebellum. Experimental data suggest that DCNn can reversibly switch between two states: the firing of spikes (F state) and a stable depolarized state (SD state). We introduce a new biophysical model of the DCNn membrane electro-responsiveness to investigate how the interplay between the documented conductances identified in DCNn give rise to these states. In the model, the F state emerges as an isola of limit cycles, i.e. a closed loop of periodic solutions disconnected from the branch of SD fixed points. This bifurcation structure endows the model with the ability to reproduce the [Formula: see text] transition triggered by hyperpolarizing current pulses. The model also reproduces the [Formula: see text] transition induced by blocking Ca currents and ascribes this transition to the blocking of the high-threshold Ca current. The model suggests that intracellular current injections can trigger fully reversible [Formula: see text] transitions. Investigation of low-dimension reduced models suggests that the voltage-dependent Na current is prominent for these dynamical features. Finally, simulations of the model suggest that physiological synaptic inputs may trigger [Formula: see text] transitions. These transitions could explain the puzzling observation of positively correlated activities of connected Purkinje cells and DCNn despite the former inhibit the latter.
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Affiliation(s)
- Hugues Berry
- INRIA, 69603 Villeurbanne, France
- LIRIS UMR5205, Université de Lyon, 69622 Villeurbanne, France
| | - Stéphane Genet
- Sorbonne Université, CNRS, Institut des Systèmes Intelligents et de Robotique, ISIR, F-75005 Paris, France
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6
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Bhatti AF, Choubeh RR, Kirilovsky D, Wientjes E, van Amerongen H. State transitions in cyanobacteria studied with picosecond fluorescence at room temperature. Biochim Biophys Acta Bioenerg 2020; 1861:148255. [PMID: 32619427 DOI: 10.1016/j.bbabio.2020.148255] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 11/30/2022]
Abstract
Cyanobacteria can rapidly regulate the relative activity of their photosynthetic complexes photosystem I and II (PSI and PSII) in response to changes in the illumination conditions. This process is known as state transitions. If PSI is preferentially excited, they go to state I whereas state II is induced either after preferential excitation of PSII or after dark adaptation. Different underlying mechanisms have been proposed in literature, in particular i) reversible shuttling of the external antenna complexes, the phycobilisomes, between PSI and PSII, ii) reversible spillover of excitation energy from PSII to PSI, iii) a combination of both and, iv) increased excited-state quenching of the PSII core in state II. Here we investigated wild-type and mutant strains of Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 using time-resolved fluorescence spectroscopy at room temperature. Our observations support model iv, meaning that increased excited-state quenching of the PSII core occurs in state II thereby balancing the photochemistry of photosystems I and II.
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Affiliation(s)
- Ahmad Farhan Bhatti
- Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands
| | | | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (12BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Emilie Wientjes
- Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands
| | - Herbert van Amerongen
- Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands; MicroSpectroscopy Research Facility, Wageningen University, Wageningen, the Netherlands.
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7
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Kimmel JC, Hwang AB, Scaramozza A, Marshall WF, Brack AS. Aging induces aberrant state transition kinetics in murine muscle stem cells. Development 2020; 147:dev183855. [PMID: 32198156 PMCID: PMC7225128 DOI: 10.1242/dev.183855] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/17/2020] [Indexed: 12/12/2022]
Abstract
Murine muscle stem cells (MuSCs) experience a transition from quiescence to activation that is required for regeneration, but it remains unknown if the trajectory and dynamics of activation change with age. Here, we use time-lapse imaging and single cell RNA-seq to measure activation trajectories and rates in young and aged MuSCs. We find that the activation trajectory is conserved in aged cells, and we develop effective machine-learning classifiers for cell age. Using cell-behavior analysis and RNA velocity, we find that activation kinetics are delayed in aged MuSCs, suggesting that changes in stem cell dynamics may contribute to impaired stem cell function with age. Intriguingly, we also find that stem cell activation appears to be a random walk-like process, with frequent reversals, rather than a continuous linear progression. These results support a view of the aged stem cell phenotype as a combination of differences in the location of stable cell states and differences in transition rates between them.
