Identification of cancer/testis-antigen genes by massively parallel signature sequencing.

Massively parallel signature sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a single RNA preparation. Most MPSS tags can be unambiguously assigned to genes, thereby generating a comprehensive expression profile of the tissue of origin. From the comparison of MPSS data from 32 normal human tissues, we identified 1,056 genes that are predominantly expressed in the testis. Further evaluation by using MPSS tags from cancer cell lines and EST data from a wide variety of tumors identified 202 of these genes as candidates for encoding cancer/testis (CT) antigens. Of these genes, the expression in normal tissues was assessed by RT-PCR in a subset of 166 intron-containing genes, and those with confirmed testis-predominant expression were further evaluated for their expression in 21 cancer cell lines. Thus, 20 CT or CT-like genes were identified, with several exhibiting expression in five or more of the cancer cell lines examined. One of these genes is a member of a CT gene family that we designated as CT45. The CT45 family comprises six highly similar (>98% cDNA identity) genes that are clustered in tandem within a 125-kb region on Xq26.3. CT45 was found to be frequently expressed in both cancer cell lines and lung cancer specimens. Thus, MPSS analysis has resulted in a significant extension of our knowledge of CT antigens, leading to the discovery of a distinctive X-linked CT-antigen gene family.

Length variation in HIV-1 gp120 as the product of DNA misalignment mechanism

Background: To determine whether misalignment structures such as duplications, repeats, and palindromes are associated to insertions/deletions (indels) in gp120, indicating that indels are indeed frameshift mutations generated by DNA misalignment mechanism. Methods: Cloning and sequencing of a fragment of HIV-1 gp120 spanning C2-C4 derived from plasma RNA in 12 patients with early chronic disease and naïve to antiretroviral therapy. Results: Indels in V4 involved always insertion and deletion of duplicated nucleotide segments, and AAT repeats, and were associated to the presence of palindromic sequences. No duplications were detected in V3 and C3. Palindromic sequences occurred with similar frequencies in V3, C3 and V4; the frequency of palindromes in individual genes was found to be significantly higher in structural (gp120, p ≤ 3.00E-7) and significantly lower in regulatory (Tat, p ≤ 9.00E-7) genes, as compared to the average frequency calculated over the full genome. Discussion: Indels in V4 are associated to misalignment structures (i.e. duplications repeat and palindromes) indicating DNA misalignment as the mechanism underlying length variation in V4. The finding that indels in V4 are caused by DNA misalignment has some very important implications: 1) indels in V4 are likely to occur in proviral DNA (and not in RNA), after integration of HIV into the host genome; 2) they are likely to occur as progressive modifications of the early founder virus during chronic infection, as more and more cells get infected; 3) frameshift mutations involving any number of base pairs are likely to occur evenly across gp120; however, only those mutants carrying a functional gp120 (indels as multiples of three base pairs) will be able to perpetuate the virus cycle and to keep spreading through the population.

The short-rooted phenotype of the brevis radix mutant partly reflects root abscisic acid hypersensitivity.

To gain further insight into abscisic acid (ABA) signaling and its role in growth regulation, we have screened for Arabidopsis (Arabidopsis thaliana) mutants hypersensitive to ABA-mediated root growth inhibition. As a result, we have identified a loss-of-function allele of BREVIS RADIX (BRX) in the Columbia background, named brx-2, which shows enhanced response to ABA-mediated inhibition of root growth. BRX encodes a key regulator of cell proliferation and elongation in the root, which has been implicated in the brassinosteroid (BR) pathway as well as in the regulation of auxin-responsive gene expression. Mutants affected in BR signaling that are not impaired in root growth, such as bes1-D, bzr1-D, and bsu1-D, also showed enhanced sensitivity to ABA-mediated inhibition of root growth. Triple loss-of-function mutants affected in PP2Cs, which act as negative regulators of ABA signaling, showed impaired root growth in the absence of exogenous ABA, indicating that disturbed regulation of ABA sensitivity impairs root growth. In agreement with this result, diminishing ABA sensitivity of brx-2 by crossing it with a 35S:HAB1 ABA-insensitive line allowed significantly higher recovery of root growth after brassinolide treatment. Finally, transcriptomic analysis revealed that ABA treatment negatively affects auxin signaling in wild-type and brx-2 roots and that ABA response is globally altered in brx-2. Taken together, our results reveal an interaction between BRs, auxin, and ABA in the control of root growth and indicate that altered sensitivity to ABA is partly responsible for the brx short-root phenotype.

