Genetic and epigenetic mechanisms of tumor predisposition in hereditary non-polyposis colorectal carcinoma and sporadic cancers

Individuals with inherited deficiency in DNA mismatch repair(MMR) (Lynch syndrome) LS are predisposed to different cancers in a non-random fashion. Endometrial cancer (EC) is the most common extracolonic malignancy in LS. LS represents the best characterized form of hereditary nonpolyposis colorectal carcinoma (HNPCC). Other forms of familial non-polyposis colon cancer exist, including familial colorectal cancer type X (FCCX). This syndrome resembles LS, but MMR gene defects are excluded and the predisposition genes are unknown so far. To address why different organs are differently susceptible to cancer development, we examined molecular similarities and differences in selected cancers whose frequency varies in LS individuals. Tumors that are common (colorectal, endometrial, gastric) and less common (brain, urological) in LS were characterized for MMR protein expression, microsatellite instability (MSI), and by altered DNA methylation. We also studied samples of histologically normal endometrium, endometrial hyperplasia,and cancer for molecular alterations to identify potential markers that could predict malignant transformation in LS and sporadic cases. Our results suggest that brain and kidney tumors follow a different pathway for cancer development than the most common LS related cancers.Our results suggest also that MMR defects are detectable in endometrial tissues from a proportion of LS mutation carriers prior to endometrial cancer development. Traditionally (complex) atypical hyperplasia has been considered critical for progression to malignancy. Our results suggest that complex hyperplasia without atypia is equally important as a precursor lesion of malignancy. Tumor profiles from Egypt were compared with colorectal tumors from Finland to evaluate if there are differences specific to the ethnic origin (East vs.West). Results showed for the first time a distinct genetic and epigenetic signature in the Egyptian CRC marked by high methylation of microsatellite stable tumors associated with advanced stage, and low frequency of Wnt signaling activation, suggesting a novel pathway. DNA samples from FCCX families were studied with genome wide linkage analysis using microsatellite markers. Selected genes from the linked areas were tested for possible mutations that could explain predisposition to a large number of colon adenomas and carcinomas seen in these families. Based on the results from the linkage analysis, a number of areas with tentative linkage were identified in family 20. We narrowed down these areas by additional microsatellite markers to found a mutation in the BMPR1A gene. Sequencing of an additional 17 FCCX families resulted in a BMPR1A mutation frequency of 2/18 families (11%). Clarification of the mechanisms of the differential tumor susceptibility in LS increases the understanding of gene and organ specific targets of MMR deficiency. While it is generally accepted that widespread MMR deficiency and consequent microsatellite instability (MSI) drives tumorigenesis in LS, the timing of molecular alterations is controversial. In particular, it is important to know that alterations may occur several years before cancer formation, at stages that are still histologically regarded as normal. Identification of molecular markers that could predict the risk of malignant transformation may be used to improve surveillance and cancer prevention in genetically predisposed individuals. Significant fractions of families with colorectal and/or endometrial cancer presently lack molecular definition altogether. Our findings expand the phenotypic spectrum of BMPR1A mutations and, for the first time, link FCCX families to the germline mutation of a specific gene. In particular, our observations encourage screening of additional families with FCCX for BMPR1A mutation, which is necessary in obtaining a reliable estimate of the share of BMPR1A-associated cases among all FCCX families worldwide. Clinically, the identification of predisposing mutations enables targeted cancer prevention in proven mutation carriers and thereby reduces cancer morbidity and mortality in the respective families.

H I deficiency in cluster spiral galaxies - Dependence on galaxy size

From the available H I data on spiral galaxies in three rich Abell clusters and the Virgo Cluster, it is shown that galaxies with medium to large optical sizes tend to be more severely deficient in atomic hydrogen than the small galaxies. This is so both in terms of the fractional number of galaxies that are deficient and the amount of gas lost by a galaxy. The fraction of H I-deficient galaxies increases with size over most of the size range, saturating or dropping only for the largest galaxies. A comparative study is made of various currently accepted gas removal mechanisms, namely those which are a result of galaxy-intracluster medium interactions, e.g., ram pressure stripping, as well as those due to galaxy-galaxy interactions, i.e., collisions and tidal interactions. It is shown that, with the exception of tidal interactions, all of these mechanisms would produce a size dependence in H I deficiency that is the opposite of that observed. That is, the gas in the largest galaxies would be the least affected by these mechanisms. However, if there is significant mass segregation, these processes may give the trends observed in the size dependence of H I deficiency.