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Affiliation(s)
- Jacob C Kimmel
- Eli and Edythe Broad Center for Regenerative Medicine, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
- Center for Cellular Construction, University of California, San Francisco, San Francisco, CA 94143, USA
- Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ara B Hwang
- Eli and Edythe Broad Center for Regenerative Medicine, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Annarita Scaramozza
- Eli and Edythe Broad Center for Regenerative Medicine, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Wallace F Marshall
- Center for Cellular Construction, University of California, San Francisco, San Francisco, CA 94143, USA
- Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrew S Brack
- Eli and Edythe Broad Center for Regenerative Medicine, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
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8
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Todo M. Towards the interpretation of complex visual hallucinations in terms of self-reorganization of neural networks. Neurosci Res 2020; 156:147-158. [PMID: 32112785 DOI: 10.1016/j.neures.2020.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/25/2019] [Accepted: 12/28/2019] [Indexed: 10/24/2022]
Abstract
Patients suffering from dementia with Lewy body (DLB) often see complex visual hallucinations (CVH). Despite many pathological, clinical, and neuroimaging studies, the mechanism of CVH remains unknown. One possible scenario is that top-down information is being used to compensate for the lack of bottom-up information. To investigate this possibility and understand the underlying mathematical structure of the CVH mechanism, we propose a simple computational model of synaptic plasticity with particular focus on the effect of selective damage to the bottom-up network on self-reorganization. We show neurons that undergo a change in activity from a bottom-up to a top-down network framework during the reorganization process, which can be understood in terms of state transitions. Assuming that the pre-reorganization representation of this neuron remains after reorganization, it is possible to interpret neural response induced by top-down information as the sensation of bottom-up information. This situation might correspond to a hallucinatory situation in DLB patients. Our results agree with existing experimental evidence and provide new insights into data that have hitherto not been experimentally validated on patients with DLB.
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Affiliation(s)
- Masato Todo
- Department of Mathematics, School of Science, Hokkaido University, Sapporo, Hokkaido, Japan.
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9
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Hu B, Wang D, Xia Z, Yang A, Zhang J, Shi Q, Dai H. Regulation and control roles of the basal ganglia in the development of absence epileptiform activities. Cogn Neurodyn 2020; 14:137-54. [PMID: 32015772 DOI: 10.1007/s11571-019-09559-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/02/2019] [Accepted: 09/30/2019] [Indexed: 10/25/2022] Open
Abstract
Absence epileptiform activities are traditionally considered to be primarily induced by abnormal interactions between the cortical and thalamic neurons, which form the thalamocortical circuit in the brain. The basal ganglia, as an organizational unit in the brain, has close input and output relationships with the thalamocortical circuit. Although several studies report that the basal ganglia may participate in controlling and regulating absence epileptiform activities, to date, there have been no studies regarding whether the basal ganglia directly cause absence epileptiform activities. In this paper, we built a basal ganglia-corticothalamic network model to determine the role of basal ganglia in this disease. We determined that absence epileptiform activities might be directly induced by abnormal coupling strengths on certain pivotal pathways in the basal ganglia. These epileptiform activities can be well controlled by the coupling strengths of three major pathways that project from the thalamocortical network to the basal ganglia. The results implied that the substantia nigra pars compacta (SNc) can be considered to be the effective treatment target area for inhibiting epileptiform activities, which supports the observations of previous studies. Particularly, as a major contribution of this paper, we determined that the final presentation position of the epileptic slow spike waves is not limited to the cerebral cortex; these waves may additionally appear in the thalamus, striatal medium spiny neurons, striatal fast spiking interneuron, the SNc, subthalamic nucleus, substantia nigra pars reticulata and globus pallidus pars externa. In addition, consistent with several previous studies, the delay in the network was observed to be a critical factor for inducing transitions between different types of absence epileptiform activities. Our new model not only explains the onset and control mechanism but also provides a unified framework to study similar problems in neuron systems.
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Bos P, Oosterwijk A, Koehorst R, Bader A, Philippi J, van Amerongen H, Wientjes E. Digitonin-sensitive LHCII enlarges the antenna of Photosystem I in stroma lamellae of Arabidopsis thaliana after far-red and blue-light treatment. Biochim Biophys Acta Bioenerg 2019; 1860:651-658. [PMID: 31299182 DOI: 10.1016/j.bbabio.2019.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 06/14/2019] [Accepted: 07/07/2019] [Indexed: 11/16/2022]
Abstract
Light drives photosynthesis. In plants it is absorbed by light-harvesting antenna complexes associated with Photosystem I (PSI) and photosystem II (PSII). As PSI and PSII work in series, it is important that the excitation pressure on the two photosystems is balanced. When plants are exposed to illumination that overexcites PSII, a special pool of the major light-harvesting complex LHCII is phosphorylated and moves from PSII to PSI (state 2). If instead PSI is over-excited the LHCII complex is dephosphorylated and moves back to PSII (state 1). Recent findings have suggested that LHCII might also transfer energy to PSI in state 1. In this work we used a combination of biochemistry and (time-resolved) fluorescence spectroscopy to investigate the PSI antenna size in state 1 and state 2 for Arabidopsis thaliana. Our data shows that 0.7 ± 0.1 unphosphorylated LHCII trimers per PSI are present in the stroma lamellae of state-1 plants. Upon transition to state 2 the antenna size of PSI in the stroma membrane increases with phosphorylated LHCIIs to a total of 1.2 ± 0.1 LHCII trimers per PSI. Both phosphorylated and unphosphorylated LHCII function as highly efficient PSI antenna.
