The time course of photoinactivation of photosystem II in leaves revisited

Since photosystem II (PS II) performs the demanding function of water oxidation using light energy, it is susceptible to photoinactivation during photosynthesis. The time course of photoinactivation of PS II yields useful information about the process. Depending on how PS II function is assayed, however, the time course seems to differ. Here, we revisit this problem by using two additional assays: (1) the quantum yield of oxygen evolution in limiting, continuous light and (2) the flash-induced cumulative delivery of PS II electrons to the oxidized primary donor (P700+) in PS I measured as a ‘P700 kinetics area’. The P700 kinetics area is based on the fact that the two photosystems function in series: when P700 is completely photo-oxidized by a flash added to continuous far-red light, electrons delivered from PS II to PS I by the flash tend to re-reduce P700+ transiently to an extent depending on the PS II functionality, while the far-red light photo-oxidizes P700 back to the steady-state concentration. The quantum yield of oxygen evolution in limiting, continuous light indeed decreased in a way that deviated from a single-negative exponential. However, measurement of the quantum yield of oxygen in limiting light may be complicated by changes in mitochondrial respiration between darkness and limiting light. Similarly, an assay based on chlorophyll fluorescence may be complicated by the varying depth in leaf tissue from which the signal is detected after progressive photoinactivation of PS II. On the other hand, the P700 kinetics area appears to be a reasonable assay, which is a measure of functional PS II in the whole leaf tissue and independent of changes in mitochondrial respiration. The P700 kinetics area decreased in a single-negative exponential fashion during progressive photoinactivation of PS II in a number of plant species, at least at functional PS II contents ≥6 % of the initial value, in agreement with the conclusion of Sarvikas et al. (Photosynth Res 103:7–17, 2010). That is, the single-negative-exponential time course does not provide evidence for photoprotection of functional PS II complexes by photoinactivated, connected neighbours.The support of this study by an Australian Research Council Grant (DP1093827) awarded to W.S.C., a China Scholarship Council Fellowship to J.K., JSPS Postdoctoral Fellowships for Research Abroad (21-674) to R.O. and a Knowledge Innovation Programme of the Chinese Academy of Sciences Grant (KSCX2-EW-J-1) to D.-Y.F. is gratefully acknowledged

Quantifying and monitoring functional Photosystem II and the stoichiometry of the two photosystems in leaf segments: Approaches and approximations

Given its unique function in light-induced water oxidation and its susceptibility to photoinactivation during photosynthesis, photosystem II (PS II) is often the focus of studies of photosynthetic structure and function, particularly in environmental stress conditions. Here we review four approaches for quantifying or monitoring PS II functionality or the stoichiometry of the two photosystems in leaf segments, scrutinizing the approximations in each approach. (1) Chlorophyll fluorescence parameters are convenient to derive, but the information-rich signal suffers from the localized nature of its detection in leaf tissue. (2) The gross O2 yield per single-turnover flash in CO2-enriched air is a more direct measurement of the functional content, assuming that each functional PS II evolves one O2 molecule after four flashes. However, the gross O2 yield per single-turnover flash (multiplied by four) could overestimate the content of functional PS II if mitochondrial respiration is lower in flash illumination than in darkness. (3) The cumulative delivery of electrons from PS II to P700? (oxidized primary donor in PS I) after a flash is added to steady background far-red light is a whole-tissue measurement, such that a single linear correlation with functional PS II applies to leaves of all plant species investigated so far. However, the magnitude obtained in a simple analysis (with the signal normalized to the maximum photo-oxidizable P700 signal), which should equal the ratio of PS II to PS I centers, was too small to match the independently-obtained photosystem stoichiometry. Further, an under-estimation of functional PS II content could occur if some electrons were intercepted before reaching PS I. (4) The electrochromic signal from leaf segments appears to reliably quantify the photosystem stoichiometry, either by progressively photoinactivating PS II or suppressing PS I via photo-oxidation of a known fraction of the P700 with steady far-red light. Together, these approaches have the potential for quantitatively probing PS II in vivo in leaf segments, with prospects for application of the latter two approaches in the field