Photometric calibration of the CCD camera of 1-m telescope at VBO

Calibration of the CCD camera of the 1-m telescope at the Vainu Bappu Observatory, Kavalur, to the BVR system is reported here based on the observations of stars in the 'dipper asterism' in the open cluster M 67 (NGC 2682). Transformations involving B and V have negligible colour terms, while those involving R are slightly colour dependent. The possibility of using scale-down R band fluxes to estimate the continuum flux at H-alpha is investigated by comparing the counts in R band with those through an interference filter centred at H-alpha. The scaling factor is found to remain constant over a wide range of colours. The sensitivity of the telescope-filter-CCD combination is estimated to be 2.0 per cent, 8.3 per cent and 9.7 per cent in B, V and R bands, respectively. The star F117 appears to be a small-amplitude (approximately 0.05 mag) variable.

Comment on “Southward magnetic field in the neutral sheet produced by wavy motions Propagating in the dawn‐dusk direction”

In a recent paper Nakagawa and Nishida [1989] have suggested that wavy motions of the neutral sheet can be generated by the Kelvin‐Helmholtz instability if the dawn‐dusk flow of only several tens of km/s is present. However, their mathematical analysis is based on the choice of particular magnetic field directions in the three regions consisting of north, south lobes and the neutral sheet. In an earlier paper Uberoi [1986] discussed the Kelvin‐Helmholtz instability of a similar structured plasma layer without any assumptions either on velocity field directions or on the magnetic field directions, thus pointing out the angle effect due to variation in magnetic field directions on the instability criterion. The relevance of these results to the problem of wavy motions of the neutral sheet are pointed out. In particular it is found that when the y‐component of the magnetic field in each lobe is taken into consideration the Kelvin‐Helmholtz instability can be exicted only when the dawn‐dusk flow is of several hundreds of km/s a order of ten higher than that arrived in the analysis by Nakagawa and Nishida [1989].

Polarization studies in electromagnetic scattering by small Solar-system particles

In remote-sensing studies, particles that are comparable to the wavelength exhibit characteristic features in electromagnetic scattering, especially in the degree of linear polarization. These features vary with the physical properties of the particles, such as shape, size, refractive index, and orientation. In the thesis, the direct problem of computing the unknown scattered quantities using the known properties of the particles and the incident radiation is solved at both optical and radar spectral regions in a unique way. The internal electromagnetic fields of wavelength-scale particles are analyzed by using both novel and established methods to show how the internal fields are related to the scattered fields in the far zone. This is achieved by using the tools and methods that were developed specifically to reveal the internal field structure of particles and to study the mechanisms that relate the structure to the scattering characteristics of those particles. It is shown that, for spherical particles, the internal field is a combination of a forward propagating wave with the apparent wavelength determined by the refractive index of the particle, and a standing wave pattern with the apparent wavelength the same as for the incident wave. Due to the surface curvature and dielectric nature of the particle, the incident wave front undergoes a phase shift, and the resulting internal wave is focused mostly at the forward part of the particle similar to an optical lens. This focusing is also seen for irregular particles. It is concluded that, for both spherical and nonspherical particles, the interference at the far field between the partial waves that originate from these concentrated areas in the particle interior, is responsible for the specific polarization features that are common for wavelength-scale particles, such as negative values and local extrema in the degree of linear polarization, asymmetry of the phase function, and enhancement of intensity near the backscattering direction. The papers presented in this thesis solve the direct problem for particles with both simple and irregular shapes to demonstrate that these interference mechanisms are common for all dielectric wavelength-scale particles. Furthermore, it is shown that these mechanisms can be applied to both regolith particles in the optical wavelengths and hydrometeors at microwave frequencies. An advantage from this kind of study is that it does not matter whether the observation is active (e.g., polarimetric radar) or passive (e.g., optical telescope). In both cases, the internal field is computed for two mutually perpendicular incident polarizations, so that the polarization characteristics can then be analyzed according to the relation between these fields and the scattered far field.

Light scattering in random media with wavelength-scale structures : astronomical and industrial applications