Inheritance of late flowering in natural variants of soybean cultivars under short-day conditions

The objective of this work was to determine the inheritance of the long juvenile period trait in natural variants of the Doko, BR 9 (Savana), Davis, Embrapa 1 (IAS 5RC), and BR 16 soybean cultivars. Complete diallel crosses were made between the Doko and BR 16 cultivars and their variants. A 3:1 segregation ratio was observed in the F2 populations of the 'Doko' x Doko-18T, 'Doko' x Doko-Milionária, 'Davis' x São Carlos, and 'BR 9 (Savana)' x MABR92-836 (Savanão) crosses, indicating that the long juvenile period trait is controlled by a pair of recessive genes. The difference in late flowering between the Doko cultivar and both of its variants was caused by a recessive spontaneous mutation at the same genetic locus. However, the variants Doko-18T and Doko-Milionária are identical mutants that share a pair of genes that control the long juvenile period under short-day conditions. These mutants can be used in breeding programs to develop cultivars adapted to low-latitude tropical regions.

Short-term Hydropower Planning System

The Thesis gives a decision support framework that has significant impact on the economic performance and viability of a hydropower company. The studyaddresses the short-term hydropower planning problem in the Nordic deregulated electricity market. The basics of the Nordic electricity market, trading mechanisms, hydropower system characteristics and production planning are presented in the Thesis. The related modelling theory and optimization methods are covered aswell. The Thesis provides a mixed integer linear programming model applied in asuccessive linearization method for optimal bidding and scheduling decisions inthe hydropower system operation within short-term horizon. A scenario based deterministic approach is exploited for modelling uncertainty in market price and inflow. The Thesis proposes a calibration framework to examine the physical accuracy and economic optimality of the decisions suggested by the model. A calibration example is provided with data from a real hydropower system using a commercial modelling application with the mixed integer linear programming solver CPLEX.

Short-term increase in particulate matter blunts nocturnal blood pressure dipping and daytime urinary sodium excretion

Short-term exposure to ambient particulate matter with aerodynamic diameters<10 µm were found to be positively associated with blood pressure. Yet, little information exists regarding the association between particles and circadian rhythm of blood pressure. Hence, we analyzed the association of exposure to particulate matter with aerodynamic diameters<10 µm on the day of examination and ≤7 days before with ambulatory blood pressure and with sodium excretion in 359 adults from the general population using multiple linear regression. After controlling for potential confounders, a 10-µg/m3 increase in particulate matter with aerodynamic diameters<10 µm levels was associated with nighttime systolic blood pressure (β=1.32 mm Hg 95% CI, 0.06-2.58 mm Hg at lag 0; P=0.04), nighttime diastolic blood pressure (0.72 mm Hg 95% CI, 0.03-1.42 mm Hg at lag 2; P=0.04), nocturnal systolic blood pressure dipping (-0.96 mm Hg 95% CI, -1.89 to -0.03 mm Hg at lag 0; P=0.044), and daytime urinary sodium excretion (-0.05 log-mmol/min 95% CI, -0.10 to -0.01 log-mmol/min at lag 0; P=0.027) but not with nighttime sodium excretion. The associations with blood pressure rapidly diminished with increasing lag days, and the associations with daytime sodium excretion were maximal with particulate matter with aerodynamic diameters<10 µm in exposures 2 to 5 days before. The associations of short-term increases in particulate matter with aerodynamic diameters<10 µm with higher nighttime blood pressure and blunted systolic blood pressure dipping were preceded by associations with reduced ability of the kidney to excrete sodium during daytime. The underlying mechanism linking air pollution to increased cardiovascular risk may include disturbed circadian rhythms of renal sodium handling and blood pressure.

