M.tuberculosis Pantothenate Kinase: Dual Substrate Specificity and Unusual Changes in Ligand Locations

Kinetic measurements of enzyme activity indicate that type I pantothenate kinase from Mycobacterium tuberculosis has dual substrate specificity for ATP and GTP, unlike the enzyme from Escherichia coli, which shows a higher specificity for ATP. A molecular explanation for the difference in the specificities of the two homologous enzymes is provided by the crystal structures of the complexes of the M. tuberculosis enzyme with (1) GMPPCP and pantothenate, (2) GDP and phosphopantothenate, (3) GDP, (4) GDP and pantothenate, (5) AMPPCP, and (6) GMPPCP, reported here, and the structures of the complexes of the two enzymes involving coenzyme A and different adenyl nucleotides reported earlier. The explanation is substantially based on two critical substitutions in the amino acid sequence and the local conformational change resulting from them. The structures also provide a rationale for the movement of ligands during the action of the mycobacterial enzyme. Dual specificity of the type exhibited by this enzyme is rare. The change in locations of ligands during action,observed in the case of the M. tuberculosis enzyme, is unusual, so is the striking difference between two homologous enzymes in the geometryof the binding site, locations of ligands, and specificity. Furthermore, the dual specificity of the mycobacterial enzyme appears to have been caused by a biological necessity. (C) 2010 Elsevier Ltd.All rights reserved.

Cooperative Replies to Unbelievable Assertions

We propose a dialogue protocol for situations in which an agent makes to another agent an assertion that the other agent finds impossible to believe. In this interaction, unbelievable assertions are rejected using explanations formed by logical interpolation and new assertions are being made such that all previous rebuttals are taken into account.

Structural alteration from non-B to B-form could reflect DNase I hypersensitivity

Preferential cleavage of active genes by DNase I has been correlated with a structurally altered conformation of DNA at the hypersensitive site in chromatin. To have a better understanding of the structural requirements for gene activation as probed by DNase I action, digestability by DNase I of synthetic polynucleotides having the ability to adopt B and non-B conformation (like Z-form) was studied which indicated a marked higher digestability of the B-form of DNA. Left handed Z form present within a natural sequence in supercoiled plasmid also showed marked resistance towards DNase I digestion. We show that alternating purine-pyrimidine sequences adopting Z-conformation exhibit DNAse I foot printing even in a protein free system. The logical deductions from the results indicate that 1) altered structure like Z-DNA is not a favourable substrate for DNase I, 2) both the ends of the alternating purine-pyrimidine insert showed hypersensitivity, 3) B-form with a minor groove of 12-13 A is a more favourable substrate for DNase I than an altered structure, 4) any structure of DNA deviating largely from B form with a capacity to flip over to the B-form are potential targets for the DNase I enzymic probes in naked DNA.

Monikasvoinen TAVA-partisiippi : Tutkimus suomen TAVA-partisiipin käyttökonteksteista ja verbiliittojen kieliopillistumisesta

The multifaceted passive present participle in Finnish This study investigates the uses of the passive present participle in Finnish. The participle occurs in a variety of syntactic environments and exhibits a rich polysemy. Former descriptions have treated it as a mainly modal element, but it has several non-modal uses as well. The present study provides an overview of its uses and meanings, with the main focus on the factors which trigger the modal reading. In addition, the study contains two case studies on modal periphrastic constructions consisting of the verb 'to be' and the present passive participle, the Obligation construction, e.g., on men-tä-vä [is go-pass-ptc], and the Possiblity construction, e.g., on pelaste-tta-v-i-ssa [is save-pass-ptc-pl-ine]. The study is based on empirical data of 9000 sentences obtained from i) large collections of transcribed material from Finnish dialects, ii) a corpus of modern Finnish newspaper texts, iii) corpora of Old Finnish texts. Both in colloquial and standard Finnish the reading of the participle is highly dependent of the context and determined by such factors as the overall syntactic environment and other co-occurring elements. One of the main findings here is that the Finnish passive present participle is not modal per se. The contextual modal reading arises whenever the state of affairs is conceptualized from the viewpoint of the implied subject of the participle, and the meaning of possibility or obligation depends mostly on whether the situation is pleasant or undesirable. In sections examining the grammaticalization of the Possibility and Obligation constructions, the perspective is diachronic. Both constructions have derived from copula constructions with the passive present participle as a predicate (adjective or adverb). These sections show how a linguistic change can be investigated on the basis of the patterns of usage in the empirical data. The Possibility construction is currently going through a restructuration to a passive verbal complex. The source of this construction is reflected in its present-day use by the fact that it heavily biased towards a small set of verbs. The Obligation construction has grammaticalized to a construction comparable to a compound tense. Patterns of use of the construction show that grammaticalization originates in specific syntactic constructions with an implication of practical necessity. Furthermore, it is shown that the Obligation construction has grammaticalized in different directions in standard and colloquial Finnish. Differing from the study on most typical phenomena investigated in the literature on grammaticalization of modality, the present study opens new perspectives and methods for discussion on these questions.

