Initiation of transcription of rDNA in rice

Three direct repeats of 320, 340 and 238 nucleotides were detected upstream to the 5′ end of the 18S rRNA gene of an rDNA unit present on a 9.8 kb EcoRT fragment of the rice DNA. The primer extension analysis showed that the site of initiation of transcription is in the 1st repeat at an A, the 623rd nucleotide upstream to the 5′ end of the 18S rRNA gene. Different stretches of the intergenic spacer DNA linked to the Chloramphenicol acetyl transferase gene were transcribed in the intact nuclei of rice embryos. The S1 nuclease protection analysis of the transcripts using [32P]-labelled Chloramphenicol acetyl transferase gene as the probe showed the presence of multiple promoters for rDNA transcription.

Myotonic dystrophy type 2 (DM2) : Diagnostic methods and molecular pathology

Myotonic dystrophies type 1 (DM1) and type 2 (DM2) are the most common forms of muscular dystrophy affecting adults. They are autosomal dominant diseases caused by microsatellite tri- or tetranucleotide repeat expansion mutations in transcribed but not translated gene regions. The mutant RNA accumulates in nuclei disturbing the expression of several genes. The more recently identified DM2 disease is less well known, yet more than 300 patients have been confirmed in Finland thus far, and the true number is believed to be much higher. DM1 and DM2 share some features in general clinical presentation and molecular pathology, yet they show distinctive differences, including disease severity and differential muscle and fiber type involvement. However, the molecular differences underlying DM1 and DM2 muscle pathology are not well understood. Although the primary tissue affected is muscle, both DMs show a multisystemic phenotype due to wide expression of the mutation-carrying genes. DM2 is particularly intriguing, as it shows an incredibly wide spectrum of clinical manifestations. For this reason, it constitutes a real diagnostic challenge. The core symptoms in DM2 include proximal muscle weakness, muscle pain, myotonia, cataracts, cardiac conduction defects and endocrinological disturbations; however, none of these is mandatory for the disease. Myalgic pains may be the most disabling symptom for decades, sometimes leading to incapacity for work. In addition, DM2 may cause major socio-economical consequences for the patient, if not diagnosed, due to misunderstanding and false stigmatization. In this thesis work, we have (I) improved DM2 differential diagnostics based on muscle biopsy, and (II) described abnormalities in mRNA and protein expression in DM1 and DM2 patient skeletal muscles, showing partial differences between the two diseases, which may contribute to muscle pathology in these diseases. This is the first description of histopathological differences between DM1 and DM2, which can be used in differential diagnostics. Two novel high-resolution applications of in situ -hybridization have been described, which can be used for direct visualization of the DM2 mutation in muscle biopsy sections, or mutation size determination on extended DNA-fibers. By measuring protein and mRNA expression in the samples, differential changes in expression patterns affecting contractile proteins, other structural proteins and calcium handling proteins in DM2 compared to DM1 were found. The dysregulation at mRNA level was caused by altered transciption and abnormal splicing. The findings reported here indicate that the extent of aberrant splicing is higher in DM2 compared to DM1. In addition, the described abnormalities to some extent correlate to the differences in fiber type involvement in the two disorders.

Real-Time PCR : A Molecular Approach to Investigate the Role of Intestinal Microbiota in the Pathophysiology of Irritable Bowel Syndrome

