Interaction of metal ions with nucleic acids and related compounds. II. Studies on Au(III)-nucleic acid system

The nature of interaction of Au(III) with nucleic acids was studied by using methods such as uv and ir spectrophotometry, viscometry, pH titrations, and melting-temperature measurements. Au(III) is found to interact slowly with nucleic acids over a period of several hours. The uv spectra of native calf-thymus DNA 9pH 5.6 acetate buffer containing (0.01M NaCIO4) showed a shift in λ max to high wavelengths and an increase in optical density at 260 nm. There was a fourfold decrease in viscosity (expressed as ηsp/c). The reaction was faster at pH 4.0 and also with denatured DNA (pH 5.6) and whole yeast RNA (pH 5.6). The order of preference of Au(III) (as deduced from the time of completion of reaction) for the nucleic acids in RNA > denatured DNA > DNA. The reaction was found to be completely reversible with respect KCN. Infrared spectra of DNA-Au(III) complexes showed binding to both the phosphate and bases of DNA. The same conclusions were also arrived at by melting-temperature studies of Au(III)-DNA system. pH titrations showed liberation of two hydroxylions at r = 0.12 [r = moles of HAuCl4 added per mole of DNA-(P)] and one hydrogen ion at r = 0.5. The probable binding sites could be N(1)/N(7) of adenine, N(7) and/or C(6)O of guanine, N(3) of cytosine and N(3) of thymine. DNAs differing in their (G = C)-contents [Clostridium perfingens DNA(G = C, 29%), salmon sperm DNA (G + C, 42%) and Micrococcus lysodeikticus DNA(G + C, 29%), salmon sperm DNA (G = C, 72%)] behaved differently toward Au(III). The hyperchromicity observed for DNAs differing in (G + C)-content and cyanide reversal titrations indicate selectivity toward ( A + T)-rich DNA at lw values of r. Chemical analysis and job's continuous variation studies indicated the existence of possible complexes above and below r = 1. The results indicate that Au(III) ions probably bind to hte phosphate group in the initial stages of the reaction, particularly at low values of r, and participation of the base interaction also increases. Cross-linking of the two strands by Au(III) may take place, but a complete collapse of the doulbe helix is not envisaged. It is probable that tilting of the bases or rotaiton of the bases around the glucosidic bond, resulting in a significant distrotion of the double helix, might take place due to binding of Au(III) to DNA.

Non-industrial private forest landowners’ choices of timber management strategies and potential allowable cut.

In the study, the potential allowable cut in the district of Pohjois-Savo - based on the non-industrial private forest landowners' (NIPF) choices of timber management strategies - was clarified. Alternative timber management strategies were generated, and the choices and factors affecting the choices of timber management strategies by NIPF landowners were studied. The choices of timber management strategies were solved by maximizing the utility functions of the NIPF landowners. The parameters of the utility functions were estimated using the Analytic Hierarchy Process (AHP). The level of the potential allowable cut was compared to the cutting budgets based on the 7th and 8th National Forest Inventories (NFI7 and NFI8), to the combining of private forestry plans, and to the realized drain from non-industrial private forests. The potential allowable cut was calculated using the same MELA system as has been used in the calculation of the national cutting budget. The data consisted of the NIPF holdings (from the TASO planning system) that had been inventoried compartmentwise and had forestry plans made during the years 1984-1992. The NIPF landowners' choices of timber management strategies were clarified by a two-phase mail inquiry. The most preferred strategy obtained was "sustainability" (chosen by 62 % of landowners). The second in order of preference was "finance" (17 %) and the third was "saving" (11 %). "No cuttings", and "maximum cuttings" were the least preferred (9 % and 1 %, resp.). The factors promoting the choices of strategies with intensive cuttings were a) "farmer as forest owner" and "owning fields", b) "increase in the size of the forest holding", c) agriculture and forestry orientation in production, d) "decreasing short term stumpage earning expectations", e) "increasing intensity of future cuttings", and f) "choice of forest taxation system based on site productivity". The potential allowable cut defined in the study was 20 % higher than the average of the realized drain during the years 1988-1993, which in turn, was at the same level as the cutting budget based on the combining of forestry plans in eastern Finland. Respectively, the potential allowable cut defined in the study was 12 % lower than the NFI8-based greatest sustained allowable cut for the 1990s. Using the method presented in this study, timber management strategies can be clarified for non-industrial private forest landowners in different parts of Finland. Based on the choices of timber managemet strategies, regular cutting budgets can be calculated more realistically than before.