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Affiliation(s)
- Peter Bos
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, the Netherlands
| | - Anniek Oosterwijk
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, the Netherlands
| | - Rob Koehorst
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, the Netherlands; MicroSpectroscopy Research Facility, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, the Netherlands
| | - Arjen Bader
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, the Netherlands; MicroSpectroscopy Research Facility, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, the Netherlands
| | - John Philippi
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, the Netherlands
| | - Herbert van Amerongen
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, the Netherlands; MicroSpectroscopy Research Facility, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, the Netherlands
| | - Emilie Wientjes
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET Wageningen, the Netherlands.
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Ventimiglia E, Van Hemelrijck M, Lindhagen L, Stattin P, Garmo H. How to measure temporal changes in care pathways for chronic diseases using health care registry data. BMC Med Inform Decis Mak 2019; 19:103. [PMID: 31146754 PMCID: PMC6543619 DOI: 10.1186/s12911-019-0823-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 05/20/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Disease trajectories for chronic diseases can span over several decades, with several time-dependent factors affecting treatment decisions. Thus, there is a need for long-term predictions of disease trajectories to inform patients and healthcare professionals on the long-term outcomes and provide information on the need of future health care. Here, we propose a state transition model to describe and predict disease trajectories up to 25 years after diagnosis in men with prostate cancer (PCa), as a proof of principle. METHODS States, state transitions, and transition probabilities were identified and estimated in Prostate Cancer data Base of Sweden (PCBaSeTraject), using nationwide population-based data from 118,743 men diagnosed with PCa. A state transition model in discrete time steps (i.e., 4 weeks) was developed and applied to capture all possible transitions (PCBaSeSim). Transition probabilities were estimated for changes in both treatment and comorbidity. These models combined yielded parameter estimates to run an individual-level simulation based on the state-transition model to obtain prediction estimates. Predicted estimates were then compared to real world data in PCBaSeTraject. RESULTS PCBaSeSim estimates for the cumulative incidence of first and second transitions, death from PCa and death from other causes were compared to observed transitions in PCBaSeTraject. A good agreement was found between simulated and observed estimates. CONCLUSIONS We developed a reliable and accurate simulation tool, PCBaSeSim that provides information on disease trajectories for subjects with a chronic disease on an individual and population-based level.
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Affiliation(s)
- Eugenio Ventimiglia
- Division of Experimental Oncology/Unit of Urology, IRCCS Ospedale San Raffaele, Milan, Italy.,Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Mieke Van Hemelrijck
- King's College London, School of Cancer and Pharmaceutical Sciences, Translational Oncology & Urology Research (Tour), 3rd Floor, Bermondsey Wing, Guy's Hospital, London, SE1 9RT, UK
| | | | - Pär Stattin
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Hans Garmo
- King's College London, School of Cancer and Pharmaceutical Sciences, Translational Oncology & Urology Research (Tour), 3rd Floor, Bermondsey Wing, Guy's Hospital, London, SE1 9RT, UK. .,Regional Cancer Centre, Uppsala Örebro, Uppsala, Sweden.
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12
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Yuan M, Hong W, Li P. Identification of regulatory variables for state transition of biological networks. Biosystems 2019; 181:71-81. [PMID: 31071365 DOI: 10.1016/j.biosystems.2019.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/04/2019] [Accepted: 05/05/2019] [Indexed: 01/02/2023]
Abstract
Attractors represent steady states of biological networks. Recent studies have shown that regulatory variables can be used to steer a network state transition from an undesired attractor, such as a cancerous state, to a desired healthy one. Therefore, it is important to identify the regulatory variables and determine their time-dependent profile for state transition of a given network. However, this is a challenging task since regulatory variables have to be identified among numerous candidates in a large-scale biological network. In this study, we developed a new method for identifying regulatory variables in large-scale biological networks for the purpose of state transition. As a result, a set of optimal regulatory variables can be determined based on formulating and solving a mixed-integer nonlinear dynamic optimization problem. A relaxation scheme is used to overcome the difficulties in solving this complex problem containing a large number of binary variables. The solution to this problem simultaneously identifies the optimal regulatory variables, provides strength of regulatory interactions, and obtains the minimal control time to realize the required state transition. In addition, by adjusting the objective function, various combinations of the strength of regulatory interactions and the transition time can be achieved according to the requirement for disease therapy. Results of three case studies (a myeloid differentiation regulatory network, a cancer gene regulatory network, and a T-LGL signaling network) demonstrate the efficacy of the proposed approach. Therefore, this study establishes an appropriate framework for identifying the regulatory variables for state transition of complex biological networks.
