The Crystal Structure of Pivaloyl- D- prolyl-L- prolyl- L-alanyl-N- methylamide

Pivaloyl-D-prolyl-L-prolyl-L-analyl-N-methylam~de (I), C1UH32N40c4r,y stallizes in the orthorhombic space group P21212,w ith four molecules in a unit cell of dimensions a = 9.982 (l),b = 10.183 (3), c = 20.746 (2)A . The structure has been refined to R 0.048 for 1 745 observed reflections. All the peptide bonds in the molecule are trans and both the prolyl residues are in the CY-exo-conformation. The molecule assumes a highly folded conformation in which a Type II' DL bend is followed by a Type I LL bend, both stabilised by intramolecular 4 + 1 hydrogen bonds. This conformation, which has been observed for the first time, is of interest in relation to the structure of gramicidin S.

Understanding the organic chain : The framework of the interaction between the actors in organic chains in relation to ecological modernisation of food production

The sustainability of food production has increasingly attracted the attention of consumers, farmers, food and retailing companies, and politicians. One manifestation of such attention is the growing interest in organic foods. Organic agriculture has the potential to enhance the ecological modernisation of food production by implementing the organic method as a preventative innovation that simultaneously produces environmental and economic benefits. However, in addition to the challenges to organic farming, the small market share of organic products in many countries today and Finland in particular risks undermining the achievement of such benefits. The problems identified as hindrances to the increased consumption of organic food are the poor availability, limited variety and high prices of organic products, the complicated buying decisions and the difficulties in delivering the intangible value of organic foods. Small volumes and sporadic markets, high costs, lack of market information, as well as poor supply reliability are obstacles to increasing the volume of organic production and processing. These problems shift the focus from a single actor to the entire supply chain and require solutions that involve more interaction among the actors within the organic chain. As an entity, the organic food chain has received very little scholarly attention. Researchers have mainly approached the organic chain from the perspective of a single actor, or they have described its structure rather than the interaction between the actors. Consequently, interaction among the primary actors in organic chains, i.e. farmers, manufacturers, retailers and consumers, has largely gone unexamined. The purpose of this study is to shed light on the interaction of the primary actors within a whole organic chain in relation to the ecological modernisation of food production. This information is organised into a conceptual framework to help illuminate this complex field. This thesis integrates the theories and concepts of three approaches: food system studies, supply chain management and ecological modernisation. Through a case study, a conceptual system framework will be developed and applied to a real life-situation. The thesis is supported by research published in four articles. All examine the same organic chains through case studies, but each approaches the problem from a different, complementary perspective. The findings indicated that regardless of the coherent values emphasising responsibility, the organic chains were loosely integrated to operate as a system. The focus was on product flow, leaving other aspects of value creation largely aside. Communication with consumers was rare, and none of the actors had taken a leading role in enhancing the market for organic products. Such a situation presents unsuitable conditions for ecological modernisation of food production through organic food and calls for contributions from stakeholders other than those directly involved in the product chain. The findings inspired a revision of the original conceptual framework. The revised framework, the three-layer framework , distinguishes the different layers of interaction. By gradually enlarging the chain orientation the different but interrelated layers become visible. A framework is thus provided for further research and for understanding practical implications of the performance of organic food chains. The revised framework provides both an ideal model for organic chains in relation to ecological modernisation and demonstrates a situation consistent with the empirical evidence.

Microbial indicators related to yield and disease and changes in soil microbial community structure with ginger farm management practices

TRFLP (terminal restriction fragment length polymorphism) was used to assess whether management practices that improved disease suppression and/or yield in a 4-year ginger field trial were related to changes in soil microbial community structure. Bacterial and fungal community profiles were defined by presence and abundance of terminal restriction fragments (TRFs), where each TRF represents one or more species. Results indicated inclusion of an organic amendment and minimum tillage increased the relative diversity of dominant fungal populations in a system dependant way. Inclusion of an organic amendment increased bacterial species richness in the pasture treatment. Redundancy analysis showed shifts in microbial community structure associated with different management practices and treatments grouped according to TRF abundance in relation to yield and disease incidence. ANOVA also indicated the abundance of certain TRFs was significantly affected by farming system management practices, and a number of these TRFs were also correlated with yield or disease suppression. Further analyses are required to determine whether identified TRFs can be used as general or soil-type specific bio-indicators of productivity (increased and decreased) and Pythium myriotylum suppressiveness.

