Changes in the Electron Transfer Symmetry in the Photosystem I Reaction Centers upon Removal of Iron–Sulfur Clusters

Biochemistry (Moscow) - In photosynthetic reaction centers of intact photosystem I (PSI) complexes from cyanobacteria, electron transfer at room temperature occurs along two symmetrical branches of...     

A Closed Parameterization of DNA–Damage by Charged Particles,as a Function of Energy — A Geometrical Approach

Purpose

To present a closed formalism calculating charged particle radiation damage induced in DNA. The formalism is valid for all types of charged particles and due to its closed nature is suited to provide fast conversion of dose to DNA-damage.

Methods

The induction of double strand breaks in DNA–strings residing in irradiated cells is quantified using a single particle model. This leads to a proposal to use the cumulative Cauchy distribution to express the mix of high and low LET type damage probability generated by a single particle. A microscopic phenomenological Monte Carlo code is used to fit the parameters of the model as a function of kinetic energy related to the damage to a DNA molecule embedded in a cell. The model is applied for four particles: electrons, protons, alpha–particles, and carbon ions. A geometric interpretation of this observation using the impact ionization mean free path as a quantifier, allows extension of the model to very low energies.

Results

The mathematical expression describes the model adequately using a chi–square test (). This applies to all particle types with an almost perfect fit for protons, while the other particles seem to result in some discrepancies at very low energies. The implementation calculating a strict version of the RBE based on complex damage alone is corroborated by experimental data from the measured RBE. The geometric interpretation generates a unique dimensionless parameter for each type of charged particle. In addition, it predicts a distribution of DNA damage which is different from the current models.     

Reconsideration of the term ‘vitrification’ as used in micropropagation

The term vitrification is currently used to describe two types of processes related to tissue-cultured plant material. The first is used to describe organs and tissues having an abnormal morphological appearance and physiological function. The second is used to describe the transition from liquid to solid state, i.e. the formation of ice during low temperature storage of in vitro cultured cells, tissues and organs. Use of the same term to define two greatly different processes in the same research area can only lead to confusion, especially for key words. Thus it is appropriate to reconsider the usage of vitrification in the first sense mentioned above. It is recommended that the term vitrification should no longer be used to indicate plant material with an abnormal morphological appearance and physiological function, and should be substituted by the term hyperhydricity.This paper was written as a follow up of the discussions held during the workshop on Vitrification at the IAPTC-Congress in Amsterdam (1990). Different eminent research workers in the field of vitrification were invited to formulate their preference for a new terminology, and they came to a consensus.     

Biapenem Inactivation by B2 Metallo β-Lactamases: Energy Landscape of the Hydrolysis Reaction

Background

A general mechanism has been proposed for metallo β-lactamases (MβLs), in which deprotonation of a water molecule near the Zn ion(s) results in the formation of a hydroxide ion that attacks the carbonyl oxygen of the β-lactam ring. However, because of the absence of X-ray structures that show the exact position of the antibiotic in the reactant state (RS) it has been difficult to obtain a definitive validation of this mechanism.

Methodology/Principal Findings

We have employed a strategy to identify the RS, which does not rely on substrate docking and/or molecular dynamics. Starting from the X-ray structure of the enzyme:product complex (the product state, PS), a QM/MM scan was used to drive the reaction uphill from product back to reactant. Since in this process also the enzyme changes from PS to RS, we actually generate the enzyme:substrate complex from product and avoid the uncertainties associated with models of the reactant state. We used this strategy to study the reaction of biapenem hydrolysis by B2 MβL CphA. QM/MM simulations were carried out under 14 different ionization states of the active site, in order to generate potential energy surfaces (PESs) corresponding to a variety of possible reaction paths.

Conclusions/Significance

The calculations support a model for biapenem hydrolysis by CphA, in which the nucleophile that attacks the β-lactam ring is not the water molecule located in proximity of the active site Zn, but a second water molecule, hydrogen bonded to the first one, which is used up in the reaction, and thus is not visible in the X-ray structure of the enzyme:product complex.     

A Four-Level Theory on Energy Transfer of the Light-Harvesting Complex ￠ò in PS ￠ò in Higher Plants (in English)

With reference to the recent achivements about the structure, spectra and kinetics of light-harvesting complex (LHCⅡ) in PSⅡ of higher plants, a four-level model was provided to simulate the energy transfer process from LHCⅡ to the reaction center. On the basis of this model, a set of rate equation was established. Analysis of its algebra solution led to a general picture of energy transfer process in LHCⅡ of higher plants and the strong interaction among pigment molecules in this process. Based on the spectra, kinetics and biological structural data providing some information of energy transfer path and energy dissipation mechanism, it has been found that energy transfer mainly happened between the pigments whose energy level was most closely adjacent, the loss of energy had a close relation to the process of energy transfer and tended to increase with the decrease of energy level. The protective mechanism of antenna system was also discussed.     

