Probing the role of the C-H center dot center dot center dot O hydrogen bond stabilized polypeptide chain reversal at the C-terminus of designed peptide helices. Structural characterization of three decapeptides

The structural characterization in crystals of three designed decapeptides containing a double D-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val- (D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all L analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed a-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-(HO)-O-... hydrogen bond between residue 4 (CH)-H-alpha and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C-alpha atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt at conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-(HO)-O-... hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.

Tibetan Written Images : A Study of Imagery in the Writings of Dhondup Gyal

Dhondup Gyal (Don grub rgyal, 1953 - 1985) was a Tibetan writer from Amdo (Qinghai, People's Republic of China). He wrote several prose works, poems, scholarly writings and other works which have been later on collected together into The Collected Works of Dhondup Gyal, in six volumes. He had a remarkable influence on the development of modern Tibetan literature in the 1980s. Examining his works, which are characterized by rich imagery, it is possible to notice a transition from traditional to modern ways of literary expression. Imagery is found in both the poems and prose works of Dhondup Gyal. Nature imagery is especially prominent and his writings contain images of flowers and plants, animals, water, wind and clouds, the heavenly bodies and other environmental elements. Also there are images of parts of the body and material and cultural images. To analyse the images, most of which are metaphors and similes, the use of the cognitive theory of metaphor provides a good framework for making comparisons with images in traditional Tibetan literature and also some images in Chinese, Indian and Western literary works. The analysis shows that the images have both traditional and innovative features. The source domains of images often appear similar to those found in traditional Tibetan literature and are slow to change. However, innovative shifts occur in the way they are mapped on their target domains, which may express new meanings and are usually secular in nature if compared to the religiosity which often characterizes traditional Tibetan literature. Dhondup Gyal's poems are written in a variety of styles, ranging from traditional types of verse compositions and poems in the ornate kāvya-style to modern free verse poetry. The powerful central images of his free verse poems and some other works can be viewed as structurally innovative and have been analysed with the help of the theory of conceptual blending. They are often ambiguous in their meaning, but can be interpreted to express ideas related to creativity, freedom and the need for change and development.

Propagation of quasi-simple waves in a compressible rotating atmosphere

A class of self-propagating linear and nonlinear travelling wave solutions for compressible rotating fluid is studied using both numerical and analytical techiques. It is shown that, in general, a three dimensional linear wave is not periodic. However, for some range of wave numbers depending on rotation, horizontally propagating waves are periodic. When the rotation ohgr is equal to $$\sqrt {(\gamma - 1)/(4\gamma )}$$ , all horizontal waves are periodic. Here, gamma is the ratio of specific heats. The analytical study is based on phase space analysis. It reveals that the quasi-simple waves are periodic only in some plane, even when the propagation is horizontal, in contrast to the case of non-rotating flows for which there is a single parameter family of periodic solutions provided the waves propagate horizontally. A classification of the singular points of the governing differential equations for quasi-simple waves is also appended.

Bear Shields of Plains Indians : Motifs and Meanings

The study is the outcome of two research projects on the North American Indian traditions: the role of the shields within the Plains Indians traditional culture and religion, and the bear ceremonialism of the Native North America, especially the significance of the bear among the Plains Indians. This article-based dissertation includes seven separately published scholar papers, forming Chapters 6 12. The introduction formulates the objectives and frame of reference of the study and the conclusions pulls together its results. The study reconsiders the role of the Plains Indian shields with bear motifs. Such shields are found in rock art, in the Plains Indian s paintings and drawings, and in various collections, the main source material being the shields in European and North American museums. The aim is not only to study shields with bear power motifs and the meanings of the bear, but also to discuss appropriate methods for studying these subjects. There are three major aims of the study: to consider methodical questions in studying Plains Indian shields, to examine the complexity of the Plains Indian shields with the bear power motifs, and to offer new interpretations for the basic meanings of the bear among the Plains Indians and the interrelationship between individualism and collectivism in the Plains Indians visionary art that show bear power motifs on the shields. The study constructs a view on the bear shields taking account of all sources of information available and analysing the shields both as physical artefacts and religious objects from different perspectives, studying them as a part of the ensemble of Plains culture and religious traditions. The bear motifs represented the superhuman power that medicine men and warriors could exploit through visions. For the Plains Indians, the bear was a wise animal from which medicine men could get power for healing but also a dangerous animal from which warriors could get power for warfare. The shields with bear motifs represented the bear powers of the owners of the shields. The bear shield was made to represent the vision, and the principal interpretation of the symbolism was based on the individual experience of spiritual world and its powers. The study argues that the bear shield as personal medicine object is based on wider tribal traditions, and the basic meaning is derived from the collective tradition. This means that the bear seen in vision represented particular affairs and it was represented on the shield surface using conventional ways of traditional artistry. In consequence of this, the bear shields reflect not only the individual experiences of bear power but whole field of tribal traditions that legitimated the experiences and offered acceptable interpretations and conventional modes for the bear symbols.

