Effect of mutation and genetic background on drug resistance in Mycobacterium tuberculosis.

Bacterial factors may contribute to the global emergence and spread of drug-resistant tuberculosis (TB). Only a few studies have reported on the interactions between different bacterial factors. We studied drug-resistant Mycobacterium tuberculosis isolates from a nationwide study conducted from 2000 to 2008 in Switzerland. We determined quantitative drug resistance levels of first-line drugs by using Bactec MGIT-960 and drug resistance genotypes by sequencing the hot-spot regions of the relevant genes. We determined recent transmission by molecular methods and collected clinical data. Overall, we analyzed 158 isolates that were resistant to isoniazid, rifampin, or ethambutol, 48 (30.4%) of which were multidrug resistant. Among 154 isoniazid-resistant strains, katG mutations were associated with high-level and inhA promoter mutations with low-level drug resistance. Only katG(S315T) (65.6% of all isoniazid-resistant strains) and inhA promoter -15C/T (22.7%) were found in molecular clusters. M. tuberculosis lineage 2 (includes Beijing genotype) was associated with any drug resistance (adjusted odds ratio [OR], 3.0; 95% confidence interval [CI], 1.7 to 5.6; P < 0.0001). Lineage 1 was associated with inhA promoter -15C/T mutations (OR, 6.4; 95% CI, 2.0 to 20.7; P = 0.002). We found that the genetic strain background influences the level of isoniazid resistance conveyed by particular mutations (interaction tests of drug resistance mutations across all lineages; P < 0.0001). In conclusion, M. tuberculosis drug resistance mutations were associated with various levels of drug resistance and transmission, and M. tuberculosis lineages were associated with particular drug resistance-conferring mutations and phenotypic drug resistance. Our study also supports a role for epistatic interactions between different drug resistance mutations and strain genetic backgrounds in M. tuberculosis drug resistance.

L'ostéolyse expansive familiale : manifestations otologiques et dentaires d'origine génétique

RESUME Nous rapportons l'étude d'une famille de 49 membres sur 5 générations. Parmi 35 membres étudiés, 18 sont atteints d'Osteolyse Expansive Familiale (OEF). L'OEF est une dysplasie osseuse génétique rare, autosomique dominante, dont les altérations locales et générales du squelette ont une distribution périphérique prédominante qui devient manifeste à partir de la deuxième décennie de vie. Une résorption ostéoclastique progressive, accompagnée d'une faible activité ostéoblastique, est à l'origine d'une expansion médullaire osseuse. Cette dernière est caractérisée par une raréfaction de la moelle osseuse qui est remplacée par du tissu fibreux et de la graisse. L'amincissement de la moelle osseuse aboutit à des déformations invalidantes, sévères et douloureuses du squelette, avec tendance aux fractures spontanées. La première manifestation clinique de la maladie est une surdité de transmission très précoce résultant d'une lyse de la chaîne ossiculaire. Radiologiquement, il existe toujours une pneumatisation marquée de la mastoïde et du rocher. Les dents montrent des signes importants de résorption osseuse au niveau de la région apicale et/ou du collet, dont l'aspect est caractéristique et unique. La phosphatase alcaline sérique, l'hydroxyproline et la deoxypiridoline urinaire sont élevées à des taux variables. Le taux de calcium et d'hormone parathyroïdienne est normal. Le traitement par les diphosphonates, la calcitonine et la vitamine D est inefficace. Histologiquement, l'OEF présente des similitudes avec la maladie de Paget, mais l'âge de début, la distribution des lésions osseuses, les altérations dentaires et de l'oreille moyenne, ainsi que la progression clinique sont différents. Il en va de même pour la dysplasie fibreuse, l'ostéite fibro-kystique et l'ostéogénèse imparfaite. Le gêne responsable de la maladie se localise dans la région du chromosome 18q21-22. Récemment, des mutations du TNFRSF 11A, gêne qui codifie le RANK, ont été identifiées comme étant la cause de l'OEF. La duplication de la 18ème paire de base au niveau de l'exon 1 suggère qu'il correspond au site de l'anomalie. La technique chirurgicale et les résultats audiométriques à court et long terme de 13 interventions chez 8 patients sont présentés. ABSTRACT Objectives: Familial Expansive Osteolysis (EEO) is a rare autosomal dominant bone dys¬plasia. The disease can show general and focal skeletal alterations, the latter having a pre¬dominantly peripheral distribution. Onset occurs after the second decade of life. Patients and methods: We present the study, of 30 years, of a family consisting of 49 members covering five generations. Results: Among the 35 members studied, 18 have familial expansive osteolysis (FEO). The first clinical sign of the condition is transmission deafness at an early age. The features of the teeth has a unique and characteristic appearance. Thinning of the corti¬cal bone leads to severe, painful, disabling deformities. Serum alkaline phosphatase, and urinary hydroxyproline and deoxipyridinoline are elevated. Calcium and parathyroid hor¬mone are normal. Treatment with diphosphonates, calcitonin and vitamin D has been unsuccessful. We present the surgical technology and the results to short and long term of 13 interventions on 8 patients. Conclusion: Progressive osteoclastic reabsorption accompanied by weak osteoblastic activ¬ity results in medullary expansion characterized by rarefaction of the bone marrow, which is replaced by fibrous tissue and fat. FE0 is histologically similar to Paget disease, but the age of onset, the distribution of the bone lesions, the dental and middle ear alterations, and the clin¬ical progression are different. These features also differentiate FE0 from fibrous dysplasia, fibrocystic osteitis and imperfect osteogenesis. The gene responsible for EEO is located in the 18q21-22 chromosome region. Mutations in TNFRSF11A, the gene encoding receptor activa¬tor of nuclear factor-kappa-B (RANK), has been recently identified as the cause of FEO. A duplication of 18 base pairs in exon 1 of the TNFRSF11A gene suggests that this corresponds to the site of the anomaly and can be considered a "hot spot" for mutations.

