Genes outside The Hla Region affecting Susceptibility to Type 1 Diabetes - The Role of Iddm2 and Iddm9 in the Finnish Population

Tyypin 1 diabeteksen perinnöllinen alttius Suomessa - HLA-alueen ulkopuolisten alttiuslokusten IDDM2 ja IDDM9 rooli taudin periytymisessä HLA-alue, joka sijaitsee kromosomissa 6p21.3, vastaa noin puolesta perinnöllisestä alttiudesta sairastua tyypin 1 diabetekseen. Myös HLA-alueen ulkopuolisten lokusten on todettu liittyvän sairausalttiuteen. Näistä kolmen lokuksen on varmistettu olevan todellisia alttiuslokuksia ja lisäksi useiden muiden, vielä varmistamattomien lokusten, on todettu liittyvän sairausalttiuteen. Tässä tutkimuksessa 12:n HLA-alueen ulkopuolisen alttiuslokuksen kytkentä tyypin 1 diabetekseen tutkittiin käyttäen 107:aa suomalaista multiplex-perhettä. Jatkotutkimuksessa analysoitiin IDDM9-alueen kytkentä ja assosiaatio sairauteen laajennetuissa perhemateriaaleissa sekä IDDM2-alueen mahdollinen interaktio HLA-alueen kanssa sairauden muodostumisessa. Lisäksi suoritettiin IDDM2-alueen suojaavien haplotyyppien alatyypitys tarkoituksena tutkia eri haplotyyppien käyttökelpoisuutta sairastumisriskin tarkempaa ennustamista varten. Ensimmäisessä kytkentätutkimuksessa ei löytynyt koko genomin tasolla merkitsevää tai viitteellistä kytkentää tutkituista HLA-alueen ulkopuolisista lokuksista. Voimakkain havaittu nimellisen merkitsevyyden tavoittava kytkentä nähtiin IDDM9-alueen markkerilla D3S3576 (MLS=1.05). Tutkimuksessa ei kyetty varmistamaan tai sulkemaan pois aiempia kytkentähavaintoja tutkituilla lokuksilla, mutta IDDM9-alueen jatkotutkimuksessa havaittu voimakas kytkentä (MLS=3.4) ja merkitsevä assosiaatio (TDT p=0.0002) viittaa vahvasti siihen, että 3q21-alueella sijaitsee todellinen tyypin 1 diabeteksen alttiusgeeni, jolloin alueen kattava assosiaatiotutkimus olisi perusteltu jatkotoimenpide. Sairauteen altistava IDDM2-alueen MspI-2221 genotyyppi CC oli nimellisesti yleisempi matalan tai kohtalaisen HLA-sairastumisriskin diabeetikoilla, verrattuna korkean HLA-riskin potilaisiin (p=0.05). Myös genotyyppijakauman vertailu osoitti merkitsevää eroa ryhmien välillä (p=0.01). VNTR-haplotyyppitutkimus osoitti, että IIIA/IIIA-homotsygootin sairaudelta suojaava vaikutus on merkitsevästi voimakkaampi kuin muiden luokka III:n genotyypeillä. Nämä tulokset viittaavat IDDM2-HLA -vuorovaikutukseen sekä siihen että IDDM2-alueen haplotyyppien välillä esiintyy etiologista heterogeniaa. Tämän johdosta IDDM2-alueen haplotyyppien tarkempi määrittäminen voisi tehostaa tyypin 1 diabeteksen riskiarviointia.

DnaSP Version 5. DNA Sequence Polymorphism

DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.

Cancer incidence in Vaud (2003-2007)

CANCER CARE FACILITIES: In 2005, the registration area had about 3200 hospital beds available for cancer diagnosis and treatment (about 5 per 1000 residents). There were about 3600 hospital medical residents and private practitioners (1 per 180 residents). The canton has a major, multidisciplinary, public university oncology and radiotherapy centre and two private radiotherapy units (available to all residents), as well as several peripheral (mostly hospital-based) medical and surgical oncology facilities and specialists. REGISTRY STRUCTURE AND METHODS: The registry is part of the Cancer Epidemiology Unit of the Institute of Social and Preventive Medicine within the Faculty of Biology and Medicine of the University of Lausanne. Notiĺcation is voluntary. The registry's main sources of information are the University Institute of Pathology at the University of Lausanne and three major private pathology laboratories. Passive and active follow-up are conducted. Data on all deaths in the canton (including cancer deaths) are available. Other features of the registry are good registration of non-melanoma skin cancers, linkage of reports of selected preneoplastic conditions to the registry database (to study subsequent cancer risk), analysis.

