New applications of photoacoustics to the study of photosynthesis

Photoacoustic methods offer unique capabilities for photosynthesis research. Phenomena that are readily observed by photoacoustics include the storage of energy by electron transport, oxygen evolution by leaf tissue at microsecond time resolution, and the conformational changes of photosystems caused by charge separation. Despite these capabilities, photoacoustic methods have not been widely exploited in photosynthesis research. One factor that has contributed to their slow adoption is uncertainty in the interpretation of photoacoustic signals. Careful experimentation is resolving this uncertainty, however, and technical refinements of photoacoustic methods continue to be made. This review provides an overview of the application of photoacoustics to the study of photosynthesis with an emphasis on the resolution of uncertainties in the interpretation of photoacoustic signals. Recent developments in photoacoustic technology are also presented, including a microphotoacoustic spectrometer, gas permeable photoacoustic cells, the use of photoacoustics to monitor phytoplankton populations, and the use of photoacoustics to study protein dynamics. This revised version was published online in June 2006 with corrections to the Cover Date.     

Photoacoustic Spectroscopy and its Application in Plant Science

The principles of photoacoustic spectroscopy are outlined. This new and still developing technique enables one to detect non-radiative de-excitation processes. It is possible to distinguish between signals emenating from different depths of the sample. In plant science photoacoustic spectroscopy has mainly been applied in photosynthesis research. Here it allows the detection of gross oxygen evolution and gives information about the energy balance of the primary photosynthetic reaction.     

The carboxyl-terminal processing of precursor D1 protein of the photosystem II reaction center

The D1 protein, a key subunit of photosystem II reaction center, is synthesized as a precursor form with a carboxyl-terminal extension, in oxygenic photosynthetic organisms with some exceptions. This part of the protein is removed by the action of an endopeptidase, and the proteolytic processing is indispensable for the manifestation of oxygen-evolving activity in photosynthesis. The carboxyl-terminus of mature D1 protein, which appears upon the cleavage, has recently been demonstrated to be a ligand for a manganese atom in the Mn₄Ca-cluster, which is responsible for the water oxidation chemistry in photosystem II, based on the isotope-edited Fourier transform infrared spectroscopy and the X-ray crystallography. On the other hand, the structure of a peptidase involved in the cleavage of precursor D1 protein has been resolved at a higher resolution, and the enzyme–substrate interactions have extensively been analyzed both in vivo and in vitro. The present article briefly summarizes the history of research and the present state of our knowledge on the carboxyl-terminal processing of precursor D1 protein in the photosystem II reaction center.     

适用于植物光合作用的光声池设计研究进展

光声光谱检测可很好地应用在植物光合作用的研究领域,可更有效于传统检测方法并已在大量检测研究中得以证明。在一套光声光谱仪检测装置中,光声池是其核心部件,其设计好坏直接影响着实验的结果。文章阐述了适用于植物光合作用的光声池的设计方法及其需要关注的关键问题;展望了植物光合作用的光声光谱检测与其他检测方法联用的重点及其研究方向;提出了光声池设计中应着重关注其活体实时在线检测及其相关技术问题。     

Importance of canopy structure on photosynthesis in single- and multi-species assemblages of marine macroalgae

