Trivaline Molecular Complexes with Trinucleotides Form in Solution the Extended,about 1000 Å in Length Structures

Abstract

The fluorescence, flow linear dichroism and electron microscopy (EM) have shown the trivaline ability to interact in solution with certain molecules of trinucleotides. This interaction results in formation of extended structures up to several. thousand angstroms in length. Such structures were observed for trivaline complexes with homopurine, homopyrimidine or random sequences of deoxyribo- and ribonucleotides, independently of the presence or absence of the terminal 5′-phosphate residue. A model of such a structural organization is proposed. An elementary structural unit consists of a trivaline β-dimer and adsorbed trinucleotide. So, “dimeric” complex is formed. Two such “dimeric” complexes combine with each other by means of peptide-peptide contacts (as with β-sandwich). So, “tetrameric” complex is formed It has a dyad axis. Two such structural units combine with each other by means of Hoogsteen's hydrogen bonds. So, “octamreic” complex is formed. It has three mutually perpendicular dyad axes. The “octameric” complexes appear to be able to combine with each other by means of stacking interactions, and to form the regular organized aggregates consisting of many dozens of elementary units. So, “stacking” structure is formed. The “octameric” complex is the symmetry translational unit of such a stucture. The spatial position of the bases in all these structures is additionally fixed by the nucleo-peptide interactions. These aggregates have the appearance of extended structures on electron micrographs.     

Modeling Critical Infrastructure Interdependency: The Case of the Mexico City Metro Transport System

ABSTRACT

“Critical infrastructures” are exceedingly complex and highly interconnected. In order to gain a full understanding and comprehensive awareness of the risks associated with critical infrastructures it becomes essential to consider in a coherent way all the aspects that may cause a failure of such systems. That is, there is a need for a systemic approach to interdependencies among critical infrastructures. The article presents the application of a systemic safety management system (SSMS) model to interdependency modeling for the case of the Mexico City Metro transport network. The model has highlighted that interdependencies occur vertically and horizontally. Horizontal interdependency occurs at every level of recursion and can be: operational, managerial, and environmental. Vertical interdependency, on the other hand, occurs between two levels of recursion only. The SSMS model has shown the potential to be used to model interdependencies among critical infrastructures. It is hoped that the approach presented may help to gain a better understanding of critical infrastructure interdependency.     

Binding Studies of Eukaryotic Initiation Factor eIF4E with Novel mRNA Dinucleotide Cap Analogues

Abstract

Studies on the interaction of the murine translation initiation factor 4E with two new-synthesized cap-analogues, modified at C2′ of 7-methylguanosine, have been performed by means of the fluorescence titration method. No difference in the binding affinity for eIF4E was observed compared with the “anti reversed” cap analogues, possessing the analogous modifications at C3′. Potential significance of the novel caps as research tools for examination of the nuclear cap binding complex CBC80/20 has been discussed.     

Studies on the electrogenic action of acetylcholine with Torpedo marmorata electric organ: V. Qualitative correlation between pharmacological effects and equilibration processes of the cholinergic receptor protein as revealed by the structural probe quinacrine

When the differential fluorescence emission at 515 nm of receptor-rich membrane fragments from Torpedo marmorata labelled with quinacrine is followed by energy transfer, addition of a high concentration of an agonist such as 0.4 mm-carbamylcholine or 0.4 mm-phenyltrimethylammonium causes a fast (unresolved) increase of fluorescence intensity followed by a slow (minute range) decrease, which leads to a final stable level. On the other hand, a stepwise addition of agonist at low concentrations gives only a slow fluorescence increase. Antagonists, such as flaxedil and d-tubocurarine, at all the concentrations tested, bring about exclusively slow fluorescence increases. Decamethonium at 0.4 mm gives no slow reaction but only a fast (unresolved) increase without transient overshoot.Addition of a local anaesthetic reduces the amplitude of the fluorescence response to carbamylcholine. The α-toxin from Naja nigricollis does not cause any change of fluorescence intensity but blocks the effect of the cholinergic agonists and antagonists.Dissolution of the membrane fragments by a non-ionic detergent abolishes the fast transient reaction triggered by the agonists but preserves the slow ones observed in the presence of agonists or antagonists. The data are interpreted in terms of a three-state model, a revised version of the model of Katz & Thesleff (1957): the fast transient reaction brought about by the agonists being assigned to the “activation” of the receptor-ionophore complex and the slow one to its “desensitization”.     