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Affiliation(s)
- Meichen Yuan
- College of Energy Engineering, Zhejiang University, Hangzhou, 310027, China; Process Optimization Group, Institute of Automation and Systems Engineering, Technische Universität Ilmenau, Ilmenau, 98684, Germany
| | - Weirong Hong
- College of Energy Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Pu Li
- Process Optimization Group, Institute of Automation and Systems Engineering, Technische Universität Ilmenau, Ilmenau, 98684, Germany.
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13
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Calzadilla PI, Muzzopappa F, Sétif P, Kirilovsky D. Different roles for ApcD and ApcF in Synechococcus elongatus and Synechocystis sp. PCC 6803 phycobilisomes. Biochim Biophys Acta Bioenerg 2019; 1860:488-498. [PMID: 31029593 DOI: 10.1016/j.bbabio.2019.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 10/27/2022]
Abstract
The phycobilisome, the cyanobacterial light harvesting complex, is a huge phycobiliprotein containing extramembrane complex, formed by a core from which rods radiate. The phycobilisome has evolved to efficiently absorb sun energy and transfer it to the photosystems via the last energy acceptors of the phycobilisome, ApcD and ApcE. ApcF also affects energy transfer by interacting with ApcE. In this work we studied the role of ApcD and ApcF in energy transfer and state transitions in Synechococcus elongatus and Synechocystis PCC6803. Our results demonstrate that these proteins have different roles in both processes in the two strains. The lack of ApcD and ApcF inhibits state transitions in Synechocystis but not in S. elongatus. In addition, lack of ApcF decreases energy transfer to both photosystems only in Synechocystis, while the lack of ApcD alters energy transfer to photosystem I only in S. elongatus. Thus, conclusions based on results obtained in one cyanobacterial strain cannot be systematically transferred to other strains and the putative role(s) of phycobilisomes in state transitions need to be reconsidered.
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Affiliation(s)
- Pablo I Calzadilla
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Fernando Muzzopappa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Pierre Sétif
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France.
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14
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Mishra KB, Mishra A, Kubásek J, Urban O, Heyer AG. Low temperature induced modulation of photosynthetic induction in non-acclimated and cold-acclimated Arabidopsis thaliana: chlorophyll a fluorescence and gas-exchange measurements. Photosynth Res 2019; 139:123-143. [PMID: 30306531 DOI: 10.1007/s11120-018-0588-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 03/26/2018] [Accepted: 09/24/2018] [Indexed: 05/23/2023]
Abstract
Cold acclimation modifies the photosynthetic machinery and enables plants to survive at sub-zero temperatures, whereas in warm habitats, many species suffer even at non-freezing temperatures. We have measured chlorophyll a fluorescence (ChlF) and CO2 assimilation to investigate the effects of cold acclimation, and of low temperatures, on a cold-sensitive Arabidopsis thaliana accession C24. Upon excitation with low intensity (40 µmol photons m- 2 s- 1) ~ 620 nm light, slow (minute range) ChlF transients, at ~ 22 °C, showed two waves in the SMT phase (S, semi steady-state; M, maximum; T, terminal steady-state), whereas CO2 assimilation showed a linear increase with time. Low-temperature treatment (down to - 1.5 °C) strongly modulated the SMT phase and stimulated a peak in the CO2 assimilation induction curve. We show that the SMT phase, at ~ 22 °C, was abolished when measured under high actinic irradiance, or when 3-(3, 4-dichlorophenyl)-1, 1- dimethylurea (DCMU, an inhibitor of electron flow) or methyl viologen (MV, a Photosystem I (PSI) electron acceptor) was added to the system. Our data suggest that stimulation of the SMT wave, at low temperatures, has multiple reasons, which may include changes in both photochemical and biochemical reactions leading to modulations in non-photochemical quenching (NPQ) of the excited state of Chl, "state transitions," as well as changes in the rate of cyclic electron flow through PSI. Further, we suggest that cold acclimation, in accession C24, promotes "state transition" and protects photosystems by preventing high excitation pressure during low-temperature exposure.
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Affiliation(s)
- Kumud B Mishra
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00, Brno, Czech Republic.
