The energy flux theory 35 years later: formulations and applications

Several models have been proposed for the energetic behavior of the photosynthetic apparatus and a variety of experimental techniques are nowadays available to determine parameters that can quantify this behavior. The Energy Flux Theory (EFT) developed by Strasser 35 years ago provides a straightforward way to formulate any possible energetic communication between any complex arrangement of interconnected pigment systems and any energy transduction by these systems. We here revisit the EFT, starting from the basic general definitions and equations and presenting applications in formulating the energy distribution in photosystem (PS) II units with variable connectivity, as originally derived, where certain simplifications were adopted. We then proceed to the derivation of equations for a PSII model of higher complexity, which corresponds, from the formalistic point of view, to the later formulated and now broadly accepted exciton–radical-pair model. We also compare the formulations derived with the EFT with those obtained, by different approaches, in the classic papers on energetic connectivity. Moreover, we apply the EFT for the evaluation of the excitation energy distribution between PSII and PSI and the distinction between state transitions and PSII to PSI excitation energy migration. Our analysis demonstrates that the EFT is a powerful approach for the formulation of any possible model, at any complexity level, even of models that may be proposed in the future, with the advantage that any possible energetic communication or energy transduction can be easily formulated mathematically by trivial algebraic equations. Moreover, the biophysical parameters introduced by the EFT and applicable for any possible model can be linked with obtainable experimental signals, provided that the theoretical resolution of the model does not go beyond the experimental resolution.     

20 years since the introduction of DNA barcoding: from theory to application

Traditionally, taxonomic identification has relied upon morphological characters. In the last two decades, molecular tools based on DNA sequences of short standardised gene fragments, termed DNA barcodes, have been developed for species discrimination. The most common DNA barcode used in animals is a fragment of the cytochrome c oxidase (COI) mitochondrial gene, while for plants, two chloroplast gene fragments from the RuBisCo large subunit (rbcL) and maturase K (matK) genes are widely used. Information gathered from DNA barcodes can be used beyond taxonomic studies and will have far-reaching implications across many fields of biology, including ecology (rapid biodiversity assessment and food chain analysis), conservation biology (monitoring of protected species), biosecurity (early identification of invasive pest species), medicine (identification of medically important pathogens and their vectors) and pharmacology (identification of active compounds). However, it is important that the limitations of DNA barcoding are understood and techniques continually adapted and improved as this young science matures.     

Mechanism of inhibition of cytoplasmic streaming by myrmicacin (Β-hydroxydecanoic acid) inChara andSpirogyra

Summary Myrmicacin (-hydroxydecanoic acid) applied externally inhibited the cytoplasmic streaming ofChara cells in acidic (pH 4.5) but not in neutral (pH 7.5) solution. Application by intracellular perfusion at neutral pH also did not inhibit the streaming. Other carboxylic acids could inhibit the streaming when given as an acidic external solution. Inhibition of the cytoplasmic streaming was concluded to occur due to acidification of the intracellular pH upon application of an acidic external medium of these carboxylic acids. The cytoplasmic streaming ofSpirogyra was also inhibited by myrmicacin and acetic acid in acidic solution.Abbreviations APW artificial pond water - CB cytochalasin B - DMGA 3.3-dimethylglutaric acid - DMSO dimethylsulfoxide - EGTA ethyleneglycol-bis-(\-aminoethyl ether)N - N tetraacetic acid - HEPES 2-hydroxyethylpiperazine - N ethanesulfonic acid - MES 2-(N-morpholino)ethanesulfonic acid - pH _i intracellular pH - Tris trishydroxyaminomethane     

The discovery of state transitions in photosynthesis 40 years ago

In the late 1960s, I identified an aspect of the kinetics of chlorophyll fluorescence in algal cells that I was unable to explain in terms of photochemical quenching. I proposed a novel regulatory mechanism for the distribution of light energy to photosystems I and II, which is now known by the term of “state transitions.” I also examined the “cation-dependent redistribution of light energy” to photosystems I and II and the “energy-dependent quenching” of chlorophyll fluorescence. At that time, financial constraints prevented me from measuring the emission and action spectra of chlorophyll fluorescence at liquid-nitrogen temperature and the light quality-dependent changes in the yield of chlorophyll fluorescence at room temperature. The financial problems were solved by constructing several pieces of electronic equipment using skills obtained by repairing radios when I was a high-school and college student.     

