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.     

Not Looking a Gift Horse in the Mouth: Exploring the Merits of a Student–Teacher–Scientist Partnership

One major emphasis of reform initiatives in science education is the importance of extended inquiry experiences for students through authentic collaborations with scientists. As such, unique partnerships have started to emerge between science and education in an ongoing effort to capture the interest and imaginations of students as they make sense of the world around them. One such partnership is called the student–teacher–scientist partnership, in which teachers and their students participate in and contribute to the research of scientists. This article explores a partnership between a 10th-grade biology teacher, her students, and practicing scientists who collaborated in the design, implementation and evaluation of a horse evolution unit. The primary goal of the collaborative activity was to involve teachers and students in a process of conceptual change as a means of eliminating common misconceptions implicit in horse evolution displays in museums in various parts of the country. The evidence-based lessons developed enhanced students’ understanding of concepts in macroevolution but also connected the science classroom with a community of scientists whose personalization of the horse evolution unit situated biological concepts and the learning experience within the context of real-world issues.     

Phytoplankton pigments designation–an application of RP-HPLC in qualitative and quantitative analysis

An account is given of the use of RP-HPLC (reverse-phase high performance liquid chromatography) analysis of high purity chlorophylls and carotenoids standards originating from reference phytoplankton monocultures. All important chromatography parameters were established: retention time, detection limit, spectrum, wavelength of maximum absorption, calibration curve, response factors. Data were also obtained for pigment mixtures in naturalphytoplankton populations in Spitsbergen and the Gulf of Gdask. The identity and purity of all pigments were confirmed by co-elution with standards, including canthaxanthin as an internal standard. The data presented enable the qualitative and quantitative analysis of naturally existing phytoplankton pigments at concentrations down to 0.1 g L^-1 to be carried out without the need for standards from commercial sources.     

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.     

NMR assignment of the apo-form of a Desulfovibrio gigas protein containing a novel Mo–Cu cluster

We report the 98% assignment of the apo-form of an orange protein, containing a novel Mo–Cu cluster isolated from Desulfovibrio gigas. This protein presents a region where backbone amide protons exchange fast with bulk solvent becoming undetectable. These residues were assigned using ¹³C-detection experiments.     

Phytoplankton–bacterioplankton interactions in a neotropical floodplain lake (Laguna Bufeos,Bolivia)

Laguna Bufeos is a floodplain lake of the river Ichilo, a tributary of the Amazon basin situated in Bolivia. Nutrient addition assays involving whole water (<200 μm) as well as fractionated water (<0.8 μm) treatments were carried out in incubation tubes to test whether bacterial growth is limited by the availability of inorganic nutrients and to test whether bacteria are able to utilize inorganic nutrients directly or are stimulated by inorganic nutrients through increased production of phytoplankton. The assays were carried out during two extreme hydrological conditions, the high-water and the low-water period. During the high-water period experiment, neither N or P limited bacterial growth rates. During the low-water period, bacterial growth was P limited. Bacterial growth was stimulated in the fractionated as well as in the whole water treatments, indicating that bacterial growth was directly stimulated by P. Bacterial growth corrected for grazing losses (determined by means of dilution experiments) was significantly higher in the fractionated water containing only bacteria when compared to the whole water containing also grazers and phytoplankton. This suggests that bacterial growth was suppressed by competition with phytoplankton rather than stimulated through the production of dissolved organic matter by phytoplankton.     

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.     

Preliminary Evaluation of a White-Rot Fungal Reactor in the Treatment of a Waste Oil–Recycling Wastewater

An investigation of the treatment of a complex waste oil–recycling hydrocarbon wastewater was made by employing white-rot fungal strains immobilized in a pinewood chip-packed reactor. The reactor was operated in sequencing batch mode. The fungal reactor was evaluated in a preliminary bench-scale reactor followed by intermediate-scale operation. Substantial chemical oxygen demand (COD) reduction (> 96% in 48-h batch cycles) and removal of specific influent compound constituents, alkanes (n-C8, n-C10–C12) and aromatic compound (o-xylene), was shown in diluted and undiluted (COD > 37 g L^?1) influent. Industrial application of the fungal reactor was evaluated in a 14-m³ pilot plant erected on-site at a waste oil–processing facility. The scale-up implication and optimization of the field plant is discussed in relation to the process-monitoring programme.     

Recovery of the motor function of the arm with the aid of a hand exoskeleton controlled by a brain–computer interface in a patient with an extensive brain lesion

The dynamics of motor function recovery in a patient with an extensive brain lesion has been investigated during a course of neurorehabilitation assisted by a hand exoskeleton controlled by a brain–computer interface. Biomechanical analysis of the movements of the paretic arm recorded during the rehabilitation course was used for an unbiased assessment of motor function. Fifteen procedures involving hand exoskeleton control (one procedure per week) yielded the following results: (a) the velocity profile for targeted movements of the paretic hand became nearly bell-shaped; (b) the patient began to extend and abduct the hand, which was flexed and adducted at the beginning of the course; and (c) the patient started supinating the forearm, which was pronated at the beginning of the rehabilitation course. The first result is interpreted as improvement of the general level of control over the paretic hand, and the two other results are interpreted as a decrease in spasticity of the paretic hand.     

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.     

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.     

The use of the logarithmic transformation in the calculation of the transport parameters of a system that obeys Michaelis–Menten kinetics

1. A logarithmic method is described for the calculation of the transport parameters, K(m) and V(max.)' of a biological system obeying Michaelis-Menten kinetics. 2. This logarithmic method leads to a way of estimating the transport parameters that has not apparently been used previously. It allows the separation of variance due to V(max.) from other variance, and so reduces the fiducial limits that can be placed on an estimation of K(m). 3. The results of studies on the transport of l-histidine and l-monoiodohistidine by rat intestinal sacs in vitro have been used to illustrate the application of the new method. Estimates of the transport parameters have also been made by two alternative procedures. The relative merits of the three methods are discussed.     