Microbiological characterisation of soils : Evaluation of some critical steps in data collection and experimental design

The study of soil microbiota and their activities is central to the understanding of many ecosystem processes such as decomposition and nutrient cycling. The collection of microbiological data from soils generally involves several sequential steps of sampling, pretreatment and laboratory measurements. The reliability of results is dependent on reliable methods in every step. The aim of this thesis was to critically evaluate some central methods and procedures used in soil microbiological studies in order to increase our understanding of the factors that affect the measurement results and to provide guidance and new approaches for the design of experiments. The thesis focuses on four major themes: 1) soil microbiological heterogeneity and sampling, 2) storage of soil samples, 3) DNA extraction from soil, and 4) quantification of specific microbial groups by the most-probable-number (MPN) procedure. Soil heterogeneity and sampling are discussed as a single theme because knowledge on spatial (horizontal and vertical) and temporal variation is crucial when designing sampling procedures. Comparison of adjacent forest, meadow and cropped field plots showed that land use has a strong impact on the degree of horizontal variation of soil enzyme activities and bacterial community structure. However, regardless of the land use, the variation of microbiological characteristics appeared not to have predictable spatial structure at 0.5-10 m. Temporal and soil depth-related patterns were studied in relation to plant growth in cropped soil. The results showed that most enzyme activities and microbial biomass have a clear decreasing trend in the top 40 cm soil profile and a temporal pattern during the growing season. A new procedure for sampling of soil microbiological characteristics based on stratified sampling and pre-characterisation of samples was developed. A practical example demonstrated the potential of the new procedure to reduce the analysis efforts involved in laborious microbiological measurements without loss of precision. The investigation of storage of soil samples revealed that freezing (-20 °C) of small sample aliquots retains the activity of hydrolytic enzymes and the structure of the bacterial community in different soil matrices relatively well whereas air-drying cannot be recommended as a storage method for soil microbiological properties due to large reductions in activity. Freezing below -70 °C was the preferred method of storage for samples with high organic matter content. Comparison of different direct DNA extraction methods showed that the cell lysis treatment has a strong impact on the molecular size of DNA obtained and on the bacterial community structure detected. An improved MPN method for the enumeration of soil naphthalene degraders was introduced as an alternative to more complex MPN protocols or the DNA-based quantification approach. The main advantage of the new method is the simple protocol and the possibility to analyse a large number of samples and replicates simultaneously.

Making Music, Making Muslims : A Case Study of Islamic Hip Hop and the Discursive Construction of Muslim Identities on the Internet