Cancer incidence in Neuchâtel (2003-2007)

REGISTRATION AREA: The Neuchâtel Cancer Registry covers the Frenchspeaking canton of Neuchâtel in western Switzerland, which shares a border with France. The canton is mainly rural, with only two cities (of approximately 35 000 residents each). Almost all residents are Caucasian; 38% are Protestant and 31% are Catholic. Foreign residents (predominantly of Mediterranean origin) account for about 23% of the population. The main occupational sectors in the canton are watch-making and the microtechnical industry (35%), agriculture (4%), and services (61%). REGISTRY STRUCTURE AND METHODS: The bulk of information is provided by the Neuchâtel Institute of Pathology (INAP) through submission of biopsy, cytology, and autopsy reports. Notiĺcation is voluntary for medical institutions. Additional information is abstracted by the registry staff from computerized hospital charts. The registry routinely integrates abstracts of medical records into its database, and performs periodic electronic linkage between the registry database and the centralized cantonal administrative population database (for the purpose of active follow-up). All death certiĺcates are checked annually against the registry ĺles.

Breeding, genetic and genomic of citrus for disease resistance

Although the citriculture is one of the most important economic activities in Brazil, it is based on a small number of varieties. This fact has contributed for the vulnerability of the culture regarding the phytosanitary problems. A higher number of varieties/genotypes with potential for commercial growing, either for the industry or fresh market, has been one of the main objectives of citrus breeding programs. The genetic breeding of citrus has improved, in the last decades, due to the possibility of an association between biotechnological tools and classical methods of breeding. The use of molecular markers for early selection of zygotic seedlings from controlled crosses resulted in the possibility of selection of a high number of new combination and, as a consequence, the establishment of a great number of hybrids in field experiments. The faster new tools are incorporated in the program, the faster is possibility to reach new genotypes that can be tested as a new variety. Good traits should be kept or incorporate, whereas bad traits have to be excluded or minimized in the new genotype. Scion and rootstock can not be considered separately, and graft compatibility, fruit quality and productivity are essential traits to be evaluated in the last stages of the program. The mapping of QTLs has favored breeding programs of several perennial species and in citrus it was possible to map several characteristics with qualitative and quantitative inheritance. The existence of linkage maps and QTLs already mapped, the development of EST and BAC library and the sequencing of the Citrus complete genome altogether make very demanding and urgent the exploration of such data to launch a wider genetic study of citrus. The rising of information on genome of several organisms has opened new approaches looking for integration between breeding, genetic and genome. Genome assisted selection (GAS) involves more than gene or complete genome sequencing and is becoming an import support in breeding programs of annual and perennial species. An huge information amount can be derivate from genome analysis. The use and benefit of such informations will depend on the genetic basis of the breeding program.

Targeting Oxidative Stress and Aberrant Critical Period Plasticity in the Developmental Trajectory to Schizophrenia.

Schizophrenia is a neurodevelopmental disorder reflecting a convergence of genetic risk and early life stress. The slow progression to first psychotic episode represents both a window of vulnerability as well as opportunity for therapeutic intervention. Here, we consider recent neurobiological insight into the cellular and molecular components of developmental critical periods and their vulnerability to redox dysregulation. In particular, the consistent loss of parvalbumin-positive interneuron (PVI) function and their surrounding perineuronal nets (PNNs) as well as myelination in patient brains is consistent with a delayed or extended period of circuit instability. This linkage to critical period triggers (PVI) and brakes (PNN, myelin) implicates mistimed trajectories of brain development in mental illness. Strategically introduced antioxidant treatment or later reinforcement of molecular brakes may then offer a novel prophylactic psychiatry.

Dysfunctional SEMA3E signaling underlies gonadotropin-releasing hormone neuron deficiency in Kallmann syndrome.

Individuals with an inherited deficiency in gonadotropin-releasing hormone (GnRH) have impaired sexual reproduction. Previous genetic linkage studies and sequencing of plausible gene candidates have identified mutations associated with inherited GnRH deficiency, but the small number of affected families and limited success in validating candidates have impeded genetic diagnoses for most patients. Using a combination of exome sequencing and computational modeling, we have identified a shared point mutation in semaphorin 3E (SEMA3E) in 2 brothers with Kallmann syndrome (KS), which causes inherited GnRH deficiency. Recombinant wild-type SEMA3E protected maturing GnRH neurons from cell death by triggering a plexin D1-dependent (PLXND1-dependent) activation of PI3K-mediated survival signaling. In contrast, recombinant SEMA3E carrying the KS-associated mutation did not protect GnRH neurons from death. In murine models, lack of either SEMA3E or PLXND1 increased apoptosis of GnRH neurons in the developing brain, reducing innervation of the adult median eminence by GnRH-positive neurites. GnRH neuron deficiency in male mice was accompanied by impaired testes growth, a characteristic feature of KS. Together, these results identify SEMA3E as an essential gene for GnRH neuron development, uncover a neurotrophic function for SEMA3E in the developing brain, and elucidate SEMA3E/PLXND1/PI3K signaling as a mechanism that prevents GnRH neuron deficiency.