- Department of Experimental Biology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
| | - Anamika Mishra
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00, Brno, Czech Republic
| | - Jiří Kubásek
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00, Brno, Czech Republic
| | - Otmar Urban
- Global Change Research Institute, Czech Academy of Sciences, Bělidla 986/4a, 603 00, Brno, Czech Republic
| | - Arnd G Heyer
- Department of Plant Biotechnology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70567, Stuttgart, Germany
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15
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Madireddi SK, Nama S, Devadasu E, Subramanyam R. Thylakoid membrane dynamics and state transitions in Chlamydomonas reinhardtii under elevated temperature. Photosynth Res 2019; 139:215-226. [PMID: 30030686 DOI: 10.1007/s11120-018-0562-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 03/17/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
Moderately elevated temperatures can induce state transitions in higher plants by phosphorylation of light-harvesting complex II (LHCII). In this study, we exposed unicellular algae Chlamydomonas reinhardtii to moderately elevated temperatures (38 °C) for short period of time in the dark to understand the thylakoid membrane dynamics and state transition mechanism. Here we report that under elevated temperatures (1) LHCII gets phosphorylated similar to higher plants and (2) there is decreased absorption cross section of photosystem II (PSII), whereas (3) there is no change in absorption cross section of photosystem I (PSI) indicating that LHCII trimers are largely disconnected with both photosystems under moderately elevated temperatures and (4) on return to room temperature after elevated temperature treatment there is a formation of state transition complex comprising of PSII-LHCII-PSI. The temperature-induced state transition mechanism also depends on stt7 kinase-like in light-induced state transition. The protein content was stable at the moderately elevated temperature treatment of 40 °C; however, at 45 °C severe downregulation in photosynthetic performance and protein content was observed. In addition to the known changes to photosynthetic apparatus, elevated temperatures can destabilize the PSII-LHCII complex that can result in decreased photosynthetic efficiency in C. reinhardtii. We concluded that the membrane dynamics of light-induced state transitions differs considerably from temperature-induced state transition mechanisms in C. reinhardtii.
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Affiliation(s)
- Sai Kiran Madireddi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Srilatha Nama
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Elsinraju Devadasu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
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16
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He H, Xu J, Xie W, Guo QL, Jiang FL, Liu Y. Reduced state transition barrier of CDK6 from open to closed state induced by Thr177 phosphorylation and its implication in binding modes of inhibitors. Biochim Biophys Acta Gen Subj 2017; 1862:501-512. [PMID: 29108955 DOI: 10.1016/j.bbagen.2017.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 01/15/2023]
Abstract
BACKGROUND CDK6 is considered as a highly validated anticancer drug target due to its essential role in regulating cell cycle progression at G1 restriction point. Activation of CDK6 requires the phosphorylation of Thr177 on A-loop, but the structural insights of the activation mechanism remain unclear. METHODS Herein, all-atoms molecular dynamics (MD) simulations were used to study the effects of Thr177 phosphorylation on the dynamic structure of CDK6-Vcyclin complex. RESULTS MD results indicated that the free energy barrier of the transition from open to closed state decreased ~47.2% after Thr177 phosphorylation. Key steps along the state transition process were obtained from a cluster analysis. Binding preference of ten different inhibitors to open or closed state were also investigated through molecular docking along with MD simulations methods. CONCLUSIONS Our results indicated that Thr177 phosphorylation increased the flexibility around the ATP-binding pocket. The transition of the ATP-binding pocket between open and closed states should be considered for understanding the binding of CDK6 inhibitors. GENERAL SIGNIFICANCE This work could deepen the understanding of CDKs activation mechanism, and provide useful information for the discovery of new CDKs inhibitors with high affinity and specificity.
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Affiliation(s)
- Huan He
- State Key Laboratory of Virology & Key Laboratory of Analytical Chemistry for Biology and Medicine (MOE) & Key Laboratory of Biomedical Polymer Materials (MOE), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Juan Xu
- State Key Laboratory of Virology & Key Laboratory of Analytical Chemistry for Biology and Medicine (MOE) & Key Laboratory of Biomedical Polymer Materials (MOE), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Wen Xie
- Department of Clinical Laboratory, Zhongnan Hospital, Wuhan University, Wuhan 430071, PR China
| | - Qing-Lian Guo
- Department of Clinical Laboratory, Zhongnan Hospital, Wuhan University, Wuhan 430071, PR China
| | - Feng-Lei Jiang
- State Key Laboratory of Virology & Key Laboratory of Analytical Chemistry for Biology and Medicine (MOE) & Key Laboratory of Biomedical Polymer Materials (MOE), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China.
| | - Yi Liu
- State Key Laboratory of Virology & Key Laboratory of Analytical Chemistry for Biology and Medicine (MOE) & Key Laboratory of Biomedical Polymer Materials (MOE), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China; Key Laboratory of Coal Conversion and Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, PR China; College of Chemistry and Material Sciences, Guangxi Teachers Education University, Nanning 530001, PR China.