Origin of eukaryotic cells: 40 years on

The year 1970 saw the publication of Origin of Eukaryotic Cells by Lynn Margulis. This influential book brought the exciting and weighty problems of cellular evolution to the scientific mainstream, simultaneously breaking new ground and ‘re-discovering’ the decades-old ideas of German and Russian biologists. In this commemorative review, I discuss the 40 years that have elapsed since this landmark publication, with a focus on the ‘molecular era’: how DNA sequencing and comparative genomics have proven beyond all doubt the central tenets of the endosymbiont hypothesis for the origin of mitochondria and plastids, and, at the same time, revealed a genetic and genomic complexity in modern-day eukaryotes that could not have been imagined in decades past.     

On 20 years of Lophotrochozoa

Lophotrochozoa is a protostome clade that includes disparate animals such as molluscs, annelids, bryozoans, and flatworms, giving it the distinction of including the most body plans of any of the three major clades of Bilateria. This extreme morphological disparity has prompted numerous conflicting phylogenetic hypotheses about relationships among lophotrochozoan phyla. Here, I review the current understanding of lophotrochozoan phylogeny with emphasis on recent insights gained through approaches taking advantage of high-throughput DNA sequencing (phylogenomics). Of significance, Platyzoa, a hypothesized clade of mostly small-bodied animals, appears to be an artifact of long-branch attraction. Recent studies recovered Gnathifera (Syndermata, Gnathostomulida, and Micrognathozoa) sister to all other lophotrochozoans and a clade called Rouphozoa (Platyhelminthes and Gastrotricha) sister to the remaining non-gnathiferan lophotrochozoans. Although Bryozoa was traditionally grouped with Brachiopoda and Phoronida (Lophophorata), most molecular studies have supported a clade including Entoprocta, Cycliophora, and Bryozoa (Polyzoa). However, recent phylogenomic work has shown that entoprocts and bryozoans have compositionally heterogeneous genomes that may cause systematic artifacts affecting their phylogenetic placement. Lastly, relationships within Trochozoa (Mollusca, Annelida, and relatives) largely remain ambiguous. Recent work has shown that phylogenomic studies must identify and reduce sources of systematic error, such as amino acid compositional heterogeneity and long-branch attraction. Still, other approaches such as the analysis of rare genomic changes may be needed to overcome challenges to standard phylogenomic approaches. Resolving lophotrochozoan phylogeny will provide important insight into how these complex and diverse body plans evolved and provide a much-needed framework for comparative studies.     

Brain Connectivity: The Feel of Blindsight

A visual subcortical pathway to the amygdala that undergoes structural plastic strengthening in blindsight has been identified in humans?-?neuroanatomical evidence for a pathway that might mediate rapid non-conscious processing of salient information.     

Explaining the “Pulse of Protoplasm”: The search for molecular mechanisms of protoplasmic streaming

Explanations for protoplasmic streaming began with appeals to contraction in the eighteenth century and ended with appeals to contraction in the twentieth. During the intervening years, biologists prop...     

The weak effects of climatic change on Plantago pollen concentration: 17 years of monitoring in Northwestern Spain

Plantago L. species are very common in nitrified areas such as roadsides and their pollen is a major cause of pollinosis in temperate regions. In this study, we sampled airborne pollen grains in the city of León (NW, Spain) from January 1995 to December 2011, by using a Burkard® 7-day-recording trap. The percentage of Plantago pollen compared to the total pollen count ranged from 11 % (1997) to 3 % (2006) in the period under study. Peak pollen concentrations were recorded in May and June. Our 17-year analysis failed to disclose significant changes in the seasonal trend of plantain pollen concentration. In addition, there were no important changes in the start dates of pollen release and the meteorological parameters analyzed did not show significant variations in their usual trends. We analyzed the influence of several meteorological parameters on Plantago pollen concentration to explain the differences in pollen concentration trends during the study. Our results show that temperature, sun hours, evaporation, and relative humidity are the meteorological parameters best correlated to the behavior of Plantago pollen grains. In general, the years with low pollen concentrations correspond to the years with less precipitation or higher temperatures. We calculated the approximate Plantago flowering dates using the cumulative sum of daily maximum temperatures and compared them with the real bloom dates. The differences obtained were 4 days in 2009, 3 days in 2010, and 1 day in 2011 considering the complete period of pollination.     