The Hoechst 33258 covalent dimer covers a total turn of the double-stranded DNA

With the goal to design ligands recognizing extended regions on dsDNA, a covalent dimer of the fluorescent dye Hoechst 33258 [bis-HT(NMe)] composed of two dye molecules linked via the phenol oxygen atoms with a (CH2)3-N+ H(CH3)-(CH2)3 fragment was constructed using computer modeling and then synthesized. Its interactions with the double-stranded DNA (dsDNA) were studied by fluorescent and UV-Vis spectroscopy and circular (CD) and linear dichroism (LD). Based on variations in the affinity to the dsDNA, it was shown that complexes of three types are formed. The first type complexes result from binding of a bis-HT(NMe) monomer in the open conformation; in this case the ligand covers the total dsDNA turn and is located in the minor groove according to the positive value of CD at 370 nm. In addition, the ability to form bis-HT(NMe)-bridges between two dsDNA molecules, i.e., each of the two bis-HT(NMe) ends binds to two different dsDNA molecules, was demonstrated for the first type complexes. Spectral characteristics (maximal absorption at 362 nm, positive sign, and maximal value of CD at 370 nm) of the first type complexes conform to those of the specific Hoechst 33258 complex with poly[d(A-T)] x poly[d(A-T]. The second type complexes correspond to the bis-HT(NMe) sandwich (as an inter- or intramolecular) binding to dsDNA with stoichiometry > or = 5 bp. Thereby, a negative LD at 360 nm and the location of bis-HT(NMe) sandwiches in the minor groove of B form dsDNA seems contradictory. Spectral characteristics (maximal positive CD at 345 nm, a dramatic decrease in fluorescence intensity and the shift of its maximum to 490 nm) of these complexes favor a suggestion that this binding correlates to the formation of nonspecific dimeric Hoechst 33258 complex with dsDNA. The third type complexes are characterized by stoichiometry of one bis-HT(NMe) molecule per approximately 2 bp and the tendency to zero of LD values at 270 and 360 nm. We assume that in these complexes bis-HT(NMe) sandwich dimers are formed on dsDNA. The complexes of this type conform to the aggregation type complex of Hoechst 33258 with dsDNA. The ability of bis-HT(NMe) to cover the whole dsDNA turn or form bridges with two dsDNA upon the formation of the first type complexes essentially distinguishes it from Hoechst 33258, which can only occupy 5 bp and does not form such bridges. This specific property of bis-HT(NMe) may support new biological activities.     

Cation-Mediated Interplay of Loops in Chaperonin-10

Abstract

The ubiquitously occurring chaperonins consist of a large tetradecameric Chaperonin-60, forming a cylindrical assembly, and a smaller heptameric Chaperonin-10. For a functional protein folding cycle, Chaperonin-10 caps the cylindrical Chaperonin-60 from one end forming an asymmetric complex. The oligomeric assembly of Chaperonin-10 is known to be highly plastic in nature. In Mycobacterium tuberculosis, the plasticity has been shown to be modulated by reversible binding of divalent cations. Binding of cations confers rigidity to the metal binding loop, and also promotes stability of the oligomeric structure. We have probed the conformational effects of cation binding on the Chaperonin-10 structure through fluorescence studies and molecular dynamics simulations. Fluorescence studies show that cation binding induces reduced exposure and flexibility of the dome loop. The simulations corroborate these results and further indicate a complex landscape of correlated motions between different parts of the molecule. They also show a fascinating interplay between two distantly spaced loops, the metal binding “dome loop” and the GroEL-binding “mobile loop”, suggesting an important cation-mediated role in the recognition of Chaperonin-60. In the presence of cations the mobile loop appears poised to dock onto the Chaperonin-60 structure. The divalent metal ions may thus act as key elements in the protein folding cycle, and trigger a conformational switch for molecular recognition.     