Puutavaranosturin teleskooppipuomin kehittäminen ultralujilla teräksillä toteutettavaksi

Diplomityössä on tutkittu ultralujien terästen käyttömahdollisuuksia puutavaranosturin puomirakenteissa. Työn tavoitteena on ollut suunnitella uusi puomikonstruktio, joka on kevyempi kuin aiemmat ratkaisut, mutta täyttää kuitenkin sovellettavien standardien asettamat vaatimukset väsymisen, staattisen kestävyyden ja stabiliteetin suhteen. Työ on tehty vertailemalla erilaisten uusien profiilien ja rakenneyksityiskohtien ominaisuuksia toisiinsa ja vanhaan rakenteeseen. Vertailukriteereinä on käytetty elastista taivutuskapasiteettia, kriittistä lommahduskuormaa, väsymislujuutta sekä hitsaus- ja materiaalikustannuksia. Työn lopputuloksena saatiin ehdotus uudeksi teleskooppipuomiksi, joka on noin 8 % kevyempi kuin nykyinen ratkaisu.

A Graphical Pattern Editor for Java Frameworks

Ohjelmistojen uudelleenkäyttö on hyvin tärkeä käsite ohjelmistotekniikan alueella.Ohjelmistojen uudelleenkäyttötekniikat parantavat ohjelmistokehitysprosessin laatua. Yleisiä ratkaisuja sekä ohjelmiston suunnittelun että arkkitehtuurin uudelleenkäyttöön ovat olio-ohjelmointi ja sovelluskehykset. Tähän asti ei ole ollut olemassa yleisiä tapoja sovelluskehysten erikoistamiseen. Monet nykyääntunnetuista sovelluskehyksistä ovat hyvin suuria ja mutkikkaita. Tällaisten sovelluskehyksien käyttö on monimutkaista myös kokeneille ohjelmoijille. Hyvin dokumentoidut uudelleenkäytettävät sovelluskehyksen rajapinnat parantavat kehyksen käytettävyyttä ja tehostavat myös erikoistamisprosessiakin sovelluskehyksen käyttäjille. Sovelluskehyseditori (framework editor, JavaFrames) on prototyyppityökalu, jota voidaan käyttää yksinkertaistamaan sovelluskehyksen käyttöä. Perusajatus JavaFrames lähestymistavassa ovat erikoistamismallit, joita käytetään kuvamaan sovelluskehyksen uudelleenkäytettäviä rajapintoja. Näihin malleihin perustuen JavaFrames tarjoaa automaattisen lähdekoodi generaattorin, dokumentoinninja arkkitehtuurisääntöjen tarkistuksen. Tämä opinnäyte koskee graafisen mallieditorin kehittämistä JavaFrames ympäristöön. Työssä on laadittu työkalu,jonka avulla voidaan esittää graafisesti erikoistamismalli. Editori sallii uusien mallien luomisen, vanhojen käyttämättä olevien poistamisen, kuten myös yhteyksien lisäämisen mallien välille. Tällainen graafinen tuki JavaFrames ympäristöönvoi huomattavasti yksinkertaistaa sen käyttöä ja tehdä sovellusten kehittämisprosessista joustavamman.