Non-industrial private forest landowners’ choices of timber management strategies.

The factors affecting the non-industrial, private forest landowners' (hereafter referred to using the acronym NIPF) strategic decisions in management planning are studied. A genetic algorithm is used to induce a set of rules predicting potential cut of the landowners' choices of preferred timber management strategies. The rules are based on variables describing the characteristics of the landowners and their forest holdings. The predictive ability of a genetic algorithm is compared to linear regression analysis using identical data sets. The data are cross-validated seven times applying both genetic algorithm and regression analyses in order to examine the data-sensitivity and robustness of the generated models. The optimal rule set derived from genetic algorithm analyses included the following variables: mean initial volume, landowner's positive price expectations for the next eight years, landowner being classified as farmer, and preference for the recreational use of forest property. When tested with previously unseen test data, the optimal rule set resulted in a relative root mean square error of 0.40. In the regression analyses, the optimal regression equation consisted of the following variables: mean initial volume, proportion of forestry income, intention to cut extensively in future, and positive price expectations for the next two years. The R2 of the optimal regression equation was 0.34 and the relative root mean square error obtained from the test data was 0.38. In both models, mean initial volume and positive stumpage price expectations were entered as significant predictors of potential cut of preferred timber management strategy. When tested with the complete data set of 201 observations, both the optimal rule set and the optimal regression model achieved the same level of accuracy.

A participatory approach to tactical forest planning.

The paper examines the needs, premises and criteria for effective public participation in tactical forest planning. A method for participatory forest planning utilizing the techniques of preference analysis, professional expertise and heuristic optimization is introduced. The techniques do not cover the whole process of participatory planning, but are applied as a tool constituting the numerical core for decision support. The complexity of multi-resource management is addressed by hierarchical decision analysis which assesses the public values, preferences and decision criteria toward the planning situation. An optimal management plan is sought using heuristic optimization. The plan can further be improved through mutual negotiations, if necessary. The use of the approach is demonstrated with an illustrative example, it's merits and challenges for participatory forest planning and decision making are discussed and a model for applying it in general forest planning context is depicted. By using the approach, valuable information can be obtained about public preferences and the effects of taking them into consideration on the choice of the combination of standwise treatment proposals for a forest area. Participatory forest planning calculations, carried out by the approach presented in the paper, can be utilized in conflict management and in developing compromises between competing interests.

Bicriterion differential games with qualitative outcomes

Combat games are studied as bicriterion differential games with qualitative outcomes determined by threshold values on the criterion functions. Survival and capture strategies of the players are defined using the notion of security levels. Closest approach survival strategies (CASS) and minimum risk capture strategies (MRCS) are important strategies for the players identified as solutions to four optimization problems involving security levels. These are used, in combination with the preference orderings of the qualitative outcomes by the players, to delineate the win regions and the secured draw and mutual kill regions for the players. It is shown that the secured draw regions and the secured mutual kill regions for the two players are not necessarily the same. Simple illustrative examples are given.

DNA polymorphism and local variation in base-pair orientation: a theoretical rationale

Basepair stacking calculations have been carried out to understand the conformational polymorphism of DNA and its sequence dependence. The recently developed self-consistent parameter set, which is specially suitable for describing irregular DNA structures, has been used to describe the geometry of a basepair doublet. While for basepairs without any propeller, the favourable stacking patterns do not appear to have very strong features, much more noticeable sequence dependent stacking patterns emerge once a propeller is applied to the basepairs. The absolute minima for most sequences occurs for a doublet geometry close to the B-DNA fibre models. Hence in the B-DNA region, no strong sequence dependent features are found, but the range of doublet geometries observed in the crystal structures generally lie within the low energy contours, obtained from stacking energy calculations. The doublet geometry corresponding to the A-DNA fibre model is not energetically favourable for the purine-pyrimidine sequences, which prefer small roll angle values when the slide has a large negative value as in A-DNA. However positive roll with large negative slide is allowed for GG, GA, AG and the pyrimidine-purine steps. This is consistent with the observed geometries of various steps in A-DNA crystals. Thus the general features of the basepair doublets predicted from these theoretical studies agree very well with the results from crystal structure analysis. However, since most sequences show an overall preference for B-type doublet geometry, the B --> A transition for random sequence DNA cannot be explained on the basis of basepair stacking interactions.

