Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition

The rapid increase in genome sequence information has necessitated the annotation of their functional elements, particularly those occurring in the non-coding regions, in the genomic context. Promoter region is the key regulatory region, which enables the gene to be transcribed or repressed, but it is difficult to determine experimentally. Hence an in silico identification of promoters is crucial in order to guide experimental work and to pin point the key region that controls the transcription initiation of a gene. In this analysis, we demonstrate that while the promoter regions are in general less stable than the flanking regions, their average free energy varies depending on the GC composition of the flanking genomic sequence. We have therefore obtained a set of free energy threshold values, for genomic DNA with varying GC content and used them as generic criteria for predicting promoter regions in several microbial genomes, using an in-house developed tool `PromPredict'. On applying it to predict promoter regions corresponding to the 1144 and 612 experimentally validated TSSs in E. coli (50.8% GC) and B. subtilis (43.5% GC) sensitivity of 99% and 95% and precision values of 58% and 60%, respectively, were achieved. For the limited data set of 81 TSSs available for M. tuberculosis (65.6% GC) a sensitivity of 100% and precision of 49% was obtained.

Young driver perceptions of police traffic enforcement and self reported driving offences

Purpose Road policing is a key method used to improve driver compliance with road laws. However, we have a very limited understanding of the perceptions of young drivers regarding police enforcement of road laws. This paper addresses this gap. Design/Methodology/Approach Within this study 238 young drivers from Queensland, Australia, aged 17-24 years (M = 18, SD = 1.54), with a provisional (intermediate) driver’s licence completed an online survey regarding their perceptions of police enforcement and their driver thrill seeking tendencies. This study considered whether these factors influenced self-reported transient (e.g., travelling speed) and fixed (e.g., blood alcohol concentration) road violations by the young drivers. Findings The results indicate that being detected by police for a traffic offence, and the frequency with which they display P-plates on their vehicle to indicate their licence status, are associated with both self-reported transient and fixed rule violations. Licence type, police avoidance behaviours and driver thrill seeking affected transient rule violations only, while perceptions of police enforcement affected fixed rule violations only. Practical implications This study suggests that police enforcement of young driver violations of traffic laws may not be as effective as expected and that we need to improve the way in which police enforce road laws for young novice drivers. Originality/value: This paper identifies that perceptions of police enforcement by young drivers does not influence all types of road offences.

Clinical Phenotype and Genetic Epidemiology of Schizophrenia in a Finnish Isolate

This study is part of the joint project "The Genetic Epidemiology and Molecular Genetics of schizophrenia in Finland" between the Departments of Mental Health and Alcohol Research, and Molecular Medicine at the National Public Health Institute. In the study, we utilized three nationwide health care registers: 1) the Hospital Discharge Register, 2) the Free Medication Register, and 3) the Disability Pension Register, plus the National Population Register, in order to identify all patients with schizophrenia born from 1940 to 1976 (N=33,731) in Finland, and their first degree-relatives. 658 patients with at least one parent born in a homogeneous isolate in northeastern Finland were identified, as well as 4904 familial schizophrenia patients with at least two affected siblings from the whole country. The comparison group was derived from the Health 2000 Study. We collected case records and reassessed the register diagnosis. Were contacted the isolate patients and a random sample of patients from the whole country to make diagnostic clinical interviews and to assess the negative and positive symptoms and signs of schizophrenia. In addition to these patients, we interviewed siblings who were initially healthy according to the Hospital Discharge Register. Of those with a register diagnosis of schizophrenia, schizoaffective or schizophreniform disorder, 69% received a record-based consensus diagnosis and 63% an interview-based diagnosis of schizophrenia. Patients with schizophrenia having first-degree relatives with psychotic disorder had more severe affective flattening and alogia than those who were the only affected individuals in their family. The novel findings were: 1) The prevalence of schizophrenia in the isolate was relatively high based on register (1.5%), case record (0.9-1.3%), and interview (0.7-1.2%) data. 2) Isolate patients, regardless of their familial loading for schizophrenia, had less delusions and hallucinations than the whole country familial patients, which may be related to the genetic homogeneity in the isolate. This phenotype encourages the use of endophenotypes in genetic analyses instead of diagnoses alone. 3) The absence of register diagnosis does not confirm that siblings are healthy, because 7.7% of siblings had psychotic symptoms already before the register diagnoses were identified in 1991. For genetic research, the register diagnosis should therefore be reassessed using either a structured interview or a best- estimate case note consensus diagnosis. Structured clinical interview methods need be considered also in clinical practice.