Using a botanic garden collection to test a bioclimatic vegetation scheme

Vegetation maps and bioclimatic zone classifications communicate the vegetation of an area and are used to explain how the environment regulates the occurrence of plants on large scales. Many practises and methods for dividing the world’s vegetation into smaller entities have been presented. Climatic parameters, floristic characteristics, or edaphic features have been relied upon as decisive factors, and plant species have been used as indicators for vegetation types or zones. Systems depicting vegetation patterns that mainly reflect climatic variation are termed ‘bioclimatic’ vegetation maps. Based on these it has been judged logical to deduce that plants moved between corresponding bioclimatic areas should thrive in the target location, whereas plants moved from a different zone should languish. This principle is routinely applied in forestry and horticulture but actual tests of the validity of bioclimatic maps in this sense seem scanty. In this study I tested the Finnish bioclimatic vegetation zone system (BZS). Relying on the plant collection of Helsinki University Botanic Garden’s Kumpula collection, which according to the BZS is situated at the northern limit of the hemiboreal zone, I aimed to test how the plants’ survival depends on their provenance. My expectation was that plants from the hemiboreal or southern boreal zones should do best in Kumpula, whereas plants from more southern and more northern zones should show progressively lower survival probabilities. I estimated probability of survival using collection database information of plant accessions of known wild origin grown in Kumpula since the mid 1990s, and logistic regression models. The total number of accessions I included in the analyses was 494. Because of problems with some accessions I chose to separately analyse a subset of the complete data, which included 379 accessions. I also analysed different growth forms separately in order to identify differences in probability of survival due to different life strategies. In most analyses accessions of temperate and hemiarctic origin showed lower survival probability than those originating from any of the boreal subzones, which among them exhibited rather evenly high probabilities. Exceptionally mild and wet winters during the study period may have killed off hemiarctic plants. Some winters may have been too harsh for temperate accessions. Trees behaved differently: they showed an almost steadily increasing survival probability from temperate to northern boreal origins. Various factors that could not be controlled for may have affected the results, some of which were difficult to interpret. This was the case in particular with herbs, for which the reliability of the analysis suffered because of difficulties in managing their curatorial data. In all, the results gave some support to the BZS, and especially its hierarchical zonation. However, I question the validity of the formulation of the hypothesis I tested since it may not be entirely justified by the BZS, which was designed for intercontinental comparison of vegetation zones, but not specifically for transcontinental provenance trials. I conclude that botanic gardens should pay due attention to information management and curational practices to ensure the widest possible applicability of their plant collections.

On the fundamentals of coherence theory

In the thesis I study various quantum coherence phenomena and create some of the foundations for a systematic coherence theory. So far, the approach to quantum coherence in science has been purely phenomenological. In my thesis I try to answer the question what quantum coherence is and how it should be approached within the framework of physics, the metatheory of physics and the terminology related to them. It is worth noticing that quantum coherence is a conserved quantity that can be exactly defined. I propose a way to define quantum coherence mathematically from the density matrix of the system. Degenerate quantum gases, i.e., Bose condensates and ultracold Fermi systems, form a good laboratory to study coherence, since their entropy is small and coherence is large, and thus they possess strong coherence phenomena. Concerning coherence phenomena in degenerate quantum gases, I concentrate in my thesis mainly on collective association from atoms to molecules, Rabi oscillations and decoherence. It appears that collective association and oscillations do not depend on the spin-statistics of particles. Moreover, I study the logical features of decoherence in closed systems via a simple spin-model. I argue that decoherence is a valid concept also in systems with a possibility to experience recoherence, i.e., Poincaré recurrences. Metatheoretically this is a remarkable result, since it justifies quantum cosmology: to study the whole universe (i.e., physical reality) purely quantum physically is meaningful and valid science, in which decoherence explains why the quantum physical universe appears to cosmologists and other scientists very classical-like. The study of the logical structure of closed systems also reveals that complex enough closed (physical) systems obey a principle that is similar to Gödel's incompleteness theorem of logic. According to the theorem it is impossible to describe completely a closed system within the system, and the inside and outside descriptions of the system can be remarkably different. Via understanding this feature it may be possible to comprehend coarse-graining better and to define uniquely the mutual entanglement of quantum systems.