Irritable bowel syndrome (IBS) is a common multifactorial functional intestinal disorder, the pathogenesis of which is not completely understood. Increasing scientific evidence suggests that microbes are involved in the onset and maintenance of IBS symptoms. The microbiota of the human gastrointestinal (GI) tract constitutes a massive and complex ecosystem consisting mainly of obligate anaerobic microorganisms making the use of culture-based methods demanding and prone to misinterpretation. To overcome these drawbacks, an extensive panel of species- and group-specific assays for an accurate quantification of bacteria from fecal samples with real-time PCR was developed, optimized, and validated. As a result, the target bacteria were detectable at a minimum concentration range of approximately 10 000 bacterial genomes per gram of fecal sample, which corresponds to the sensitivity to detect 0.000001% subpopulations of the total fecal microbiota. The real-time PCR panel covering both commensal and pathogenic microorganisms was assessed to compare the intestinal microbiota of patients suffering from IBS with a healthy control group devoid of GI symptoms. Both the IBS and control groups showed considerable individual variation in gut microbiota composition. Sorting of the IBS patients according to the symptom subtypes (diarrhea, constipation, and alternating predominant type) revealed that lower amounts of Lactobacillus spp. were present in the samples of diarrhea predominant IBS patients, whereas constipation predominant IBS patients carried increased amounts of Veillonella spp. In the screening of intestinal pathogens, 17% of IBS samples tested positive for Staphylococcus aureus, whereas no positive cases were discovered among healthy controls. Furthermore, the methodology was applied to monitor the effects of a multispecies probiotic supplementation on GI microbiota of IBS sufferers. In the placebo-controlled double-blind probiotic intervention trial of IBS patients, each supplemented probiotic strain was detected in fecal samples. Intestinal microbiota remained stable during the trial, except for Bifidobacterium spp., which increased in the placebo group and decreased in the probiotic group. The combination of assays developed and applied in this thesis has an overall coverage of 300-400 known bacterial species, along with the number of yet unknown phylotypes. Hence, it provides good means for studying the intestinal microbiota, irrespective of the intestinal condition and health status. In particular, it allows screening and identification of microbes putatively associated with IBS. The alterations in the gut microbiota discovered here support the hypothesis that microbes are likely to contribute to the pathophysiology of IBS. The central question is whether the microbiota changes described represent the cause for, rather than the effect of, disturbed gut physiology. Therefore, more studies are needed to determine the role and importance of individual microbial species or groups in IBS. In addition, it is essential that the microbial alterations observed in this study will be confirmed using a larger set of IBS samples of different subtypes, preferably from various geographical locations.

A possible model for fifth force

Recent reanalysis of the data of the Eötvös experiment suggested the existence of a new force. We show that a negative energy massive scalar field minimally coupled to gravity in a background Schwarzschild metric naturally leads to a potential which can explain the small anomalous effect in the Eötvös experiment.

Heme regulates cytochrome P-450 gene transcription elongation

Administration of 3-methylcholanthrene (MC) to rats results in a striking increase in the transcription of cytochrome P-450 (c+d) messenger RNA with isolated nuclei, which is blocked by the simultaneous administration of cobalt chloride, an inhibitor of heme biosynthesis. Transcription of cytochrome P-450 (c+d) mRNAs with nuclei isolated from MC treated rats shows a linear increase with time of incubation, whereas it shows a progressive decrease with incubation time in the case of nuclei isolated from MC+CoCl2 treated rats. Addition of heme in vitro (10−6M) to the latter nuclei results in a significant counteraction of the decreased cytochrome P-450 (c+d) mRNA transcription. The inhibition in transcription rates observed in MC+CoCl2 treated rat liver nuclei is more pronounced with the seventh exon probe than with the second exon probe. Once again, in vitro heme addition can counteract the inhibition observed with both the probes. Since run off transcription with isolated nuclei represents essentially elongation of the initiated transcripts, the data obtained can be interpreted on the basis that heme regulates cytochrome P-450 gene transcription elongation.

Hot gaseous coronae of early-type galaxies and their radio luminosity function

Recent X-ray observations have revealed that early-type galaxies (which usually produce extended double radio sources) generally have hot gaseous haloes extending up to approx102kpc1,2. Moreover, much of the cosmic X-ray background radiation is probably due to a hotter, but extremely tenuous, intergalactic medium (IGM)3. We have presented4–7 an analytical model for the propagation of relativistic beams from galactic nuclei, in which the beams' crossing of the pressure-matched interface between the IGM and the gaseous halo, plays an important role. The hotspots at the ends of the beams fade quickly when their advance becomes subsonic with respect to the IGM. This model has successfully predicted (for typical double radio sources) the observed8 current mean linear-size (approx2Dsime350 kpc)4,5, the observed8–11 decrease in linear-size with cosmological redshift4–6 and the slope of the linear-size versus radio luminosity10,12–14 relation6. We have also been able to predict the redshift-dependence of observed numbers and radio luminosities of giant radio galaxies7,15. Here, we extend this model to include the propagation of somewhat weaker beams. We show that the observed flattening of the local radio luminosity function (LRLF)16–20 for radio luminosity Papproximately 1024 W Hz-1 at 1 GHz can be explained without invoking ad hoc a corresponding break in the beam power function Phi(Lb), because the heads of the beams with Lb < 1025 W Hz-1 are decelerated to sonic velocity within the halo itself, which leads to a rapid decay of radio luminosity and a reduced contribution of these intrinsically weaker sources to the observed LRLF.