HIV outbreak among injecting drug users in Finland

An HIV outbreak among Finnish injecting drug users (IDUs) occurred in 1998. By the end of 2005, 282 IDUs were in-fected, most of them by recombinant virus CRF01_AE of HIV. After a rapid spread, the outbreak subsided, and the prevalence of HIV among IDUs remained low (<2%). The purpose of the study was to describe the outbreak in order to recognise factors that have influenced the spread and restriction of the outbreak, and thus to find tools for HIV preven-tion. Data on Finnish IDUs newly diagnosed HIV-positive between 1998 and 2005 was collected through interviews and patient documents. Study I compared markers of disease progression between 93 Finnish IDUs and 63 Dutch IDUs. In study II, geographical spread of the HIV outbreak was examined and compared with the spatial distribution of employed males. In study III, risk behaviour data from interviews of 89 HIV-positive and 207 HIV-negative IDUs was linked, and prevalence and risk factors for unprotected sex were evaluated. In study IV, data on 238 newly diagnosed IDUs was combined with data on 675 sexually transmitted HIV cases, and risk factors for late HIV diagnosis (CD4 cell count <200/µL, or AIDS at HIV diagnosis) were analysed. Finnish IDUs infected with CRF01_AE exhibited higher viral loads than did Amsterdam IDUs infected with subtype B, but there was no difference in CD4 development. The Finnish IDU outbreak spread and was restricted socially in a marginalised IDU population and geographically in areas characterised by low proportions of employed males. Up to 40% of the cases in the two clusters outside the city centre had no contact with the centre, where needle exchange services were available since 1997. Up to 63% of HIV-positive and 80% of HIV-negative sexually active IDUs reported inconsistent condom use, which was associated with steady relationships and recent inpatient addiction care. Com-pared to other transmission groups, HIV-positive IDUs were diagnosed earlier in their infection. The proportion of late diagnosed HIV cases in all transmission groups was 23%, but was only 6% among IDUs diagnosed during the first four years of the epidemic. The high viral load in early HIV infection may have contributed to the rapid spread of recombinant virus in the Finnish outbreak. The outbreak was restricted to a marginalised IDU population, and limited spatially to local pockets of pov-erty. To prevent HIV among IDUs, these pockets should be recognised and reached early through outreach work and the distribution of needle exchange and other prevention activities. To prevent the sexual transmission of HIV among IDUs, prevention programmes should be combined with addiction care services and targeted at every IDU. The early detection of the outbreak and early implementation of needle exchange programmes likely played a crucial role in re-versing the IDU outbreak.

Cyclosporine population pharmacokinetics in pediatric renal transplant recipients