Whole-tissue determination of the rate coefficients of photoinactivation and repair of photosystem II in cotton leaf discs based on flash-induced P700 redox kinetics

Using radioactively labelled amino acids to investigate repair of photoinactivated photosystem II (PS II) gives only a relative rate of repair, while using chlorophyll fluorescence parameters yields a repair rate coefficient for an undefined, variable location within the leaf tissue. Here, we report on a whole-tissue determination of the rate coefficient of photoinactivation k i , and that of repair k r in cotton leaf discs. The method assays functional PS II via a P700 kinetics area associated with PS I, as induced by a single-turnover, saturating flash superimposed on continuous background far-red light. The P700 kinetics area, directly proportional to the oxygen yield per single-turnover, saturating flash, was used to obtain both k i and k r . The value of k i , directly proportional to irradiance, was slightly higher when CO2 diffusion into the abaxial surface (richer in stomata) was blocked by contact with water. The value of k r , sizable in darkness, changed in the light depending on which surface was blocked by contact with water. When the abaxial surface was blocked, k r first peaked at moderate irradiance and then decreased at high irradiance. When the adaxial surface was blocked, k r first increased at low irradiance, then plateaued, before increasing markedly at high irradiance. At the highest irradiance, k r differed by an order of magnitude between the two orientations, attributable to different extents of oxidative stress affecting repair (Nishiyama et al., EMBO J 20: 5587–5594, 2001). The method is a whole-tissue, convenient determination of the rate coefficient of photoinactivation k i and that of repair k r .The support of this work by an Australian Research Council Grant (DP1093827) awarded to W. S. C., the Joint Funds of the National Natural Science Foundation of China Grant (No. U1203283) and a National Key Technology R and D Program of China Grant (2007BAD44B07) to Z. W. F., and a Knowledge Innovation Program of the Chinese Academy of Sciences grant (KZCX2- XB3-09-02) to D. -Y. F. is gratefully acknowledged

The effect of bleach duration and age on the ERG photostress test

Background: The ERG photostress test assesses the recovery of the focal 41 Hz ERG following exposure to a bright light that bleaches a significant proportion of photopigment. The aims of this study were: 1) to compare the repeatability of the ERG photostress test recovery time constant following long and short duration light exposure, and 2) to determine the effect of age on the ERG photostress test recovery time constant. Methods: Focal 41 Hz ERGs were recorded from 23 participants (age range 20–71 years) at 20-second intervals for 5 minutes following either a short-duration (photoflash) or long-duration (equilibrium) light exposure. After a 5-minute wash-out period, the procedure was repeated using the second bleach modality. The time constant of cone recovery was determined by fitting an exponential model to the amplitude recovery data. The whole procedure was repeated on a second occasion. The co-efficient of repeatability (CoR) was calculated for each bleaching technique. The relationship between the time constant of recovery and age was investigated (Pearson’s correlation coefficient). Results: The time constant of recovery following an equilibrium bleach was more repeatable than recovery following a photoflash (CoR = 85s and 184s respectively). Eight trials (from seven participants) failed to show a reduction in amplitude following the photoflash, suggesting that a blink or fixation loss had occurred. All participants were reliably light-adapted by the equilibrium bleach. For the equilibrium bleach data, the time constant of recovery increased with age at a rate of 27 seconds per decade. Conclusions: The equilibrium bleach was more reliable and repeatable than the photoflash. Increasing participant age was shown to result in a lengthening of the recovery time constant, of a magnitude comparable to previously published psychophysical data

Optimising the linear electron transport rate measured by chlorophyll a fluorescence to empirically match the gross rate of oxygen evolution in white light: towards improved estimation of the cyclic electron flux around photosystem I in leaves