Evidence for an endogenous circannual component in the control of the annual gonadal cycle in spotted munia

Abstract

For the first time evidence has been provided for a circannual gonadal cycle in any avian species (male spotted munia Lonchura punctulata, Estrildidae) held on continuous light. A model has thus been rendered available in which the “entraining effects” of photoperiod could be clearly distinguished from its direct “driving effects”.     

Comparison of heavy metal accumulation and cadmium phytoextraction rates among ten leading tobacco (Nicotiana tabacum L.) cultivars in China

Abstract

Cadmium (Cd) contamination is one of the most serious global environmental problems, and phytoremediation, which uses Cd-accumulator plants, is potentially one of the sustainable solutions. Pot experiments with natural and Cd-amended soils were conducted to investigate the accumulation of heavy metals in 10 leading cultivars of tobacco in China. The extraction ability and profiles of Cd accumulation among plant organs were also analyzed. The tobacco roots accumulated cobalt, nickel, and Cd, while the leaf highly bioaccumulated Cd and lowly accumulated zinc, selenium and mercury. The transport from the tobacco stem to the leaf plays a critical role in the accumulation of these elements. The ratios of Cd concentration in the leaves at lower, middle and upper positions were comparatively stable. The high Cd-extracting cultivars were “Hongda”, “NC89” and “Zhongyan 100” when grown in normal soils, “CuiBi 1” and “Hongda” in moderately contaminated soils, and “YuYan 87”, “LongJiang 851” and “K326” in severely contaminated soils. Tobacco leaves could accumulate about 80% of the total Cd extracted from the soil by the plant. Considering the Cd-extraction limitations exhibited by leading tobacco cultivars, screening of germplasm resources for high or low levels of Cd-accumulation is still an important target for the future.     

Neutron Diffraction of Alpha,Beta and Gamma Cyclodextrins: Hydrogen Bonding Patterns

Abstract

Cyclodextrins (CD's) have proved useful as model systems for the study of hydrogen bonding. They are torus-shaped molecules composed of six(α), seven (β) or eight(γ) (1?4) linked glucoses. Because of their particular geometry, they are able to act as a “host” to form inclusion complexes with “guest” molecules very much like enzymes. Cyclodextrins have been shown to exert catalytic activity on suitable included-substrate molecules; they catalyze the hydrolysis of phenylacetates, of organic pyrophosphates and of penicillin derivatives. They also accelerate aromatic chlorinations and diazo coupling by means of their primary and/or secondary hydroxyl groups, so that the rates of hydrolysis are enhanced by up to a factor of 400. In order to understand the hydrogen bonding in these enzyme models, neutron diffraction data were collected to unambiguously determine the hydrogen atom positions, which could not be done from the x-ray diffraction data. α-CD has been shown to have two different structures with well-defined hydrogen bonds, one “tense” and the other “relaxed”. An “induced-fit”-like mechanism for α-CD complex formation has been proposed. Circular hydrogen bond networks have also been found for α-CD due to the energetically favored cooperative effect. β-CD with a disordered water structure possesses an unusual flip-flop hydrogen bonding system of the type O-H…H-O representing an equilibrium between two states: O-H…O?O…O. γ-CD with a disordered water structure similar to β-CD also possesses the flip-flop hydrogen bond. This study demonstrates that hydrogen bonds are operative in disordered systems and display dynamics even in the solid state.     