Analysis of the genetic basis of periodic fever with aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome.

PFAPA syndrome is the most common autoinflammatory syndrome in children from Western countries. In spite of its strong familial clustering, its genetic basis and inheritance pattern are still unknown. We performed a comprehensive genetic study on 68 individuals from 14 families. Linkage analysis suggested a susceptibility locus on chromosome 8, but direct molecular sequencing did not support this initial statistical finding. Exome sequencing revealed the absence of any gene that was mutated in all patients. Exhaustive screening of genes involved in other autoinflammatory syndromes or encoding components of the human inflammasome showed no DNA variants that could be linked to PFAPA molecular pathology. Among these, the previously-reported missense mutation V198M in the NLRP3 gene was clearly shown not to co-segregate with PFAPA. Our results on this relatively large cohort indicate that PFAPA syndrome is unlikely to be a monogenic condition. Moreover, none of the several genes known to be involved in inflammation or in autoinflammatory disorders seem to be relevant, alone, to its etiology, suggesting that PFAPA results from oligogenic or complex inheritance of variants in multiple disease genes and/or non-genetic factors.

Mortality risk associated with underweight : a census-linked cohort of 31,578 individuals with up to 32 years of follow-up

BACKGROUND: In contrast to obesity, information on the health risks of underweight is sparse. We examined the long-term association between underweight and mortality by considering factors possibly influencing this relationship. METHODS: We included 31,578 individuals aged 25-74 years, who participated in population based health studies between 1977 and 1993 and were followed-up for survival until 2008 by record linkage with the Swiss National Cohort (SNC). Body Mass Index (BMI) was calculated from measured (53% of study population) or self-reported height and weight. Underweight was defined as BMI < 18.5 kg/m2. Cox regression models were used to determine mortality Hazard Ratios (HR) of underweight vs. normal weight (BMI 18.5- < 25.0 kg/m2). Covariates were study, sex, smoking, healthy eating proxy, sports frequency, and educational level. RESULTS: Underweight individuals represented 3.0% of the total study population (n = 945), and were mostly women (89.9%). Compared to normal weight, underweight was associated with increased all-cause mortality (HR: 1.37; 95% CI: 1.14-1.65). Increased risk was apparent in both sexes, regardless of smoking status, and mainly driven by excess death from external causes (HR: 3.18; 1.96-5.17), but not cancer, cardiovascular or respiratory diseases. The HR were 1.16 (0.88-1.53) in studies with measured BMI and 1.59 (1.24-2.05) with self-reported BMI. CONCLUSIONS: The increased risk of dying of underweight people was mainly due to an increased mortality risk from external causes. Using self-reported BMI may lead to an overestimation of mortality risk associated with underweight.

Liikesimulaattorialustan kehittäminen virtuaaliprototyypin avulla

Työn tarkoituksena oli kehittää kuuden vapausasteen liikesimulaattorialusta virtuaaliprototyypin avulla siten, että alustan dynamiikka mallinnetaan Adams-ohjelmistolla ja ohjaus- ja säätöpiiri Matlab Simulink:llä. Tarkoituksena oli tutkia dynaamisen mallin ja säätöteknisen mallin yhdistämistä ja niiden yhteen toimimista. Tarkoituksena oli myös selvittää tulevaisuudessa rakennettavan Stewart:n alustan mekaniikan mitat ja hydraulikomponenttien koot. Työssä tutkittiin alustan käyttäytymistä halutulla liikealueella, nopeuksia joita saavutetaan ja mekaanisia rajoitteita. Työn tuloksesta on tarkoitus rakentaa fyysinen prototyyppi liittyen KONSI-projektiin, jossa kehitetään satamanosturisimulaattori nosturiohjaajan koulutuksen tueksi. Malli tullaan kytkemään Teppo Lehtisen diplomityönä tehtyyn satamanosturi kontin simulointimalliin ja koko järjestelmän on tarkoitus toimia reaaliaikaisena.