Peroxisomes: 40 years of histochemical staining,personal reminiscences

The historical circumstances that led to the discovery of the 3,3′-diamino-benzidine (DAB) method for staining of peroxisomes 40 years ago are reviewed. In the course of studies on the uptake and absorption of horse radish peroxidase in mammalian liver, in sections incubated for detection of peroxidase activity in DAB, it was noted that peroxisomes also stained positively for peroxidase activity. Subsequently, it was revealed that the peroxidatic activity of catalase, which is abundantly present in peroxisomes, is responsible for that staining. This notion was confirmed in quantitative biochemical studies with crystalline beef liver catalase and in tracer studies using catalase as an ultrastructural tracer. The application of the DAB method led to the discovery of peroxisomes as a ubiquitous eukaryotic cell organelle, attracting great interest in their investigation in biomedical research.     

The mitochondrial theory of aging: dead or alive?

The mitochondrial theory of aging is based around the idea of a vicious cycle, in which somatic mutation of mtDNA engenders respiratory chain dysfunction, enhancing the production of DNA-damaging oxygen radicals. In turn, this is proposed to result in the accumulation of further mtDNA mutations. Finally, a bioenergetic crisis leads to overt tissue dysfunction and degeneration. A substantial body of circumstantial evidence seems to support this idea. However, the extent of detectable mtDNA mutation is far less than can easily be reconciled to this hypothesis, unless it is assumed that a subset of cells with much higher than average mtDNA mutation load is systematically lost by apoptosis. A rigorous test of the hypothesis remains to be undertaken, but would require a direct manipulation of the rate of mtDNA mutagenesis, to test whether this could alter the kinetics of aging.     

Quantum simulation of nanosized materials: 100 years of mystery is solved

Application of alpha-oscillator theory to quantum electrodynamics (QED) solves the mystery (as Feynman said) of the double-slit phenomenon involved in the foundation of quantum mechanics (QM). Even if with the same initial condition given, different spots on the screen can be predicted deterministically with no introduction of hidden variables. The general proof has already been published in Ref. [3] and “what is new in this paper” is the concrete numerical algorithm of the extended normal mode technique in section “Concrete numerical algorithm of the extended normal mode technique” and concrete trajectory of one electron in section “Current of one electron”. The interference pattern is similar to, but cannot be reproduced quantitatively by, that of QM wave function, contrary to many-years-anticipation: a new prediction, awaiting experimental test over and above the Bohr–Einstein gedanken experiment. QED paves the way for the new generic quantitative theory of electronic structure and dynamics over and above QM. Alpha-oscillator theory presents new aspects of QED from basic physics to material sciences with mathematical rigor. Quantum simulation of nanosized materials is a realization of the new-generation quantum theory. A new era of quantum simulation of nanosized materials is realized. Correct theory of the double-slit phenomenon is QED. Correct quantum theoretical view of the double-slit phenomenon is relativistic quantum field theory (QFT).     

The fish community of a newly restored southern California estuary: ecological perspective 3 years after restoration

Bays and estuaries are considered essential fish habitat, yet in many parts of the world, these areas have been degraded or destroyed. In southern California, habitat restoration has become a widely used approach for protecting coastal ecosystems; however, there is little information available on the success of these efforts. Monthly abundance surveys were employed to examine spatial and temporal trends in the fish assemblages 3 years after the restoration of the Bolsa Chica Full Tidal Basin (BCFTB). This was used as a short-term success assessment of the BCFTB restoration, as well as an important baseline against which future studies can determine the long-term trajectory of the restoration. Forty-four species of fish were caught inside the BCFTB, at an average density of 116.8 fish 100 m^?2 and an average biomass of 4.2 kg 100 m^?2. There was a seasonal pattern in fish abundances but no overall increase or decrease in abundances during the entire study period. Marine, estuarine and migrant fish species were found in the BCFTB, each showing different seasonal patterns in abundance, similar to nearby estuaries, with 14 species driving these patterns. Water temperature and season were the most influential factors on the species composition of the fish community in the BCFTB. Therefore, 3 years after restoration the BCFTB is providing habitat for coastal fish species where none existed previously, and shows a community structure similar to natural estuaries in southern California. The BCFTB restoration has been initially successful but needs to be monitored periodically to assess its long-term success.