Hip-hopin juuret juontavat 1970-luvulle Yhdysvaltoihin, mutta hip-hop-kulttuuri ja musiikkityyli ovat sen jälkeen levinneet ympäri maailmaa osana globalisaatiokehitystä. Myös monet nuoret muslimit tekevät nykyään hip-hop-musiikkia, ja yhä useampi tuo myös sanoituksiinsa vaikutteita Islamista ja elämästään muslimina. Musiikin asema on islamissa varsin kiistelty, eikä sitä ole selvästi sallittu (halal) tai kielletty (haram) muslimeilta. Muslimien tekemää hip-hoppia on toistaiseksi tutkittu hyvin vähän. Tutkielmassa tarkastellaan diskurssianalyysin keinoin, miten tapaustutkimuksena toimivalla muslimhiphop.com-internetsivustolla argumentoidaan ja konstruoidaan käsityksiä muslimi-identiteetistä. Teoreettisena ja analyyttisenä viitekehyksenä toimii sosiaalikonstruktivistinen näkemys identiteetistä kontekstisidonnaisena sekä puheessa ja teksteissä diskursiivisesti rakentuvana. Tutkielma kyseenalaistaa aiempien tutkimusten oletuksen hip-hopista vaikutuksiltaan yksinomaan positiivisena muslimi-identiteetille sekä muslimeja yhdentävänä tekijänä. Aineisto on kerätty edellä mainitulta sivustolta syksyn 2010 ja kevään 2011 aikana, josta analyysiin on rajattu vain itse sivusto ja sen hip-hoppia käsittelevät osiot. Sivusto ja sen perustaja ovat yhdysvaltalaisia, mutta sivustolla esiteltävien artistien tausta on hyvin monikulttuurinen. Moni on myös maahanmuuttajana nykyisessä kotimaassaan. Aineistossa esiintyviä teemoja ja diskursseja eritellään ja analysoidaan tutkielmassa lainauksien avulla. Sivuston periaatteissa ja artistien esillepääsyn kriteereissä määritellään tarkasti asennoituminen Islamin ja musiikin yhdistämiseen: mikäli sanoitukset ja artistit noudattavat Islamin oppeja, on muslimin sallittua tehdä ja kuunnella tällaista musiikkia. Islam-aiheisen hip-hopin perustellaan olevan ennen kaikkea vaihtoehto valtavirran hip-hopille, jota konstruoidaan aineistossa moraalisesti arveluttavaksi. Hip-hopille sekä muslimeille sallittuja ja kiellettyjä elementtejä erottelevan halal-haram-diskurssin ohella aineistosta nousee esiin opetusdiskurssi. Muslimien tekemän hip-hopin perustellaan edistävän Islamin opettamista erityisesti nuorille muslimeille ja siten vahvistavan positiivista muslimi-identiteettiä. Myös positiivisen muutoksen diskurssia käytetään aineistossa runsaasti liittyen mm. muslimiyhteisöihin sekä muslimeihin kohdistuviin taloudellisiin ja sosiaalipoliittisiin epäkohtiin ja stereotypioihin; musiikin sisältöä ja sen tekemistä perustellaan sen voimalla muuttaa asioita parempaan suuntaan. Monet muslimiartistit kamppailevat yhdistääkseen toisaalta Islamin ja taiteellisen luovuuden ja ilmaisuvapauden, toisaalta menestyäkseen kaupallisesti unohtamatta uskonnollista vakaumustaan. Monilla heistä hip-hop on ollut vahvasti läsnä kasvuympäristössä, mutta sen yhdistäminen Islamin periaatteisiin aiheuttaa kysymyksiä ja kyseenalaistuksia oman musiikillisen ja uskonnollisen identiteetin muodosta ja sisällöstä. Aineiston perusteella monet muslimiartistit ja Islam-aiheista hip-hoppia kuuntelevat muslimit joutuvat jatkuvasti puolustamaan musiikkia siihen kielteisesti suhtautuville muslimeille sekä ei-muslimeille, jotka vierastavat sen uskonnollisuutta. Muslimi-identiteettiä neuvotellaan jatkuvasti, ja se näyttäytyy aineistossa moniulotteisena ja tilanteisesti rakentuvana. Avainsanat: Muslimit, Islam, hip-hop, identiteetti, Internet, diskurssi, diskurssianalyysi

Specific-heat measurements during cooling through the glass-transition region

In this paper we report the measurements of specific heats of five glass formers as they are cooled through the glass-transition region. The measurements are compared with other specific-heat measurements such as adiabatic-calorimetry and ac-calorimetry measurements. The data are then analyzed using a model of enthalpy relaxation and nonequilibrium cooling, which can track the nonequilibrium relaxation time tau(S). The relevant parameters that describe tau(S) are obtained, allowing us to compare the enthalpy-relaxation times obtained from this method with other methods. We display the clear connection of the unrelaxed enthalpy with the nonequilibrium relaxation time and also show the role played by the delayed heat release from the unrelaxed enthalpy in the glass-transition region. We have also made certain definite observations regarding the equilibrium configurational specific heat and the Vogel-Fulcher law, which describes tau(S).

Amino acid selective unlabeling for sequence specific resonance assignments in proteins

Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective `unlabeling' or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly C-13/N-15 labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {(CO)-C-12 (i) -N-15 (i+1)}-filtered HSQC, which aids in linking the H-1(N)/N-15 resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i - 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to H-2 labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of N-14 at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies.

