Chlorophyll a fluorescence induction: a personal perspective of the thermal phase, the J–I–P rise

The fast (up to 1?s) chlorophyll (Chl) a fluorescence induction (FI) curve, measured under saturating continuous light, has a photochemical phase, the O-J rise, related mainly to the reduction of Q(A), the primary electron acceptor plastoquinone of Photosystem II (PSII); here, the fluorescence rise depends strongly on the number of photons absorbed. This is followed by a thermal phase, the J-I-P rise, which disappears at subfreezing temperatures. According to the mainstream interpretation of the fast FI, the variable fluorescence originates from PSII antenna, and the oxidized Q(A) is the most important quencher influencing the O-J-I-P curve. As the reaction centers of PSII are gradually closed by the photochemical reduction of Q(A), Chl fluorescence, F, rises from the O level (the minimal level) to the P level (the peak); yet, the relationship between F and [Q(A) (-)] is not linear, due to the presence of other quenchers and modifiers. Several alternative theories have been proposed, which give different interpretations of the O-J-I-P transient. The main idea in these alternative theories is that in saturating light, Q(A) is almost completely reduced already at the end of the photochemical phase O-J, but the fluorescence yield is lower than its maximum value due to the presence of either a second quencher besides Q(A), or there is an another process quenching the fluorescence; in the second quencher hypothesis, this quencher is consumed (or the process of quenching the fluorescence is reversed) during the thermal phase J-I-P. In this review, we discuss these theories. Based on our critical examination, that includes pros and cons of each theory, as well mathematical modeling, we conclude that the mainstream interpretation of the O-J-I-P transient is the most credible one, as none of the alternative ideas provide adequate explanation or experimental proof for the almost complete reduction of Q(A) at the end of the O-J phase, and for the origin of the fluorescence rise during the thermal phase. However, we suggest that some of the factors influencing the fluorescence yield that have been proposed in these newer theories, as e.g., the membrane potential ΔΨ, as suggested by Vredenberg and his associates, can potentially contribute to modulate the O-J-I-P transient in parallel with the reduction of Q(A), through changes at the PSII antenna and/or at the reaction center, or, possibly, through the control of the oxidation-reduction of the PQ-pool, including proton transfer into the lumen, as suggested by Rubin and his associates. We present in this review our personal perspective mainly on our understanding of the thermal phase, the J-I-P rise during Chl a FI in plants and algae.     

Vascular epiphytes in the temperate zones–a review

Vascular epiphytes are typically associated with tropical rainforests, whereas their occurrence in temperate forests is little appreciated. This review summarises the available information on epiphytism in the temperate zones (> 23.5 latitude), which has not been reviewed omprehensively for more than a century, and critically analyses the proposed mechanisms behind the observed biogeographical patterns. Although in the temperate zone epiphytic vascular plants are rarely as impressive as in tropical forests, there are noteworthy exceptions. Temperate rain forests of Chile and New Zealand, or montane forests in the Himalayas are comparable to many tropical forests in terms of epiphyte biomass and diversity, but differ in their taxonomic spectrum temperate epiphyte communities are generally dominated by ferns and fern-allies. Other temperate areas are not, however, necessarily barren of epiphytes, as repeatedly implied. Quite in contrast, local populations of epiphytes in a large number of other non-tropical areas in both the southern and the northern hemisphere can be quite conspicuous. The proposed reasons for the latitudinal gradients in epiphyte abundance and diversity (water scarcity or low tempera-tures). are not fully convincing and, moreover, still await experimental verification. Other factors, both historical (e.g., Pleistocene extinctions) and ecological (e.g., prevalence of conifers in the northern hemisphere), should also be taken into consideration to obtain a comprehensive explanation of the extant global distribution of vascular epiphytes.     

On the Neimark–Sacker bifurcation in a discrete predator–prey system

A two-parameter family of discrete models describing a predator–prey interaction is considered, which generalizes a model discussed by Murray, and originally due to Nicholson and Bailey, consisting of two coupled nonlinear difference equations. In contrast to the original case treated by Murray, where the two populations either die out or may display unbounded growth, the general member of this family displays a somewhat wider range of behaviour. In particular, the model has a nontrivial steady state which is stable for a certain range of parameter values, which is explicitly determined, and also undergoes a Neimark–Sacker bifurcation that produces an attracting invariant curve in some areas of the parameter space and a repelling one in others.     