A modified structural stress method for fatigue assessment of welded structures

Fatigue life assessment of weldedstructures is commonly based on the nominal stress method, but more flexible and accurate methods have been introduced. In general, the assessment accuracy is improved as more localized information about the weld is incorporated. The structural hot spot stress method includes the influence of macro geometric effects and structural discontinuities on the design stress but excludes the local features of the weld. In this thesis, the limitations of the structural hot spot stress method are discussed and a modified structural stress method with improved accuracy is developed and verified for selected welded details. The fatigue life of structures in the as-welded state consists mainly of crack growth from pre-existing cracks or defects. Crack growth rate depends on crack geometry and the stress state on the crack face plane. This means that the stress level and shape of the stress distribution in the assumed crack path governs thetotal fatigue life. In many structural details the stress distribution is similar and adequate fatigue life estimates can be obtained just by adjusting the stress level based on a single stress value, i.e., the structural hot spot stress. There are, however, cases for which the structural stress approach is less appropriate because the stress distribution differs significantly from the more common cases. Plate edge attachments and plates on elastic foundations are some examples of structures with this type of stress distribution. The importance of fillet weld size and weld load variation on the stress distribution is another central topic in this thesis. Structural hot spot stress determination is generally based on a procedure that involves extrapolation of plate surface stresses. Other possibilities for determining the structural hot spot stress is to extrapolate stresses through the thickness at the weld toe or to use Dong's method which includes through-thickness extrapolation at some distance from the weld toe. Both of these latter methods are less sensitive to the FE mesh used. Structural stress based on surface extrapolation is sensitive to the extrapolation points selected and to the FE mesh used near these points. Rules for proper meshing, however, are well defined and not difficult to apply. To improve the accuracy of the traditional structural hot spot stress, a multi-linear stress distribution is introduced. The magnitude of the weld toe stress after linearization is dependent on the weld size, weld load and plate thickness. Simple equations have been derived by comparing assessment results based on the local linear stress distribution and LEFM based calculations. The proposed method is called the modified structural stress method (MSHS) since the structural hot spot stress (SHS) value is corrected using information on weld size andweld load. The correction procedure is verified using fatigue test results found in the literature. Also, a test case was conducted comparing the proposed method with other local fatigue assessment methods.

Diphenyl urea derivatives as inhibitors of transketolase: a structure-based virtual screening.

Transketolase is an enzyme involved in a critical step of the non-oxidative branch of the pentose phosphate pathway whose inhibition could lead to new anticancer drugs. Here, we report new human transketolase inhibitors, based on the phenyl urea scaffold, found by applying structure-based virtual screening. These inhibitors are designed to cover a hot spot in the dimerization interface of the homodimer of the enzyme, providing for the first time compounds with a suggested novel binding mode not based on mimicking the thiamine pyrophosphate cofactor.

Allosteric conversation in the androgen receptor ligand-binding domain surfaces

Androgen receptor (AR) is a major therapeutic target that plays pivotal roles in prostate cancer (PCa) and androgen insensitivity syndromes. We previously proposed that compounds recruited to ligand-binding domain (LBD) surfaces could regulate AR activity in hormone-refractory PCa and discovered several surface modulators of AR function. Surprisingly, the most effective compounds bound preferentially to a surface of unknown function [binding function 3 (BF-3)] instead of the coactivator-binding site [activation function 2 (AF-2)]. Different BF-3 mutations have been identified in PCa or androgen insensitivity syndrome patients, and they can strongly affect AR activity. Further, comparison of AR x-ray structures with and without bound ligands at BF-3 and AF-2 showed structural coupling between both pockets. Here, we combine experimental evidence and molecular dynamic simulations to investigate whether BF-3 mutations affect AR LBD function and dynamics possibly via allosteric conversation between surface sites. Our data indicate that AF-2 conformation is indeed closely coupled to BF-3 and provide mechanistic proof of their structural interconnection. BF-3 mutations may function as allosteric elicitors, probably shifting the AR LBD conformational ensemble toward conformations that alter AF-2 propensity to reorganize into subpockets that accommodate N-terminal domain and coactivator peptides. The induced conformation may result in either increased or decreased AR activity. Activating BF-3 mutations also favor the formation of another pocket (BF-4) in the vicinity of AF-2 and BF-3, which we also previously identified as a hot spot for a small compound. We discuss the possibility that BF-3 may be a protein-docking site that binds to the N-terminal domain and corepressors. AR surface sites are attractive pharmacological targets to develop allosteric modulators that might be alternative lead compounds for drug design.