The superfluid as a source of all interactions

The superfluid state of fermion-antifermion fields developed in our previous papers is generalized to include higher orbital and spin states. In addition to single-particle excitations, the system is capable of having real and virtual bound or quasibound composite excitations which are akin to bosons of spinJ P equal to0 �, 1�, 2+, etc. These pseudoscalar, vector, and tensor bosons can be massive or massless and provide the vehicles for strong, electromagnetic, weak, and gravitational interactions. The concept that the basic (unmanifest) fermion-antifermion interaction can lead to a multiplicity of manifest interactions seems to provide a basis for a unified field theory.

A study of interactions in He2 1 in terms of the electronic forces

The He+He+1 interactions have been studied, as a function of the internuclear separation R, in terms of the electronic forces acting on the nuclei and the change in the charge distribution. The analysis reveals that at large R the atomic densities are polarized inwards, causing an attractive force on each nucleus, while at small R the difference in the nature of the interactions in the 2Σu and 2Σg systems is noted. It is seen that the He+He+1 (2Σu) interaction is less attractive than the He+1+He+1 interaction at lower values of R.

Towards understanding the unusual Indian monsoon in 2009

The Indian summer monsoon season of 2009 commenced with a massive deficit in all-India rainfall of 48% of the average rainfall in June. The all-India rainfall in July was close to the normal but that in August was deficit by 27%. In this paper, we first focus on June 2009, elucidating the special features and attempting to identify the factors that could have led to the large deficit in rainfall. In June 2009, the phase of the two important modes, viz., El Nino and Southern Oscillation (ENSO) and the equatorial Indian Ocean Oscillation (EQUINOO) was unfavourable. Also, the eastern equatorial Indian Ocean (EEIO) was warmer than in other years and much warmer than the Bay. In almost all the years, the opposite is true, i.e., the Bay is warmer than EEIO in June. It appears that this SST gradient gave an edge to the tropical convergence zone over the eastern equatorial Indian Ocean, in competition with the organized convection over the Bay. Thus, convection was not sustained for more than three or four days over the Bay and no northward propagations occurred. We suggest that the reversal of the sea surface temperature (SST) gradient between the Bay of Bengal and EEIO, played a critical role in the rainfall deficit over the Bay and hence the Indian region. We also suggest that suppression of convection over EEIO in association with the El Nino led to a positive phase of EQUINOO in July and hence revival of the monsoon despite the El Nino. It appears that the transition to a negative phase of EQUINOO in August and the associated large deficit in monsoon rainfall can also be attributed to the El Nino.

Spin and mass content of linearized Poincaré gauge theories

A unified gauge theory of massless and massive spin-2 fields is of considerable current interest. The Poincaré gauge theories with quadratic Lagrangian are linearized, and the conditions on the parameters are found which will lead to viable linear theories with massive gauge particles. As well as the 2+ massless gravitons coming from the translational gauge potential, the rotational gauge potentials, in the linearized limit, give rise to 2+ and 2− particles of equal mass, as well as a massive pseudoscalar.

Population genetics of the invasive plant species Impatiens glandulifera in Southern Finland

