Recollections of Thomas John Wydrzynski

In appreciation of his contribution to the Photosystsem II research and commemoration of the book Photosystem II: The Light-Driven Water-Plastoquinone Oxido-Reductase, co-edited with Kimiyuki Satoh, I present here some of my recollections of Thomas John Wydrzynski and by several others with whom he has associated over the years at Urbana (Illinois), Berkeley (California), Standard Oil Company-Indiana (Illinois), Berlin (Germany), Gothenburg (Sweden), and Canberra (Australia). We not only recognize him for his unique career path in Photosystem II research, but also for his qualities as a collaborative scientist working on the only system on Earth that has the ability to oxidize water to molecular oxygen using the energy of sunlight.     

The Mystery of Oxygen Evolution: Analysis of Structure and Function of Photosystem II,the Water-Plastoquinone Oxido-Reductase

Photosystem II (PS II) of thylakoid membrane of photosynthetic organisms has drawn attention of researchers over the years because it is the only system on Earth that provides us with oxygen that we breathe. In the recent past, structure of PS II has been the focus of research in plant science. The report of X-ray crystallographic structure of PS II complex by the research groups of James Barber and So Iwata in UK (K.N. Ferreira et al. Science 303: 1831–38, 2004) is a milestone in the area of research in photosynthesis. It follows the pioneering and elegant work from the laboratories of Horst Witt and W. Saenger in Germany (A. Zouni et al. Nature 409: 739–743, 2001), and J. Shen in Japan (N. Kamiya and J. Shen, Proc Natl Acad Sci USA 100: 98–103, 2003). It is time to analyze the historic events during the long journey made by the researchers to arrive at this point. This review makes an attempt to critically review the growth of the advancement of concepts and knowledge on the photosystem in the background of technological development. We conclude the review with perspectives on research and technology that should reveal the complete story of PS II of thylakoid in the future.     

The time of a conscious sensory experience and mind-brain theories

Libet et al. and Popper & Eccles have the view that some single hypothesis about the time of a conscious sensory experience has certain consequences for various mind-brain theories. The view involves a fundamental inconsistency, which may cast doubt on experimental findings, and two hypotheses rather than one. The preferable hypothesis is doubtful. The preferable hypothesis has been thought to have mind-brain consequences principally because it has not been distinguished from a different hypothesis. The preferable hypothesis in fact does not have the supposed mind-brain consequences. The different hypothesis, which in fact does have the given consequences, is entirely unacceptable.     

