Index to Authors,Volume 6

Abstract

The refractive indices of wet-spun films of CsDNA have been measured for light polarized parallel and perpendicular to the helical axis as a function of relative humidity (RH). These data have been combined with previously published data (Biopolymers 30 (1990) 877–887) for the volume per base pair and water content as a function of RH in order to extract the optical polarizabilities. This work was motivated by the study of Weidlich et al. (Biopolymers 26 (1987) 439–453) who reported a ～35% increase at the A-to-B transition in the parallel and perpendicular polarizabilities of NaDNA. In contrast, a much smaller increase in the polarizabilities of CsDNA is found near the A-to-B transition: ～ 12% for the perpendicular direction and < 4% for the parallel direction.     

Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2

Abstract

The empirical conformational energy program for peptides (ECEPP2) and molecular mechanics (MM2) have been used for the simulation of the For-Gly-NH₂ backbone. I propose two different methods for the calculation of the polarization energy term: the polarization procedure by non-interacting induced dipoles (NID) which assumes scalar isotropic point polarizabilities and the polarization scheme by interacting induced dipoles (ID) which calculates tensor effective anisotropic point polarizabilities (method of Applequist). I present a comparative study of ECEPP2 and MM2 + polarization. I discuss molecular mechanics results including the total energy differences, partitional analyses of the total steric energies and torsion dihedral angles. The γ global and the α, β and Δ local minima are stabilized by intramolecular hydrogen bonds. Although ECEPP2-based calculations rather under or over-estimate the relative energy of some local minima, the ID polarization energy term represents a significant correction to the total relative energy.     

Bimolecular systems: II. Nonlinear systems of complexes

This paper deals with bimolecular systems in which also complex-complex interactions occur. Because of the complexity of the problem, an approximation in a form of coupled linear systems of complexes (Bull. Math. Biophysics,29, 1–16, 1967) is considered. Two types of couplings, serial and parallel, are studied. In the serial coupling the nonlinear system of complexes has the same behavior as its subsystems. An entity, initial sensitivity, has interesting properties: in serial coupling it is at most equal to the product and in parallel coupling, at most equal to the sum of partial initial sensitivities.     

A suggestion of a new approach to the theory of some biological periodicities

Previous studies of L. Danziger and G. Elmergreen (Bull. Math. Biophysics,16, 15–21, 1954;18, 1–13, 1956) of possible biochemical periodicities in organisms assumed non-linear biochemical interaction between different metabolites, because linear systems do not lead to undamped ocsillations. They treated homogeneous systems. Later N. Rashevsky generalized their results to a more realistic case where the non-homogeneity due to the histological structure is considered. (Some Medical Aspects of Mathematical Biology, Springfield, Illinois: Charles C. Thomas, Publisher, 1964;Bull. Math. Biophysics,29, 389–393, 1967.) As long as the histological structure remains constant, the existence of sustained periodicities requires the assumption of non-linearity of biochemical interactions. If, however, the secretions of an endocrine gland affect the histological structure of the target organ, notably as in the menstrual cycle, and if there is a feed-back, the equations become non-linear and may admit sustained periodic solutions even if the purely biochemical interactions are linear.     

Design,synthesis, spectral analysis and in vitro microbiological evaluation of 2-phenyl-3-(4,6-diarylpyrimidin-2-yl)thiazolidin-4-ones

A series of novel 2-phenyl-3-(4,6-diarylpyrimidin-2-yl)thiazolidin-4-ones 23-33 were synthesized, and studied for their in vitro antibacterial and antifungal activities against clinically isolated strains. Generally compounds possessing electron donating groups showed good antibacterial activity. Compound 31, which contain both electron withdrawing chloro and electron donating methyl groups showed potent activity against all the tested Gram positive and Gram negative bacterial strains whereas compounds 32 and 33 which contain electron donating methoxy functional group at the para position of the phenyl ring attached to pyrimidine ring showed promising activity against S.aureus, S.typhii and E.coli. Compounds 32 and 33, both containing electron withdrawing groups (-Cl, -F) showed excellent activities against all the tested A. flavus, Mucor, Rhizopus and M.gypsuem fungal strains. while against Mucor, compound 27 which contains an electron donating methyl group at the para position of the phenyl ring attached to pyrimidine ring showed promising activity. Also compound 31, which contains both electron withdrawing chloro and electron donating methyl groups showed potent activity against A. flavus and Rhizopus.     

