NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution

d[G4(T4G4)3] has been folded into a unimolecular G-quadruplex in the presence of 15NH4+ ions. NMR spectroscopy confirmed that its topology is the same as the solution state structure determined earlier by Wang and Patel (J. Mol. Biol., 1995; 251: 76-94) in the presence of Na+ ions. The d[G4(T4G4)3] G-quadruplex exhibits four G-quartets with three 15NH4+-ion-binding sites (O1, I and O2). Quantitative analysis utilizing 15NH4+ ions as a NMR probe clearly demonstrates that there is no unidirectional 15NH4+ ion movement through the central cavity of the G-quadruplex. 15NH4+ ions move back and forth between the binding sites within the G-quadruplex and exchange with ions in bulk solution. 15NH4+ ion movement is controlled by the thermodynamic preferences of individual binding sites, steric restraints of the G-quartets for 15NH4+ ion passage and diagonal versus edge-type arrangement of the T4 loops. The movement of 15NH4+ ions from the interior of the G-quadruplex to bulk solution is faster than exchange within the G-quadruplex. The structural details of the G-quadruplex define stiffness of individual G-quartets that intimately affects 15NH4+ ion movement. The stiffness of G-quartets and steric hindrance imposed by thymine residues in the loops contribute to the 5-fold difference in the exchange rate constants through the outer G-quartets.     

A self-stabilized model of the chymotrypsin catalytic pocket. The energy profile of the overall catalytic cycle

A model of the catalytic triad of chymotrypsin is built assuring the arrangement and properties as they are within the complete enzyme. The model contains 18 amino acid residues of chymotrypsin and its substrate. A total of 135 atoms (including 70 heavy atoms) were subjected to full ab initio geometry optimizations through 127 individual steps along the reaction coordinate of the complete catalytic mechanism. It was shown that the described model of the catalytic apparatus forms a self-stabilized molecule ensemble without the rest of the enzyme and substrate. According to the calculations, the formations of the first and second tetrahedral intermediates in the model have 20.3 and 15.7 kcal/mol activation energy barriers, respectively. Removing elements of the catalytic apparatus such as the (1) catalytic aspartate or (2) the anion hole, as well as (3) inserting a water molecule "early" in the catalytic process, or (4) introducing conformational rigidity of the substrate, results in an increase of the above energy barrier of the first catalytic step in the model by 6.4, 13.7, 3.7, and 4.1 kcal/mol, respectively. Based on the calculated process one can conclude that the catalytic reaction in this model is much more similar to the reaction in the enzyme than to the reference reaction. To our knowledge, this is the first model system that mimics the complete catalytic mechanism.     

Feeding enhances photosynthetic efficiency in the carnivorous pitcher plant Nepenthes talangensis

Background and Aims

Cost–benefit models predict that carnivory can increase the rate of photosynthesis (A_N) by leaves of carnivorous plants as a result of increased nitrogen absorption from prey. However, the cost of carnivory includes decreased A_N and increased respiration rates (R_D) of trapping organs. The principal aim of the present study was to assess the costs and benefits of carnivory in the pitcher plant Nepenthes talangensis, leaves of which are composed of a lamina and a pitcher trap, in response to feeding with beetle larvae.

Methods

Pitchers of Nepenthes grown at 200 µmol m⁻² s⁻¹ photosynthetically active radiation (PAR) were fed with insect larvae for 2 months, and the effects on the photosynthetic processes were then assessed by simultaneous measurements of gas exchange and chlorophyll fluorescence of laminae and pitchers, which were correlated with nitrogen, carbon and total chlorophyll concentrations.