A C-H…O hydrogen bond stabilized polypeptide chain reversal motif at the C-terminus helices in proteins.

The serendipitous observation of a C–Hcdots, three dots, centeredO hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been examined. The C–Hcdots, three dots, centeredO interaction between the T−4 CαH and T+1 C=O group (Ccdots, three dots, centeredO≤3.5 Å) becomes possible only when the T+1 residue adopts an extended β conformation (T is defined as the helix terminating residue adopting an αL conformation). In all, 111 examples of this chain reversal motif have been identified and the compositional and conformational preferences at positions T−4, T, and T+1 determined. A marked preference for residues like Ser, Glu and Gln is observed at T−4 position with the motif being further stabilized by the formation of a side-chain–backbone Ocdots, three dots, centeredH–N hydrogen bond involving the side-chain of residue T−4 and the N–H group of residue T+3. In as many as 57 examples, the segment following the helix was extended with three to four successive residues in β conformation. In a majority of these cases, the succeeding β strand lies approximately antiparallel with the helix, suggesting that the backbone C–Hcdots, three dots, centeredO interactions may provide a means of registering helices and strands in an antiparallel orientation. Two examples were identified in which extended registry was detected with two sets of C–Hcdots, three dots, centeredO hydrogen bonds between (T−4) CαHcdots, three dots, centeredC=O (T+1) and (T−8) CαHcdots, three dots, centeredC=O (T+3).

Microsite occupancy and spatial structure of regeneration in three late-successional Norway spruce forests in northern Europe

A comparison of microsite occupancy and the spatial structure of regeneration in three areas of late-successional Norway spruce dominated forest. Pallas-Ylläs is understood to have been influenced only by small-scale disturbance; Dvina-Pinega has had sporadic larger-scale disturbances; Kazkim has been affected by fire. All spruce and birch trees with diameter at breast height (DBH) ?10 cm were mapped in five stands on 40 m x 400 m transects, and those with DBH < 10 cm on 2 or 4 m x 400 m subplots. Microsite type was inventoried at 1m intervals along the centre line and for each tree with DBH < 10 cm. At all study areas small seedlings (h < 0.3 m, DBH < 10 cm) preferentially occupied disturbed microsites. In contrast, spruce saplings (h ? 1.3 m, DBH <10 cm) at all study areas showed less, or no, preference. At Pallas-Ylläs spruce seedlings (h < 1.3 m, DBH < 10 cm) and saplings (h ? 1.3 m, DBH < 10 cm) exhibited spatial correlation at scales from 32-52 m. At Dvina-Pinega saplings of both spruce and birch exhibited spatial correlation at scales from 32-81 m. At Kazkim spatial correlation of seedlings and saplings of both species was exhibited over variable distances. No spatial cross-correlation was found between overstorey basal area (DBH ? 10 cm) and regeneration (h ? 1.3 m, DBH < 10 cm) at any study area. The results confirm the importance of disturbed microsites for seedling establishment, but suggest that undisturbed microsites may sometimes be more advantageous for long-term tree survival. The regeneration gap concept may not be useful in describing the regeneration dynamics of late-successional boreal forests.

Symmetry preservation during radiation damage

An examination of radiation-damage processes consequent to high-energy irradiation in certain ammonium salts studied using ESR of free radical together with the structural information available from neutron diffraction studies shows that, other factors being equal/nearly equal, symmetry-related bonds are preserved in preference to those unrelated to one another by any symmetry.