Plant secondary compounds and soil microbial processes in carbon and nitrogen cycling in relation to tree species

The aim of this study was to explore soil microbial activities related to C and N cycling and the occurrence and concentrations of two important groups of plant secondary compounds, terpenes and phenolic compounds, under silver birch (Betula pendula Roth), Norway spruce (Picea abies (L.) Karst) and Scots pine (Pinus sylvestris L.) as well as to study the effects of volatile monoterpenes and tannins on soil microbial activities. The study site, located in Kivalo, northern Finland, included ca. 70-year-old adjacent stands dominated by silver birch, Norway spruce and Scots pine. Originally the soil was very probably similar in all three stands. All forest floor layers (litter (L), fermentation layer (F) and humified layer (H)) under birch and spruce showed higher rates of CO2 production, greater net mineralisation of nitrogen and higher amounts of carbon and nitrogen in microbial biomass than did the forest floor layers under pine. Concentrations of mono-, sesqui-, di- and triterpenes were higher under both conifers than under birch, while the concentration of total water-soluble phenolic compounds as well as the concentration of condensed tannins tended to be higher or at least as high under spruce as under birch or pine. In general, differences between tree species in soil microbial activities and in concentrations of secondary compounds were smaller in the H layer than in the upper layers. The rate of CO2 production and the amount of carbon in the microbial biomass correlated highly positively with the concentration of total water-soluble phenolic compounds and positively with the concentration of condensed tannins. Exposure of soil to volatile monoterpenes and tannins extracted and fractionated from spruce and pine needles affected carbon and nitrogen transformations in soil, but the effects were dependent on the compound and its molecular structure. Monoterpenes decreased net mineralisation of nitrogen and probably had a toxic effect on part of the microbial population in soil, while another part of the microbes seemed to be able to use monoterpenes as a carbon source. With tannins, low-molecular-weight compounds (also compounds other than tannins) increased soil CO2 production and nitrogen immobilisation by soil microbes while the higher-molecular-weight condensed tannins had inhibitory effects. In conclusion, plant secondary compounds may have a great potential in regulation of C and N transformations in forest soils, but the real magnitude of their significance in soil processes is impossible to estimate.

The Spin-Statistics Relation and Noncommutative Quantum Field Theory

The efforts of combining quantum theory with general relativity have been great and marked by several successes. One field where progress has lately been made is the study of noncommutative quantum field theories that arise as a low energy limit in certain string theories. The idea of noncommutativity comes naturally when combining these two extremes and has profound implications on results widely accepted in traditional, commutative, theories. In this work I review the status of one of the most important connections in physics, the spin-statistics relation. The relation is deeply ingrained in our reality in that it gives us the structure for the periodic table and is of crucial importance for the stability of all matter. The dramatic effects of noncommutativity of space-time coordinates, mainly the loss of Lorentz invariance, call the spin-statistics relation into question. The spin-statistics theorem is first presented in its traditional setting, giving a clarifying proof starting from minimal requirements. Next the notion of noncommutativity is introduced and its implications studied. The discussion is essentially based on twisted Poincaré symmetry, the space-time symmetry of noncommutative quantum field theory. The controversial issue of microcausality in noncommutative quantum field theory is settled by showing for the first time that the light wedge microcausality condition is compatible with the twisted Poincaré symmetry. The spin-statistics relation is considered both from the point of view of braided statistics, and in the traditional Lagrangian formulation of Pauli, with the conclusion that Pauli's age-old theorem stands even this test so dramatic for the whole structure of space-time.

Unusual effects of anisotropic bonding in Cu(II) and Ni(II) oxides with K2NiF4 structure