Novel insulated gamma and lentis retroviral vectors towards safer genetic modification of stem cells

In otherwise successful gene therapy trials insertional mutagenesis has resulted in leukemia. The identification of new short synthetic genetic insulator elements (GIE) which would both prevent such activation effects and shield the transgene from silencing, is a main challenge. Previous attempts with e.g. b-globin HS4, have met with poor efficacy and genetic instability. We have investigated potential improvement with two new candidate synthetic GIEs in SIN-gamma and lentiviral vectors. With each constructs two internal promoters have been tested: either the strong Fr- MuLV-U3 or the housekeeping hPGK.We could identify a specific combination of insulator 2 repeats which translates into best functional activity, high titers and boundary effect in both gammaretro and lentivectors. In target cells a dramatic shift of expression is observed with an homogenous profile the level of which strictly depends on the promoter strength. These data remain stable in both HeLa cells over three months and cord blood HSCs for two months, irrespective of the multiplicity of infection (MOI). In comparison, control native and SIN vectors expression levels show heterogeneous, depend on the MOI and prove unstable. We have undertaken genotoxicity assessment in comparing integration patterns ingenuity in human target cells sampled over three months using high-throughput pyro-sequencing. Data will be presented. Further genotoxicity assessment will include in vivo studies. We have established insulated vectors which harbour both boundary and enhancer-blocking effect and show stable in prolonged in vitro culture conditions. Work performed with support of EC-DG research FP6-NoE, CLINIGENE: LSHB-CT-2006-018933

Terrestrial Trunked Radio - verkossa toimivan reaaliaikaisen Short Data Service - viesteihin perustuvan telemetriasovelluksen ohjelmistokehitys

Tämä diplomityö tarkastelee TETRA-verkon soveltuvuutta turvallisuusviranomaisille tarkoitettuun telemetriasovellukseen, jossa erilaiset mittausdatat ja hälytystiedot kulkevat verkon yli SDS-viestiliikenteenä. Diplomityön tarkoituksena on tehdä kaksi sulautettua ohjelmistoa sekä yksi PCohjelmisto, joita käytetään rakennettavassa demolaitteistossa. Lisäksi selvitetään TETRA-verkon toimivuus ja rajoitukset sovelluksessa eri olosuhteissa ja eri kuormitustilanteissa. Diplomityön teoriaosassa käydään läpi työn määrittely ja ohjelmistonkehitysprosessin läpivienti eri osa-alueilla. Loppuosassa kuvataan tehdyt ohjelmistot erikseen ja yhdessä suunnittelusta toteutukseen, sekä lopullisen järjestelmän testaus.

Gold investments and short- and long-run price determinants of the price of gold

Tämän tutkielman tavoitteena on tutkia tekijöitä jotkavaikuttavat lyhyellä ja pitkällä aikavälillä kullan hintaan. Toiseksi tutkielmassa selvitetään mitä eri sijoitusmahdollisuuksia löytyy kultaan sijoitettaessa. Aineistona käytetään kuukausitasoista dataa Yhdysvaltain ja maailman hintaindekseistä, Yhdysvaltain ja maailman inflaatiosta ja inflaation volatiliteetista, kullan beetasta, kullan lainahinnasta, luottoriskistä ja Yhdysvaltojen ja maailman valuuttakurssi indeksistä joulukuulta 1972 elokuulle 2006. Yhteisintegraatio regressiotekniikoita käytettiin muodostamaan malli jonka avullatutkittiin päätekijöitä jotka vaikuttavat kullan hintaan. Kirjallisuutta tutkimalla selvitettiin miten kultaan voidaan sijoittaa. Empiirisettulokset ovat yhteneväisiä edellisten tutkimusten kanssa. Tukea löytyi sille, että kulta on pitkän ajan suoja inflaatiota vastaan ja kulta ja Yhdysvaltojen inflaatio liikkuvat pitkällä aikavälillä yhdessä. Kullan hintaan vaikuttavat kuitenkin lyhyen ajan tekijät pitkän ajan tekijöitä enemmän. Kulta on myös sijoittajalle helppo sijoituskohde, koska se on hyvin saatavilla markkinoilla ja eri instrumentteja on lukuisia.