Tänään ostetaan.. vuodet Pera Pirkolana mainonnan ihmemaassa

Tutkimuksen tavoitteena on valottaa tekijöitä, jotka vaikuttivat Pera Pirkolan päätymiseen mainosmusiikin tekijäksi, sekä millaisena hän tänä päivänä näkee uravalintansa ja sen tulevaisuuden näkymät. Tutkimus toteutettiin 11.10.2006 tehdyn teemahaastattelun muodossa, joka sitten kirjoitettiin sanatarkaksi tekstiksi ja analysoitiin käyttäen laadullista sisältöanalyysiä ja järjestettiin teemojen mukaan loogisiksi kokonaisuuksiksi. Kävi ilmi, että haastateltava kokee olevansa täydellisesti itselleen sopivalla alalla, eikä voi kuvitellakaan tekevänsä mitään ainakaan kovin paljon nykyisestä toimenkuvastaan poikkeavaa. Haastateltava kuvaili avoimesti uraansa ja mm. firmansa Hot Spot syntyvaiheita. Kesällä 1985 hän oli ajautunut vappuna perustettuun Radio Cityyn töihin ja päätynyt sitä kautta tekemään radiomainontaa. Aseman yhteyteen perustettu Miracle Sound tarjosi työpaikan tuleviksi vuosiksi ennen Hot Spotin perustamista 1988. Radiomainonta Suomessa syntyi 80-luvun loppupuolella. Alan alku oli villiä aikaa. Kenelläkään ei ollut käsitystä kuinka asioita pitäisi tehdä, yrityksen ja erehdyksen kautta ala kuitenkin vuosien myötä koulutti tekijänsä. Töitä oli alan alkuaikoina vaikka muille jakaa, joten oman yrityksen perustaminen tuntui luonnolliselta jatkolta hyvin alkaneelle uralle Radio Cityssä. Alan liki olemattomat kouluttautumismahdollisuudet Suomessa ovat yksi keskeinen ongelma johon haastateltava toivoisi parannusta. Muita haastattelussa sivuttuja teemoja ovat mm. muusikoiden erilainen rooli kun tehdään musiikkia mainontaan, asiakkaan esittämät mahdolliset referenssiäänitteet haetusta musiikkityylistä ja niiden suhde omaan luovaan työhön - kuinka lähelle uskaltaa mennä sekä haastateltavan työskentelytavat ja niiden kehitys yhdessä yhtiökumppani Pekka Witikan kanssa.

Titaanisen valkaisutornin korjaussuunnitelma

Tämän työn tarkoituksena on poistaa toistuvasti esiintyneet vauriot titaanisessa valkaisutornissa Kuusankosken paperitehtailla. Vauriot esiintyivät melko pian käyttöönoton jälkeen ja niitä esiintyi toistuvasti jokaisen korjauksen jälkeen. Jatkuvatoimisen prosessin vuoksi käyttökatkokset eivät olleet suotavia. Aikataulu suunnittelulle ja korjaukselle oli erittäin tiukka, jolloin kenttämittauksia ei ollut mahdollista tehdä laskelmien tueksi. Tämän vuoksi tähän työtön parhaiten soveltuvaksi menetelmäksi valittiin FEA. Alkuperäisessä rakenteessa pääsäiliöön oli hitsattu pintatasku, jota käytettiin välisäiliönä varastoimaan suuri määrä vaarallista nestettä. Tämä aiheutti valkaisutornin vaipalle murtumia ja vuotoja sekä suuronnettomuuden riskin koko valkaisutornille. Kuormitustietojen puutteesta johtuen kuormitukset mallinnettiin virtuaalisesti FE-menetelmällä ja analyyttisin keinoin. Kuormitusten suuruudet arvioitiin konservatiivisesti. Tämän työn tärkein oivallus oli määritellä uudelleen pintataskun toiminto siten, että sitä ei enää käytetty nesteen välivarastona, vaan ohjaimena nesteelle. Tämä innovatiivinen ongelmankorjauskonsepti on havaittu onnistuneeksi, koska vaurioita ei ole enää esiintynyt viimeisimmän korjauksen jälkeen.