The Solar Action Spectrum of Photosystem II Damage

The production of oxygen and the supply of energy for life on earth rely on the process of photosynthesis using sunlight. Paradoxically, sunlight damages the photosynthetic machinery, primarily photosystem II (PSII), leading to photoinhibition and loss of plant performance. However, there is uncertainty about which wavelengths are most damaging to PSII under sunlight. In this work we examined this in a simple experiment where Arabidopsis (Arabidopsis thaliana) leaves were exposed to different wavelengths of sunlight by dispersing the solar radiation across the surface of the leaf via a prism. To isolate only the process of photodamage, the repair of photodamaged PSII was inhibited by infiltration of chloramphenicol into the exposed leaves. The extent of photodamage was then measured as the decrease in the maximum quantum yield of PSII using an imaging pulse amplitude modulation fluorometer. Under the experimental light conditions, photodamage to PSII occurred most strongly in regions exposed to ultraviolet (UV) or yellow light. The extent of UV photodamage under incident sunlight would be greater than we observed when one corrects for the optical efficiency of our system. Our results suggest that photodamage to PSII under sunlight is primarily associated with UV rather than photosynthetically active light wavelengths.Plants absorb sunlight to power the productive photochemical reactions of photosynthesis. Absorption of sunlight may also lead to deleterious photochemistry that damages the photosynthetic machinery. The PSII protein complex is important in this regard as it seems to be most susceptible to photodamage that results in photoinhibition and ultimately suppresses photosynthetic CO₂ assimilation, growth, and productivity (Long et al., 1994; Takahashi and Murata, 2008). Although plants have photoprotection mechanisms (Niyogi, 1999) and can effectively repair photodamaged PSII through the PSII repair cycle (Aro et al., 1993), photoinhibition still occurs under stressful environmental conditions (Nishiyama et al., 2006; Murata et al., 2007; Takahashi and Murata, 2008).The onset of photoinhibition is strongly correlated with the absorption of excessive excitation energy for photosynthesis. Therefore, photodamage to PSII was most readily assumed to be attributed to the excess light absorbed by photosynthetic pigments (Melis, 1999). However, the extent of photodamage that is measured under conditions where the repair of photodamaged PSII is prevented by inhibiting chloroplast protein synthesis (i.e. lincomycin or chloramphenicol) is directly proportional to the intensity of light (Mattoo et al., 1984; Tyystjärvi and Aro, 1996; Nishiyama et al., 2001, 2004; Allakhverdiev and Murata, 2004; Chow et al., 2005). Furthermore, recent studies have demonstrated that interruption of the Calvin cycle (Hakala et al., 2005; Takahashi and Murata, 2005; Takahashi et al., 2007) and inhibition of electron transfer between Q_A and Q_B (Jegerschöld et al., 1990; Kirilovsky et al., 1994; Allakhverdiev et al., 2005) have no effect on the rate of photodamage to PSII, but in fact cause inhibition of the repair of photodamaged PSII due to suppression of the de novo synthesis of PSII proteins (Allakhverdiev et al., 2005; Takahashi and Murata, 2005, 2006). Thus, photodamage to PSII is paradoxically not associated with the excess light absorbed by photosynthetic pigments (Nishiyama et al., 2006; Murata et al., 2007; Takahashi and Murata, 2008).Studies of the effect of monochromatic light on the photodamage process have suggested that photodamage to PSII primarily occurs at the manganese cluster of the oxygen-evolving complex (OEC) through a direct photoexcitation of manganese (Hakala et al., 2005; Ohnishi et al., 2005). Release of manganese ions (Mn²⁺) from thylakoid membranes is accompanied by photodamage to PSII (Hakala et al., 2005; Zsiros et al., 2006), suggesting that disruption of the manganese cluster upon absorption of light might be a primary event in photodamage. It is likely that the reaction center of PSII is secondarily damaged by light absorbed by photosynthetic pigments after inactivation of the OEC (Hakala et al., 2005; Ohnishi et al., 2005), if an alternative electron transfer donor from lumenal ascorbate is not available (Mano et al., 2004; Tóth et al., 2009). These findings have lead to a recent photodamage model called the manganese (or two-step; Ohnishi et al., 2005) mechanism of photoinhibition (Tyystjärvi, 2008).Studies of the action spectrum of photodamage to PSII have shown that UV damages PSII more effectively than visible light (Jones and Kok, 1966; Jung and Kim, 1990; Hakala et al., 2005; Ohnishi et al., 2005). Thus, under identical light intensity, UV is the most damaging wavelength to PSII. However, inferring damage under natural sunlight is not straight forward as there is a need to account for the spectral distribution and intensity of sunlight. It is unclear which wavelengths of sunlight are most damaging to PSII and we cannot discount the premise that significant primary photodamage to PSII is caused by light absorbed by photosynthetic pigments (Vass and Cser, 2009). To identify which wavelengths of sunlight are most damaging to PSII, sunlight was spectrally dispersed via a prism onto an Arabidopsis (Arabidopsis thaliana) leaf infiltrated with chloramphenicol and decrease in the maximum quantum yield of PSII (F_v/F_m) was measured using an imaging pulse amplitude modulation (PAM) fluorometer. This simple but powerful approach revealed the in vivo spectral dependence of photodamage that had two peaks at UV and yellow wavelengths. Since the spectral efficiency of our optical system decreased below 400 nm, we calculated photodamage to PSII under incident sunlight. Our results show that photodamage to PSII was primarily associated with UV wavelengths and secondarily with yellow light wavelengths. This finding indicates that photodamage to PSII is less associated with light absorbed by photosynthetic pigments under sunlight and suggest that most of photodamage to PSII is potentially avoidable during photosynthesis.     