Key Results

A_N and maximum (F_v/F_m) and effective quantum yield of photosystem II (Φ_PSII) were greater in the fed than unfed laminae but not in the fed compared with unfed pitchers. Respiration rate was not significantly affected in fed compared with unfed plants. The unfed plants had greater non-photochemical quenching (NPQ) of chlorophyll fluorescence. Higher NPQ in unfed lamina did not compensate for their lower Φ_PSII, resulting in lower photochemical quenching (QP) and thus higher excitation pressure on PSII. Biomass and nitrogen and chlorophyll concentration also increased as a result of feeding. The cost of carnivory was shown by lower A_N and Φ_PSII in pitchers than in laminae, but R_D depended on whether it was expressed on a dry weight or a surface area basis. Correlation between nitrogen and A_N in the pitchers was not found. Cost–benefit analysis showed a large beneficial effect on photosynthesis from feeding as light intensity increased from 200 to 1000 µmol m⁻² s⁻¹ PAR after which it did not increase further. All fed plants began to flower.

Conclusion

Feeding pitchers with insect larvae increases A_N of leaf laminae, due to higher nutrient acquisition, with strong correlation with nitrogen concentration, but A_N of pitchers does not increase, despite increased nitrogen concentration in their tissue. Increased A_N improves growth and reproduction and is likely to increase the competitive advantage of carnivorous over non-carnivorous plants in nutrient-poor habitats.Key words: carnivorous plants, chlorophyll fluorescence, Nepenthes talangensis, nitrogen, pitcher plant, photosynthetic rate, photosystem II, respiration rate     

The role of cytokinins in shoot organogenesis in apple

Effective regeneration in vitro is a necessary precondition for the implementation of different biotechnological approaches in plant breeding. Numerous studies have reported on regeneration from apple somatic tissues, and organogenesis has been proved to be influenced by several factors including mother shoots (genotype, size, type, and age of explant), in vitro conditions (dark period, light intensity, and quality), and others (wounding, orientation of leaf explants). However, one of the most important factors before and during the regeneration process is the type and concentration of cytokinin applied. Thidiazuron and benzyladenine are the most frequently used cytokinins in the regeneration systems, but their efficiency depends on genotype and other factors. Other cytokinins (e.g., zeatin and kinetin) have also been tested in several experiments and they were found in general to be less active. The organogenic ability of explants can also be increased by a properly selected cytokinin pre-treatment. Cytokinins applied in the pre-treatments can influence the leaf structure, which in turn can alter the regeneration capacity of the leaf explant. Interactions between factors of pre-treatments (hormones, light, and culture conditions) and factors of the regeneration phase should be considered. This review brings into focus the role of different cytokinins during in vitro shoot development, discussing their effects on the histology of leaves developed in vitro, and how this affects the subsequent regeneration process.     

Trap closure and prey retention in Venus flytrap (Dionaea muscipula) temporarily reduces photosynthesis and stimulates respiration

Background and Aims

The carnivorous plant Venus flytrap (Dionaea muscipula) produces a rosette of leaves: each leaf is divided into a lower part called the lamina and an upper part, the trap, with sensory trigger hairs on the adaxial surface. The trap catches prey by very rapid closure, within a fraction of a second of the trigger hairs being touched twice. Generation of action potentials plays an important role in closure. Because electrical signals are involved in reduction of the photosynthetic rate in different plant species, we hypothesized that trap closure and subsequent movement of prey in the trap will result in transient downregulation of photosynthesis, thus representing the energetic costs of carnivory associated with an active trapping mechanism, which has not been previously described.

Methods

Traps were enclosed in a gas exchange cuvette and the trigger hairs irritated with thin wire, thus simulating insect capture and retention. Respiration rate was measured in darkness (R_D). In the light, net photosynthetic rate (A_N), stomatal conductance (g_s) and intercellular CO₂ concentration (c_i) were measured, combined with chlorophyll fluorescence imaging. Responses were monitored in the lamina and trap separately.