Biological invasions affect biodiversity worldwide, and, consequently, the invaded ecosystems may suffer from significant losses in economic and cultural values. Impatiens glandulifera Royle (Balsaminaceae) is an invasive annual herb, native to the western Himalayas and introduced into Europe in the 19th century as a garden ornamental plant. The massive invasion of I. glandulifera is due to its high reproductive output, rapid growth and its ability to outcompete native species. In Finland, the first observations regarding the presence of I. glandulifera date from the year 1947, and today it is considered a serious problem in riparian habitats. The aim of this master’s thesis research is to reveal the population genetic structure of I. glandulifera in Finland and to find out whether there have been one or multiple invasions in Finland. The study focuses on investigating the origin of I. glandulifera in Southern Finland, by comparing plant samples from the Helsinki region with those from its native region and other regions of invasion. Samples from four populations in Helsinki and from the United Kingdom, Canada, India and Pakistan were collected and genotyped using 11 microsatellite markers. The genetic analyses were evaluated using the programs Arlequin and Structure. The results of the genetic analyses suggested that I. glandulifera has been introduced to Finland more than once. Multiple introductions are supported by the higher level of genetic diversity detected within and among Finnish populations than would be expected for a single introduction. Results of the Bayesian Structure analysis divided the four Finnish populations into four clusters. This geographical structure was further supported by pairwise Fst values among populations. The causes and potential consequences of such multiple introductions of I. glandulifera in Finland and further perspectives are discussed.

Mode of action of antitumour antibiotics-III: Modulation of permeability of nuclear membrane in the presence of the antibiotics

The binding characteristics of the antibiotics to nuclei and their effect on the permeability of nuclear membrane with respect to histones and ribonucleic acids have been investigated. The binding constant for chromomycin A3 was found to be 1.4 × 104M?1 and number of binding sites was equal to 3.48 ± 1.08 × 1012 molecules/nuclei. The antibiotic chromomycin A3 enhanced the uptake of lysine-rich histone, actinomycin D decreased the uptake and ethidium bromide had no effect. Chromomycin A3 also enhanced the release of acid insoluble fraction containing RNA from the nuclei, actinomycin D and ethidium bromide inhibited the release of acid insoluble fraction containing RNA. The relevance of this finding to the role of nuclear envelope in understanding the mechanism of action of the antibiotic has been discussed.

A Triggering Mechanism for Enhanced Star-Formation in Colliding Galaxies

We propose a physical mechanism to explain the origin of the intense burst of massive-star formation seen in colliding/merging, gas-rich, field spiral galaxies. We explicitly take account of the different parameters for the two main mass components, H-2 and H I, of the interstellar medium within a galaxy and follow their consequent different evolution during a collision between two galaxies. We also note that, in a typical spiral galaxy-like our galaxy, the Giant Molecular Clouds (GMCs) are in a near-virial equilibrium and form the current sites of massive-star formation, but have a low star formation rate. We show that this star formation rate is increased following a collision between galaxies. During a typical collision between two field spiral galaxies, the H I clouds from the two galaxies undergo collisions at a relative velocity of approximately 300 km s-1. However, the GMCs, with their smaller volume filling factor, do not collide. The collisions among the H I clouds from the two galaxies lead to the formation of a hot, ionized, high-pressure remnant gas. The over-pressure due to this hot gas causes a radiative shock compression of the outer layers of a preexisting GMC in the overlapping wedge region. This makes these layers gravitationally unstable, thus triggering a burst of massive-star formation in the initially barely stable GMCs.The resulting value of the typical IR luminosity from the young, massive stars from a pair of colliding galaxies is estimated to be approximately 2 x 10(11) L., in agreement with the observed values. In our model, the massive-star formation occurs in situ in the overlapping regions of a pair of colliding galaxies. We can thus explain the origin of enhanced star formation over an extended, central area approximately several kiloparsecs in size, as seen in typical colliding galaxies, and also the origin of starbursts in extranuclear regions of disk overlap as seen in Arp 299 (NGC 3690/IC 694) and in Arp 244 (NGC 4038/39). Whether the IR emission from the central region or that from the surrounding extranuclear galactic disk dominates depends on the geometry and the epoch of the collision and on the initial radial gas distribution in the two galaxies. In general, the central starburst would be stronger than that in the disks, due to the higher preexisting gas densities in the central region. The burst of star formation is expected to last over a galactic gas disk crossing time approximately 4 x 10(7) yr. We can also explain the simultaneous existence of nearly normal CO galaxy luminosities and shocked H-2 gas, as seen in colliding field galaxies.This is a minimal model, in that the only necessary condition for it to work is that there should be a sufficient overlap between the spatial gas distributions of the colliding galaxy pair.