生物表面活性剂的合成与提取研究进展*

生物表面活性剂（Biosurfactant）是由微生物产生的具有高表面活性的生物分子。相对于化学合成的表面活性剂,生物表面活性剂对生态系统的毒性较低,且可生物降解。因此,生物表面活性剂开始应用于环境污染治理的各个方面。中从生物表面活性剂生产菌的筛选、培养基的优化及生物表面活性剂的提取等方面对近年来生物表面活性剂的研究进展进行了总结,并对未来的发展方向作了展望。     

Photosynthetic acclimation of Tradescantia albiflora to growth irradiance: morphological, ultrastructural and growth responses

Tradescantia albiflora (Kunth), a trailing ground species naturally occurring in deep shade in rainforests, has an unusual photosynthetic acclimation profile for growth irradiance. Although capable of increasing its capacity for electron transport, photophosphorylation and carbon fixation when grown in full sunlight, Tradescantia has constant chlorophyll alb ratios, photosystem reaction centre stoichiometry and pigment-protein composition at all growth irradiances (Chow et al. 1991. Physiol. Plant. 81: 175–182). To gain an insight into the compensatory strategies which allow Tradescantia to grow in both high and low lights, plants were grown under shade cloth (100 to 1.4% relative growth irradiance) and leaf and chloroplast attributes were compared. While shade Tradescantia chloroplasts had three times more chlorophyll per chloroplast and twice the length of thylakoid membranes compared to plants grown in full sunlight, the ratios of appressed to nonappressed thylakoid membranes were constant. The average net surface charge density of destacked thylakoids was the same for plants grown at moderate and low-irradiance, consistent with their similar stacking profiles. Tradescantia plants grown in direct sunlight had 10-times more fresh and dry weight per plant compared to plants grown in shade, despite a lower photosynthetic capacity on a leaf area basis with partial photoinhibition. We conclude that having a light-harvesting apparatus permanently locked into the "shade-plant mode " does not necessarily prevent a plant from thriving in high light. Analyses of leaf growth at different irradiances provide a partial explanation of the manner in which Tradescantia compensates for very low photosynthetic capacity per unit leaf in sunlight.     

New insights into the evolutionary history of photoreceptor cells

Although the common descent of all life has been widely accepted since Darwin's time, new research occasionally provides us with arresting reminders of the unity of evolutionary history. Recent papers by Arendt et al. and Panda et al. provide one such reminder. They illustrate that the two classes of animal photoreceptors, ciliary and rhabdomeric photoreceptors, are likely to share an ancient common ancestor and have been evolving in parallel since their duplication over 600 million years ago.     

Photosynthesis: a blueprint for solar energy capture and biohydrogen production technologies.

Solar energy capture, conversion into chemical energy and biopolymers by photoautotrophic organisms, is the basis for almost all life on Earth. A broad range of organisms have developed complex molecular machinery for the efficient conversion of sunlight to chemical energy over the past 3 billion years, which to the present day has not been matched by any man-made technologies. Chlorophyll photochemistry within photosystem II (PSII) drives the water-splitting reaction efficiently at room temperature, in contrast with the thermal dissociation reaction that requires a temperature of ca. 1550 K. The successful elucidation of the high-resolution structure of PSII, and in particular the structure of its Mn(4)Ca cluster provides an invaluable blueprint for designing solar powered biotechnologies for the future. This knowledge, combined with new molecular genetic tools, fully sequenced genomes, and an ever increasing knowledge base of physiological processes of oxygenic phototrophs has inspired scientists from many countries to develop new biotechnological strategies to produce renewable CO(2)-neutral energy from sunlight. This review focuses particularly on the potential of use of cyanobacteria and microalgae for biohydrogen production. Specifically this article reviews the predicted size of the global energy market and the constraints of global warming upon it, before detailing the complex set of biochemical pathways that underlie the photosynthetic process and how they could be modified for improved biohydrogen production.     