Plant communities utilize available irradiance with different efficiency depending not only on their photosynthetic characteristics but also on the canopy structure and density. The importance of canopy structure are well studied in terrestrial plant communities but poorly studied in aquatic plant communities. The objective of this study was to evaluate macroalgal community photosynthesis in artificial constructed communities of one to four species with different morphologies along a range of leaf (i.e.=thallus) area densities. In a laboratory set-up we measured net photosynthesis and dark respiration in constructed assemblages of macroalgae, excluding effects other than photosynthesis of individual tissue and distribution of photons in the canopy from influencing metabolism. We hypothezised that 1) canopy structure determines the actual rates of photosynthesis relative to the optimal rates and 2) multi-species communities attain higher maximum photosynthetic rates than single species communities. We found that differences in canopy structure outweighed large differences in tissue photosynthesis resulting in relatively similar maximum community photosynthetic rates among the different single and multi-species assemblages (20.1–40.5 μmol O₂ m⁻² s⁻¹). Canopy structure influenced community photosynthesis both at low and high leaf area densities because it determines the ability of macroalgae to use the photosynthetic potential of their individual tissues. Due to an averaging effect the photosynthetic rate at high leaf area density was more similar among multi-species community than among single-species communities. Multi-species communities had, on average, a slightly higher photosynthetic production than expected from photosynthesis of single species communities. Moreover multi-species communities were capable of exposing new tissue to irradiance up to high densities thereby avoiding a decrease in net photosynthesis. This finding suggests that multi-species communities may be able to maintain higher biomass per unit ground area than single-species communities.     

The structure, function and dynamics of photosystem two

One of the greatest challenges in modern photosynthesis research is to elucidate fully the structural and functional properties of photosystem two (PSII). This water-plasto-quinone oxidoreductase is located in a membrane complex composed of more than 25 subunits. The primary and secondary structures of all known subunits which constitute the central core of PSII are reviewed. How these subunits interact with each other to produce the tertiary and quaternary structure of PSII in vivo is not fully understood. However, electron microscopy is helping to fill this gap in our knowledge both by single particle analysis and electron crystallography. These studies suggest that active PSII is dimeric, although the functional significance of this oligomeric state is not yet understood. Moreover, the elucidation of the structure of photosystem one (PSI) by X-ray crystallography has revealed features which are likely to be relevant to PSII structure. It seems highly likely that the D1 protein with CP43 and D2 protein with CP47 (summing 11 transmembrane helices in each case) will have structural similarities to the organisation of PsaA and PsaB. It is likely that the turnover of the D1 protein is aided by the relatively easy removal of CP43 from this arrangement of the PSII core.     

缙云山森林林隙与非林隙物种多样性比较研究

运用Gleason物种丰富度指数、Shannon-Wiener指数、Pielou均匀度指数、Simpson指数、生态优势度指数、均优多指数和群落优势度指数对缙云山森林群落林隙与非缃隙物种多样性进行了研究,对群落稳定性进行了探讨。结果表明,林隙以个体数为基础的物种丰富度为12.14,Shannon-Wiener指数为4.62,均匀度为0.70,Simpson指数为13.32,灌木层所起作用较大;非林隙林分各项物种多样性指数明显低于林隙,依次为6.32、3.74、0.66、8.16。林隙植物群落物种多样性指数显著高于非林隙,而生态优势度和群落优势度又明显低于非林隙,表明作为自然干扰和人为干扰的产物,林隙的存在增加了群落物种多样性,但同时也降低了群落的稳定性。     

Does dinocyst wall composition really reflect trophic affinity? New evidence from ATR micro-FTIR spectroscopy measurements

Attenuated total reflection (ATR) microscope Fourier transform infrared (micro-FTIR) spectroscopy was used to investigate the dinosporin composition in the walls of modern, organic-walled dinoflagellate resting cysts (dinocysts). Variable cyst wall compositions were observed, which led to the erection of four spectrochemical groups, some with striking similarities to other resistant biomacromolecules such as sporopollenin and algaenan. Furthermore, possible proxies derivable from the spectrochemical composition of modern and fossil dinocysts were discussed. The color of the dinocyst walls was reflected in the spectral data. When comparing that color with a standard and the results of a series of bleaching experiments with oxidative agents, eumelanin was assigned as a likely pigment contributing to the observed color. Following this assignment, the role of eumelanin as an ultraviolet sunscreen in colored dinocysts was hypothesized, and its implications on the autofluorescence and morphological preservation of dinocysts were further discussed. Unlike what had previously been assumed, it was shown that micro-FTIR data from dinocysts cannot be used to unambiguously infer trophic affinities of their associated cells. Finally, using methods with high spatial resolutions (synchrotron transmission micro-FTIR and optical photothermal infrared spectroscopy), it was shown that dinocyst wall layers are chemically homogenous at the probed scales. This study fills a large knowledge gap in our understanding of the chemical nature of dinocyst walls and has nuanced certain assumptions and interpretations made in the past.     