On the Modal Content of A Posteriori Necessities

This paper challenges the Kripkean interpretation of a posteriori necessities. It will be demonstrated, by an analysis of classic examples, that the modal content of supposed a posteriori necessities is more complicated than the Kripkean line suggests. We will see that further research is needed concerning the a priori principles underlying all a posteriori necessities. In the course of this analysis it will emerge that the modal content of a posteriori necessities can be best described in terms of a Finean conception of modality – by giving essences priority over modality. The upshot of this is that we might be able to establish the necessity of certain supposed a posteriori necessities by a priori means.

Purification and characterization of three toxins and two agglutinins from Abrus precatorius seed by using lactamyl-Sepharose affinity chromatography

Three toxins, abrin-I, -II, and -III, and two agglutinins, APA-I and -II, were purified from the seeds of Abrus precatorius by lactamyl-Sepharose affinity chromatography followed by gel filtration and DEAE-Sephacel column chromatography. abrin-I did not bind on DEAE-Sephacel column chromatography and the bound abrin-II, abrin-III, APA-I, and APA-II were eluted with a sodium acetate gradient. The identity of each protein was established by sodium dodecylsulfate-polyacrylamide gel electrophoresis and isoelectric focusing. The relative molecular weights are abrin-I, 64,000; abrin-II and abrin-III, 63,000 each: APA-I, 130,000; and APA-II, 128,000. Isoelectric focusing revealed microheterogeneity due to the presence of isoforms in each protein. Toxicity and binding studies further confirmed the differences among the lectins. The time course of inhibition of protein synthesis in thymocytes by the toxins showed lag times of 78, 61, and 72 min with Ki's of 0.55, 0.99, and 0.74 ms−1 at a 0.63 nImage concentration of each of abrin-I, -II, and -III, respectively. A Scatchard plot obtained from the equilibrium measurement for the lectins binding to lactamyl-Sepharose beads showed nonlinearity, indicating a cooperative mode of binding which was not observed for APA-I binding to Sepharose 4B beads. Further, by the criterion of the isoelectric focusing profile, it was shown that the least toxic abrin-I and the highly toxic abrin-II isolated by lactamyl-Sepharose chromatography were not retained on a low-affinity Sepharose 4B matrix, which signifies the necessity of using a high-affinity matrix for the purification of the lectins.

”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.

Työntekijän näkökulmat ja oppiminen ulkoistusprojektissa : "Aluks pelkää muutosta ja sit pelkää, ettei mikään muutukaan."

The aim of this master s thesis was to clarify employees views on outsourcing. The main questions of the study were 1) How the employees dealt with the change created by outsourcing and what things they felt important when implementing the change? 2) What kind of organizational questions the employees paid attention to when moving from one organization to another? 3) What kind of management issues the employees brought up in the outsourcing process? and 4) How the employees reflected change while experienced outsourcing? The theoretical foundations of the study were Jack Mezirow s theory of transformational learning and Yrjö Engeström s theory of expansive learning. The management of outsourcing was viewed by John P. Kotter s change management model. Research casted light on transformation and learning on four levels of analysis: on individual, organizational and management levels and on the level of reflection. The target of the study were the outsourced employees, who were moved from a Finnish public corporation to a private ITC organization along with the services they produce. The study material was eleven interviews from the outsourced employees. The study was implemented by fenomenographical theme analysis. The analysis revealed results in all four levels. On the individual level the main results were the importance of systematic and open information, meaning of social and technical integration and the feeling of employee s own control. On the organizational level the move from the public sector to private and all the changes in organizational culture and in fringe benefitswere fundamental. Organizational learning was analyzed with expansive learning theory. Expanding was perceived in four dimensions: temporal dimension, spatial dimension, responsibility-moral dimension and developmental dimension. On the management level the actions of one s closest manager was vital, as was the upper management s clear engagement and a shared view of the necessity of a change. In the data was found employees reflective talking, which was indicating the meaning of the change and which was interpreted from the learning point of view. According to this study, it is possible to identify and analyze reflective talk and that way have information about employees learning in an organizational change. It was prominent to notice how reflection in the process of outsourcing is extremely versatile and extensive.