Three essays on short-term macroeconomics : business fluctuations, large devaluations and inflation dynamics

Résumé: At least since the Great Depression, explaining why there are business fluctuations has been one of the biggest challenges that the science of economics has had to face. The hope is that if we could better understand recessions, then we could also be more successful in overcoming them. This dissertation consists of three papers that are part of the general endeavor of economists to understand these fluctuations. The first paper discusses, for a particular model, whether a result related to fluctuations would still hold if time were modeled as continuous rather than discrete. The two other papers focus on price stickiness. The second paper discusses why, after a large devaluation, prices of non-tradables may change by only a small amount in comparison to the magnitude of the devaluation. The third paper examines price adjustment in a model in which information is imperfect and it is costly to change prices.

Cardiovascular effects of short term exposure to electric and magnetic fields of electricity power transmission

In the electrical industry the 50 Hz electric and magnetic fields are often higher than in the average working environment. The electric and magnetic fields can be studied by measuring or by calculatingthe fields in the environment. For example, the electric field under a 400 kV power line is 1 to 10 kV/m, and the magnetic flux density is 1 to 15 µT. Electricand magnetic fields of a power line induce a weak electric field and electric currents in the exposed body. The average current density in a human being standing under a 400 kV line is 1 to 2 mA/m2. The aim of this study is to find out thepossible effects of short term exposure to electric and magnetic fields of electricity power transmission on workers' health, in particular the cardiovascular effects. The study consists of two parts; Experiment I: influence on extrasystoles, and Experiment II: influence on heart rate. In Experiment I two groups, 26 voluntary men (Group 1) and 27 transmission-line workers (Group 2), were measured. Their electrocardiogram (ECG) was recorded with an ambulatory recorder both in and outside the field. In Group 1 the fields were 1.7 to 4.9 kV/m and 1.1 to 7.1 pT; in Group 2 they were 0.1 to 10.2 kV/m and 1.0 to 15.4 pT. In the ECG analysis the only significant observation was a decrease in the heart rate after field exposure (Group 1). The drop cannot be explained with the first measuring method. Therefore Experiment II was carried out. In Experiment II two groups were used; Group 1 (26 male volunteers) were measured in real field exposure, Group 2 (15 male volunteers) in "sham" fields. The subjects of Group 1 spent 1 h outside the field, then 1 h in the field under a 400 kV transmission line, and then again 1 h outside the field. Under the 400 kV linethe field strength varied from 3.5 to 4.3 kV/m, and from 1.4 to 6.6 pT. Group 2spent the entire test period (3 h) in a 33 kV outdoor testing station in a "sham" field. ECG, blood pressure, and electroencephalogram (EEG) were measured by ambulatory methods. Before and after the field exposure, the subjects performed some cardiovascular autonomic function tests. The analysis of the results (Experiments I and II) showed that extrasystoles or arrythmias were as frequent in the field (below 4 kV/m and 4 pT) as outside it. In Experiment II there was no decrease detected in the heart rate, and the systolic and diastolic blood pressure stayed nearly the same. No health effects were found in this study.

Short communication. Persistence of point crop yield subjective estimates

En este trabajo se investiga la persistencia de las estimaciones puntuales subjetivas de rendimientos en cultivos anua- les realizadas por un amplio grupo de agricultores. La persistencia en el tiempo es una condición necesaria para la co- herencia y la confiabilidad de las estimaciones subjetivas de variables aleatorias. Los sujetos entrevistados estimaron valores puntuales de rendimientos de cultivos anuales (rendimientos medio, mayor, mínimo y más frecuente). Se han encontrado diferencias relativas poco importantes en todas las variables, excepto en los rendimientos mínimos, donde existe una alta dispersión. Los resultados son interesantes para estimar la adecuación de las técnicas de estimación de probabilidades subjetivas para ser utilizadas en los sistemas de ayuda en la toma de decisiones en agricultura.