Analysis of the Putative Remains of a European Patron Saint–St. Birgitta

Saint Birgitta (Saint Bridget of Sweden) lived between 1303 and 1373 and was designated one of Europe''s six patron saints by the Pope in 1999. According to legend, the skulls of St. Birgitta and her daughter Katarina are maintained in a relic shrine in Vadstena abbey, mid Sweden. The origin of the two skulls was assessed first by analysis of mitochondrial DNA (mtDNA) to confirm a maternal relationship. The results of this analysis displayed several differences between the two individuals, thus supporting an interpretation of the two skulls not being individuals that are maternally related. Because the efficiency of PCR amplification and quantity of DNA suggested a different amount of degradation and possibly a very different age for each of the skulls, an orthogonal procedure, radiocarbon dating, was performed. The radiocarbon dating results suggest an age difference of at least 200 years and neither of the dating results coincides with the period St. Birgitta or her daughter Katarina lived. The relic, thought to originate from St. Birgitta, has an age corresponding to the 13^th century (1215–1270 cal AD, 2σ confidence), which is older than expected. Thus, the two different analyses are consistent in questioning the authenticity of either of the human skulls maintained in the Vadstena relic shrine being that of St. Birgitta. Of course there are limitations when interpreting the data of any ancient biological materials and these must be considered for a final decision on the authenticity of the remains.     

Broadscale Specificity in a Bark Beetle–Fungal Symbiosis: a Spatio-temporal Analysis of the Mycangial Fungi of the Western Pine Beetle

Whether and how mutualisms are maintained through ecological and evolutionary time is a seldom studied aspect of bark beetle–fungal symbioses. All bark beetles are associated with fungi and some species have evolved structures for transporting their symbiotic partners. However, the fungal assemblages and specificity in these symbioses are not well known. To determine the distribution of fungi associated with the mycangia of the western pine beetle (Dendroctonus brevicomis), we collected beetles from across the insect’s geographic range including multiple genetically distinct populations. Two fungi, Entomocorticium sp. B and Ceratocystiopsis brevicomi, were isolated from the mycangia of beetles from all locations. Repeated sampling at two sites in Montana found that Entomocorticium sp. B was the most prevalent fungus throughout the beetle’s flight season, and that females carrying that fungus were on average larger than females carrying C. brevicomi. We present evidence that throughout the flight season, over broad geographic distances, and among genetically distinct populations of beetle, the western pine beetle is associated with the same two species of fungi. In addition, we provide evidence that one fungal species is associated with larger adult beetles and therefore might provide greater benefit during beetle development. The importance and maintenance of this bark beetle–fungus interaction is discussed.     

Growth of Pseudomonas chlororaphis on apolyester–polyurethane and the purification andcharacterization of a polyurethanase–esterase enzyme

A Pseudomonas chlororaphis was found to degrade and utilize apolyester polyurethane as a sole carbon and energy source. Polyurethane utilization by P.chlororaphis followed simple Michaelis–Menten kinetics. The K_s and μ_max values were 0.802 mg·ml⁻¹ and 1.316 doublings·h⁻¹, respectively. The enzymes from P. chlororaphis responsible for polyurethanedegradation were found to be extracellular. Analysis of the polyurethane degrading proteins, usingnon-denaturing polyacrylamide gel electrophoresis, revealed three active protein bands with R_f values of 0.25, 0.417 and 0.917. A polyurethane degrading enzyme was purifiedand displayed esterase activity. This enzyme was inhibited by phenylmethylsulfonyl fluoride andhad a molecular weight of 27,000 daltons.     

Phytoplankton of the extremely acidic mining lakes of Lusatia (Germany) with pH ≤3

Most of the flooded, open-cast lignite mining lakes of Lusatia (Germany) impacted by the oxidation of iron sulphides (pyrite and marcasite) are extremely acidic. Of 32 lakes regularly studied from 1995 to 1998, 14 have a pH <3 (median pH 2.3–2.9). These lakes are typically buffered by high concentrations of Fe (III) and have high conductivity (1000–5000 S cm^–1). Concentrations of dissolved inorganic carbon (DIC) and phosphorus are typically extremely low. These factors result in a very different environment for algae than found in neutral and acid-rain impacted lakes. The planktonic algal flora is generally dominated by flagellates belonging to genera of Chlorophyta (Chlamydomonas), Heterokontophyta of the class Chrysophyceae (Ochromonas, Chromulina), Cryptophyta (Cyathomonas) and Euglenophyta (Lepocinclis, Euglena mutabilis). Near-spherical non-motile Chlorophyta (Nanochlorum sp.), Heterokontophyta of the class Bacillariophyceae (Eunotia exigua, Nitzschia), Dinophyta (Gymnodinium, Peridinium umbonatum), other Chlorophyta (Scourfieldia cordiformis) and Cryptophyta (Rhodomonas minuta) are also found.     

Methylene blue as a suppessor of the genotoxic effect of ultraviolet radiation with a wavelength of 300–400 nm

Ultraviolet radiation with a wavelength of 300–400 nm is characteristic of sunlight at the earth surface and causes DNA damage mediated by energy transfer to O₂ with the transformation of the latter in the singlet state. In connection with this, scavengers of reactive oxygen species (ROSs) are potential protectors against the genotoxic effect of this kind of radiation. It was found that the methylene blue dye at doses differing by several orders of magnitude from those that are toxic for humans is able to suppress completely the SOS response induced by UV with a wavelength of 300–400 nm in Escherichia coli.