Cyclosporine is an immunosuppressant drug with a narrow therapeutic index and large variability in pharmacokinetics. To improve cyclosporine dose individualization in children, we used population pharmacokinetic modeling to study the effects of developmental, clinical, and genetic factors on cyclosporine pharmacokinetics in altogether 176 subjects (age range: 0.36–20.2 years) before and up to 16 years after renal transplantation. Pre-transplantation test doses of cyclosporine were given intravenously (3 mg/kg) and orally (10 mg/kg), on separate occasions, followed by blood sampling for 24 hours (n=175). After transplantation, in a total of 137 patients, cyclosporine concentration was quantified at trough, two hours post-dose, or with dose-interval curves. One-hundred-four of the studied patients were genotyped for 17 putatively functionally significant sequence variations in the ABCB1, SLCO1B1, ABCC2, CYP3A4, CYP3A5, and NR1I2 genes. Pharmacokinetic modeling was performed with the nonlinear mixed effects modeling computer program, NONMEM. A 3-compartment population pharmacokinetic model with first order absorption without lag-time was used to describe the data. The most important covariate affecting systemic clearance and distribution volume was allometrically scaled body weight i.e. body weight**3/4 for clearance and absolute body weight for volume of distribution. The clearance adjusted by absolute body weight declined with age and pre-pubertal children (< 8 years) had an approximately 25% higher clearance/body weight (L/h/kg) than did older children. Adjustment of clearance for allometric body weight removed its relationship to age after the first year of life. This finding is consistent with a gradual reduction in relative liver size towards adult values, and a relatively constant CYP3A content in the liver from about 6–12 months of age to adulthood. The other significant covariates affecting cyclosporine clearance and volume of distribution were hematocrit, plasma cholesterol, and serum creatinine, explaining up to 20%–30% of inter-individual differences before transplantation. After transplantation, their predictive role was smaller, as the variations in hematocrit, plasma cholesterol, and serum creatinine were also smaller. Before transplantation, no clinical or demographic covariates were found to affect oral bioavailability, and no systematic age-related changes in oral bioavailability were observed. After transplantation, older children receiving cyclosporine twice daily as the gelatine capsule microemulsion formulation had an about 1.25–1.3 times higher bioavailability than did the younger children receiving the liquid microemulsion formulation thrice daily. Moreover, cyclosporine oral bioavailability increased over 1.5-fold in the first month after transplantation, returning thereafter gradually to its initial value in 1–1.5 years. The largest cyclosporine doses were administered in the first 3–6 months after transplantation, and thereafter the single doses of cyclosporine were often smaller than 3 mg/kg. Thus, the results suggest that cyclosporine displays dose-dependent, saturable pre-systemic metabolism even at low single doses, whereas complete saturation of CYP3A4 and MDR1 (P-glycoprotein) renders cyclosporine pharmacokinetics dose-linear at higher doses. No significant associations were found between genetic polymorphisms and cyclosporine pharmacokinetics before transplantation in the whole population for which genetic data was available (n=104). However, in children older than eight years (n=22), heterozygous and homozygous carriers of the ABCB1 c.2677T or c.1236T alleles had an about 1.3 times or 1.6 times higher oral bioavailability, respectively, than did non-carriers. After transplantation, none of the ABCB1 SNPs or any other SNPs were found to be associated with cyclosporine clearance or oral bioavailability in the whole population, in the patients older than eight years, or in the patients younger than eight years. In the whole population, in those patients carrying the NR1I2 g.-25385C–g.-24381A–g.-205_-200GAGAAG–g.7635G–g.8055C haplotype, however, the bioavailability of cyclosporine was about one tenth lower, per allele, than in non-carriers. This effect was significant also in a subgroup of patients older than eight years. Furthermore, in patients carrying the NR1I2 g.-25385C–g.-24381A–g.-205_-200GAGAAG–g.7635G–g.8055T haplotype, the bioavailability was almost one fifth higher, per allele, than in non-carriers. It may be possible to improve individualization of cyclosporine dosing in children by accounting for the effects of developmental factors (body weight, liver size), time after transplantation, and cyclosporine dosing frequency/formulation. Further studies are required on the predictive value of genotyping for individualization of cyclosporine dosing in children.

Epigenetics Underpinning DNA Damage Repair

Epigenetics is the study of heritable changes in gene expression that are not the result of genetic alterations. These changes include DNA methylation, histone modifications, or indeed microRNA expression. Chromatin is a tightly compacted DNA–protein complex that allows approximately two meters of DNA to be packaged inside a cell, only a few micrometers across. Although the resulting DNA structure is very stable, it is not very amiable to DNA-dependent processes, so mechanisms have to exist to allow processes such as transcription, replication, and DNA repair to occur. This chapter will look at how a cell responds to and deals with genomic instability at the epigenetic level and highlight how critical chromatin remodeling is for correct DNA repair and cell survival following DNA damage. This chapter will initially look at the DNA repair pathways that function in human cells and then at how the repair of DNA damage is controlled by epigenetics.

Intonation of Finnish Verbs

A production experiment investigated the tonal shape of Finnish finite verbs in transitive sentences without narrow focus. Traditional descriptions of Finnish stating that non- focused finite verbs do not receive accents were only partly supported. Verbs were found to have a consistently smaller pitch range than words in other word classes, but their pitch contours were neither flat nor explainable by pure interpolation.