Geometric constraints present in A2BO4 compounds with the tetragonal-T structure of K2NiF4 impose a strong pressure on the B---OII---B bonds and a stretching of the A---OI---A bonds in the basal planes if the tolerance factor is t congruent with RAO/√2 RBO < 1, where RAO and RBO are the sums of the A---O and B---O ionic radii. The tetragonal-T phase of La2NiO4 becomes monoclinic for Pr2NiO4, orthorhombic for La2CuO4, and tetragonal-T′ for Pr2CuO4. The atomic displacements in these distorted phases are discussed and rationalized in terms of the chemistry of the various compounds. The strong pressure on the B---OII---B bonds produces itinerant σ*x2−y2 bands and a relative stabilization of localized dz2 orbitals. Magnetic susceptibility and transport data reveal an intersection of the Fermi energy with the d2z2 levels for half the copper ions in La2CuO4; this intersection is responsible for an intrinsic localized moment associated with a configuration fluctuation; below 200 K the localized moment smoothly vanishes with decreasing temperature as the d2z2 level becomes filled. In La2NiO4, the localized moments for half-filled dz2 orbitals induce strong correlations among the σ*x2−y2 electrons above Td reverse similar, equals 200 K; at lower temperatures the σ*x2−y2 electrons appear to contribute nothing to the magnetic susceptibility, which obeys a Curie-Weiss law giving a μeff corresponding to S = 1/2, but shows no magnetic order to lowest temperatures. These surprising results are verified by comparison with the mixed systems La2Ni1−xCuxO4 and La2−2xSr2xNi1−xTixO4. The onset of a charge-density wave below 200 K is proposed for both La2CuO4 and La2NiO4, but the atomic displacements would be short-range cooperative in mixed systems. The semiconductor-metallic transitions observed in several systems are found in many cases to obey the relation Ea reverse similar, equals kTmin, where varrho = varrho0exp(−Ea/kT) and Tmin is the temperature of minimum resistivity varrho. This relation is interpreted in terms of a diffusive charge-carrier mobility with Ea reverse similar, equals ΔHm reverse similar, equals kT at T = Tmin.

Use of structure-directed DNA ligands to probe the binding of recA protein to narrow and wide grooves of DNA and on its ability to promote homologous pairing

We have used circular dichroism and structure-directed drugs to identify the role of structural features, wide and narrow grooves in particular, required for the cooperative polymerization, recognition of homologous sequences, and the formation of joint molecules promoted by recA protein. The path of cooperative polymerization of recA protein was deduced by its ability to cause quantitative displacement of distamycin from the narrow groove of duplex DNA. By contrast, methyl green bound to the wide groove was retained by the nucleoprotein filaments comprised of recA protein-DNA. Further, the mode of binding of these ligands and recA protein to DNA was confirmed by DNaseI digestion. More importantly, the formation of joint molecules was prevented by distamycin in the narrow groove while methyl green in the wide groove had no adverse effect. Intriguingly, distamycin interfered with the production of coaggregates between nucleoprotein filaments of recA protein-M13 ssDNA and naked linear M13 duplex DNA, but not with linear phi X174 duplex DNA. Thus, these data, in conjunction with molecular modeling, suggest that the narrow grooves of duplex DNA provide the fundamental framework required for the cooperative polymerization of recA protein and alignment of homologous sequences. These findings and their significance are discussed in relation to models of homologous pairing between two intertwined DNA molecules.

Comparative life-history traits in a fig wasp community: implications for community structure

1. Whether life-history traits can determine community composition and structure is an important question that has been well explored theoretically, but has received scant empirical attention. Life-history traits of a seven-member community of galler and parasitoid fig wasp species (Chalcidoidea), developing within the inflorescences (syconia) of Ficus racemosa (Moraceae) in India, were determined and used to examine community structure and ecology. 2. Gallers were pro-ovigenic (all eggs are mature upon adult emergence) whereas parasitoids were synovigenic (eggs mature progressively during adult lifespan). Initial egg load was correlated with body size for some species, and there was a trade-off between egg number and egg size across all species. Although all species completed their development and left the syconium concurrently, they differed in their adult and pre-adult lifespans. Providing sucrose solutions increased parasitoid lifespan but had no effect on the longevity of some galler species. While feeding regimes and body size affected longevity in most species, an interaction effect between these variables was detected for only one species. 3. Life-history traits of wasp species exhibited a continuum in relation to their arrival sequence at syconia for oviposition during syconium development, and therefore reflected their ecology. The largest number of eggs, smallest egg sizes, and shortest longevities were characteristic of the earliest-arriving galling wasps at the smallest, immature syconia; the converse characterised the later-arriving parasitoids at the larger, already parasitised syconia. Thus life history is an important correlate of community resource partitioning and can be used to understand community structure. 4. This is the first comprehensive study of life-history traits in a fig wasp community. The comparative approach revealed constraints and flexibility in trait evolution.