Hydrogen bonding interactions in noradrenaline-DMSO complexes: DFT and QTAIM studies of structure,properties and topology

The hydrogen bonding interactions between noradrenaline (NA) and DMSO were studied with density functional theory (DFT) regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and the natural bond orbital (NBO) analyses were employed to elucidate the hydrogen bonding interaction characteristics in noradrenaline-DMSO complexes. The H-bonds involving the hydroxyls hydrogen in NA and the O atom in DMSO are dominant intermolecular H-bonds and are stronger than other H-bonds involving the methyl hydrogen of DMSO as a H-donor. The weak H-bonds also include a π H-bond which involves the benzene ring as a H-donor or H-acceptor. QTAIM identified the weak H-bonds formed between the methyl hydrogen of DMSO and the N atom in NA in some complexes (AB5, AB6 and AB7), which cannot be further confirmed by NBO and other methods, so there are probably no interactions between hydrogen and nitrogen atoms among these complexes. A good linear relationship between logarithmic electron density (lnρ _b ) at the bond critical point (BCP) and structural parameter (δR _H···Y) was found. The formations of new H-bonds in some complexes are helpful to strengthen the original intramolecular H-bond, this is attributed to the cooperativity of H-bonds in complexes and can be learned from the structure results and the NBO and QTAIM analyses. Analysis of various physically meaningful contributions arising from the energy decomposition procedures show that the orbital interactions of H-bond is predominant during the formation of the complex, moreover, both the hydrogen bonding interaction and the structural deformation are responsible for the stability of the complexes.     

Calcium wave propagation by calcium-induced calcium release: An unusual excitable system

We discuss in detail the behaviour of a model, proposed by Goldbeteret al. (1990.Proc. natn. Acad. Sci. 87, 1461–1465), for intracellular calcium wave propagation by calcium-induced calcium release, focusing our attention on excitability and the propagation of waves in one spatial dimension. The model with no diffusion behaves like a generic excitable system, and threshold behaviour, excitability and oscillations can be understood within this general framework. However, when diffusion is included, the model no longer behaves like a generic excitable system; the fast and slow variables are not distinct and previous results on excitable systems do not necessarily apply. We consider a piecewise linear simplification of the model, and construct travelling pulse and periodic plane wave solutions to the simplified model. The analogous behaviour in the full model is studied numerically. Goldbeter's model for calciuminduced calcium release is an excitable system of a type not previously studied in detail.     

Patterns of phylogenetic community structure of sand dune plant communities in the Yucatan Peninsula: the role of deterministic and stochastic processes in community assembly

ABSTRACT

Background: Tropical sand dunes are ideal systems for understanding drivers of community assembly as dunes are subject to both deterministic and stochastic processes. However, studies that evaluate the factors that mediate plant community assembly in these ecosystems are few.

Aims: We evaluated phylogenetic community structure to elucidate the role of deterministic and stochastic processes in mediating the assembly of plant communities along the north of the Yucatan Peninsula, Mexico.

Methods: We used plastid genetic markers to evaluate phylogenetic relationships in 16 sand-dune communities. To evaluate the role of climate in shaping plant community structure we carried out linear regressions between climatic variables and mean phylogenetic distance. We estimated the Net Relatedness Index and Nearest Taxon Index to identify ecological processes mediating community assembly.

Results: Observed phylogenetic structure was not different from random, suggesting that stochastic processes are the major determinants of community assembly. Climate was slightly correlated with phylogenetic diversity suggesting that abiotic environment plays a minimal role in community assembly.

Conclusions: Random assembly appears to be the primary factor structuring the studied sand dune plant communities. Environmental filters may represent a secondary factor contributing to the observed phylogenetic structure. Thus, both processes may act simultaneously to mediate the assembly of sand-dune plant communities.     

Complexes of graphene nanoribbons with porphyrins and metal-encapsulated C28 as molecular rectifiers: a theoretical study

The rectification properties of porphyrin–graphene nanoflake complexes and endohedral complexes of C28 fullerene with metal atoms have been studied using the fully ab initio method. D3 dispersion-corrected PBE/-def2-SVP model was used for the optimisations and the electronic energy evaluation. In porphyrin–graphene nanoflake complexes dispersion dominates, while in the endohedral complexes of C28 dispersion does not play an important role. All studied systems do rectify. In the case of fullerenes, the rectification is possible due to the reduction in the molecular symmetry of the fullerene caused by the interaction with electrodes and the endohedral complex formation. The origin of the rectification is the asymmetrical deformation of the electron density under direct and inverse voltages which creates different currents in opposite directions. It seems that peculiar geometry of Au-TPP-Cd/NF diode is responsible for its high rectification ratio. The Cd ion is notably out of the porphyrin plane making close contact with the neighbouring electrode, increasing the asymmetry of the diode compared to other TPP/NF complexes.     