Target for improvement: a cluster randomised trial of public involvement in quality-indicator prioritisation (intervention development and study protocol)

Background

Violence against women (VAW) is a major public health problem. Translation of VAW research to policy and practice is an area that remains understudied, but provides the opportunity to examine knowledge translation and exchange (KTE) processes in a complex, multi-stakeholder context. In a series of studies including two randomized trials, the McMaster University VAW Research Program studied one key research gap: evidence about the effectiveness of screening women for exposure to intimate partner violence. This project developed and evaluated KTE strategies to share research findings with policymakers, health and community service providers, and women's advocates.

Methods

A longitudinal cross-sectional design, applying concurrent mixed data collection methods (surveys, interviews, and focus groups), was used to evaluate the utility of specific KTE strategies, including a series of workshops and a day-long Family Violence Knowledge Exchange Forum, on research sharing, uptake, and use.

Results

Participants valued the opportunity to meet with researchers, provide feedback on key messages, and make personal connections with other stakeholders. A number of factors specific to the knowledge itself, stakeholders' contexts, and the nature of the knowledge gap being addressed influenced the uptake, sharing, and use of the research. The types of knowledge use changed across time, and were specifically related to both the types of decisions being made, and to stage of decision making; most reported use was conceptual or symbolic, with few examples of instrumental use. Participants did report actively sharing the research findings with their own networks. Further examination of these second-order knowledge-sharing processes is required, including development of appropriate methods and measures for its assessment. Some participants reported that they would not use the research evidence in their decision making when it contradicted professional experiences, while others used it to support apparently contradictory positions. The online wiki-based 'community of interest' requested by participants was not used.

Conclusions

Mobilizing knowledge in the area of VAW practice and policy is complex and resource-intensive, and must acknowledge and respect the values of identified knowledge users, while balancing the objectivity of the research and researchers. This paper provides important lessons learned about these processes, including attending to the potential unintended consequences of knowledge sharing.     

Characterization of azido-NAD to assess its potential as a two-dimensional infrared probe of enzyme dynamics

Enzyme active-site dynamics at femtosecond to picosecond time scales are of great biochemical importance, but remain relatively unexplored due to the lack of appropriate analytical methods. Two-dimensional infrared (2D IR) spectroscopy is one of the few methods that can examine chemical biological motions at this time scale, but all the IR probes used so far were specific to a few unique enzymes. The lack of IR probes of broader specificity is a major limitation to further 2D IR studies of enzyme dynamics. Here we describe the synthesis of a general IR probe for nicotinamide-dependent enzymes. This azido analog of the ubiquitous cofactor nicotinamide adenine dinucleotide is found to be stable and bind to several dehydrogenases with dissociation constants similar to that for the native cofactor. The infrared absorption spectra of this probe bound to several enzymes indicate that it has significant potential as a 2D IR probe to investigate femtosecond dynamics of nicotinamide-dependent enzymes.     

应用CiteSpace对生态学科meta分析的文献计量学和可视化分析

Meta分析是针对一系列独立研究结果进行定量综合分析的方法。从20世纪90年代初开始被应用于生态学的研究中,已经对这一学科的数据汇总方式产生重大影响。为了探究meta分析方法在生态学领域的研究现状及热点,以Web of Science论文核心合集为检索数据库,通过输入关键词检索了1992至2018年之间的论文,并利用Web of Science自带的文献分析工具和Histcite对检索的文献信息进行统计分析,分析了不同年份、国家、期刊、学科基础知识论文的发表和被引情况,用CiteSpace软件对其进行热点分析并绘制了知识图谱。研究发现,我国生态学研究在meta分析方法的改进和利用方面与美国、英国等国家相比尚有差距;使用meta分析方法开展研究越来越多,但研究方向上出现了一些转变,越来越多的研究关注全球变化背景下植物光合作用、物种入侵的机理以及模拟氮循环过程对物候和植被生产力的影响及价值评估的研究,并成为本领域的研究前沿。     