Solving the decentralised gathering problem with a reaction–diffusion–chemotaxis scheme

The decentralised gathering problem consists in grouping in a compact cluster agents that are initially randomly scattered. We propose a bio-inspired algorithm, the Reaction–Diffusion–Chemotaxis aggregation scheme, to group agents that have limited abilities. The agents and their environment are described with a stochastic model inspired by the aggregation of the Dictyostelium discoideum cellular slime mold. The environment is an active lattice, whose cells transmit information according to a reaction–diffusion mechanism. The agents are virtual amoebae; they trigger excitations randomly and move by following reaction–diffusion waves. We demonstrate that despite its simplicity, this model exhibits interesting properties of self-organisation and is efficient for gathering agents. Moreover, observations show that the system is robust to various perturbations, such as the presence of obstacles on the lattice or noise in the movements of the agents.     

From the inverse density–area relationship to the minimum patch size of a host–parasitoid system

The minimum amount of suitable habitat (MASH) is an important concept in conservation biological control. Two methods for estimating the MASH have been proposed by McCoy and Mushinsky based on an inverse density–area relationship. Using data of the population densities of aphid host–parasitoid–hyperparasitoid collected from wheat fields of different habitat sizes, we argued that the inverse density–area relationship may be an artifact. Significant correlations between population densities and patch sizes from all three trophic levels were found once the population density had been log-transformed. We could not obtain the same results if the population density had not been log-transformed. We estimated that the MASH for the aphid M. avena, S. graminum, A. avenae, A. gifuensis, P. aphidis, and Alloxysta sp. were 246, 246, 479, 495, 949, and 835 m² according to the methods of McCoy and Mushinsky. The scale-dependence and the systematic spatial variations of the host–parasitoid interaction suggests that we can achieve an optimal effect of biological control by manipulating the habitat patch sizes, although not based on the inverse density–area relationship.     

Fano Resonance in a Gear-Shaped Nanocavity of the Metal–Insulator–Metal Waveguide

The filter function of the metal–insulator–metal (MIM) waveguide with a gear-shaped nanocavity is investigated using the finite-difference time-domain method. Since the gear breaks the symmetric distribution of the resonance, Fano resonance occurs in the gear-shaped nanocavity. Fano resonance strongly depends on the structural parameters of the gear. Compared to the MIM waveguide with a disk-shaped nanocavity, the MIM waveguide with a gear-shaped nanocavity allows for a much more sensitive detection of small refractive index changes of the filled media inside the nanocavity, which reveals a potential sensor application of the MIM waveguide with a gear-shaped nanocavity.     

Tentative identification of a vasopressin–neurophysin and an oxytocin–neurophysin in the rat

1. Rat neurohypophysial extracts have been examined by polyacrylamide-gel electrophoresis. 2. Three of the proteins were tentatively identified as neurophysins by their acidic nature and their disappearance after dehydration of the animals. 3. These proteins were radioactive 24h after intracisternal injection of [(35)S]cysteine. 4. Two of the proteins were present in much greater quantities than the third, and these two were present in the gland in the same ratio as the hormones vasopressin and oxytocin. 5. One of these proteins was absent from glands of rats homozygous for diabetes insipidus but present in heterozygous animals. 6. It is suggested that these two proteins are the vasopressin-neurophysin and oxytocin-neurophysin of the rat.     

Small-scale indirect effects determine the outcome of a tripartite plant–disperser–granivore interaction