The cyclic electron flux (CEF) around photosystem I (PSI) was discovered in isolated chloroplasts more than six decades ago, but its quantification has been hampered by the absence of net formation of a product or net consumption of a substrate. We estimated in vivo CEF in leaves as the difference (ΔFlux) between the total electron flux through PSI (ETR1) measured by a near infrared signal, and the linear electron flux through both photosystems by optimised measurement of chlorophyll a fluorescence (LEFfl). Chlorophyll fluorescence was excited by modulated green light from a light-emitting diode at an optimal average irradiance, and the fluorescence was detected at wavelengths >710 nm. In this way, LEFfl matched the gross rate of oxygen evolution multiplied by 4 (LEFO2) in broad-spectrum white actinic irradiance up to half (spinach, poplar and rice) or one third (cotton) of full sunlight irradiance. This technique of estimating CEF can be applied to leaves attached to a plant.This work was supported by a China Scholarship Council Fellowship (to M-M. Z.), and a grant from the Australian Research Council (to WSC, DP1093827)

Identification and Characterization of RcMADS1, an AGL24 Ortholog from the Holoparasitic Plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae)

10.1371/journal.pone.0067243PLoS ONE86-POLN

Standardised Outcomes in Nephrology-Polycystic Kidney Disease (SONG-PKD): study protocol for establishing a core outcome set in polycystic kidney disease

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is the most common potentially life threatening inherited kidney disease and is responsible for 5-10% of cases of end-stage kidney disease (ESKD). Cystic kidneys may enlarge up to 20 times the weight of a normal kidney due to the growth of renal cysts, and patients with ADPKD have an increased risk of morbidity, premature mortality, and other life-time complications including renal and hepatic cyst and urinary tract infection, intracranial aneurysm, diverticulosis, and kidney pain which impair quality of life. Despite some therapeutic advances and the growing number of clinical trials in ADPKD, the outcomes that are relevant to patients and clinicians, such as symptoms and quality of life, are infrequently and inconsistently reported. This potentially limits the contribution of trials to inform evidence-based decision-making. The Standardised Outcomes in Nephrology-Polycystic Kidney Disease (SONG-PKD) project aims to establish a consensus-based set of core outcomes for trials in PKD (with an initial focus on ADPKD but inclusive of all stages) that patients and health professionals identify as critically important. METHODS: The five phases of SONG-PKD are: a systematic review to identify outcomes that have been reported in existing PKD trials; focus groups with nominal group technique with patients and caregivers to identify, rank, and describe reasons for their choices; qualitative stakeholder interviews with health professionals to elicit individual values and perspectives on outcomes for trials involving patients with PKD; an international three-round Delphi survey with all stakeholder groups (including patients, caregivers, healthcare providers, policy makers, researchers, and industry) to gain consensus on critically important core outcome domains; and a consensus workshop to review and establish a set of core outcome domains and measures for trials in PKD. DISCUSSION: The SONG-PKD core outcome set is aimed at improving the consistency and completeness of outcome reporting across ADPKD trials, leading to improvements in the reliability and relevance of trial-based evidence to inform decisions about treatment and ultimately improve the care and outcomes for people with ADPKD

Applications of interpretable deep learning in neuroimaging: a comprehensive review

Clinical adoption of deep learning models has been hindered, in part, because the black-box nature of neural networks leads to concerns regarding their trustworthiness and reliability. These concerns are particularly relevant in the field of neuroimaging due to the complex brain phenotypes and inter-subject heterogeneity often encountered. The challenge can be addressed by interpretable deep learning (iDL) methods that enable the visualisation and interpretation of the inner workings of deep learning models. This study systematically reviewed the literature on neuroimaging applications of iDL methods and critically analysed how iDL explanation properties were evaluated. Seventy-five studies were included, and ten categories of iDL methods were identified. We also reviewed five properties of iDL explanations that were analysed in the included studies: biological validity, robustness, continuity, selectivity, and downstream task performance. We found that the most popular iDL approaches used in the literature may be sub-optimal for neuroimaging data, and we discussed possible future directions for the field