Role of the oxidized secondary acceptor Q B of Photosystem II in the delayed ‘afterglow’ chlorophyll luminescence

Leaf discs of dark-adapted tobacco plants were excited by 2 flashes and kept in darkness at 20 °C for various time periods, then thermoluminescence emission was recorded without freezing the sample. The B band at 30 °C decreased with a half-time t_1/2~1 min and the AG band at 45 °C with a t_1/2~5 min. This corresponds to the decay kinetics of S_2/3 in PS II centres in the state S_2/3 Q_B^- (B band) or S_2/3 Q_B. Assuming that the 45 °C band is an ‘afterglow’ emission originating from those centres with an oxidized Q_B on which an electron is back-transferred from stroma reductants through a pathway induced by warming, the theoretical ratio of the B and AG band was compared to that measured experimentally. After 2 or 3 flashes producing mainly S₃, the intensity of AG band encompassed several fold that of the B band, because recombining S₃ recreated S₂ Q_B AG-emitting centres. In order to confirm that the AG band is governed by the heat-induced activation of a dark Q_B-reducing pathway rather than by PS II charge recombination, the AG emission was characterized in triazine-resistant Chenopodium album weed biotypes. In these mutants where the Q_B pocket is altered, the B band is strongly downshifted to 18 °C, compared to 32 °C in the wild type, whereas the AG band is only downshifted by 3 or 4 °C, demonstrating that S_2/3 Q_B^- is not the limiting step of the AG emission.     

Heritage of the Romantic Philosophy in Post-Linnaean Botany Reichenbach’s Reception of Goethe’s Metamorphosis of Plants as a Methodological and Philosophical Framework

This paper demonstrates the importance of the reception and development of Goethe’s metamorphosis of plants as a methodological and philosophical framework in the history of botanical theories. It proposes a focus on the textbooks written by the German botanist Ludwig Reichenbach and his first attempt to use Goethe’s idea of metamorphosis of plants as fundamental to his natural system of plants published under the title ‘Botany for Women’, in German Botanik für Damen (1828). In this book, Reichenbach paid particular attention to Goethe’s sensitive views on the essence of nature; he regarded Goethe’s idea of metamorphosis in the plant kingdom as an ideal model to interpret connections of natural phenomena, in particular as a conceptual frame for a natural system. Furthermore, he aimed to develop the philosophical statement of the metamorphosis, in which he called for nature-philosophical conceptions in order to materialize his representation of plant “affinities,” and of a kind of “ontogeny” of the whole plant kingdom. This paper demonstrates that, between speculative views and empirical attempts, the extent to which Reichenbach actually belonged to a new “school” of thought, which left its mark on the history and philosophy of botany.     

The Efficiency of Energy Transfer from Quantum Dots to Photosynthetic Reaction Centers of Rhodobacter sphaeroides in the Temperature Range of 100–310 K

Biophysics - The temperature dependence of the efficiency of energy transfer from polymer coated CdSe/CdS/ZnS quantum dots bearing terminal carboxyl groups to the reaction centers of purple...     

‘HypothesisFinder:’ A Strategy for the Detection of Speculative Statements in Scientific Text

Speculative statements communicating experimental findings are frequently found in scientific articles, and their purpose is to provide an impetus for further investigations into the given topic. Automated recognition of speculative statements in scientific text has gained interest in recent years as systematic analysis of such statements could transform speculative thoughts into testable hypotheses. We describe here a pattern matching approach for the detection of speculative statements in scientific text that uses a dictionary of speculative patterns to classify sentences as hypothetical. To demonstrate the practical utility of our approach, we applied it to the domain of Alzheimer''s disease and showed that our automated approach captures a wide spectrum of scientific speculations on Alzheimer''s disease. Subsequent exploration of derived hypothetical knowledge leads to generation of a coherent overview on emerging knowledge niches, and can thus provide added value to ongoing research activities.     