The microhabitat in which plants grow affects the outcome of their interactions with animals, particularly non-specialist consumers. Nevertheless, as most research on this topic has dealt with either mutualists or antagonists, little is known about the indirect effects of plant microhabitats on the outcome of tripartite interactions involving plants and both mutualists (e.g. seed dispersers) and antagonists (e.g. granivores). During three consecutive years, we analysed small-scale variations in the interaction of a perennial myrmecochore, Helleborus foetidus, with its seed dispersers and consumers as a function of the intensity of plant cover. Most seeds were released during the day and were rapidly removed by ants. Nevertheless, the proportion of ant-removed seeds was higher for plants located in open microhabitats than for plants surrounded by dense vegetation and rocky cover. Ant sampling revealed that seed removers were equally abundant, irrespective of the level of cover. By contrast, a few tiny ant species that feed on the reward without transporting the seeds were more abundant in highly covered microhabitats, irrespective of hellebore diaspore availability. These “cheaters” decrease the chance of removal by removers and increase the probability of seeds remaining on the ground until night, when granivore mice Apodemus sylvaticus become active. Mice also preferred foraging in covered microhabitats, where they consumed a larger proportion of seeds. Therefore, the density of cover indirectly increased seed predation risk by attracting more seed predators and cheater ants that contribute to increase seed availability for seed predators. Our results emphasize the importance of considering the indirect effects of plant microhabitat on their dispersal success. They highlight the indirect effect of cheaters that are likely to interfere in mutualisms and may lead to their collapse unless external factors such as spatio-temporal heterogeneity in seed availability constrain their effect. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Mechanisms driving the density–area relationship in a saproxylic beetle

Mechanisms underlying density–area relationships (correlations between population density and patch size) have rarely been tested experimentally. It is often assumed that higher density on large patches is evidence that large patches are high quality (i.e. have greater survival and reproduction), but the same pattern could result from disproportionate movement from small to large patches. Movement-based and within-patch processes must be experimentally separated to show that large patches are indeed of higher quality, but few studies have done so. We experimentally tested movement-based and within-patch hypotheses to explain the positive density–area relationship observed for a saproxylic (decayed wood-dependent) beetle, Odontotaenius disjunctus Illiger (Coleoptera: Passalidae). In separate experiments we quantified (1) immigration into and (2) finite growth rate within logs (=patches) that varied in size and density of conspecific beetles. A log was 11.7-fold [95 % confidence interval (CI) 3.4–40.8) and 10.5-fold (95 % CI 2.7–40.9) more likely to contain a new immigrant if it was large or contained a conspecific pair of beetles, respectively. Neither log size nor conspecific density was associated with changes in finite growth rate that would lead to higher density: decreased log size and increased conspecific density reduced finite growth rate in direct proportion to the loss in available resources per mating pair. We conclude that movement behavior rather than habitat quality is responsible for the positive density–area relationship for O. disjunctus. An important implication of our results is that population density is an imperfect indicator of habitat quality.     

Structure of the UreD–UreF–UreG–UreE complex in Helicobacter pylori: a model study

The molecular details of the protein complex formed by UreD, UreF, UreG, and UreE, accessory proteins for urease activation in the carcinogenic bacterium Helicobacter pylori, have been elucidated using computational modeling. The calculated structure of the complex supports the hypothesis of UreF acting as a GTPase activation protein that facilitates GTP hydrolysis by UreG during urease maturation, and provides a rationale for the design of new drugs against infections by ureolytic bacterial pathogens.     

Targeting the ICB2 site of the topoisomerase IIα promoter with a formamido-pyrrole–imidazole–pyrrole H-pin polyamide

The synthesis, DNA binding characteristics and biological activity of an N-formamido pyrrole- and imidazole-containing H-pin polyamide (f-PIP H-pin, 2) designed to selectively target the ICB2 site on the topoIIα promoter, is reported herein. Thermal denaturation, circular dichroism, isothermal titration calorimetry, surface plasmon resonance and DNase I footprinting studies demonstrated that 2 maintained the selectivity of the unlinked parent monomer f-PIP (1) and with a slight enhancement in binding affinity (K_eq = 5 × 10⁵ M^?1) to the cognate site (5′-TACGAT-3′). H-pin 2 also exhibited comparable ability to inhibit NF-Y binding to 1, as demonstrated by gel shift studies. However, in stark contrast to monomer 1, the H-pin did not affect the up-regulation of topoisomerase IIα (topoIIα) in cells (Western blot), suggesting that the H-pin does not enter the nucleus. This study is the first to the authors’ knowledge that reports such a markedly different cellular response between two compounds of almost identical binding characteristics.     