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17
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Ogawa T, Misumi M, Sonoike K. Estimation of photosynthesis in cyanobacteria by pulse-amplitude modulation chlorophyll fluorescence: problems and solutions. Photosynth Res 2017; 133:63-73. [PMID: 28283890 DOI: 10.1007/s11120-017-0367-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [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: 10/25/2016] [Accepted: 03/02/2017] [Indexed: 05/09/2023]
Abstract
Cyanobacteria are photosynthetic prokaryotes and widely used for photosynthetic research as model organisms. Partly due to their prokaryotic nature, however, estimation of photosynthesis by chlorophyll fluorescence measurements is sometimes problematic in cyanobacteria. For example, plastoquinone pool is reduced in the dark-acclimated samples in many cyanobacterial species so that conventional protocol developed for land plants cannot be directly applied for cyanobacteria. Even for the estimation of the simplest chlorophyll fluorescence parameter, F v/F m, some additional protocol such as addition of DCMU or illumination of weak blue light is necessary. In this review, those problems in the measurements of chlorophyll fluorescence in cyanobacteria are introduced, and solutions to those problems are given.
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Affiliation(s)
- Takako Ogawa
- Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, 162-8480, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Masahiro Misumi
- Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, 162-8480, Japan
| | - Kintake Sonoike
- Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, 162-8480, Japan.
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18
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Schuurmans RM, Matthijs JCP, Hellingwerf KJ. Transition from exponential to linear photoautotrophic growth changes the physiology of Synechocystis sp. PCC 6803. Photosynth Res 2017; 132:69-82. [PMID: 28108865 PMCID: PMC5357262 DOI: 10.1007/s11120-016-0329-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 12/16/2016] [Indexed: 05/03/2023]
Abstract
Phototrophic microorganisms like cyanobacteria show growth curves in batch culture that differ from the corresponding growth curves of chemotrophic bacteria. Instead of the usual three phases, i.e., lag-, log-, and stationary phase, phototrophs display four distinct phases. The extra growth phase is a phase of linear, light-limited growth that follows the exponential phase and is often ignored as being different. Results of this study demonstrate marked growth phase-dependent alterations in the photophysiology of the cyanobacterium Synechocystis sp. PCC 6803 between cells harvested from the exponential and the linear growth phase. Notable differences are a gradual shift in the energy transfer of the light-harvesting phycobilisomes to the photosystems and a distinct change in the redox state of the plastoquinone pool. These differences will likely affect the result of physiological studies and the efficiency of product formation of Synechocystis in biotechnological applications. Our study also demonstrates that the length of the period of exponential growth can be extended by a gradually stronger incident light intensity that matches the increase of the cell density of the culture.
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Affiliation(s)
- R M Schuurmans
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - J C P Matthijs
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - K J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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19
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Marutani Y, Yamauchi Y, Higashiyama M, Miyoshi A, Akimoto S, Inoue K, Ikeda KI, Mizutani M, Sugimoto Y. Essential role of the PSI-LHCII supercomplex in photosystem acclimation to light and/or heat conditions by state transitions. Photosynth Res 2017; 131:41-50. [PMID: 27432175 DOI: 10.1007/s11120-016-0295-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 03/01/2016] [Accepted: 07/11/2016] [Indexed: 05/22/2023]
Abstract
Light and temperature affect state transitions through changes in the plastoquinone (PQ) redox state in photosynthetic organisms. We demonstrated that light and/or heat treatment induced preferential photosystem (PS) I excitation by binding light-harvesting complex II (LHCII) proteins. The photosystem of wheat was in state 1 after dark overnight treatment, wherein PQ was oxidized and most of LHCII was not bound to PSI. At the onset of the light treatment [25 °C in the light (100 µmol photons m-2 s-1)], two major LHCIIs, Lhcb1 and Lhcb2 were phosphorylated, and the PSI-LHCII supercomplex formed within 5 min, which coincided with an increase in the PQ oxidation rate. Heat treatment at 40 °C of light-adapted wheat led to further LHCII protein phosphorylation of, resultant cyclic electron flow promotion, which was accompanied by ultrafast excitation of PSI and structural changes of thylakoid membranes, thereby protecting PSII from heat damage. These results suggest that LHCIIs are required for the functionality of wheat plant PSI, as it keeps PQ oxidized by regulating photochemical electron flow, thereby helping acclimation to environmental changes.
