Phytoplankton Photophysiology Utilities: A Python Toolbox for the Standardization of Processing Active Chlorophyll-a Fluorescence Data

The uptake and application of single turnover chlorophyll fluorometers to the study of phytoplankton ecosystem status and microbial functions has grown considerably in the last two decades. However, standardization of measurement protocols, processing of fluorescence transients and quality control of derived photosynthetic parameters is still lacking and makes community goals of large global databases of high-quality data unrealistic. We introduce the Python package Phytoplankton Photophysiology Utilities (PPU), an adaptable and open-source interface between Fast Repetition Rate and Fluorescence Induction and Relaxation instruments and python. The PPU package includes a variety of functions for the loading, processing and quality control of single turnover fluorescence transients from many commercially available instruments. PPU provides the user with greater flexibility in the application of the Kolber-Prasil-Falkowski model; tools for plotting, quality control, correcting instrument biases and high-throughput processing with ease; and a greater appreciation for the uncertainties in derived photosynthetic parameters. Using data from three research cruises across different biogeochemical regimes, we provide example applications of PPU to fit raw active chlorophyll-a fluorescence data from three commercial instruments and demonstrate tools which help to reduce uncertainties in the final fitted parameters.

Phenotypic Characteristics of Strawberry related to Photo-physiological Parameters according to Temperature and Relative Humidity in a Greenhouse after Planting

The low relative humidity (RH) levels in a greenhouse during the daytime in a strawberry (Fragaria × ananassa Duch) cultivation period negatively affect the growth of strawberry related to photo-physiology. Therefore, this study was conducted to confirm an efficient RH management method by analyzing the phenotypic characteristics related to photo-physiology by controlling the RH in a greenhouse during the daytime with a fog system. Strawberry plants were grown respectively in a greenhouse affected by natural RH changes (control) and in a greenhouse with 40% ~ 50% RH adjusted during the daytime using a fog system. In the greenhouse, with controlled RH, the temperature decreased, and the RH was higher in the initial growth stage of strawberry planting than the control. It was observed a significant increase in the survival rate of the strawberry plant, as well as the incidence of powdery mildew, was lowered. In addition, the photosynthetic rate and OJIP chlorophyll a fluorescence transients related to photosystem II efficiency of strawberry leaves were significantly higher in the fog treatment than in the control. In winter, during the day, the number of days on which the temperature dropped below 20℃ has increased, the greenhouse temperature with controlled RH was lower due to the fog system. When the yield per strawberry plant in January and February was investigated, the control was higher than the RH treatment. Therefore, RH management using a fog system must be controlled at a level where a temperature range is adequate for plant growth, in which the efficient control of these parameters increases strawberry productivity.

Using Rapid Chlorophyll Fluorescence Transients to Classify Vitis Genotypes

When a dark-adapted leaf is illuminated with saturating light, a fast polyphasic rise of fluorescence emission (Kautsky effect) is observed. The shape of the curve is dependent on the molecular organization of the photochemical apparatus, which in turn is a function of the interaction between genotype and environment. In this paper, we evaluate the potential of rapid fluorescence transients, aided by machine learning techniques, to classify plant genotypes. We present results of the application of several machine learning algorithms (k-nearest neighbors, decision trees, artificial neural networks, genetic programming) to rapid induction curves recorded in different species and cultivars of vine grown in the same environmental conditions. The phylogenetic relations between the selected Vitis species and Vitis vinifera cultivars were established with molecular markers. Both neural networks (71.8%) and genetic programming (75.3%) presented much higher global classification success rates than k-nearest neighbors (58.5%) or decision trees (51.6%), genetic programming performing slightly better than neural networks. However, compared with a random classifier (success rate = 14%), even the less successful algorithms were good at the task of classifying. The use of rapid fluorescence transients, handled by genetic programming, for rapid preliminary classification of Vitis genotypes is foreseen as feasible.

The impact of reporter kinetics on the interpretation of data gathered with fluorescent reporters

Fluorescent reporters of biological functions are used to monitor biochemical events and signals in cells and tissue. For neurobiology, these have been particularly useful for monitoring signals in the brains of behaving animals. In order to enhance signal-to-noise, fluorescent reporters typically have kinetics that are slower than that of the underlying biological process. This low-pass filtering by the reporter renders the fluorescence transient a leaking integrated version of the biological signal. Here I discuss the effects that low-pass filtering, or more precisely of integrating by convolving with an exponentially decaying kernel, has on the interpretation of the relationship between the reporter fluorescence transient and the events that underlie it. Unfortunately, when the biological events being monitored are impulse-like, such as the firing of an action potential or the release of neurotransmitter, filtering greatly reduces the maximum correlation coefficient that can be found between the events and the fluorescence signal. This can erroneously support the conclusion that the fluorescence transient and the biological signal that it reports are only weakly related. Furthermore, when examining the encoding of behavioral state variables by nervous system, filtering by the reporter kinetics will favor the interpretation that fluorescence transients encode integrals of measured variables as opposed to the variables themselves. For these reasons, it is necessary to take into account the filtering effects of the indicator by deconvolving with the convolution kernel and recovering the underlying biological events before making conclusions about what is encoded in the signals emitted by fluorescent reporters.

Comprehensive Evaluation for Cold Tolerance in Wucai (Brassica campestris L.) by the Performance Index on an Absorption Basis (PIabs)

Wucai is a biannual leafy vegetable that is more sensitive to cold than most Brassicaceae vegetables. Here, phenotypic differences in wucai were investigated to identify those genotypes with high cold tolerance at low temperature, which could allow their cultivation in cold climates. In all, on the basis of PIabs, 20 wucai genotypes (10 lower PIabs and 10 higher PIabs) were selected from a collection of 124 genotypes. Both W16-13 and SW-3 (higher PIabs) and the LS-6 and W15-16 (lower PIabs) were screened from the 20 wucai genotypes according to several key plant physiological traits: net photosynthetic rate, electrolyte leakage, chilling injury index, specific leaf area, malondialdehyde contents, and PIabs. To further verify the reliability of PIabs, four genotypes were grown under low temperature gradient conditions and their morphological indexes, chlorophyll content, total antioxidant capacity, fluorescence transients (OJIP transients), leaf cell ultrastructure, and gene expression were measured. These indicators strongly demonstrated that the W16-13 and SW-3, which had higher PIabs, possessed higher resistance to cold stress, while both LS-6 and W15-16 were sensitive to cold. As this study shows, the easily measured performance index, PIabs, could be applied to wucai genotypes to screen for one or more varieties characterized by higher cold tolerance.