Spectroscopic properties of the Chlorophyll a–Chlorophyll c 2–Peridinin-Protein-Complex (acpPC) from the coral symbiotic dinoflagellate Symbiodinium

Femtosecond time-resolved transient absorption spectroscopy was performed on the chlorophyll a–chlorophyll c ₂–peridinin-protein-complex (acpPC), a major light-harvesting complex of the coral symbiotic dinoflagellate Symbiodinium. The measurements were carried out on the protein as well on the isolated pigments in the visible and the near-infrared region at 77 K. The data were globally fit to establish inter-pigment energy transfer paths within the scaffold of the complex. In addition, microsecond flash photolysis analysis was applied to reveal photoprotective capabilities of carotenoids (peridinin and diadinoxanthin) in the complex, especially the ability to quench chlorophyll a triplet states. The results demonstrate that the majority of carotenoids and other accessory light absorbers such as chlorophyll c ₂ are very well suited to support chlorophyll a in light harvesting. However, their performance in photoprotection in the acpPC is questionable. This is unusual among carotenoid-containing light-harvesting proteins and may explain the low resistance of the acpPC complex against photoinduced damage under even moderate light conditions.     

Demosponge distribution in the eastern Mediterranean: a NW–SE gradient

The purpose of this paper was to investigate patterns of demosponge distribution along gradients of environmental conditions in the biogeographical subzones of the eastern Mediterranean (Aegean and Levantine Sea). The Aegean Sea was divided into six major areas on the basis of its geomorphology and bathymetry. Two areas of the Levantine Sea were additionally considered. All available data on demosponge species numbers and abundance in each area, as well as their vertical and general geographical distribution were taken from the literature. Multivariate analysis revealed a NW–SE faunal gradient, showing an apparent dissimilarity among the North Aegean, the South Aegean and the Levantine Sea, which agrees with the differences in the geographical, physicochemical and biological characteristics of the three areas. The majority of demosponge species has been recorded in the North Aegean, while the South Aegean is closer, in terms of demosponge diversity, to the oligotrophic Levantine Sea. The number of studies in the Aegean and Levantine subareas was positively correlated with the number of species recorded within each Aegean subarea. Demosponge species with an Altanto-Mediterranean distribution prevailed in the Aegean and the Levantine. The reduced contribution of the endemic component, as compared to the western Mediterranean, is consistent with the general NW–SE decrease in the number of endemic species in the Mediterranean. Demosponge distribution at the order level showed also a NW–SE gradient, similar to that observed in the entire Atlantic–Mediterranean region, suggesting a warm water affinity. Sublittoral, circalittoral and bathyal zones were clearly distinguishable in the Aegean Sea on the basis of their sponge fauna. The total number of species was an exponential negative function of depth.     

Metallo-β-lactamases and a tug-of-war for the available zinc at the host–pathogen interface

Metallo-β-lactamases (MBLs) are zinc-dependent hydrolases that inactivate virtually all β-lactam antibiotics. The expression of MBLs by Gram-negative bacteria severely limits the therapeutic options to treat infections. MBLs bind the essential metal ions in the bacterial periplasm, and their activity is challenged upon the zinc starvation conditions elicited by the native immune response. Metal depletion compromises both the enzyme activity and stability in the periplasm, impacting on the resistance profile in vivo. Thus, novel inhibitory approaches involve the use of chelating agents or metal-based drugs that displace the native metal ion. However, newer MBL variants incorporate mutations that improve their metal binding abilities or stabilize the metal-depleted form, revealing that metal starvation is a driving force acting on MBL evolution. Future challenges require addressing the gap between in cell and in vitro studies, dissecting the mechanism for MBL metalation and determining the metal content in situ.     