The attenuation of concentrations model: a new method for assessing mercury mobility in sediments

In this work we propose a new approach for the determination of the mobility of mercury in sediments based on spatial distribution of concentrations. We chose the Tainheiros Cove, located in the Todos os Santos Bay, Brazil, as the study area, for it has a history of mercury contamination due to a chloro-alkali plant that was active during 12 years. Twenty-six surface sediment samples were collected from the area and mercury concentrations were measured by cold vapour atomic absorption spectrophotometry. A contour map was constructed from the results, indicating that mercury accumulated in a "hot spot" where concentrations reach more than 1 µg g-1. The model is able to estimate mobility of mercury in the sediments based on the distances between iso-concentration contours that determines an attenuation of concentrations factor. Values of attenuation ranged between 0.0729 (East of the hot spot, indicating higher mobility) to 0.7727 (North of the hot spot, indicating lower mobility).

Fitossociologia e estrutura diamétrica da mata de galeria do Taquara, na reserva ecológica do IBGE, DF

(Florística e estrutura na mata do Taquara, Reserva Ecológica do IBGE, DF). As matas de Galeria, apesar de legalmente protegidas, vêm sendo sistematicamente substituídas visando a outras finalidades. As árvores (DAP³ 5 cm) na mata de Galeria do córrego do Taquara, na Reserva Ecológica do IBGE, no Distrito Federal, foram amostradas pelo método de quadrantes, com 250 pontos, dispostos em linhas estabelecidas ao longo do comprimento do córrego, desde as margens até os limites entre a mata e o cerrado. A amostragem de 1.000 árvores resultou na composição florística, na fitossociologia e na distribuição dos diâmetros dos troncos. No total foram amostradas 110 espécies de 49 famílias. O índice de diversidade de Shannon & Wiener foi estimado em 4,25 nats.ind-1. As famílias mais importantes foram: Leguminosae (lato sensu), Rubiaceae, Anacardiaceae, Euphorbiaceae e Sapindaceae, enquanto as espécies principais foram: Tapirira guianensis, Copaifera langsdorffii, Lamanonia ternata, Anadenanthera colubrina var. cebil, Piptocarpha macropoda, Alibertia macrophylla, Matayba guianensis, Pera glabrata, Guettarda viburnioides e Ixora warmingii. As estimativas da densidade e da área basal total foram de 1.573 árvores.ha-1, e 38,5 m².ha-1 respectivamente. A distribuição diamétrica indicou uma curva tendendo para o `J' invertido, evidenciando os baixos níveis de distúrbios ocorridos na mata. Uma comparação florística conduzida entre 21 matas de Galeria no Distrito Federal apontou a mata do Taquara como uma área rica, com 110 (29,1%) das 378 espécies listadas e similaridade de Sørensen variando entre 0,34 e 0,80, nas matas incluídas.

Laser-TIG hybrid welding process

Joining processes and techniques need to meet the trend of new applications and the development of new materials. The application in connection with thick and thin plates in industrial fields is wide and the joining technology is in very urgent need. The laser-TIG hybrid welding technology can play the respective advantages of both of them. One major advantage of the hybrid laser-TIG welding technology is its efficient use of laser energy. Additionally, it can develop into a high and new advanced welding technology and become a hot spot in both the application and research area. This thesis investigated laser –TIG hybrid welding with the aim of enlightening the reader on its advantages, disadvantages and future areas of improvement. The main objective is to investigate laser-TIG hybrid on the welding of various metals (steels, magnesium, aluminium etc.). In addition, it elaborates on various possible combinations on hybrid laser-TIG welding technology and their benefits. The possibility of using laser-TIG hybrid in welding of thick materials was investigated. The method applied in carrying out this research is by using literature review. The results showed that hybrid laser-TIG is applicable to almost all weldable metals. Also it proves to be effective in welding refractive metals. The possibility of welding with or without filler materials is of economic advantage especially in welding of materials with no filler material. Thick plate’s hybrid laser-TIG welding is showing great prospects although it normally finds its used in welding thin materials in the range of 0.4 to 0.8 mm. The findings show that laser-TIG hybrid welding can be a versatile welding process and therefore will be increasingly used industrially due to its numerous advantages and the development of new TIG arc that enhances its capabilities.