Covariance NMR in higher dimensions: application to 4D NOESY spectroscopy of proteins

Elucidation of high-resolution protein structures by NMR spectroscopy requires a large number of distance constraints that are derived from nuclear Overhauser effects between protons (NOEs). Due to the high level of spectral overlap encountered in 2D NMR spectra of proteins, the measurement of high quality distance constraints requires higher dimensional NMR experiments. Although four-dimensional Fourier transform (FT) NMR experiments can provide the necessary kind of spectral information, the associated measurement times are often prohibitively long. Covariance NMR spectroscopy yields 2D spectra that exhibit along the indirect frequency dimension the same high resolution as along the direct dimension using minimal measurement time. The generalization of covariance NMR to 4D NMR spectroscopy presented here exploits the inherent symmetry of certain 4D NMR experiments and utilizes the trace metric between donor planes for the construction of a high-resolution spectral covariance matrix. The approach is demonstrated for a 4D (13)C-edited NOESY experiment of ubiquitin. The 4D covariance spectrum narrows the line-widths of peaks strongly broadened in the FT spectrum due to the necessarily short number of increments collected, and it resolves otherwise overlapped cross peaks allowing for an increase in the number of NOE assignments to be made from a given dataset. At the same time there is no significant decrease in the positive predictive value of observing a peak as compared to the corresponding 4D Fourier transform spectrum. These properties make the 4D covariance method a potentially valuable tool for the structure determination of larger proteins and for high-throughput applications in structural biology.     

活性污泥微生物菌群研究方法进展

活性污泥是活性污泥法处理污水系统的功能主体。人类对活性污泥微生物菌群的认识随着其研究方法的发展而逐步深入。传统培养方法只能检测到活性污泥中1％～15％的微生物。随着一系列基于免培养的分子生物学技术的出现,活性污泥中菌群的复杂性和多样性以惊人的速度被人们认识,大量依靠传统检测方法未能发现却在活性污泥中起关键作用的微生物逐渐被发现。许多模拟活性污泥菌群生存环境条件的现代培养技术开始发展,且已成功培养了一部分传统培养方法不能培养的细菌类群,这为研究基于免培养方法发现的大量新的微生物菌群的生理特性和作用机制提供了可能,也无疑将把人们对活性污泥菌群的认识推向一个新的层次．主要介绍活性污泥微生物菌群研究的一系列方法,从传统培养方法到基于免培养的现代分子生物学技术,再到现代培养技术,着重论述了现代分子生物学技术及其在活性污泥微生物菌群研究中的进展。     

Introduction to optical methods in photosynthesis

Optical spectroscopy is widely used to study structure and function of photosynthetic systems. Due to the large variety of different methods, these studies have contributed a lot to the identification of the cofactors involved in the primary reactions of photosynthesis and to the elucidation of the kinetics of the light-induced energy and electron transfer reactions. Within other aspects of photosynthesis research as e.g. photoinhibition, these techniques play an important role as well. In this brief introduction, I will focus on the basic principles of the different methods and the information obtained by applying these various techniques. In the reviews that follow, under the section “Optical Methods”, these methods are discussed in detail.     