Conformationally restricted formyl methionyl tripeptide chemoattractants: a three-dimensional structure-activity study of analogs incorporating a C alpha,alpha-dialkylated glycine at position 2

The conformationally restricted CHO-L-Met-Xxx-L-Phe-OY (where Xxx = Aib, Ac3c, Ac5c, Ac6c, and Ac7c; Y = H, Me) tripeptides, analogs of the chemoattractant CHO-L-Met-L-Leu-L-Phe-OH, have been synthesized in solution by classical methods and fully characterized. Compounds were compared to determine the combined effect of backbone conformational preferences and side-chain bulkiness on the relation of three-dimensional structure to biological activity. Each peptide was tested for its ability to induce granule enzyme secretion from rabbit peritoneal polymorphonuclear leukocytes. In parallel, a conformational analysis on the CHO-blocked peptide and their tertbutyloxycarbonylated synthetic precursors was performed in the crystal state and in solution using X-ray diffraction, infrared absorption, and 1H nuclear magnetic resonance. The biological and conformational data are discussed in relation to the proposed model of the chemotactic peptide receptor of rabbit neutrophils.

Influence of crossed electric and quantizing magnetic fields on the Einstein relation in nonlinear optical, optoelectronic and related materials: Simplified theory, relative comparison and suggestion for experimental determination

An attempt is made to study the Einstein relation for the diffusivity-to-mobility ratio (DMR) under crossed fields' configuration in nonlinear optical materials on the basis of a newly formulated electron dispersion law by incorporating the crystal field in the Hamiltonian and including the anisotropies of the effective electron mass and the spin-orbit splitting constants within the framework of kp formalisms. The corresponding results for III-V, ternary and quaternary compounds form a special case of our generalized analysis. The DMR has also been investigated for II-VI and stressed materials on the basis of various appropriate dispersion relations. We have considered n-CdGeAs2, n-Hg1-xCdxTe, n-In1-xGaxAsyP1-y lattice matched to InP, p-CdS and stressed n-InSb materials as examples. The DMR also increases with increasing electric field and the natures of oscillations are totally band structure dependent with different numerical values. It has been observed that the DMR exhibits oscillatory dependences with inverse quantizing magnetic field and carrier degeneracy due to the Subhnikov-de Haas effect. An experimental method of determining the DMR for degenerate materials in the present case has been suggested. (C) 2010 Elsevier B.V. All rights reserved.

Crystallographic identification of a ‘stepped-cubane’ structure for the Cu4O4 core in [Cu4L2(bipy)4(µ3-OH)2][ClO4]4(HL = 5-hydroxy-6-methylpyridine-,4-dimethanol, bipy = 2,2′-bipyridine)

The structure of [Cu4L2(bipy)4(µ3-OH)2][ClO4]4 containing a Vitamin B6 ligand, pyridoxine (5-hydroxy-6-methylpyridine-3,4-dimethanol, HL), and 2,2′-bipyridine (bipy) has been determined by single-crystal X-ray analysis. This is the first report on a copper(II) complex having a ‘stepped-cubane’ structure. The compound crystallizes in the triclinic space group P[1 with combining macron](Z= 1) with a= 11.015(3), b= 11.902(1), c= 13.142(2)Å, α= 105.07(1), β= 102.22(1) and γ= 99.12(1)°; R= 0.054). The co-ordination geometry around each copper is trigonally distorted square pyramidal. Two of the basal sites are occupied by bipyridyl nitrogens in a bidentate fashion. The remaining basal positions for Cu(1) are filled by a phenolic oxygen and a 4-hydroxymethyl oxygen of the L moiety, whereas for Cu(2) they are occupied by two µ3-OH oxygens. The axial sites are occupied by a µ3-OH oxygen and the 4-hydroxymethyl oxygen of the same pyridoxine for Cu(1) and Cu(2), respectively. Both the bridging nature of the 4-hydroxymethyl oxygen of the L moiety and the unsymmetrical bridging nature of the µ3-OH groups with axial–equatorial bridging are novel features. The structure is discussed in relation to stepped-cubane structures reported in the literature. A comparative study is also made with µ3-hydroxo-bridged copper(II) complexes. Both the plasticity effect of CuII and the stacking interactions between the various rings appear to be important in stabilizing this unusual structure.