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Affiliation(s)
- Yoko Marutani
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan
- Technology Innovation Center, Sumika Chemical Analysis Service, Ltd., 3-1-135, Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan
| | - Yasuo Yamauchi
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan.
| | - Mari Higashiyama
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan
| | - Akihito Miyoshi
- Faculty of Agriculture, Kobe University, Nada-ku, Kobe, 657-8501, Japan
| | - Seiji Akimoto
- Molecular Photoscience Research Center, Kobe University, Nada-ku, Kobe, 657-8501, Japan
| | - Kanako Inoue
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Ken-Ichi Ikeda
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan
| | - Masaharu Mizutani
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan
| | - Yukihiro Sugimoto
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan
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20
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Stephenson R, Caron AM, Famina S. Significance of the zero sum principle for circadian, homeostatic and allostatic regulation of sleep-wake state in the rat. Physiol Behav 2016; 167:35-48. [PMID: 27594095 DOI: 10.1016/j.physbeh.2016.08.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 08/08/2016] [Accepted: 08/31/2016] [Indexed: 11/17/2022]
Abstract
Sleep-wake behavior exhibits diurnal rhythmicity, rebound responses to acute total sleep deprivation (TSD), and attenuated rebounds following chronic sleep restriction (CSR). We investigated how these long-term patterns of behavior emerge from stochastic short-term dynamics of state transition. Male Sprague-Dawley rats were subjected to TSD (1day×24h, N=9), or CSR (10days×18h TSD, N=7) using a rodent walking-wheel apparatus. One baseline day and one recovery day following TSD and CSR were analyzed. The implications of the zero sum principle were evaluated using a Markov model of sleep-wake state transition. Wake bout duration (a combined function of the probability of wake maintenance and proportional representations of brief and long wake) was a key variable mediating the baseline diurnal rhythms and post-TSD responses of all three states, and the attenuation of the post-CSR rebounds. Post-NREM state transition trajectory was an important factor in REM rebounds. The zero sum constraint ensures that a change in any transition probability always affects bout frequency and cumulative time of at least two, and usually all three, of wakefulness, NREM and REM. Neural mechanisms controlling wake maintenance may play a pivotal role in regulation and dysregulation of all three states.
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Affiliation(s)
- Richard Stephenson
- University of Toronto, Department of Cell and Systems Biology, 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada.
| | - Aimee M Caron
- University of Toronto, Department of Cell and Systems Biology, 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada
| | - Svetlana Famina
- University of Toronto, Department of Cell and Systems Biology, 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada
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21
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Misumi M, Katoh H, Tomo T, Sonoike K. Relationship Between Photochemical Quenching and Non-Photochemical Quenching in Six Species of Cyanobacteria Reveals Species Difference in Redox State and Species Commonality in Energy Dissipation. Plant Cell Physiol 2016; 57:1510-1517. [PMID: 26712847 PMCID: PMC4937784 DOI: 10.1093/pcp/pcv185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 10/01/2015] [Accepted: 10/12/2015] [Indexed: 05/20/2023]
Abstract
Although the photosynthetic reaction center is well conserved among different cyanobacterial species, the modes of metabolism, e.g. respiratory, nitrogen and carbon metabolism and their mutual interaction, are quite diverse. To explore such uniformity and diversity among cyanobacteria, here we compare the influence of the light environment on the condition of photosynthetic electron transport through Chl fluorescence measurement of six cyanobacterial species grown under the same photon flux densities and at the same temperature. In the dark or under weak light, up to growth light, a large difference in the plastoquinone (PQ) redox condition was observed among different cyanobacterial species. The observed difference indicates that the degree of interaction between respiratory electron transfer and photosynthetic electron transfer differs among different cyanobacterial species. The variation could not be ascribed to the phylogenetic differences but possibly to the light environment of the original habitat. On the other hand, changes in the redox condition of PQ were essentially identical among different species at photon flux densities higher than the growth light. We further analyzed the response to high light by using a typical energy allocation model and found that 'non-regulated' thermal dissipation was increased under high-light conditions in all cyanobacterial species tested. We assume that such 'non-regulated' thermal dissipation may be an important 'regulatory' mechanism in the acclimation of cyanobacterial cells to high-light conditions.