奥奈达希瓦氏菌CctA介导周质甲基橙还原的电子传递机理

电活性微生物奥奈达希瓦氏菌的胞外电子传递（extracellular electron transfer,EET）在污染物降解、环境修复、生物电化学传感、能源利用等方面具有广泛的应用潜力;四血红素细胞色素CctA （small tetraheme cytochrome）是希瓦氏菌周质空间中最丰富的蛋白质之一,能够参与多种氧化还原过程,但目前对CctA在EET中的行为和机理认识仍然有限。【目的】研究阐明CctA蛋白在希瓦氏菌模式菌株MR-1周质空间以偶氮染料作为电子受体的EET中的作用,补充和拓展希瓦氏菌的厌氧呼吸产能机制。【方法】以周质还原型偶氮染料甲基橙（methyl orange,MO）作为电子受体,在mteal reduction （Mtr）蛋白缺失菌株Δmtr中研究MO的周质还原特点,并通过基因敲除和回补表达研究CctA蛋白在周质电子传递中的作用。【结果】在缺失Mtr通道的情况下,细胞色素CctA可以介导周质空间的电子传递而还原MO。重组表达CctA在低水平时,MO在周质空间中的还原速率与其表达水平呈正相关,更高水平的CctA表达无助于进一步提高MO的还原速率。蛋白膜伏安结果展示了CctA与周质空间内其他高电位氧化还原蛋白的显著区别,可能参与构成一条低电位的MO还原通道。【结论】从分子动力学层面揭示了CctA在周质MO还原中的独特电子传递行为,为进一步推进对细菌周质电子传递机制的理解,以及通过合成生物学设计或改造胞外氧化还原系统、强化生物电化学在污染物降解中的应用提供了重要信息。     

Processi di Neoformazione di Mitocondri Nella Cellula Vegetale

Abstract

Processes of formation of new mitochondria in plant cells. — While studying with the electron microscope the quiescent centre in the onion (Allium cepa) root tips, the writer was able to observe the endoplasmic reticulum arranged into peculiar concentric ring systems, which are here described. In some of the ring structures, between a ring and the contigous one, mitochondria-like bodies are formed, which are then detached by a kind of budding process. A short review of the current literature on formation of the mitochondria is also reported.     

An Electron Microscope Study of Different Plants Infected with Grapevine Fanleaf Virus

Abstract

The alterations caused by GFV in the leaves and roots of Vitis vinifera, and in the leaves of Nicotiana clevelandii and Chenopodium amaranticolor were studied in the electron microscope. In Nicotiana and Vitis, the main alterations were found in the chloroplasts, while in Chenopodium they were found in the cytoplasm. In all cases, the tonoplast appeared more electron opaque than normal and showed irregular densities over its surface. The presence of virus-like particles was demonstrated only in two cases.     

An electron microscopical study of the genus Tortula Hedw., with special reference to exine ornamentation

Abstract

Spores of ten North European species of the genus Tortula Hedw. were studied in the transmission electron microscope. In all the sporoderm was more or less covered with finely papillate processes of several different types which divide the genus into a number of groups different from the previously suggested sections. The ornamentation of leaves, peristomes, and spores of T. norvegica (Web. f.) Wahlenb. has been studied in the scanning electron microscope. The leaf papillae are not c-shaped as suggested in the literature, but branched in a rather complex way. The borders of the basal membrane cells of the peristome appeared to be a continuation of the filamentous portion of the teeth. A comparison with T. ruralis (Hedw.) Gaertn., Meyer & Scherb. revealed the ornamentation to be of the same basic type in the two species.     

Proton transfer and polarizability of hydrogen bonds in proteins coupled with conformational changes. I. Infrared investigation of poly(glutamic acid) with various N Bases

The nature of hydrogen bonds formed between carboxylic acid residues and histidine residues in proteins is studied by ir spectroscopy. Poly(glutamic acid) [(Glu)_n] is investigated with various monomer N bases. The position of the proton transfer equilibrium OH…?N ? O^?…?H⁺N is determined considering the bands of the carboxylic group. It is shown that largely symmetrical double minimum energy surfaces are present in the OH…?N ? O^?…?H⁺N bonds when the pK_a of the protonated N base is two values larger than that of the carboxylic groups of (Glu)_n. Hence OH…?N ? O^?…?H⁺N bonds between glutamic and aspartic acid residues and histidine residues in proteins may be easily polarizable proton transfer hydrogen bonds. The polarizability of these bonds is one to two orders of magnitude larger than usual electron polarizabilities; therefore, these bonds strongly interact with their environment. It is demonstrated that water molecules shift these proton transfer equilibria in favor of the polar proton boundary structure. The access of water molecules to such bonds in proteins and therefore the position of this proton transfer equilibrium is dependent on conformation. The amide bands show that (Glu)_n is α-helical with all systems. The only exception is the (Glu)_n-n-propylamine system. When this system is hydrated (Glu)_n is α-helical, too. When it is dried, however, (Glu)_n forms antiparallel β-structure. This conformational transition, dependent on degree of hydration, is reversible. An excess of n-propylamine has the same effect on conformation as hydration.     