Analysis of the effects of amino-acid-sequence on the structure of proteins

The conformation of amino acid side chains as observed in well-determined structures of globular proteins has earlier been extensively investigated. In contrast, the structural features of the polypeptide backbone that result from the occurrence of specific amino acids along the polypeptide have not been analysed. In this article, we present the statistically significant features in the backbone geometry that appear to be a consequence of the occurrence of rotamers of different amino acid side chains by analysing 102 well-refined structures that form a random collection of proteins. It is found that the persistence of helical segments around each residue is influenced by the residue type. Several residues exert asymmetrical influence between the carboxyl and amino terminal polypeptide segments. The degree to which secondary structures depart from an average geometry also appears to depend on residue type. These departures are correlated to the corresponding Chou and Fasman parameters of amino acid residues. The frequency distribution of the side chain rotamers is influenced by polypeptide secondary structure. In turn, the rotamer conformation of side chain affects the extension of the secondary structure of the backbone. The strongest correlation is found between the occurrence of g+ conformation and helix propagation on the carboxyl side of many residues.

Growth of alkali metal periodates from silica gel and their characterization

Single crystals (up to 1 cm size) of K, Rb and Cs periodates have been grown in silica gel. In general, good quality crystals were obtained in gel of specific gravity 1.04 and pH 4. The metal/iodine ratios were determined and compared with calculated values. Morphological studies were carried out using a bicircle optical goniometer. Other characterization methods include X-ray diffraction, optical absorption, differential scanning calorimetry and optical microscopy. Microscopic examination of CsIO4 crystals in particular has revealed the existence of ferroelastic domains in the crystal. The structural basis for the occurence of ferroelasticity in this crystal is discussed and the high temperature space group is predicted.

Characterization and Acceptor Preference of a Soluble Meningococcal Group C Polysialyltransferase

Vaccines against Neisseria meningitidis group C are based on its alpha-2,9-linked polysialic acid capsular polysaccharide. This polysialic acid expressed on the surface of N. meningitidis and in the absence of specific antibody serves to evade host defense mechanisms. The polysialyltransferase (PST) that forms the group C polysialic acid (NmC PST) is located in the cytoplasmic membrane. Until recently, detailed characterization of bacterial polysialyltransferases has been hampered by a lack of availability of soluble enzyme preparations. We have constructed chimeras of the group C polysialyltransferase that catalyzes the formation alpha-2,9-polysialic acid as a soluble enzyme. We used site-directed mutagenesis to determine the region of the enzyme necessary for synthesis of the alpha-2,9 linkage. A chimera of NmB and NmC PSTs containing only amino acids 1 to 107 of the NmB polysialyltransferase catalyzed the synthesis of alpha-2,8-polysialic acid. The NmC polysialyltransferase requires an exogenous acceptor for catalytic activity. While it requires a minimum of a disialylated oligosaccharide to catalyze transfer, it can form high-molecular-weight alpha-2,9-polysialic acid in a nonprocessive fashion when initiated with an alpha-2,8-polysialic acid acceptor. De novo synthesis in vivo requires an endogenous acceptor. We attempted to reconstitute de novo activity of the soluble group C polysialyltransferase with membrane components. We found that an acapsular mutant with a defect in the polysialyltransferase produces outer membrane vesicles containing an acceptor for the alpha-2,9-polysialyltransferase. This acceptor is an amphipathic molecule and can be elongated to produce polysialic acid that is reactive with group C-specific antibody.

Role of neutral metabolites in microbial conversion of 3beta-acetoxy-19-hydroxycholest-5-ene into estrone

Biotransformation of 3 beta-acetoxy-19-hydroxycholest-5-ene (19-HCA, 6 g) by Moraxella sp. was studied. Estrone (712 mg) was the major metabolite formed. Minor metabolites identified were 5 alpha-androst-1-en-19-ol-3,17-dione (33 mg), androst-4-en-19-ol-3,17-dione (58 mg), androst-4-en-9 alpha,19-diol-3,17-dione (12 mg), and androstan-19-ol-3,17-dione (1 mg). Acidic metabolites were not formed. Time course experiments on the fermentation of 19-HCA indicated that androst-4-en-19-ol-3,17-dione was the major metabolite formed during the early stages of incubation. However with continuing fermentation its level dropped, with a concomitant increase in estrone. Fermentation of 19-HCA in the presence of specific inhibitors or performing the fermentation for a shorter period (48 h) did not result in the formation of acidic metabolites. Resting-cell experiments carried out with 19-HCA (200 mg) in the presence of alpha,alpha'-bipyridyl led to the isolation of three additional metabolites, viz., cholestan-19-ol-3-one (2 mg), cholest-4-en-19-ol-3-one (10 mg), and cholest-5-en-3 beta,19-diol (12 mg). Similar results were also obtained when n-propanol was used instead of alpha,alpha'-bipyridyl. Resting cells grown on 19-HCA readily converted both 5 alpha-androst-1-en-19-ol-3,17-dione and androst-4-en-19-ol-3,17-dione into estrone. Partially purified 1,2-dehydrogenase from steroid-induced Moraxella cells transformed androst-4-en-19-ol-3,17-dione into estrone and formaldehyde in the presence of phenazine methosulfate, an artificial electron acceptor. These results suggest that the degradation of the hydrocarbon side chain of 19-HCA does not proceed via C-22 phenolic acid intermediates and complete removal of the C-17 side chain takes place prior to the aromatization of the A ring in estrone. The mode of degradation of the sterol side chain appears to be through the fission of the C-17-C-20 bond. On the basis of these observations, a new pathway for the formation of estrone from 19-HCA in Moraxella sp. has been proposed.