Global change and biological invasions

Invasion by exotic species is one of the serious socio-economic, environmental and ecological problems currently faced by mankind. Biological invasions have changed the species composition, structure and function of ecosystems, and are seriously threatening global biodiversity, economy and human health (Iqbal et al. 2021; Wang et al. 2020; Yang et al. 2021; Zhao et al. 2020; Zheng et al. 2015). Biological invasions have resulted in an economic loss of at least US$ 1.288 trillion over the past few decades worldwide (Diagne et al. 2021). As a consequence of these far-reaching impacts, biological invasions have become a hot research topic in modern ecology, and attract major attention from international organizations, governments and scientists all over the world. There is a complex interaction between biological invasions and global environmental change. Biological invasions are not only passengers of global change, but can also be major drivers of global change (MacDougall and Turkington 2005). Other components of global change, such as atmospheric CO₂ enrichment, global warming, nitrogen deposition, changes in precipitation regimes, habitat fragmentation and land-use change, affect species distributions and resource dynamics of ecosystems, and consequently drive invasion success of many exotic species. On the other hand, invasion by exotic species can also alter basic ecosystem properties, which in turn affect many components of global change. Research on the patterns, processes and mechanisms of biological invasion can shed light on the drivers and consequences of biological invasions in the light of global change, and serve as a scientific basis for forward-thinking management plans. The overarching challenge is to understand the basic ecological interactions of, e.g., invasive and native species, plants and soil, and plants and animals.     

Prebiotic phosphate: a problem insoluble in water ? ]

It is well-known that in water phosphate readily reacts with calcium, precipitating as insoluble apatite. How phosphorus could have been available for prebiotic reactions is still an open problem. We suggest that phosphorus-containing compounds might have accumulated in a hydrophobic medium, since the absence of calcium ions would have prevented them from precipitating as apatite. Hydrophobic compounds may have been synthesized on the early Earth through the polymerization of methane or through Fischer-Tropsch-type reactions. Moreover, hydrophobic compounds would have been delivered to the early Earth by extraterrestrial infall. In previous articles (Morchio and Traverso [1999], Morchio et al. [2001]) we suggested that such hydrophobic material would have formed a hydrophobic layer on the surface of the sea, which would have provided an environment thermodynamically more suitable than water for the concentration and polymerization of organic molecules fundamental to life, particularly amino acids and (pyrimidine) bases. It may be hypothesized that elemental phosphorus or phosphorus-containing compounds (such as phosphite) deriving from volcanic eruptions would have ended up raining down into the hydrophobic layer, accumulating due to the absence of calcium ions, in an environment protected against hydrolysis. Phosphorus-containing compounds might have interacted with hydrophobic molecules in the layer giving rise to polymers. In particular, phosphite might have reacted with the hydrophobic amino acids, giving rise to phosphoamino acids, which, in turn, might have interacted with pyrimidine bases (relatively abundant in the layer) giving rise to peptides and oligonucleotide-like polymers. Indeed, it has been experimentally shown (Zhou et al. [1996]) that, in an anhydrous organic medium (pyridine), dialkilphosphite reacts with amino acids to form phosphoamino acids, which interact with pyrimidine nucleosides to give nucleotides, short oligonucleotides and phosphoryl peptides.     

Impact constraints on the environment for chemical evolution and the continuity of life

The Moon and the Earth were bombarded heavily by planetesimals and asteroids that were capable of interfering with chemical evolution and the origin of life. In this paper, we explore the frequency of giant terrestrial impacts able to stop prebiotic chemistry in the probable regions of chemical evolution. The limited time available between impacts disruptive to prebiotic chemistry at the time of the oldest evidence of life suggests the need for a rapid process for chemical evolution of life. The classical hypothesis for the origin of life through the slow accumulation of prebiotic reactants in the primordial soup in the entire ocean may not be consistent with constraints imposed by the impact history of Earth. On the other hand, rapid chemical evolution in cloud systems and lakes or other shallow evaporating water bodies would have been possible because reactants could have been concentrated and polymerized rapidly in this environment. Thus, life probably could have originated near the surface between frequent surface sterilizing impacts. There may not have been continuity of life depending on sunlight because there is evidence that life, existing as early as 3.8 Gyr ago, may have been destroyed by giant impacts. The first such organisms on Earth where probably not the ancestors of present life.     