Language universals and linguistic complexity : Three case studies in core argument marking

In this dissertation I study language complexity from a typological perspective. Since the structuralist era, it has been assumed that local complexity differences in languages are balanced out in cross-linguistic comparisons and that complexity is not affected by the geopolitical or sociocultural aspects of the speech community. However, these assumptions have seldom been studied systematically from a typological point of view. My objective is to define complexity so that it is possible to compare it across languages and to approach its variation with the methods of quantitative typology. My main empirical research questions are: i) does language complexity vary in any systematic way in local domains, and ii) can language complexity be affected by the geographical or social environment? These questions are studied in three articles, whose findings are summarized in the introduction to the dissertation. In order to enable cross-language comparison, I measure complexity as the description length of the regularities in an entity; I separate it from difficulty, focus on local instead of global complexity, and break it up into different types. This approach helps avoid the problems that plagued earlier metrics of language complexity. My approach to grammar is functional-typological in nature, and the theoretical framework is basic linguistic theory. I delimit the empirical research functionally to the marking of core arguments (the basic participants in the sentence). I assess the distributions of complexity in this domain with multifactorial statistical methods and use different sampling strategies, implementing, for instance, the Greenbergian view of universals as diachronic laws of type preference. My data come from large and balanced samples (up to approximately 850 languages), drawn mainly from reference grammars. The results suggest that various significant trends occur in the marking of core arguments in regard to complexity and that complexity in this domain correlates with population size. These results provide evidence that linguistic patterns interact among themselves in terms of complexity, that language structure adapts to the social environment, and that there may be cognitive mechanisms that limit complexity locally. My approach to complexity and language universals can therefore be successfully applied to empirical data and may serve as a model for further research in these areas.

”Ihanan överi ja juhlallinen jakku olisi kyllä kiva lisä vaatekaappiin” – tutkimus kuluttamisesta ja professionalisoitumisesta elämäntyyliblogeissa

Tarkastelen tutkimuksessani muotibloggaajien kulutuspuhetta. Tutkimuksen tarkoituksena on selvittää, millaista kuluttajuutta muotiblogeissa ilmaistaan ja millainen kehityskaari muotiblogeissa on tapahtunut vuodesta 2007 tämän tutkimuksen tekemiseen asti tutkimusaineiston sekä tekemieni havaintojen perusteella. Tutkimus on toteutettu laadullisia tutkimusmenetelmiä käyttämällä. Olen kerännyt aineistoni kymmenestä naisten kirjoittamasta muotiblogista kahtena eri ajanjaksona vuonna 2009. Lisäksi tutkimuksessa on sekä etnografisen että netnografisen havainnoinnin piirteitä. Aineiston analysoinnin apuna olen käyttänyt teemoittelua sekä tyypittelyä. Tutkimuksesta selvisi, että muotibloggaajien näkeminen identiteettiään etsivänä liittyy oman tyylin etsimiseen ja erottautumisen haluun. Perinteinen näkemys kuluttajasta valitsijana ja passiivisena markkinoilla toimijana on väistymässä, sillä muotibloggaajat näyttäytyvät tutkimuksessa aktiivisina toimijoina ja tuottajina. Muotibloggaajat hakevat myös jatkuvasti uusia kulutuselämyksiä ja kommunikoivat toistensa kanssa välittämällä merkityksiä kuluttamisensa kautta. Muotibloggaajien kulutuspuheet näyttäytyvät tutkimuksessa ekonomistisen kulutuseetoksen ja perinteisen suomalaisen kulutuspuheen mukaisesti järkevinä. Säästäväisyyttä pidetään hyveellisenä ja tuotteiden hinnat vaikuttavat ostopäätösten tekemiseen. Muotibloggaajat osaavat kuitenkin kontrolloidusti nauttia kuluttamisesta. Kulutuspuheet noudattavat myös ekologis-eettisen kulutuseetoksen perinnettä, mikä ilmenee fanaattisuuden välttämisenä sekä perinteisten että sosiaalisen median kirpputorien suosimisena. Lisäksi muotibloggaajien kulutuspuheet käyvät ilmi sosiaalisena pakkona, sillä muotiblogin pitäminen mielenkiintoisena vaatii jatkuvaa himoa uusia kulutustuotteita kohtaan. Tutkimuksen perusteella muotiblogeissa korostuu yhteisöllisyys ja kuluttaminen on hyvin naisellista. Tutkimusaineistosta sekä havainnoista tekemieni päätelmien mukaan muotiblogit ovat muuttumassa elämäntyyliblogeiksi, sillä niissä kerrotaan yhä enemmän myös muista kuin kuluttamiseen liittyvistä aiheista. Samalla muotibloggaajat ovat kehittymässä tavallisesta kuluttajasta kohti asiantuntijuutta eli professionalisoitumassa. Professionalisoitumisen myötä muotibloggaajat toimivat uuden ajan kuluttajavalistajina ja muotiblogeissa syntyy uusia sanoja ja merkityksiä. Lisäksi muotibloggaajille on kehittynyt sellaisia tietoja ja taitoja, joita voi myydä. Muotibloggaajista onkin tulossa muodin ammattilaisia, joille maksetaan tulevaisuudessa bloggaamisesta myös palkkaa.