DTC-induktiomoottorikäytön soveltaminen keskitaajuusalueelle

Työssä tarkastellaan olemassa olevan suoraa vääntömomentin säätöä käyttävän taajuudenmuuttajan soveltamista keskitaajuusalueella toimiviin induktiomoottorikäyttöihin. Keskinopeusalueen sovellusten pyörimisnopeudet ovat tyypillisesti 6000…30000rpm. Tällöin invertterin lähtötaajuuden on nelinapaista moottoria ohjattaessa ulotuttava 1000Hz:iin. ABB:n ACS600 taajuudenmuuttajan nykyinen syöttötaajuus ulottuu noin 400Hz:iin ja sen keskimääräinen kytkentätaajuus on luokkaa 3kHz. Taajuudenmuuttajan keskimääräistä kytkentätaajuutta ei haluta tästä merkittävästi nostaa, koska tällöin pääteasteen mitoitusta ja rakennetta on muutettava. Tarkastelussa keskitytään täten jännitemodulointiin, joka määrittelee invertterin lähtöjännitteen käyrämuodon ja pääteasteen tehokytkimien kytkentätaajuuden. Työssä esitetään suoran käämivuon säädön periaatetta soveltava 30-kulmainen modulointimenetelmä (30-modulointi), jolla moottorin syöttövirrasta voidaan eliminoida 5. ja 7. yliharmoninen komponentti. Yliharmonisten komponenttien eliminointi mahdollistaa passiivisilla komponenteilla toteutetun alipäästösuodattimen asentamisen invertterin lähtöön, jolloin moottorissa tapahtuvat tehohäviöt saadaan pieniksi. 30-moduloinnin ohjaukseen ja säätöön esitetään menetelmät, jotka mahdollistavat sen toteuttamisen nykyiseen taajuudenmuuttajaan ohjelmallisesti ilman suuria laitteistomuutoksia. 30-moduloinnin ominaisuuksia tarkastellaan analyyttisin menetelmin ja sen toimintaa testataan esitettyjen teorioiden perusteella simuloimalla. 30-moduloinnin ohjelmallinen implementointi nykyiseen ACS600:een mahdollistaa periaatteessa noin 600Hz:n syöttötaajuuden saavuttamisen. Tällöin invertterin keskimääräinen kytkentätaajuus voidaan säätää koko pyörimisnopeusalueella alle 4kHz:n tasolle.

Selection on a genetic polymorphism counteracts ecological speciation in a stick insect.

The interplay between selection and aspects of the genetic architecture of traits (such as linkage, dominance, and epistasis) can either drive or constrain speciation [1-3]. Despite accumulating evidence that speciation can progress to "intermediate" stages-with populations evolving only partial reproductive isolation-studies describing selective mechanisms that impose constraints on speciation are more rare than those describing drivers. The stick insect Timema cristinae provides an example of a system in which partial reproductive isolation has evolved between populations adapted to different host plant environments, in part due to divergent selection acting on a pattern polymorphism [4, 5]. Here, we demonstrate how selection on a green/melanistic color polymorphism counteracts speciation in this system. Specifically, divergent selection between hosts does not occur on color phenotypes because melanistic T. cristinae are cryptic on the stems of both host species, are resistant to a fungal pathogen, and have a mating advantage. Using genetic crosses and genome-wide association mapping, we quantify the genetic architecture of both the pattern and color polymorphism, illustrating their simple genetic control. We use these empirical results to develop an individual-based model that shows how the melanistic phenotype acts as a "genetic bridge" that increases gene flow between populations living on different hosts. Our results demonstrate how variation in the nature of selection acting on traits, and aspects of trait genetic architecture, can impose constraints on both local adaptation and speciation.