Nest Site Preference and Fidelity of Chinese Alligator(Alligator sinensis)

Oviparous female reptiles select nesting sites with optimal ecological factors that contribute to egg development. Chinese alligator(Alligator sinensis), an oviparous reptile, is a critically endangered crocodilian with temperature-dependent sex determination. Research on its nesting behavior may facilitate the protection of this species. In this study, we monitored nesting behavior over eight years. We compared selected frequency of nest sites, distance from nest site to water, height from nest site top to the water surface, distance from nest site to human activity region, and canopy density between nest sites on the island and bank. The results showed that 45 nest sites were used by female alligators over eight years and each site was selected from one to 10 times. The selected frequency of nest site occurrence on the island was higher than that on the bank(P 0.001). We observed that 88% of the individual alligators(15/17) showed different degrees of nest site fidelity. However, Chinese alligators might not always be loyal to only one nest site because of environmental changes or interspecific competition at nest sites. Our findings suggest that female alligators prefer to nest at island, which might be because of the nests on the island had a higher canopy density(P = 0.010) and were further from the human activity region(P 0.001) than those on the bank did. It would be beneficial to reduce human activities during the breeding season and protect the vegetation of Chinese alligator habitats in the future. of the beach(Ali et al., 2005; Kamel and Mrosovsky, 2005; Turkozan et al., 2012). Other species such as snakes and lizards select nest sites with more moist substrates, which significantly increases their body size at hatching(Brown and Shine, 2004; Reedy et al., 2013). Nest site preference may be maintained for one or more breeding seasons(Janzen and Morjan, 2001; Kamel et al., 2006). When female chose the same site or area during different years, it is called nest site fidelity(Switzer, 1993). This nest choice behavior may influence offspring survival(Lindeman, 1992) and nest site fidelity has been documented in numerous species such as birds(Lindberg and Sedinger, 1997), turtles(Mitrus, 2006; Walde et al., 2007), tuatara(Refsnider et al., 2010), and crocodilians(Elsey et al., 2008).Chinese alligator(Alligator sinensis) is a critically endangered freshwater crocodilian endemic to China(Thorbjarnarson and Wang, 1999). Recent investigations show that there are no more than 130 Chinese alligators     

An Improvement of Robust Biometrics-Based Authentication and Key Agreement Scheme for Multi-Server Environments Using Smart Cards

In multi-server environments, user authentication is a very important issue because it provides the authorization that enables users to access their data and services; furthermore, remote user authentication schemes for multi-server environments have solved the problem that has arisen from user’s management of different identities and passwords. For this reason, numerous user authentication schemes that are designed for multi-server environments have been proposed over recent years. In 2015, Lu et al. improved upon Mishra et al.’s scheme, claiming that their remote user authentication scheme is more secure and practical; however, we found that Lu et al.’s scheme is still insecure and incorrect. In this paper, we demonstrate that Lu et al.’s scheme is vulnerable to outsider attack and user impersonation attack, and we propose a new biometrics-based scheme for authentication and key agreement that can be used in multi-server environments; then, we show that our proposed scheme is more secure and supports the required security properties.     

The split-end model for homologous recombination at double-strand breaks and at Chi

In recent years two different styles of model for homologous recombination have been discussed, depending on whether or not the recombination event occurs in the vicinity of a double-strand break in DNA. The models of Holliday and Meselson and Radding exemplify those that do not involve a break whereas the model of Szostak et al is taken as an example of those that do. Recent advances in understanding a prototypic recombination system thought to promote exchange distant from DNA ends, at Chi sites, suggest a mechanism of initiation neither like Holliday/Meselson-Radding nor like Szostak et al. In those models, only one strand of DNA may invade a homologous DNA molecule. We propose a model for Chi in which exonuclease degrades DNA from a double-strand break to the Chi site; the exonuclease is converted into a helicase upon interaction with Chi; unwinding produces a recombinagenic split-end, and both 3'- and 5'-ending strands at the split-end are capable of invading a homologue. Different genetic consequences are proposed to result from invasion by each. We review evidence supporting the split-end model and suggest its application in at least some cases previously considered to proceed via the Meselson/Radding model and by the double-strand-break repair model of Szostak et al.     