A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein

The structure and properties of the double-helical form of the alternating copolymer poly(dA-dT) are considered. Different lines of evidence are interpreted in terms of a structure in which every second phosphate-diester linkage has a conformation different from that of the normal B form. A rationale for this “alternating-B” structure is given which provides an explanation for the effects of chemical modifications of the T residues on the binding of the poly(dA-dT)· poly(dA-dT) to the lac repressor of Escherichia coli.

Protein Hydration and Water Structure: X-ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content

Low-humidity monoclinic lysozyme, resulting from a water-mediated transformation, has one of the lowest solvent contents (22% by volume) observed in a protein crystal. Its structure has been solved by the molecular replacement method and refined to an R value of 0.175 for 7684 observed reflections in the 10–1.75 Å resolution shell. 90% of the solvent in the well ordered crystals could be located. Favourable sites of hydration on the protein surface include side chains with multiple hydrogen-bonding centres, and regions between short hydrophilic side chains and the main-chain CO or NH groups of the same or nearby residues. Major secondary structural features are not disrupted by hydration. However, the free CO groups at the C terminii and, to a lesser extent, the NH groups at the N terminii of helices provide favourable sites for water interactions, as do reverse turns and regions which connect β-structure and helices. The hydration shell consists of discontinuous networks of water molecules, the maximum number of molecules in a network being ten. The substrate-binding cleft is heavily hydrated, as is the main loop region which is stabilized by water interactions. The protein molecules are close packed in the crystals with a molecular coordination number of 14. Arginyl residues are extensively involved in intermolecular hydrogen bonds and water bridges. The water molecules in the crystal are organized into discrete clusters. A distinctive feature of the clusters is the frequent occurrence of three-membered rings. The protein molecules undergo substantial rearrangement during the transformation from the native to the low-humidity form. The main-chain conformations in the two forms are nearly the same, but differences exist in the side-chain conformation. The differences are particularly pronounced in relation to Trp 62 and Trp 63. The shift in Trp 62 is especially interesting as it is also known to move during inhibitor binding.

Recovery of tropical rainforest avifauna in relation to vegetation succession following shifting cultivation in Mizoram, north-east India

1. Recovery of rainforest bird community structure and composition, in relation to forest succession after slash-and-burn shifting cultivation or jhum was studied in Mizoram, north-east India. Replicate fallow sites abandoned after shifting cultivation 1, 5, 10, 25 and approximate to 100 years ago, were compared with primary evergreen and semi-evergreen forest using transect and quadrat sampling. 2. Vegetation variables such as woody plant species richness, tree density and vertical stratification increased with fallow age in a rapid. nun-linear, asymptotic manner. Principal components analysis of vegetation variables summarized 92.8% of the variation into two axes: PC1 reflecting forest development and woody plant succession (variables such as tree density, woody plant species richness), and PC2 depicting bamboo density, which increased from 1 to 25 years and declined thereafter. 3. Bird species richness, abundance and diversity, increased rapidly and asymptotically during succession paralleling vegetation recovery as shown by positive correlations with fallow age and PC1 scores of sites. Bamboo density reflected by PC2 had a negative effect on bird species richness and abundance. 4. The bird community similarity (Morisita index) of sites with primary forest also increased asymptotically with fallow age indicating sequential species turnover during succession. Bird community similarity of sites with primary forest (or between sites) was positively correlated with both physiognomic and floristic similarities with primary forest (or between sites). 5. The number of bird species in guilds associated with forest development and woody plants (canopy insectivores, frugivores: bark feeders) was correlated with PCI scores of the sites. Species in other guilds (e. g. granivores, understorey insectivores) appeared to dominate during early and mid-succession. 6. The non-linear relationships imply that fallow periods less than a threshold of 25 years for birds, and about 50-75 years for woody plants, are likely to cause substantial community alteration. 7. As 5-10-year rotation periods or jhum cycles prevail in many parts of north-east India. there is a need to protect and conserve tracts of late-successional and primary forest.

Plant Diversity in the Sharavathi River Basin in Relation to Human Disturbance

Changes in vegetation are taking place due to anthropogenic activities since the colonization of the evergreen forest zone of Western Ghats. The forests of the Western Ghats were contiguous and uniformly rich in endemism within each climatic and physiographic regime. The region continues to be one of the biodiversity hot spots of the world. However unplanned developmental activities are altering the balance of the ecosystem. This study focuses on the floristic structure, composition and diversity of forests with varying degree of human disturbances. Based on the investigations, various strategies for conservation and sustainable utilization of forest resources were proposed.