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Affiliation(s)
- Masahiro Misumi
- Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Hiroshi Katoh
- Division of Plant Functional Genomics, Life Science Research Center, Mie University, Kurimamachiya 1577, Tsu, Mie, 514-8507 Japan
| | - Tatsuya Tomo
- Department of Biology, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-Ku, Tokyo, 162-8601 Japan
| | - Kintake Sonoike
- Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
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22
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Ivanov AG, Morgan-Kiss RM, Krol M, Allakhverdiev SI, Zanev Y, Sane PV, Huner NPA. Photoinhibition of photosystem I in a pea mutant with altered LHCII organization. J Photochem Photobiol B 2015; 152:335-46. [PMID: 26321219 DOI: 10.1016/j.jphotobiol.2015.08.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 05/31/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 11/18/2022]
Abstract
Comparative analysis of in vivo chlorophyll fluorescence imaging revealed that photosystem II (PSII) photochemical efficiency (Fv/Fm) of leaves of the Costata 2/133 pea mutant with altered pigment composition and decreased level of oligomerization of the light harvesting chlorophyll a/b-protein complexes (LHCII) of PSII (Dobrikova et al., 2000; Ivanov et al., 2005) did not differ from that of WT. In contrast, photosystem I (PSI) activity of the Costata 2/133 mutant measured by the far-red (FR) light inducible P700 (P700(+)) signal exhibited 39% lower steady state level of P700(+), a 2.2-fold higher intersystem electron pool size (e(-)/P700) and higher rate of P700(+) re-reduction, which indicate an increased capacity for PSI cyclic electron transfer (CET) in the Costata 2/133 mutant than WT. The mutant also exhibited a limited capacity for state transitions. The lower level of oxidizable P700 (P700(+)) is consistent with a lower amount of PSI related chlorophyll protein complexes and lower abundance of the PsaA/PsaB heterodimer, PsaD and Lhca1 polypeptides in Costata 2/133 mutant. Exposure of WT and the Costata 2/133 mutant to high light stress resulted in a comparable photoinhibition of PSII measured in vivo, although the decrease of Fv/Fm was modestly higher in the mutant plants. However, under the same photoinhibitory conditions PSI photochemistry (P700(+)) measured as ΔA820-860 was inhibited to a greater extent (50%) in the Costata 2/133 mutant than in the WT (22%). This was accompanied by a 50% faster re-reduction rate of P700(+) in the dark indicating a higher capacity for CET around PSI in high light treated mutant leaves. The role of chloroplast thylakoid organization on the stability of the PSI complex and its susceptibility to high light stress is discussed.
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Affiliation(s)
- A G Ivanov
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, 1151 Richmond Street, N., London, Ontario N6A 5B7, Canada.
| | - R M Morgan-Kiss
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH 45045, USA
| | - M Krol
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, 1151 Richmond Street, N., London, Ontario N6A 5B7, Canada
| | - S I Allakhverdiev
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia; Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia; Department of Plant Physiology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Yu Zanev
- Institute of Biophysics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - P V Sane
- Jain Irrigation Systems Limited, Jain Hills, Jalgaon 425001, India
| | - N P A Huner
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, 1151 Richmond Street, N., London, Ontario N6A 5B7, Canada.
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23
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Chen Z, Zhan J, Chen Y, Yang M, He C, Ge F, Wang Q. Effects of Phosphorylation of β Subunits of Phycocyanins on State Transition in the Model Cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol 2015; 56:1997-2013. [PMID: 26315596 DOI: 10.1093/pcp/pcv118] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 04/27/2015] [Accepted: 08/09/2015] [Indexed: 05/22/2023]
Abstract
Synechocystis sp. PCC 6803 (hereafter Synechocystis) is a model cyanobacterium and has been used extensively for studies concerned with photosynthesis and environmental adaptation. Although dozens of protein kinases and phosphatases with specificity for Ser/Thr/Tyr residues have been predicted, only a few substrate proteins are known in Synechocystis. In this study, we report 194 in vivo phosphorylation sites from 149 proteins in Synechocystis, which were identified using a combination of peptide pre-fractionation, TiO(2) enrichment and liquid chromatograpy-tandem mass spectrometry (LC-MS/MS) analysis. These phosphorylated proteins are implicated in diverse biological processes, such as photosynthesis. Among all identified phosphoproteins involved in photosynthesis, the β subunits of phycocyanins (CpcBs) were found to be phosphorylated on Ser22, Ser49, Thr94 and Ser154. Four non-phosphorylated mutants were constructed by using site-directed mutagenesis. The in vivo characterization of the cpcB mutants showed a slower growth under high light irradiance and displayed fluorescence quenching to a lower level and less efficient energy transfer inside the phycobilisome (PBS). Notably, the non-phosphorylated mutants exhibited a slower state transition than the wild type. The current results demonstrated that the phosphorylation status of CpcBs affects the energy transfer and state transition of photosynthesis in Synechocystis. This study provides novel insights into the molecular mechanisms of protein phosphorylation in the regulation of photosynthesis in cyanobacteria and may facilitate the elucidation of the entire regulatory network by linking kinases to their physiological substrates.
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Affiliation(s)
- Zhuo Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China These authors contributed equally to this work.
| | - Jiao Zhan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China University of Chinese Academy of Sciences, Beijing 100094, China These authors contributed equally to this work.
| | - Ying Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Mingkun Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Chenliu He
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Qiang Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
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