Volumetric determination of tetraalkyl thiuram disulphides

A method for the volumetric determination of tetraalkyl thiuram disulphide is developed. It is based on its reaction with potassium cyanide in aqueous acetonitrile medium, when the corresponding tetraalkyl thiuram monosulphide and thiocyanate are formed. The former is removed by extraction with benzene and the latter converted into cyanogen bromide, which is estimated iodometrically.

A volumetric method for the determination of sulphoxides

A volumetric method for the quantitative determination of Sulphoxides has been developed, based on their oxidation to sulphones by dichromate in presence of 5 M sulphuric acid at 105–110°C. Excess dichromate is titrated by ferrous ammonium sulphate solution. The method is also applicable to the determination of Sulphoxides in metal sulphoxide complexes.

Toward a widely usable finite-state morphology workbench for less studied languages, 1: Desiderata

Most of the world’s languages lack electronic word form dictionaries. The linguists who gather such dictionaries could be helped with an efficient morphology workbench that adapts to different environments and uses. A widely usable workbench could be characterized, ideally, as generally applicable, extensible, and freely available (GEA). It seems that such a solution could be implemented in the framework of finite-state methods. The current work defines the GEA desiderata and starts a series of articles concerning these desiderata in finite- state morphology. Subsequent parts will review the state of the art and present an action plan toward creating a widely usable finite-state morphology workbench.

Validiusargumentin rakentuminen suullisen kielitaidon arviointiprojektissa

Artikkelissa kuvataan aluksi kielitaidon arvioinnin validiustutkimuksen keskeisiä suuntauksia, joilla kehystetään käynnissä olevan suullisen kielitaidon arviointihankkeen tutkimustehtävä. Tutkimustehtävä kohdentuu kansallisiin opetussuunnitelmaperusteisiin sisältyvän taitotasoasteikon validiuteen, jota tarkastellaan validiusargumentin rakentumisen näkökulmasta. Väitettä asteikon ja sen pohjalta laadittujen puhetehtävien pätevyydestä suullisen taidon mittareina koetellaan Toulminin mallin avulla asettamalla tätä johtopäätöstä tukevat empiiriset lähtötiedot ja niitä tukevat perusteet vastakkain väitettä horjuttavan näytön kanssa. Perusteet ja varaukset koskevat väitetyn johtopäätöksen relevanssia, hyödyllisyyttä, tarkoitettuja seurauksia ja riittävyyttä. Hankkeen tutkijoiden spesifit tutkimusongelmat kohdentuvat johonkin mainituista piirteistä. Validiusargumenttia sovelletaan suullisen kielitaidon arviointihankkeen, Hy-Talkin, kontekstissa. Ongelmanasettelussa ja menetelmävalinnoissa hyödynnetään validiustutkimuksen perinteisempiä sisältö- ja kriteeriperustaisia lähestymistapoja, mutta tehdään myös uusia avauksia tiedon syventämiseksi niistä tulkinnoista ja näkemyksistä, joita suullisten tehtävien suorittajilla ja arvioijilla ilmenee.

Sijasynkretismi morfologian koetinkivenä

Syncretism and the overlapping of morphologi- cally distinct units or entire categories have different influences on morphosyntactically cumulative and less cumulative forms. The Finnic languages, in comparison to the more eastern Finno-Ugric languages, mainly display morphologically less complex forms. Morphologically there is a clear distinction in the way syncretism is manifested in the Finnic languages that, consequently, is one of the most distinct features in the inflectional system despite the close ge- nealogical affinity. This can concretely be seen in the differences in the case inflection of the southern, such as Livonian, Estonian and Votic, and northern Finnic languages, most notably Finnish, Karelian and Veps. The comparison of syncretism in these languages shows both cross-linguistic regularity and language-specific rules that determine syncretic forms. Diachronic change and the erosion of suffixal ele- ments are closely involved in the rise of syncretism. The paper exam- ines the symmetries and asymmetries in the occurrence of syncretic forms in Finnic case paradigms.