Embryology of Clitoria ternatea (Fabaceae)

ABSTRACT

The embryology of Clitoria ternatea was studied. Anthers contain four sporangia. The anther wall comprises an epidermis, an endothecium, a middle layer and a glandular tapetum. Microspore tetrads are tetrahedral and pollen grains are shed at the 2-cell stage. The ovule is campylotropous, bitegmic and crassinucellate. The micropyle is formed by both the integuments. The megaspore tetrad is linear or T-shaped. The chalazal megaspore is functional and embryo sac development follows the monosporic Polygonum type. Endosperm development is of the nuclear type. The chalazal part of the endosperm forms a haustorium. Embryo development follows the Onagrad type.     

人工湿地反应性填料开发及其脱氮除磷性能研究

【目的】人工湿地填料作为反硝化电子供体可以高效且稳定地脱氮除磷,但是填料的选用方式和作用机理尚不明确。【方法】本文以磁黄铁矿、菱铁矿和农业废弃物(木屑等)为人工湿地填料,研究了其对人工湿地反硝化脱氮除磷的效果。【结果】结果显示,质量比1:1的矿石组合和木屑以3:1的质量比作为混合填料,驯化8个周期后NO₃^--N和PO₄^3--P的平均去除率达到88.6%和88.9%。扫描电子显微镜(scanning electron microscopy,SEM)、X射线光电子能谱(X-ray photoelectron spectroscopy,XPS)、X射线衍射仪(X-ray diffraction,XRD)和群落分析结果表明,微生物能有效利用矿石及其次生产物和木屑进行高效和持久的脱氮除磷,脱氮除磷功能菌硫杆菌(Thiobacillus)、罗姆布茨菌(Romboutsia)和溶杆菌(Lysobacter)得到了富集。【结论】本研究为人工湿地实际应用中新型填料的选择提供理论依据与指导意义。     

Possible involvement of cytoskeletal organelles in blastoderm formation of the silkworm,Bombyx mori

Summary

In this work we have studied the possibility that cytoskeletal systems are involved in energid migration and blastoderm formation of the silkworm, Bombyx mori. The results obtained suggest: (1) energid migration is mainly controlled by microtubules and perhaps secondarily by microfilaments, (2) morphological changes of microprojections covering the egg surface are regulated by microfilaments and (3) the changes of microprojections are independent of energid migration.     

Molecular modeling of 4-methylphthalonitrile for dye sensitized solar cells using quantum chemical calculations

The geometries, electronic structures, polarizabilities, and hyperpolarizabilities of organic dye sensitizer 4-Methylphthalonitrile was studied based on Hartree-Fock (HF) and density functional theory (DFT) using the hybrid functional B3LYP. Ultraviolet-visible (UV-Vis) spectrum was investigated by time dependent-density functional theory (TD-DFT). Features of the electronic absorption spectrum in the visible and near-UV regions were assigned based on TD-DFT calculations. The absorption bands are assigned to π → π* transitions. Calculated results suggest that three lowest energy excited states of 4-Methylphthalonitrile are due to photo induced electron transfer processes. The interfacial electron transfer between semiconductor TiO₂ electrode and dye sensitizer 4-Methylphthalonitrile is due to an electron injection process from excited dye to the semiconductor’s conduction band. The role of cyanine and methyl group in 4-Methylphthalonitrile in geometries, electronic structures, and spectral properties were analyzed.     

Multiple relational equilibria: Polymorphism,metamorphosis and other possibly similar phenomena

In a preceding paper (Rashevsky, 1969. “Outline of a Unified Approach to Physics, Biology and Sociology.”Bulletin of Mathematical Biophysics,31, 159–198) certain isomorphisms between biological and social systems on the one hand and physical systems on the other were studied. The notion or relational forces, of which ordinary physical forces are a particular case, was introduced. In the present paper an attempt is made to establish analogies between stable equilibria in physical systems, equilibria due to physical forces, and stable equilibria in biological and social systems which are due to purely relational forces. The notion of relational forces causing multiple equilibria similar to multiple equilibria in some physical systems is studied, and it is outlined how this notion may possibly help the understanding of such phenomena as polymorphism, metamorphosis and the existence of rudimentary organs or rudimentary functions.