A new method for modulating the activity of parvalbumin-positive neurons and cerebellar Purkinje cells in vivo

Neurons can be divided into various classes according to their location, morphology, neurochemical identity and electrical properties. They form complex interconnected networks with precise roles for each cell type. GABAergic neurons expressing the calcium-binding protein parvalbumin (Pv) are mainly interneurons, which serve a coordinating function. Pv-cells modulate the activity of principal cells with high temporal precision. Abnormalities of Pv-interneuron activity in cortical areas have been linked to neuropsychiatric illnesses such as schizophrenia. Cerebellar Purkinje cells are known to be central to motor learning. They are the sole output from the layered cerebellar cortex to deep cerebellar nuclei. There are still many open questions about the precise role of Pv-neurons and Purkinje cells, many of which could be answered if one could achieve rapid, reversible cell-type specific modulation of the activity of these neurons and observe the subsequent changes at the whole-animal level. The aim of these studies was to develop a novel method for the modulation of Pv-neurons and Purkinje cells in vivo and to use this method to investigate the significance of inhibition in these neuronal types with a variety of behavioral experiments in addition to tissue autoradiography, electrophysiology and immunohistochemistry. The GABA(A) receptor γ2 subunit was ablated from Pv-neurons and Purkinje cells in four separate mouse lines. Pv-Δγ2 mice had wide-ranging behavioral alterations and increased GABA-insensitive binding indicative of an altered GABA(A) receptor composition, particularly in midbrain areas. PC-Δγ2 mice experienced little or no motor impairment despite the lack of inhibition in Purkinje cells. In Pv-Δγ2-partial rescue mice, a reversal of motor and cognitive deficits was observed in addition to restoration of the wild-type γ2F77 subunit to the reticular nucleus of thalamus and the cerebellar molecular layer. In PC-Δγ2-swap mice, zolpidem sensitivity was restored to Purkinje cells and the administration of systemic zolpidem evoked a transient motor impairment. On the basis of these results, it is concluded that this new method of cell-type specific modulation is a feasible way to modulate the activity of selected neuronal types. The importance of Purkinje cells to motor control supports previous studies, and the crucial involvement of Pv-neurons in a range of behavioral modalities is confirmed.

Embracing Integrability in Stellar and Planetary Dynamics

Hamiltonian systems in stellar and planetary dynamics are typically near integrable. For example, Solar System planets are almost in two-body orbits, and in simulations of the Galaxy, the orbits of stars seem regular. For such systems, sophisticated numerical methods can be developed through integrable approximations. Following this theme, we discuss three distinct problems. We start by considering numerical integration techniques for planetary systems. Perturbation methods (that utilize the integrability of the two-body motion) are preferred over conventional "blind" integration schemes. We introduce perturbation methods formulated with Cartesian variables. In our numerical comparisons, these are superior to their conventional counterparts, but, by definition, lack the energy-preserving properties of symplectic integrators. However, they are exceptionally well suited for relatively short-term integrations in which moderately high positional accuracy is required. The next exercise falls into the category of stability questions in solar systems. Traditionally, the interest has been on the orbital stability of planets, which have been quantified, e.g., by Liapunov exponents. We offer a complementary aspect by considering the protective effect that massive gas giants, like Jupiter, can offer to Earth-like planets inside the habitable zone of a planetary system. Our method produces a single quantity, called the escape rate, which characterizes the system of giant planets. We obtain some interesting results by computing escape rates for the Solar System. Galaxy modelling is our third and final topic. Because of the sheer number of stars (about 10^11 in Milky Way) galaxies are often modelled as smooth potentials hosting distributions of stars. Unfortunately, only a handful of suitable potentials are integrable (harmonic oscillator, isochrone and Stäckel potential). This severely limits the possibilities of finding an integrable approximation for an observed galaxy. A solution to this problem is torus construction; a method for numerically creating a foliation of invariant phase-space tori corresponding to a given target Hamiltonian. Canonically, the invariant tori are constructed by deforming the tori of some existing integrable toy Hamiltonian. Our contribution is to demonstrate how this can be accomplished by using a Stäckel toy Hamiltonian in ellipsoidal coordinates.