Key Results

Irritation of trigger hairs resulted in decreased A_N and increased R_D, not only immediately after trap closure but also during the subsequent period when prey retention was simulated in the closed trap. Stomatal conductance remained stable, indicating no stomatal limitation of A_N, so c_i increased. At the same time, the effective quantum yield of photosystem II (Φ_PSII) decreased transiently. The response was confined mainly to the digestive zone of the trap and was not observed in the lamina. Stopping mechanical irritation resulted in recovery of A_N, R_D and Φ_PSII.

Conclusions

We put forward the first experimental evidence for energetic demands and carbon costs during insect trapping and retention in carnivorous plants, providing a new insight into the cost/benefit model of carnivory.     

The Microtubule-Associated Protein CLASP Sustains Cell Proliferation through a Brassinosteroid Signaling Negative Feedback Loop

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Complete disproportionation of duplex poly(dT)*poly(dA) into triplex poly(dT)*poly(dA)*poly(dT) and poly(dA) by coralyne

Coralyne is a small crescent-shaped molecule known to intercalate duplex and triplex DNA. We report that coralyne can cause the complete and irreversible disproportionation of duplex poly(dT)·poly(dA). That is, coralyne causes the strands of duplex poly(dT)·poly(dA) to repartition into equal molar equivalents of triplex poly(dT)·poly(dA)·poly(dT) and poly(dA). Poly(dT)·poly(dA) will remain as a duplex for months after the addition of coralyne, if the sample is maintained at 4°C. However, disproportionation readily occurs upon heating above 35°C and is not reversed by subsequent cooling. A titration of poly(dT)·poly(dA) with coralyne reveals that disproportionation is favored by as little as one molar equivalent of coralyne per eight base pairs of initial duplex. We have also found that poly(dA) forms a self-structure in the presence of coralyne with a melting temperature of 47°C, for the conditions of our study. This poly(dA) self-structure binds coralyne with an affinity that is comparable with that of triplex poly(dT)·poly(dA)·poly(dT). A Job plot analysis reveals that the maximum level of poly(dA) self-structure intercalation is 0.25 coralyne molecules per adenine base. This conforms to the nearest neighbor exclusion principle for a poly(dA) duplex structure with A·A base pairs. We propose that duplex disproportionation by coralyne is promoted by both the triplex and the poly(dA) self-structure having binding constants for coralyne that are greater than that of duplex poly(dT)·poly(dA).     

Reversibility and interaction with hepatic regeneration of toluene induced liver injury.

Acute and subacute toluene poisoning was induced in CFY rats. Routine histological, enzyme histochemical and electron microscopic investigations revealed that following discontinuation of exposure, the hepatic changes indicating an enhanced load on the detoxicating function (increased SDH activity, increase of mitochondria and smooth endoplasmic reticulum, decrease in Best carmine staining and PAS positivity) as well as degeneration (dilation of endoplasmic reticulum, accumulation positivity) as well as degeneration (dilation of endoplasmic reticulum, accumulation of autophagous vacuoles) show a rapid regression. The toxic effect of toluene and the functional load on the liver is thus reversible. In another series, toluene exposure was combined with partial hepatectomy. It has been established by routine histological, enzyme histochemical and electron microscopic techniques as well as by quantitative light and electron microscopic methods that the two interventions show a peculiar interaction: hepatic regeneration following partial hepatectomy inhibited the effect of toluene. On the other hand, the rate of regeneration was not influenced by toluene.     

The relation between the synergistic effect of cytostatics and metabolism of V 79B cells in vitro.

A single-dose simultaneous application of methotrexate (MTX; 0.002/microgram ml-1) and cisplatin (cis-Pt; 0.0002/microgram ml-1) had a permanent synergistic effect on both synchronized and asynchronous cell populations of V 79B cells. Successive combination of the drugs was manifested synergistically when MTX was applied first. The synchronized cell population was more sensitive to the cytostatics than the asynchronous population. Treatment with MTX alone, or the combination of MTX-cis-Pt, as well as their successive combination with the first drug being cis-Pt, caused gluconeogenesis.