A One-Dimensional (Proton and Phosphorus) and Two-Dimensional (Proton) In Vivo NMR Spectroscopic Study of Reversible Global Cerebral Ischemia

Abstract: The suitability of two-dimensional (2D) proton spectroscopy for monitoring, in vivo, the changes in levels of brain metabolites induced by cerebral ischemia was investigated in an experimental model of 30-min reversible ischemia induced by four-vessel occlusion in the rat. The resulting data were compared with those obtained by one-dimensional (1D) proton and phosphorus spectroscopy. Phosphorus spectra obtained during ischemia showed significant drops in levels of phosphocreatine (−73%), β-ATP (−60%), and intracellular pH (to 6.30) and an increase in inorganic phosphate level (905%). 1D and 2D proton spectra showed decreases in the N -acetylaspartate/creatine-phosphocreatine ratio that were not significantly different [−21% (1D) and −32% (2D)]. Similarly, the increases in lactate/creatine-phosphocreatine ratio were not significantly different [2,546% (1D) and 3,020% (2D)]. 2D spectroscopy also indicated a decrease in aspartate (−66%) and an increase in the inositol-choline derivative (+124%) pools during ischemia and an increase in alanine pool (+516%) during reperfusion. The glutamate-glutamine pool and taurine content did not change significantly during ischemia but decreased during reperfusion. The glucose level transiently decreased (−67%) during ischemia and increased immediately after (+261%). The levels of all the metabolites investigated returned to control values within 175 min after ischemia. 2D spectroscopy seems to be a reliable method of monitoring the changes in levels of cerebral compounds known to be involved in ischemia.     

In situ detection of heavy metal substituted chlorophylls in water plants

The in vivo substitution of magnesium, the central atom of chlorophyll, by heavy metals (mercury, copper, cadmium, nickel, zinc, lead) leads to a breakdown in photosynthesis and is an important damage mechanism in heavy metal-stressed plants. In this study, a number of methods are presented for the efficient in situ detection of this substitution (i.e. in whole plants or in chloroplasts). While macroscopic observations point to the formation of heavy metal chlorophylls at higher concentrations, fluorescence microscopy enables the detection of this reaction at very low substitution rates. Therefore, the course of the reaction can be followed by continuously measuring the fluorescence of whole plants. Furthermore absorbance spectroscopy of whole cells or isolated chloroplasts also enables the in situ detection of heavy metal chlorophylls. These methods provide practicable approaches in detecting the formation of these compounds in situ, avoiding artefacts that might occur using extraction methods based on polar solvents. In addition to the new methods for in situ detection, an extreme heterogeneity in the reaction of cells in the same tissue upon heavy metal stress was observed: while some cells are already disintegrating, others still show normal fluorescence and photosynthetic activity. Measurements of fluorescence kinetics gave a further hint that in high light intensity a substitution of Mg by heavy metals might take place specifically in PS II reaction centres.     

Keeping a positive carbon balance under adverse conditions: responses of photosynthesis and respiration to water stress

Drought and salinity (i.e. soil water stress) are the main environmental factors limiting photosynthesis and respiration and, consequently, plant growth. This review summarizes the current status of knowledge on photosynthesis and respiration under water stress. It is shown that diffusion limitations to photosynthesis under most water stress conditions are predominant, involving decreased mesophyll conductance to CO₂, an important but often neglected process. A general failure of photochemistry and biochemistry, by contrast, can occur only when daily maximum stomatal conductance ( g _s) drops below 0.05–0.10 mol H₂O m⁻² s⁻¹. Because these changes are preceded by increased leaf antioxidant activities ( g _s below 0.15–0.20 mol H₂O m⁻² s⁻¹), it is suggested that metabolic responses to severe drought occur indirectly as a consequence of oxidative stress, rather than as a direct response to water shortage. As for respiration, it is remarkable that the electron partitioning towards the alternative respiration pathway sharply increases at the same g _s threshold, although total respiration rates are less affected. Despite the considerable improvement in the understanding of plant responses to drought, several gaps of knowledge are highlighted which should become research priorities for the near future. These include how respiration and photosynthesis interact at severe stress, what are the boundaries and mechanisms of photosynthetic acclimation to water stress and what are the factors leading to different rates of recovery after a stress period.     