Substrate-mediated purification and characterization of a 3-hydroxybenzoic acid-6-hydroxylase from Micrococcus

3-Hydroxybenzoic acid-6-hydroxylase from Micrococcus sp. was purified to homogeneity in a single step using the substrate-mediated interaction of the enzyme with blue-Sepharose. The enzyme was bound to the affinity matrix in the presence of 3-hydroxybenzoic acid and was eluted in its absence. The molecular weight of the purified enzyme is 70,000 with no subunit structure. The flavoenzyme required the exogenous addition of FAD for its complete activity and had a strict preference for NADH over NADPH. The activity of the enzyme was drastically inhibited by Cu2+ and Hg2+ and the inhibition was reversed by thiol reagents.

pi.-Facial selectivities in cycloadditions to norbornyl- and norbornenyl-fused p-benzoquinones

The stereochemistry of the Diels-Alder cycloaddition of several dienes to the facially perturbed dienophiles 2,3-norbornenobenzoquinone (3) and 2,3-norbornanobenzoquinone (4) has been examined. Unambiguous structural proof for the adducts formed has been obtained from complementary 'H and I3C NMR spectral data and in two cases through X-ray crystal structure determination. While 1,3-~yclopentadiene1, ,3-~yclohexadienea, nd cyclooctatetraene exhibit preference for addition to 3 from the bottom side, the stereochemical outcome is reversed in their response to 4.1,3-DiphenyIisobenzofuran and 1,2,3,4-tetrachloro-5,5-dimethoxycyclopentadieenneg aged 3 from the top side with marked selectivity, which is further enhanced in their reaction with 4. The observed stereoselectivities seem to be essentially controlled by steric interactons at the transition state. Model calculations provide support for this interpretation.

Neural network approach for the two-dimensional assignment problem

A neural network approach for solving the two-dimensional assignment problem is proposed. The design of the neural network is discussed and simulation results are presented. The neural network obtains 10-15% lower cost placements on the examples considered, than the adjacent pairwise exchange method.

Conformational studies on beta-bend containing a cis peptide unit

Conformational studies have been carried out on the X-cis-Pro tripeptide system (a system of three linked peptide units, in the trans-cis-trans configuration) using energy minimization techniques. For X, residues Gly, L-Ala, D-Ala and L-Pro have been used. The energy minima have been classified into different groups based upon the conformational similarity. There are 15, 20, 18 and 6 minima that are possible for the four cases respectively and these fall into 11 different groups. A study of these minima shows that, (i) some minima contain hydrogen bonds - either 4-->1 or 1-->2 type, (ii) the low energy minima qualify themselves as bend conformations, (iii) cis' and trans' conformations are possible for the prolyl residue as also the C(gamma)-endo and C(gamma)-exo puckerings, and (iv) for Pro-cis-Pro, cis' at the first prolyl residue is ruled out, due to the high energy. The available crystal structure data on proteins and peptides, containing cis-Pro segment have been examined with a view to find the minima that occur in solid state. The data from protein show that they fall under two groups. The conformation at X in X-cis-Pro is near extended when it is a non-glycyl residue. In both peptides and proteins there exists a preference for trans' conformation at prolyl residue over cis' when X is a non-glycyl residue. The minima obtained can be useful in modelling studies.