Notchikololiitosten FE-analyysit

Työn kandidaatintyössä tutkittiin kolollisen levyrakenteen hot spot -jännityksiä ja väsymiskestävyyttä varioimalla kolon sädettä. Työssä haluttiin selvittää, kuinka hot spot -jännitykset, rakenteen kestoikä ja rakenteen kriittinen kohta muuttuvat, kun kolon sädettä muutetaan. Työn tavoitteena oli myös tutkia, kuinka laboratoriossa suoritettujen väsytyskokeiden ja tietokoneella laskettujen elementtimallien tulokset eroavat toisistaan.

Identification of a new human mtDNA polymorphism (A14290G) in the NADH dehydrogenase subunit 6 gene

Leber's hereditary optic neuropathy (LHON) is a maternally inherited form of retinal ganglion cell degeneration leading to optic atrophy in young adults. Several mutations in different genes can cause LHON (heterogeneity). The ND6 gene is one of the mitochondrial genes that encodes subunit 6 of complex I of the respiratory chain. This gene is a hot spot gene. Fourteen Persian LHON patients were analyzed with single-strand conformational polymorphism and DNA sequencing techniques. None of these patients had four primary mutations, G3460A, G11788A, T14484C, and G14459A, related to this disease. We identified twelve nucleotide substitutions, G13702C, T13879C, T14110C, C14167T, G14199T, A14233G, G14272C, A14290G, G14365C, G14368C, T14766C, and T14798C. Eleven of twelve nucleotide substitutions had already been reported as polymorphism. One of the nucleotide substitutions (A14290G) has not been reported. The A14290G nucleotide substitution does not change its amino acid (glutamic acid). We looked for base conservation using DNA star software (MEGALIGN program) as a criterion for pathogenic or nonpathogenic nucleotide substitution in A14290G. The results of ND6 gene alignment in humans and in other species (mouse, cow, elegans worm, and Neurospora crassa mold) revealed that the 14290th base was not conserved. Fifty normal controls were also investigated for this polymorphism in the Iranian population and two had A14290G polymorphism (4%). This study provides evidence that the mtDNA A14290G allele is a new nonpathogenic polymorphism. We suggest follow-up studies regarding this polymorphism in different populations.

Genomic alterations detected by comparative genomic hybridization in ovarian endometriomas

Endometriosis is a complex and multifactorial disease. Chromosomal imbalance screening in endometriotic tissue can be used to detect hot-spot regions in the search for a possible genetic marker for endometriosis. The objective of the present study was to detect chromosomal imbalances by comparative genomic hybridization (CGH) in ectopic tissue samples from ovarian endometriomas and eutopic tissue from the same patients. We evaluated 10 ovarian endometriotic tissues and 10 eutopic endometrial tissues by metaphase CGH. CGH was prepared with normal and test DNA enzymatically digested, ligated to adaptors and amplified by PCR. A second PCR was performed for DNA labeling. Equal amounts of both normal and test-labeled DNA were hybridized in human normal metaphases. The Isis FISH Imaging System V 5.0 software was used for chromosome analysis. In both eutopic and ectopic groups, 4/10 samples presented chromosomal alterations, mainly chromosomal gains. CGH identified 11q12.3-q13.1, 17p11.1-p12, 17q25.3-qter, and 19p as critical regions. Genomic imbalances in 11q, 17p, 17q, and 19p were detected in normal eutopic and/or ectopic endometrium from women with ovarian endometriosis. These regions contain genes such as POLR2G, MXRA7 and UBA52 involved in biological processes that may lead to the establishment and maintenance of endometriotic implants. This genomic imbalance may affect genes in which dysregulation impacts both eutopic and ectopic endometrium.