A search for predictive understanding of plant responses to elevated [CO2]

This paper reviews two decades of effort by the scientific community in a search for predictive understanding of plant responses to elevated [CO₂]. To evaluate the progress of research in leaf photosynthesis, plant respiration, root nutrient uptake, and carbon partitioning, we divided scientific activities into four phases: (I) initial assessments derived from our existing knowledge base to provide frameworks for experimental studies; (II) experimental tests of the initial assessments; (III) in cases where assessments were invalidated, synthesis of experimental results to stimulate alternative hypotheses and further experimentation; and (IV) formation of new knowledge. This paper suggests that photosynthetic research may have gone through all four phases, considering that (a) variable responses of photosynthesis to [CO₂] are generally explainable, (b) extrapolation of leaf-level studies to the global scale has been examined, and (c) molecular studies are under way. Investigation of plant respiratory responses to [CO₂] has reached the third phase: experimental results have been accumulated, and mechanistic approaches are being developed to examine alternative hypotheses in search for new concepts and/or new quantitative frameworks to understand respiratory responses to elevated [CO₂]. The study of nutrient uptake kinetics is still in the second phase: experimental evidence has contradicted some of the initial assessments, and more experimental studies need to be designed before generalizations can be made. It is quite unfortunate that we have not made much progress in understanding mechanisms of carbon partitioning during the past two decades. This is due in part to the fact that some of the holistic theories, such as functional balance and optimality, have not evolved into testable hypotheses to guide experimental studies. This paper urges modelers to play an increasing role in plant–CO₂ research by disassembling these existing theories into hypotheses and urges experimentalists to design experiments to examine these holistic concepts.     

Sun‐induced fluorescence – a new probe of photosynthesis: First maps from the imaging spectrometer HyPlant

Variations in photosynthesis still cause substantial uncertainties in predicting photosynthetic CO₂ uptake rates and monitoring plant stress. Changes in actual photosynthesis that are not related to greenness of vegetation are difficult to measure by reflectance based optical remote sensing techniques. Several activities are underway to evaluate the sun‐induced fluorescence signal on the ground and on a coarse spatial scale using space‐borne imaging spectrometers. Intermediate‐scale observations using airborne‐based imaging spectroscopy, which are critical to bridge the existing gap between small‐scale field studies and global observations, are still insufficient. Here we present the first validated maps of sun‐induced fluorescence in that critical, intermediate spatial resolution, employing the novel airborne imaging spectrometer HyPlant. HyPlant has an unprecedented spectral resolution, which allows for the first time quantifying sun‐induced fluorescence fluxes in physical units according to the Fraunhofer Line Depth Principle that exploits solar and atmospheric absorption bands. Maps of sun‐induced fluorescence show a large spatial variability between different vegetation types, which complement classical remote sensing approaches. Different crop types largely differ in emitting fluorescence that additionally changes within the seasonal cycle and thus may be related to the seasonal activation and deactivation of the photosynthetic machinery. We argue that sun‐induced fluorescence emission is related to two processes: (i) the total absorbed radiation by photosynthetically active chlorophyll; and (ii) the functional status of actual photosynthesis and vegetation stress.     

Raman spectroscopic monitoring of Lactarius latex

Lactarius is a genus of Basidiomycotina with mainly agaricoid representatives, which are characterised by the excretion of a typical milky fluid. In particular, the colour, changes and taste of this latex-like milk are often used as a taxonomically important character. When it is exuded several chemical reactions occur. To date, NMR spectroscopy is generally used for chemical investigation of this latex. However, as a vibrational spectroscopic technique Raman spectroscopy has several advantageous properties for this type of research. The aim of this study is to investigate whether Raman spectroscopy can be used as an alternative analytical technique to monitor the chemical reactions in Lactarius latex. Therefore, this paper presents the first Raman spectra of Lactarius latex and provides an interpretation of the Raman bands that are present. L. lacunarum latex spectra are thoroughly investigated by 2D correlation analysis and are compared with latex spectra of other species (L. chrysorrheus, L. deterrimus, L. fluens, L. glyciosmus and L. salmonicolor).