Changes in water colour between 1986 and 2006 in the headwaters of the River Nidd, Yorkshire, UK: a critique of methodological approaches and measurement of burning management

The effect of moorland management on the release of dissolved organic carbon (DOC) from blanket peat is currently a topic of great interest in the UK. A recent paper by Chapman et al. (Biogeochemistry, doi:10.1007/s10533-010-9474-x, 2010) reports on changes in humic colour/DOC concentrations in surface waters draining 15 upland peat catchments in the North Pennines (UK) over two decades, and examines the possible underlying drivers of those changes. Chapman et al. identify significant variation in water colour between adjacent catchments and over time. One potential driver of changes in DOC is managed moorland burning, and Chapman et al. state that their study provides evidence that burning has no effect on colour in upland catchment drainage waters. This observation counters a recent series of papers showing strong links between new moorland burn management on blanket peat soils and colour/DOC in catchment drainage waters. We have reviewed the methodological approach and results presented by Chapman et al. that relate to the assessment of managed burning, and show significant errors in the data used in their analysis. This has resulted in conclusions being drawn about the role of managed burning in DOC release that are not supported by evidence.     

Helminthiasis, bystander diseases and vaccines: analysis of interaction

Helminthiasis has assumed a new medical and veterinary significance following the recognition of its immunomodulatory consequences for the severity of bystander conditions and the efficacy of immunization against non-helminthic diseases of humans and livestock. Recent papers by Jackson et al. and Turner et al. have an important bearing on research in these areas. One of the implications of their work is that the parasitological criterion of egg-positivity versus egg-negativity is too simplistic to use in co-infection and related studies unless accompanied by immunological analysis.     

Clonal plants: beyond the patterns—ecological and evolutionary dynamics of asexual reproduction

More than 25 years have passed since publication of the first comprehensive multi-authored landmark volume on the population biology and evolution of clonal organisms (Jackson et al. 1985). Since then, no less than eight symposium volumes or special issues have appeared in scientific journals reporting on advances in the field of clonal plant research, indicating that the study of clonal organisms has remained an important topic in ecological research. The three most recent overviews were published in special issues of this journal (Stuefer et al. 2000; Tolvanen et al. 2004; Sammul et al. 2008), and these are now supplemented with a fourth special issue of Evolutionary Ecology. The articles published here reflect some of the most important contributions to a workshop on clonal plant biology held in Leuven (Belgium) in July 2009 and they illustrate some major advances that have been made over the last few years. In the following paragraphs, we first summarize some representative contributions to the current issue, and second, we put forward some personal ideas about promising and underexplored research lines in clonal plant research.     

The First Knockout Mouse Model of Retinoblastoma

The retinoblastoma susceptibility gene (RB1) was the first tumor suppressor gene identified in humans (Friend, et al., 1986) and the first tumor suppressor gene knocked out by targeted deletion in mice (Jacks, et al., Clarke, et al., Lee, et al., 1992). Children with a germline mutation in one of their RB1 alleles are likely to experience bilateral multifocal retinoblastoma; however, mice with a similar disruption of Rb1 do not develop retinoblastoma. The absence of a knock-out mouse model of retinoblastoma has slowed the progress toward developing new therapies and identifying secondary genetic lesions that occur after disruption of the Rb signaling pathway. Several advances have been made, over the past several years, in our understanding of the regulation of proliferation during retinal development (Zhang, et al., 2004; Dyer J, 2004; Dyer, Cepko, 2001) and we have built upon these earlier studies to generate the first nonchimeric knock-out mouse model of retinoblastoma. These mice are being used as a preclinical model to test new therapies for retinoblastoma and to elucidate the downstream genetic events that occur after inactivation of Rb1 or its related family members.     

Evaluation of reported sediment samples from 20 Ma using a molecular phylogenetic approach: comment on Liu et al. (2017)

Liu et al. reported the cultivation and DNA sequencing of 69 fungal isolates (Ascomycota and Basidiomycota) from ancient subseafloor sediments, suggesting that they represent living fungal populations that have persisted for over 20 million years. Because these findings could bring about a paradigm shift in our understanding of the spatial breadth of the deep subsurface biosphere as well as the longevity of ancient DNA, it is extremely important to verify that their samples represent pure ancient fungi from 20 million years ago without contamination by modern species. For this purpose, we estimated the divergence times of Dikarya (Ascomycota + Basidiomycota) and Mucoromycota fungi assuming that the fungal isolates were actually sampled from 20 Ma (mega-annum) sediments and evaluated the validity of the sample ages. Using this approach, we estimate that the age of the last common ancestor of Dikarya and Mucoromycota fungi greatly exceeds the age of the Earth. Our finding emphasizes the importance of using reliable approaches to confirm the dating of ancient samples.