Contrast : a concept in language and its development in Medieval Spanish

The purpose of this PhD thesis is to investigate a semantic relation present in the connection of sentences (more specifically: propositional units). This relation, which we refer to as contrast, includes the traditional categories of adversatives - predominantly represented by the connector but in English and pero in Modern Spanish - and concessives, prototypically verbalised through although / aunque. The aim is to describe, analyse and - as far as possible - to explain the emergence and evolution of different syntactic schemes marking contrast during the first three centuries of Spanish (also referred to as Castilian) as a literary language, i.e., from the 13th to the 15th century. The starting point of this question is a commonplace in syntax, whereby the semantic and syntactic complexity of clause linkage correlates with the degree of textual elaboration. In historical linguistics, i.e., applied to the phylogeny of a language, it is commonly referred to as the parataxis hypothesis A crucial part of the thesis is dedicated by the definition of contrast as a semantic relation. Although the label contrast has been used in this sense, mainly in functional grammar and text linguistics, mainstream grammaticography and linguistics remain attached to the traditional categories adversatives and concessives. In opposition to this traditional view, we present our own model of contrast, based on a pragma-semantic description proposed for the analysis of adversatives by Oswald Ducrot and subsequently adopted by Ekkehard König for the analysis of concessives. We refine and further develop this model in order for it to accommodate all, not just the prototypical instances of contrast in Spanish, arguing that the relationship between adversatives and concessives is a marked opposition, i.e., that the higher degree of semantic and syntactic integration of concessives restricts some possible readings that the adversatives may have, but that this difference is almost systematically neutralised by contextual factors, thus justifying the assumption of contrast as a comprehensive onomasiological category. This theoretical focus is completed by a state-of-the-question overview attempting to account for all relevant forms in which contrast is expressed in Medieval Spanish, with the aid of lexicographic and grammaticographical sources, and an empirical study investigating the expression of corpus in a corpus study on the textual functions of contrast in nine Medieval Spanish texts: Cantar de Mio Cid, Libro de Alexandre, Milagros de Nuestra Sehora, Estoria de Espana, Primera Partida, Lapidario, Libro de buen amor, Conde Lucanor, and Corbacho. This corpus is analysed using quantitative and qualitative tools, and the study is accompanied by a series of methodological remarks on how to investigate a pragma-semantic category in historical linguistics. The corpus study shows that the parataxis hypothesis fails to prove from a statistical viewpoint, although a qualitative analysis shows that the use of subordination does increase over time in some particular contexts.

Vieraalla kielellä tapahtuvan sisäisen viestinnän vaikutukset organisaation tietovarantoon postmodernin tietokäsityksen viitekehyksessä

Tutkimus pohtii tiedon ja kielitaidon välistä suhdetta kansainvälisen organisaation sisäisessä viestinnässä. Työssä keskitytään erityisesti virallisen kielen vaihtamisen vaikutuksiin organisatorisentiedon laatuun ja määrään. Aihepiiriä lähestytään käsiteanalyyttisin keinoin. Työn on kvalitatiivinen ja siinä on käytetty kirjallista materiaalia, jonka kanssa tutkijalla ei ole ollut vuorovaikutuksessa. Tutkimustulokset osoittavat että on todennäköiseksi, jopa lähes varmaa, että organisaation virallisen kielen vaihtuminen muuttaa organisaation viestintärakennetta. En seurauksena kommunikaatiosuhteet eivät perustu enää osaamiseen tai viralliseen asemaan organisaatiossa. Uudet viestintäverkostot muodostuvat kielitaidon varaan jolloin väistämättä sivutetaan henkilöitä joilla olisi tietämystä, mutta ei kielitaitoa jakaa sitä organisaatiolle. Kansainvälistyminen tuo mukanaan laajemman potentiaalisentietovarannon, joka on mahdollista saada palvelemaan organisaatiota. Näiden kahden vastakkaisen seikan kokonaisvaikutus organisaation tietovarannolle kaipaa lisätutkimusta.

Loss of function mutations in HARS cause a spectrum of inherited peripheral neuropathies.

Inherited peripheral neuropathies are a genetically heterogeneous group of disorders characterized by distal muscle weakness and sensory loss. Mutations in genes encoding aminoacyl-tRNA synthetases have been implicated in peripheral neuropathies, suggesting that these tRNA charging enzymes are uniquely important for the peripheral nerve. Recently, a mutation in histidyl-tRNA synthetase (HARS) was identified in a single patient with a late-onset, sensory-predominant peripheral neuropathy; however, the genetic evidence was lacking, making the significance of the finding unclear. Here, we present clinical, genetic, and functional data that implicate HARS mutations in inherited peripheral neuropathies. The associated phenotypic spectrum is broad and encompasses axonal and demyelinating motor and sensory neuropathies, including four young patients presenting with pure motor axonal neuropathy. Genome-wide linkage studies in combination with whole-exome and conventional sequencing revealed four distinct and previously unreported heterozygous HARS mutations segregating with autosomal dominant peripheral neuropathy in four unrelated families (p.Thr132Ile, p.Pro134His, p.Asp175Glu and p.Asp364Tyr). All mutations cause a loss of function in yeast complementation assays, and p.Asp364Tyr is dominantly neurotoxic in a Caenorhabditis elegans model. This study demonstrates the role of HARS mutations in peripheral neuropathy and expands the genetic and clinical spectrum of aminoacyl-tRNA synthetase-related human disease.