A Neutron Scattering Study of the Ternary Complex EF-Tu•GTP-valy1-tRNAVal 1A

Abstract

The complex formation between elongation factor Tu (EF-Tu), GTP, and valyl-tRNA^Val _1A has been investigated in a hepes buffer of “pH” 7.4 and 0.2 M ionic strength using the small-angle neutron scattering method at concentrations of D₂O where EF-Tu (42% D₂O) and tRNA (71% D₂O) are successively matched by the solvents. The results indicate that EF-Tu undergoes a conformational change and contracts as a result of the complex formation, since the radius of gyration decreases by 15% from 2.82 to 2.39 nm. tRNA^Val _1A, on the other hand, seems to mainly retain its conformation within the complex, since the radii of gyration for the free (after correction for interparticular scattering) and complexed form are essentially the same. 2.38 and 2.47 nm, respectively.     

Relevance of attributional and consequential information for environmental product labelling

Purpose

Considering the general agreement in the literature that environmental labelling should be based on consequential modelling, while all actually implemented environmental labelling schemes are based on attributional modelling, we investigate the arguments for this situation as provided in the literature, and whether a dual label, representing on the same label the attributional and consequential results for the same product, can be a relevant solution or at least contribute to a more informed discussion.

Methods

We developed a dual label for three hypothetical, comparable products and presented this for a small test audience, asking three questions, namely “Which product would you choose?”, “Was the attributional information useful?” and “Would you accept to have only the attributional information?”

Results and discussion

From this small pilot exercise, it appears that informed consumers may have a strong preference for consequential information and that the main problem in communicating consequential results is that they are perceived as less trustworthy and more uncertain due to the fact that the consequences are located in the future. It thus appears important to build into a consequential label some increased level of guarantee of future good behaviour.

Conclusions

We propose to apply the above questions to a more statistically representative audience to confirm or refute the findings of this little test exercise.

     

The use of steady-state treatment in the rapid kinetics of horse liver alcohol dehydrogenase. The effect of addition of product on the "burst" reaction.

The effect of addition of product on the amplitude of the “burst” reaction of horse liver alcohol dehydrogenase was studied using a stopped-flow spectrophotofluorimeter. The amplitude of the “burst” formation of enzyme-bound NADH fluorescence was completely diminished by the addition of excess acetaldehyde or benzaldehyde in the reaction with NAD⁺ and ethanol or NAD⁺ and benzylalcohol, respectively. The results indicate that a significant concentration of the ternary enzyme-coenzyme-substrate complex was formed during the steady-state in the presence of product, and this ternary complex did not exhibit NADH fluorescence. The dissociation constants for the ternary complex were determined from the amplitudes of the “burst” reactions. The “active site” titration of the enzyme with NAD⁺ in the presence of ethanol and iso-butyramide is also described.     

DNA Quadruplexes Assembled by Simple Peptide: Effects of DNA Homology and Peptide Removal

Abstract

Formation of heterologous (calf thymus dsDNA) and homologous (linearized pBR322 plasmid dsDNA) quadruplexes upon binding with the simple aliphatic tripeptide derivative (L- Val)₃?N₂H₂?DNS CF₃COOH—;DHTV) was examined by fluorimetry, flow linear (LD), circular dichroism (CD), and electron microscopy (EM). The morphology of the rod-like compact particles formed due to the association of dsDNA segments proved to be the same for both DNAs, whereas the stability of the compact DNA structure upon tripeptide removal from the complex with DNA differed substantially for homologous versus non-homologous dsDNA used. The increase in NaCl concentration in the solution up to 30 mM removes the peptide from both types of the complexes completely. At the same time at 20 mM NaCl calf thymus DNA quadruplexes readily dissociate, whereas the structures formed by plasmid DNA retain their morphology in the solution containing NaCl with concentrations up to 40 mM and are only partially disrupted at even higher NaCl concentration. These results provide an analogy between trivaline-DNA model complexes and RecA-DNA binding.     