CDNA Cloning, Overexpression in Escherichia coli, Purification and Characterization of Sheep Liver Cytosolic Serine Hydroxymethyltransferase

A sheep liver cDNA clone for the cytosolic serine hydroxymethyltransferase (SHMT) was isolated and its nucleotide sequence determined. The full-length cDNA of SHMT was placed under the control of T7 promoter in pET-3C plasmid and expressed in Escherichia coli. The overexpressed enzyme, present predominantly in the soluble fraction, was catalytically active. The recombinant SHMT was purified to homogeneity with a yield of 10 mg/l bacterial culture. The recombinant enzyme was capable of carrying out tetrahydrofolate-dependent and tetrahydrofolate-independent reactions as effectively as the native enzyme. The K-m values for serine (1 mM) and tetrahydrofolate (0.82 mM) were similar to those of the native enzyme. The recombinant enzyme had a characteristic visible spectrum indicative of the presence of pyridoxal 5'-phosphate as an internal aldimine. The apoenzyme obtained upon removal of the cofactor was inactive and could be reconstituted by the addition of pyridoxal 5'-phosphate demonstrating that the recombinant SHMT was functionally very similar to the native SHMT. This overexpression of eukaryotic tetrameric SHMT in E. coli and the purification and characterization of the recombinant enzyme should thus allow studies on the role of specific amino acids and domains in the activity of the enzyme.

Modification of photochemical reactivity on formation of inclusion complexes: photorearrangement of benzyl phenyl ethers and methyl phenoxyacetates

The photorearrangement of benzyl phenyl ethers and methyl phenoxyacetates was investigated in methanol and in complexes with cyclodextrin in both the solid state and aqueous solutions. Irradiation in cyclodextrin media leads to a large change in product distribution with a very significant ortho selectivity different from that found in methanol where the reaction is non-selective. For meta-substituted ethers and phenoxyacetates, an impressive regioselectivity between the two ortho-rearranged isomers is observed and this is significantly enhanced by increasing the substituent chain length which acts as a spacer to induce a tight fit between the host and the guest. The observed results are rationalized on the basis of specific orientations of the unsubstituted and meta-substituted ethers and phenoxyacetates in the cyclodextrin cavity.

Self-consistent microscopic treatment of the effects of self-motion of the probe on ionic and dipolar solvation dynamics

A simple but self-consistent microscopic theory for the time dependent solvation energy of both ions and dipoles is presented which includes, for the first time, the details of the self-motion of the probe on its own solvation dynamics. The theory leads to several interesting predictions. The most important of them is that, for dipolar solvation, both the rotational and the translational motions of the dipolar solute probe can significantly accelerate the rate of solvation. In addition, the rotational self-motion of the solute can also give rise to an additional mechanism of nonexponentiality in solvation time correlation functions in otherwise slow liquids. A comparison between the present theoretical predictions and the recent experimental studies of Maroncelli et al. on solvation dynamics of aniline in l-propanol seems to indicate that the said experiments have missed the initial solvent response up to about 45 ps. After mapping the experimental results on the redefined time scale, the theoretical results can explain the experimental results for solvation of aniline in 1-propanol very well. For ionic solvation, the translational motion is significant for light solutes only. For example, for Li+ in water, translational motion speeds up the solvation by about 20%. The present theory demonstrates that in dipolar solvation the partial quenching of the self-motion due to the presence of specific solute-solvent interactions (such as H-bonding) may lead to a much slower solvation than that when the self-motion is present. This point has been discussed. In addition, we present the theoretical results for solvation of aniline in propylene carbonate, Here, the solvation is predicted to be complete within 15-20 ps.