Normal state tunneling conductance of perovskite oxides: Implications for high-Tc superconductors

We have investigated tunneling conductances in disordered, normally conducting perovskite oxides close to the metal�insulator transition. We show that the normal state tunneling conductance of perovskite oxides can be cast in a general form G(V) = G0[1 + curly logical orV/V*curly logical orn] with 1?n?0.5 and where V* is an intrinsic energy scale. The exponent n graduall y increases from 0.5 to 1 as the metal-insulator (M-I) transition is approached. In the high-Tc Bi(2212) cuprates, the normally observed, linear G(V)(n=1) can be made sub-linear (n<1) by substitution of Ca with Y. From the similarity of the linear conductances, we suggest proximity to the M-I transition as a likely cause for this G(V)logical or, bar below V dependence. In systems showing linear conductances (nreverse similar, equals1), we find that ?G/?Vreverse similar, equalsG?0 with ?reverse similar, equals 1 and the intrinsic energy scale V*reverse similar, equals25�75 meV in the different oxides investigated.

The energy balance in the Ramdas layer

On calm clear nights, air at a height of a few decimetres above bare soil can be cooler than the surface by several degrees in what we shall call the Ramdas layer (Ramdas and Atmanathan, 1932). The authors have recently offered a logical explanation for such a lifted temperature minimum, together with a detailed numerical model. In this paper, we provide physical insight into the phenomenon by a detailed discussion of the energy budget in four typical cases, including one with a lifted minimum. It is shown that the net cooling rate near ground is the small difference between two dominant terms, representing respectively radiative upflux from the ground and from the air layers just above ground. The delicate energy balance that leads to the lifted minimum is upset by turbulent transport, by surface emissivity approaching unity, or by high ground cooling rates. The rapid variation of the flux emissivity of humid air is shown to dominate radiative transport near the ground.

BSSB: BLAST Server for Structural Biologists

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processing BLAST output, but none of them provide three-dimensional structure visualization. This shortcoming has been addressed in the proposed tool BLAST Server for Structural Biologists (BSSB), which maps a BLAST output onto the three-dimensional structure of the subject protein. The three-dimensional structure of the subject protein is represented using a three-color coding scheme (identical: red; similar: yellow; and mismatch: white) based on the pairwise alignment obtained. Thus, the user will be able to visualize a possible three-dimensional structure for the query protein sequence. This information can be used to gain a deeper insight into the sequence-structure correlation. Furthermore, the additional structure-level information enables the user to make coherent and logical decisions regarding the type of input model structure or fragment that can be used for molecular replacement calculations. This tool is freely available to all users at http://bioserver1.physics.iisc.ernet.in/bssb/.

From polarization to convergence: need to mend the broken patent system

For more than two hundred years, the world has discussed the issue of whether to continue the process of patenting or whether to do away with it. Developed countries remain polarized for various reasons but nevertheless the pro patent regime continued. The result was a huge volume of patents. The present article explains the implications of excessive volume of patents and conditions under which prior art search fails. This article highlights the importance and necessity of standardization efforts so as to bring about convergence of views on patenting.

Nature's Swiss Army Knives: Ovipositor Structure Mirrors Ecology in a Multitrophic Fig Wasp Community

Background: Resource partitioning is facilitated by adaptations along niche dimensions that range from morphology to behaviour. The exploitation of hidden resources may require specially adapted morphological or sensory tools for resource location and utilisation. Differences in tool diversity and complexity can determine not only how many species can utilize these hidden resources but also how they do so. Methodology and Principal Findings: The sclerotisation, gross morphology and ultrastructure of the ovipositors of a seven-member community of parasitic wasps comprising of gallers and parasitoids developing within the globular syconia (closed inflorescences) of Ficus racemosa (Moraceae) was investigated. These wasps also differ in their parasitism mode (external versus internal oviposition) and their timing of oviposition into the expanding syconium during its development. The number and diversity of sensilla, as well as ovipositor teeth, increased from internally ovipositing to externally ovipositing species and from gallers to parasitoids. The extent of sclerotisation of the ovipositor tip matched the force required to penetrate the syconium at the time of oviposition of each species. The internally ovipositing pollinator had only one type of sensillum and a single notch on the ovipositor tip. Externally ovipositing species had multiple sensilla types and teeth on their ovipositors. Chemosensilla were most concentrated at ovipositor tips while mechanoreceptors were more widely distributed, facilitating the precise location of hidden hosts in these wasps which lack larval host-seeking behaviour. Ovipositor traits of one parasitoid differed from those of its syntopic galler congeners and clustered with those of parasitoids within a different wasp subfamily. Thus ovipositor tools can show lability based on adaptive necessity, and are not constrained by phylogeny. Conclusions/Significance: Ovipositor structure mirrored the increasingly complex trophic ecology and requirements for host accessibility in this parasite community. Ovipositor structure could be a useful surrogate for predicting the biology of parasites in other communities.