The Temperature Gradient Air–Soil as a Factor in the Optimization of Net Photosynthesis in Whole Plants

The effect of soil temperature on the net photosynthetic rate was studied by the method of multifactor analysis at early growth stages of narrow-leaved lupine (Lupinus angustifolius L.), white cabbage (Brassica capitata Lisg.), spring wheat (Triticum aestivum L.), cucumber (Cucumis sativus L.), tomato (Lycopersicon esculentum Mill.), and cotton (Gossypium hirsutum L.) plant species and cultivars contrasting in their heat demand. The optimum level of the net photosynthetic rate was observed in a wide range of soil and air temperatures, from cold- to heat-hardening temperatures, irrespective of the sign of the temperature gradient, whereas the magnitude and sign of the temperature gradient favorable for the highest potential net photosynthetic rate were species- and cultivar-specific and were not related to the cold tolerance of a species or cultivar.     

Differential effects of foods traditionally regarded as ‘heating’ and ‘cooling’ on prostaglandin E2 production by a macrophage cell line

Some components of natural foods may enhance or inhibit prostaglandin formation and potentially affect the inflammation condition. A macrophage cell line, RAW264.7, was employed to examine the effects of foods traditionally regarded as heating or cooling on the production of PGE₂, a well-known proinflammatory mediator. Foods traditionally regarded as heating (litchi, longan, and dried longan) or cooling (chrysanthemum flower, bitter gourd, and lotus seed plumule) were extracted sequentially with water and ethyl acetate. The water extracts (WE) and ethyl acetate extracts (EAE) were applied to RAW264.7 macrophages in the presence or absence of LPS (lipopolysaccharide). In the absence of LPS, the WEs from the heating foods, litchi, longan, or dried longan had a dose-dependent enhancing effect on PGE₂ production, with respective EC₅₀s of 8.4, 16, and 11 mg/ml. This effect was accompanied by significant induction of COX-2 protein expression, as shown by Western blot analysis. In contrast, LPS-induced PGE₂ production was inhibited in a dose-dependent manner by the WEs of the cooling foods, chrysanthemum flower, bitter gourd, and lotus seed plumule, with respective IC₅₀s of 0.6, 0.13, and 0.08 mg/ml. At the concentrations tested, none of the EAEs had any effect on basal PGE₂ production, while LPS-induced PGE₂ production was inhibited or increased by the EAE from bitter gourd and longan, respectively. Water-soluble extracts of foods traditionally regarded as heating enhanced basal PGE₂ production, while those from cooling foods significantly inhibited LPS-induced PGE₂ production by the macrophage cell line. This subject merits further study to determine whether appropriate food selection may help patients suffering from chronic inflammatory conditions.     

Light-Induced Damage of Pheophytin a Molecule in the Isolated Photosystem Ⅱ Reaction Center D1/D2/Cyt b559 Complex

Photodamage of some pigments in the isolated photosystem Ⅱ (PS Ⅱ ) reaction center D1/D2/Cyt b559 complex from spinach has been investigated by means of high performance liquid chromatography. The light-induced damage of pheophytin a (pheo a) in the complex was observed for the first time. The content of pheo a decreased about 47 % by illumination, suggesting only one of the two pheo a molecules in the PS Ⅱ reaction center complex was damaged. No damage of β-carotene was found.     

Conformation of the C-terminal pentapeptide—the ‘message sequence’—of tachykinins as determined by consensus dynamic

The tachykinins are a family of gastrointestinal peptides comprising eight members: substance P, neurokinin A, neurokinin B, eledoisin, physalemin, uperolein, kassinin and phyllomedusin. Consensus dynamics was carried out on an ensemble of seven tachykinins to determine the binding conformation of the common C-terminal fragment: Phe-X-Gly-Leu-Met-NH ₂ ,the ’message sequence’ of tachykinins. Three binding modes for the C-terminal pentapeptide were determined. The first binding conformation is folded due to an intramolecular H-bond between the NH of the variable residue (X) and CO of Met. Other features include γ-bends at both the variable amino acid (X) and at Gly. The global minimum of the simulation has this conformation for the C-terminal pentapeptide. The other two binding modes have slightly higher energies. The second is chiefly characterized by a β-turn around the segment X-Gly-Leu-Met, with additional β-bends at the variable amino acid (X) and Met. The final binding conformation is composed of β-bends around the variable amino acid (X) and Leu, and a ’pseudo’ γ-bend at the terminal Met. This paper was presented at the MBU Silver Jubilee Symposium on Structural Biology and 24th Annual Meeting of the Indian Biophysical Society held at Indian Institute of Science, Bangalore, Dec. 9–12, 1996.     