Ricerche Sulla Flora Infestante Delle Culture in Italia

Summary

Studies on the weeds of cultivated land in italy

I. - bibliographical and methodological introduction

In the 1rst part of this paper the Author outlines the weed problem, discusses the meaning of the term “weed”, agrees with Korsmo (1930) in considering weeds as constituing a biological group characterised by certain adaptments to life.

After a short survey of the chief European and American books on weeds, he gives a more detailed account of the Italian literature which is not, the Author thinks, very rich on this subject.

In the 2nd part the Author discusses several aspects and some methodological questions of the study of weeds.

After dealing briefly with the floristic and quantitative analysis of weed floras, he goes on to outline the problem concerning the origin of the weed species of a given district; these can be considered as belonging to two main groups: local species which were present in that station before the soil was tilled, and exotic species introduced, often unwillingly, by man through his commercial and industrial activities. The line between the two groups is hard to draw, especially in countries of ancient civilization ad extensively cultivated, where in very few places the local flora has been left undisturbed. It is perhaps easier to distinguish the two main groups of species according to their geographic area of distribution and to the type of stations preferred within that area.

The study of weeds dissemination is strictly connected with the one of their origin.

The next main field of study is the ecological one: having shown the main ecological effects of agricultural technique, which also acts as a levelling agent for the vegetation of the earth, the Author agrees with E. P. Evans (1928) in stating that it is not easy “to draw any but very general conclusions” owing to the undeterminate and variable nature of the human biotic factors, which, together with natural ones, control weed growth. A great amount of research has been carried out on ecological problems a swell as sinecological and mainly agricultural ones concerning weeds. Examples are given, with reference to several Authors.

Lastly the Author stresses the importance of the biological study of weeds and describes at length the biological classification employed by Korsmo (1930), who devides weeds in three main groups, namely: “seed”, “stationary”, and “wandering” plants.

The bibliography is meant to give an useful list of references for the student, but is far from being complete, except as far as Italian literature is concerned.     

The fluorescence lifetime and quantum yield of chlorophyll a in Triton X-100 solutions

The fluorescence of chlorophyll (Chl) a in 0.007–0.1% Triton X-100 was investigated by a phase-shift technique. The Chl a concentrations varied from 0.7 to 25 μM. Parallel measurements of fluorescence lifetime (τ) and quantum yield (ψ) were made. It was concluded that homogeneous energy transfer takes place at detergent concentrations above 0.025%: (i) the transfer between uniform molecules of the pigment solubilized in Triton X-100 micelles, when τ and ψ are constant; (ii) the transfer towards the quenching centers, resulting in a proportional decrease in τ and ψ. At a Triton X-100 concentration of about 0.025% the Chl a emission becomes heterogeneous. It is evident from the disproportional decrease in τ and ψ (greater in ψ than in τ) and also from the rise of the fluorescence at 730–750 nm. As the Triton X-100 concentration becomes lower than the critical one (0.021%), the number of micelles drops abruptly and Chl a forms colloid particles in the aqueous medium. This manifests itself as a decrease in τ and as a certain stabilization of ψ. Having analyzed the complex pattern of the τ/ψ ratio, we concluded that under these conditions more than 90% of Chl a is in a weakly fluorescent form (τ < 30 ps) and about 1% is in an aggregated state fluorescing at 732 nm with τ about 0.7 ns.     