Light scattering, or scattering and absorption of electromagnetic waves, is an important tool in all remote-sensing observations. In astronomy, the light scattered or absorbed by a distant object can be the only source of information. In Solar-system studies, the light-scattering methods are employed when interpreting observations of atmosphereless bodies such as asteroids, atmospheres of planets, and cometary or interplanetary dust. Our Earth is constantly monitored from artificial satellites at different wavelengths. With remote sensing of Earth the light-scattering methods are not the only source of information: there is always the possibility to make in situ measurements. The satellite-based remote sensing is, however, superior in the sense of speed and coverage if only the scattered signal can be reliably interpreted. The optical properties of many industrial products play a key role in their quality. Especially for products such as paint and paper, the ability to obscure the background and to reflect light is of utmost importance. High-grade papers are evaluated based on their brightness, opacity, color, and gloss. In product development, there is a need for computer-based simulation methods that could predict the optical properties and, therefore, could be used in optimizing the quality while reducing the material costs. With paper, for instance, pilot experiments with an actual paper machine can be very time- and resource-consuming. The light-scattering methods presented in this thesis solve rigorously the interaction of light and material with wavelength-scale structures. These methods are computationally demanding, thus the speed and accuracy of the methods play a key role. Different implementations of the discrete-dipole approximation are compared in the thesis and the results provide practical guidelines in choosing a suitable code. In addition, a novel method is presented for the numerical computations of orientation-averaged light-scattering properties of a particle, and the method is compared against existing techniques. Simulation of light scattering for various targets and the possible problems arising from the finite size of the model target are discussed in the thesis. Scattering by single particles and small clusters is considered, as well as scattering in particulate media, and scattering in continuous media with porosity or surface roughness. Various techniques for modeling the scattering media are presented and the results are applied to optimizing the structure of paper. However, the same methods can be applied in light-scattering studies of Solar-system regoliths or cometary dust, or in any remote-sensing problem involving light scattering in random media with wavelength-scale structures.

A Multi frequency study of Radio Intensity Variations For Active Galactic Nuclei of Different Optical Classes

A study of radio intensity variations at seven frequencies in the range 0.3 to 90 GHz for compact extragalactic radio sources classified as BL Lacs and high- and low-optical polarization quasars (HPQs and LPQs) is presented. This include the results of flux-density monitoring of 33 compact sources for three years at 327 MHz with the Ooty Synthesis Radio Telescope. The degrees of 'short-term' (tau less than about 1 yr) variability for the three optical types are found to be indistinguishable at low frequencies (less than 1 GHz), pointing to an extrinsic origin for the low-frequency variability. At high frequencies, a distinct dependence on optical type is present, the variability increasing from LPQs, through HPQs to BL Lacs. This trend persists even when only sources with ultra-flat radio spectra (alpha greater than -0.2) are considered. Implications of this for the phenomenon of high-frequency variability and the proposed unification schemes for different optical types of active galactic nuclei are discussed.

Time-Dependent Dynamics of a Planar Galaxy Model

Time-dependent models of collisionless stellar systems with harmonic potentials allowing for an essentially exact analytic description have recently been described. These include oscillating spheres and spheroids. This paper extends the analysis to time-dependent elliptic discs. Although restricted to two space dimensions, the systems are richer in that their parameters form a 10-dimensional phase space (in contrast to six for the earlier models). Apart from total energy and angular momentum, two additional conserved quantities emerge naturally. These can be chosen as the areas of extremal sections of the ellipsoidal region of phase space occupied by the system (their product gives the conserved volume). The present paper describes the construction of these models. An application to a tidal encounter is given which allows one to go beyond the impulse approximation and demonstrates the effects of rotation of the perturbed system on energy and angular-momentum transfer. The angular-momentum transfer is shown to scale inversely as the cube of the encounter velocity for an initial configuration of the perturbed galaxy with zero quadrupole moment.

Radio wave heating of astrophysical plasmas

The coherent plasma process such as parametric decay instability (PDI) has been applied to a homogeneous and unmagnetized plasma. These instabilities cause anomalous absorption of strong electromagnetic radiation under specific conditions of energy and momentum conservation and thus cause anomalous heating of the plasma. The maximum plasma temperatures reached are functions of luminosity of the radio radiation and plasma parameters. We believe that these processes may be taking place in many astrophysical objects. Here, the conditions in the sources 3C 273, 3C 48 and Crab Nebula are shown to be conducive to the excitation of PDI. These processes also contribute towards the absorption of 21cm radiation

Optimum weighting function in bispectral analysis in speckle interferometry - Binary star parity detection

In order to describe the atmospheric turbulence which limits the resolution of long-exposure images obtained using ground-based large telescopes, a simplified model of a speckle pattern, reducing the complexity of calculating field-correlations of very high order, is presented. Focal plane correlations are used instead of correlations in the spatial frequency domain. General tripple correlations for a point source and for a binary are calculated and it is shown that they are not a strong function of the binary separation. For binary separations close to the diffraction limit of the telescope, the genuine triple correlation technique ensures a better SNR than the near-axis Knox-Thompson technique. The simplifications allow a complete analysis of the noise properties at all levels of light.