‘Endogenous yolk’ as the precursor of a possible fertilization envelope in a crab (Carcinus maenas)

After the egg attachment to a maternal ovigerous seta, the Carcinus maenas embryo is enclosed in a tripartite capsule. The innermost layer (envelope 2) which is also the main part of this capsule, is generally detected after egg-laying and is most probably closely related to the fecondation phenomenon. The precursor material of envelope 2, arising from the egg by a massive and very fast exocytosis process, appears as numerous ring-shaped granules. These granules, originated from numerous cortical vesicles perhaps intercommunicating with each others, are observed early in the ooplasm during oogenesis, These so-called ring-shaped granules seem very identical in form with the disc-shaped granules which are classically described as composing the endogenous or intracysternal yolk of many Decapoda crustacean oocytes. In view of our results the role of these granules, in endogenous yolk formation, is re-examined and discussed.     

Progress in deciphering the information content of the ‘glycome’ – a crescendo in the closing years of the millennium

The closing years of the second millennium have been uplifting for carbohydrate biology. Optimism that oligosaccharide sequences are bearers of crucial biological information has been borne out by the constellation of efforts of carbohydrate chemists, biochemists, immunochemists, and cell- and molecular biologists. The direct involvement of specific oligosaccharide sequences in protein targeting and folding, and in mechanisms of infection, inflammation and immunity is now unquestioned. With the emergence of families of proteins with carbohydrate-binding activities, assignments of information content for defined oligosaccharide sequences will become more common, but the pinpointing and elucidation of the bioactive domains on oligosaccharides will continue to pose challenges even to the most experienced carbohydrate biologists. The neoglycolipid technology incorporates some of the key requirements for this challenge: namely the resolution of complex glycan mixtures, and ligand binding coupled with sequence determination by mass spectrometry.     

Is the Reaction Catalyzed by 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase a Rate-Limiting Step for Isoprenoid Biosynthesis in Plants?

3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) catalyzes the irreversible conversion of 3-hydroxy-3-methylglutaryl coenzyme A to mevalonate and is considered a key regulatory step controlling isoprenoid metabolism in mammals and fungi. The rate-limiting nature of this enzyme for isoprenoid biosynthesis in plants remains controversial. To investigate whether HMGR activity could be limiting in plants, we introduced a constitutively expressing hamster HMGR gene into tabacco (Nicotiana tabaccum L.) plants to obtain unregulated HMGR activity. The impact of the resulting enzyme activity on the biosynthesis and accumulation of particular isoprenoids was evaluated. Expression of the hamster HMGR gene led to a 3- to 6-fold increase in the total HMGR enzyme activity. Total sterol accumulation was consequently increased 3- to 10-fold, whereas end-product sterols such as sitosterol, campesterol, and stigmasterol were increased only 2-fold. The level of cycloartenol, a sterol biosynthetic intermediate, was increased more than 100-fold. Although the synthesis of total sterols appears to be limited normally by HMGR activity, these results indicate that the activity of one or more later enzyme(s) in the pathway must also be involved in determining the relative accumulation of end-product sterols. The levels of other isoprenoids such as carotenoids, phytol chain of chlorophyll, and sesquiterpene phytoalexins were relatively unaltered in the transgenic plants. It appears from these results that compartmentation, channeling, or other rate-determining enzymes operate to control the accumulation of these other isoprenoid end products.     

Does Decrease in Ribulose-1,5-Bisphosphate Carboxylase by Antisense RbcS Lead to a Higher N-Use Efficiency of Photosynthesis under Conditions of Saturating CO2 and Light in Rice Plants?

Rice (Oryza sativa L.) plants with decreased ribulose-1,5-bisphosphate carboxylase (Rubisco) were obtained by transformation with the rice rbcS antisense gene under the control of the rice rbcS promoter. The primary transformants were screened for the Rubisco to leaf N ratio, and the transformant with 65% wild-type Rubisco was selected as a plant set with optimal Rubisco content at saturating CO2 partial pressures for photosynthesis under conditions of high irradiance and 25[deg]C. This optimal Rubisco content was estimated from the amounts and kinetic constants of Rubisco and the gas-exchange data. The R1 selfed progeny of the selected transformant were grown hydroponically with different N concentrations. Rubisco content in the R1 population was distributed into two groups: 56 plants had about 65% wild-type Rubisco, whereas 23 plants were very similar to the wild type. Although the plants with decreased Rubisco showed 20% lower rates of light-saturated photosynthesis in normal air (36 Pa CO2), they had 5 to 15% higher rates of photosynthesis in elevated partial pressures of CO2, (100-115 Pa CO2) than the wild-type plants for a given leaf N content. We conclude that the rice plants with 65% wild-type Rubisco show a higher N-use efficiency of photosynthesis under conditions of saturating CO2 and high irradiance.