Mixed Mode of Ligand-DNA Binding Results in S-Shaped Binding Curves

Abstract

S-shaped binding curves often characterize interactions of ligands with nucleic acid molecules as analyzed by different physicochemical and biophysical techniques. S-shaped experimental binding curves are usually interpreted as indicative of the positive cooperative interactions between the bound ligand molecules. This paper demonstrates that S-shaped binding curves may occur as a result of the “mixed mode” of DNA binding by the same ligand molecule. Mixed mode of the ligand-DNA binding can occur, for example, due to 1) isomerization or dimerization of the ligands in solution or on the DNA lattice, 2) their ability to intercalate the DNA and to bind it within the minor groove in different orientations. DNA- ligand complexes are characterized by the length of the ligand binding site on the DNA lattice (so-called “multiple-contact” model). We show here that if two or more complexes with different lengths of the ligand binding sites could be produced by the same ligand, the dependence of the concentration of the complex with the shorter length of binding site on the total concentration of ligand should be S-shaped. Our theoretical model is confirmed by comparison of the calculated and experimental CD binding curves for bis-netropsin binding to poly(dA-dT) poly(dA-dT). Bis-netropsin forms two types of DNA complexes due to its ability to interact with the DNA as monomers and trimers. Experimental S-shaped bis-netropsin-DNA binding curve is shown to be in good correlation with those calculated on the basis of our theoretical model. The present work provides new insight into the analysis of ligand-DNA binding curves.     

Cyclopropane-1,2-dicarboxylic acids as new tools for the biophysical investigation of O-acetylserine sulfhydrylases by fluorimetric methods and saturation transfer difference (STD) NMR

Abstract

Cysteine is a building block for many biomolecules that are crucial for living organisms. O-Acetylserine sulfhydrylase (OASS), present in bacteria and plants but absent in mammals, catalyzes the last step of cysteine biosynthesis. This enzyme has been deeply investigated because, beside the biosynthesis of cysteine, it exerts a series of “moonlighting” activities in bacteria. We have previously reported a series of molecules capable of inhibiting Salmonella typhimurium (S. typhymurium) OASS isoforms at nanomolar concentrations, using a combination of computational and spectroscopic approaches. The cyclopropane-1,2-dicarboxylic acids presented herein provide further insights into the binding mode of small molecules to OASS enzymes. Saturation transfer difference NMR (STD-NMR) was used to characterize the molecule/enzyme interactions for both OASS-A and B. Most of the compounds induce a several fold increase in fluorescence emission of the pyridoxal 5′-phosphate (PLP) coenzyme upon binding to either OASS-A or OASS-B, making these compounds excellent tools for the development of competition-binding experiments.     

High-sensitivity two-color detection of double-stranded DNA with a confocal fluorescence gel scanner using ethidium homodimer and thiazole orange.

Ethidium homodimer (EthD; lambda Fmax 620 nm) at EthD:DNA ratios up to 1 dye:4-5 bp forms stable fluorescent complexes with double-stranded DNA (dsDNA) which can be detected with high sensitivity using a confocal fluorescence gel scanner (Glazer, A.N., Peck, K. & Mathies, R.A. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 3851-3855). However, on incubation with unlabeled DNA partial migration of EthD takes place from its complex with dsDNA to the unlabeled DNA. It is shown here that this migration is dependent on the fractional occupancy of intercalating sites in the original dsDNA-EthD complex and that there is no detectable transfer from dsDNA-EthD complexes formed at 50 bp: 1 dye. The monointercalator thiazole orange (TO; lambda Fmax 530 nm) forms readily dissociable complexes with dsDNA with a large fluorescence enhancement on binding (Lee, L.G., Chen, C. & Liu, L.A. (1986) Cytometry 7, 508-517). However, a large molar excess of TO does not displace EthD from its complex with dsDNA. When TO and EthD are bound to the same dsDNA molecule, excitation of TO leads to efficient energy transfer from TO to EthD. This observation shows the practicability of 'sensitizing' EthD fluorescence with a second intercalating dye having a very high absorption coefficient and efficient energy transfer characteristics. Electrophoresis on agarose gels, with TO in the buffer, of preformed linearized M13mp18 DNA-EthD complex together with unlabeled linearized pBR322 permits sensitive fluorescence detection in the same lane of pBR322 DNA-TO complex at 530 nm and of M13mp18 DNA-EthD complex at 620 nm. These observations lay the groundwork for the use of stable DNA-dye intercalation complexes carrying hundreds of chromophores in two-color applications such as the physical mapping of chromosomes.