Focal plane analysis of the Knox-Thompson algorithm in speckle interferometry

For the specific case of binary stars, this paper presents signal-to-noise ratio (SNR) calculations for the detection of the parity (the side of the brighter component) of the binary using the double correlation method. This double correlation method is a focal plane version of the well-known Knox-Thompson method used in speckle interferometry. It is shown that SNR for parity detection using double correlation depends linearly on binary separation. This new result was entirely missed by previous analytical calculations dealing with a point source. It is concluded that, for magnitudes relevant to the present day speckle interferometry and for binary separations close to the diffraction limit, speckle masking has better SNR for parity detection.

Kymmenen teollisesti merkittävän puulajin kuoriuutteiden mahdollisuudet tuholaistorjunnassa

Metsäteollisuudesta kertyy vuosittain suuria määriä ylijäämämateriaalia, kuten puun kuorta ja oksia.Ylimääräinen aines käytetään pääasiassa energiantuotantoon, mutta uusia soveltamismahdollisuuksia kaivataan. Kuoren on havaittu olevan potentiaalinen lähde monille bioaktiivisille yhdisteille, joille olisi käyttöä esimerkiksi lääke- ja kemianteollisuudessa sekä maa-, metsä- ja puutarhatuotannon tuholaistorjunnassa. Tutkimus on osa Euroopan Unionin rahoittamaa ForestSpeCs-projektia, jonka tarkoituksena on selvittää metsäteollisuuden ylijäämämateriaalien vaihtoehtoisia käyttötapoja. Valittujen kymmenen teollisesti merkittävän pohjoisen puulajin (Abies nephrolepis, Betula pendula, Larix decidua, L. gmelinii, L. sibirica, Picea abies, P. ajanensis, P. pumila, Pinus sylvestris, Populus tremula) kuoresta uutettujen aineiden soveltuvuutta syönninestoaineeksi testattiin kaaliperhosen (Pieris brassicae L.) ja krysanteemiyökkösen (Spodoptera littoralis Boisduval) toukilla sekä osittain sinappikuoriaisella (Phaedon cochloreae Fabricius) ja idänlehtikuoriaisella (Agelastica alni L.). Uutteet valmistettiin yhteistyössä projektin ryhmien avulla tai itsenäisesti erilaisin menetelmin. Testaukset tehtiin laboratorio-oloissa käyttäen lehtikiekkojen valintabiotestiä sekä karkeilla uutteilla että niistä erotelluilla yksittäisillä yhdisteillä. Tehdyistä mittauksista laskettiin syönninestoindeksit (FDI). Tulosten perusteella lähes kaikki testatut uutteet vaikuttivat ainakin jossain määrin kohdehyönteisen syöntikäyttäytymiseen. Hieman yli puolet kaaliperhosella testatuista 46 uutteesta aiheuttivat yli 50 % syönnineston eli kaaliperhonen suosi kontrollilehtiä uutteella käsiteltyjä todennäköisemmin. Krysanteemiyökkösellä yli 50 %:n syönnineston aiheuttivat vain seitsemän testatuista 56 uutteesta. Lisäksi kolme uutetta lisäsi käsiteltyjen kiekkojen syöntiä merkittävästi. Idänlehtikuoriaistoukat ja -aikuiset karttoivat erityisesti abietiinihapolla käsiteltyjä lehtiä. Sinappikuoriaisella testatut uutteet toimivat myös lupaavasti. Testattujen puulajien kuoresta on mahdollista uuttaa biologisesti aktiivisia yhdisteitä, mutta tuholaistorjunnan kannalta oikeiden pitoisuuksien ja tehokkaiden uuttomenetelmien löytäminen vaatii jatkotutkimuksia. Kuoren sisältämien yhdisteiden laatu ja määrä vaihtelevat monien tekijöiden, kuten ympäristön ja genetiikan vaikutuksesta. Hyönteisten sietokyky vaihtelee myös paljon lajeittain ja yksilöidenkin välillä on eroja. Uutteista valmistettavia torjunta-aineita olisi kuitenkin mahdollista sisällyttää esimerkiksi integroituun torjuntaan muiden menetelmien rinnalle tulevaisuudessa.

Magnetorotational instability driven dynamos at low magnetic Prandtl numbers

Numerical simulations of the magnetorotational instability (MRI) with zero initial net flux in a non-stratified isothermal cubic domain are used to demonstrate the importance of magnetic boundary conditions. In fully periodic systems the level of turbulence generated by the MRI strongly decreases as the magnetic Prandtl number (Pm), which is the ratio of kinematic viscosity and magnetic diffusion, is decreased. No MRI or dynamo action below Pm=1 is found, agreeing with earlier investigations. Using vertical field conditions, which allow magnetic helicity fluxes out of the system, the MRI is found to be excited in the range 0.1