Calculation of the Three-Dimensional Structures of Two Antigenic Sequences, Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro and Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–Pro–Pro, of the Circumsporozoite Protein From a Malaria-Causing Plasmodium

Using the chain build-up procedure based on the program ECEPP, we have computed the lowest energy structures for two terminally blocked subsequences from the antigenic circumsporozoite protein of Plasmodium berghei, that is known to cause malaria in animals. The full antigenic sequence is an octapeptide proline-rich tandem repeat, (Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp)₂. We computed the structures for the first octapeptide plus one Pro from the second octapeptide, terminally blocked CH₃CO–Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–NHCH₃ as well as the first octpeptide with an additional three Pro residues from the adjoining unit, i.e., CH₃CO–Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–Pro–Pro–NHCH₃. We find that the first sequence adopts a number of different low energy structures, the most probable of which has a probability of occurrence of 56 %. Addition of two more Pro residues results in the adoption a single, unique lowest energy structure that has a probability of occurrence of over 95 % without solvation effects and 86 % when solvation effects are included in the calculations. We predict that this structure may be the one recognized as a major antigenic determinant.     

Catching the adaptor—WDFY1, a new player in the TLR–TRIF pathway

The innate immune system detects microbes and abnormal self through pattern recognition receptors (PRRs), which detect molecules that are either specific for microbes (such as lipopolysaccharide), present in much higher concentrations during infection (such as double‐stranded RNA), or present in aberrant locations (such as cytosolic DNA) 1 . The Toll‐like receptors (TLRs) are the best‐described set of PRRs. TLRs are membrane‐bound receptors localized on the plasma membrane and in endosomes, the ligand‐binding regions of which face the extracellular environment and the endosomal lumen, respectively 1 . In this issue of EMBO Reports, Hu and colleagues report that WD‐repeat and FYVE‐domain‐containing protein 1 (WDFY1) recruits the signaling adaptor TRIF to TLR3 and TLR4, thereby potentiating signaling from these PRRs (Fig  1 ); 2 .     

Phytoplankton of Lake Bol’shie Shvakshty (Belarus) during the Shift of the Ecosystem from a Macrophyte–Weakly Eutrophic to a Phytoplankton–Hypereutrophic State

Changes in the quantitative characteristics and functioning of phytoplankton in Lake Bol’shie Shvakshty have been assessed. The changes are evoked by the introduction of herbivorous fishes into the lake and the resulting disturbance of ecological balance in the ecosystem and the shift of the lake into a hypertrophic state from a weakly eutrophic state. Human interference has caused the cyanobacteria density (abundance) and biomass values in the overall phytoplankton composition to strongly exceed (3.5 × 10⁹ cells/L and above 68 μg/L chlorophyll-а, respectively) the threshold value for safe recreational use of water bodies (20 million cells/L and 10 μg/L chlorophyll-а) established by the World Health Organization (WHO). The lake can be assigned to the third level of hazard to human health within the classification proposed by the WHO, as the cyanobacteria density is higher than 100 million cells/L and chlorophyll-а content is higher than 50 μg/L. MC-producing Microcystis species were identified among the cyanobacteria that has propagated in the lake in recent years, and five microcystin variants, including the highly toxic MC-LR, have been detected in the water.     

Measuring the postfire resilience of a bird–vegetation system: a 28-year study in a Mediterranean oak woodland

Despite numerous studies on the response of Mediterranean ecosystems to fire, few have measured the respective resilience of vegetation and fauna compartments. For 28 years, we conducted an annual monitoring of avifauna composition and vegetation structure (cover profile) following a severe wildfire in a holm oak (Quercus ilex) stand in southern France. Our aim was to estimate the time necessary for this bird–vegetation system to return to a state analogous to its pre-fire state. In the burned plots, low herbaceous and shrub layers were gradually replaced by higher, woody layers of vegetation. Neither bird species richness nor inter-annual bird species turnover showed significant differences from one year to the next over the study period. In contrast, bird species composition did change steadily, leading to an almost complete replacement of early-successional species by late-successional ones. Using the first axes of multivariate analyses as ‘proxy variables’ of vegetation or avifauna recoveries, we estimated by extrapolation the recovery times of these two ecosystem components at ca. 50 and 35 years, respectively. Towards the end of the study period, the rate of change in avifauna composition decreased comparatively to that of vegetation structure. Our results show that holm oak woodlands are highly resilient and seem to tolerate a ~50-year fire interval, even if it remains to be assessed how resilient they would be in the case of increased fire frequency. More generally, our multivariate approach, which allows comparative estimations of resilience in different components of an ecosystem using qualitative as well as quantitative criteria, could be applied to various case studies in disturbance and restoration ecology.