Limiting the Extent of the RDN1 Heterochromatin Domain by a Silencing Barrier and Sir2 Protein Levels in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, transcriptional silencing occurs at the cryptic mating-type loci (HML and HMR), telomeres, and ribosomal DNA ( rDNA; RDN1). Silencing in the rDNA is unusual in that polymerase II (Pol II) promoters within RDN1 are repressed by Sir2 but not Sir3 or Sir4. rDNA silencing unidirectionally spreads leftward, but the mechanism of limiting its spreading is unclear. We searched for silencing barriers flanking the left end of RDN1 by using an established assay for detecting barriers to HMR silencing. Unexpectedly, the unique sequence immediately adjacent to RDN1, which overlaps a prominent cohesin binding site (CARL2), did not have appreciable barrier activity. Instead, a fragment located 2.4 kb to the left, containing a tRNA(Gln) gene and the Ty1 long terminal repeat, had robust barrier activity. The barrier activity was dependent on Pol III transcription of tRNA(Gln), the cohesin protein Smc1, and the SAS1 and Gcn5 histone acetyltransferases. The location of the barrier correlates with the detectable limit of rDNA silencing when SIR2 is overexpressed, where it blocks the spreading of rDNA heterochromatin. We propose a model in which normal Sir2 activity results in termination of silencing near the physical rDNA boundary, while tRNA(Gln) blocks silencing from spreading too far when nucleolar Sir2 pools become elevated.

Testicular function in adolescent boys with Klinefelter syndrome

Klinefelter syndrome (KS) is the most frequent karyotype disorder of male reproductive function. Since its original clinical description in 1942 and the identification of its chromosomal basis 47,XXY in 1959, the typical KS phenotype has become well recognized, but the mechanisms behind the testicular degeneration process have remained unrevealed. This prospective study was undertaken to increase knowledge about testicular function in adolescent KS boys. It comprised a longitudinal follow-up of growth, pubertal development, and serum reproductive hormone levels in 14 prepubertal and pubertal KS boys. Each boy had a testicular biopsy that was analyzed with histomorphometric and immunohistochemical methods. The KS boys had sufficient testosterone levels to allow normal onset and progression of puberty. Their serum testosterone levels remained within the low-normal range throughout puberty, but from midpuberty onwards, findings like a leveling-off in testosterone and insulin-like factor 3 (INSL3) concentrations, high gonadotropin levels, and exaggerated responses to gonadotropin-releasing hormone stimulation suggest diminished testosterone secretion. We also showed that the Leydig cell differentiation marker INSL3 may serve as a novel marker for onset and normal progression of puberty in boys. In the KS boys the number of germ cells was already markedly lower at the onset of puberty. The pubertal activation of the pituitary-testicular axis accelerated germ cell depletion, and germ cell differentiation was at least partly blocked at the spermatogonium or early primary spermatocyte stages. The presence of germ cells correlated with serum reproductive hormone levels. The immature Sertoli cells were incapable of transforming to the adult type, and during puberty the degeneration of Sertoli cells increased markedly. The older KS boys displayed an evident Leydig cell hyperplasia, as well as fibrosis and hyalinization of the interstitium and peritubular connective tissue. Altered immunoexpression of the androgen receptor (AR) suggested that in KS boys during puberty a relative androgen deficiency develops at testicular level. The impact of genetic features of the supernumerary X chromosome on the KS phenotype was also studied. The present study suggests that parental origin of the supernumerary X chromosome and the length of the CAG repeat of the AR gene influence pubertal development and testicular degeneration. The current study characterized by several means the testicular degeneration process in the testes of adolescent KS boys and confirmed that this process accelerates at the onset of puberty. Although serum reproductive hormone levels indicated no hypogonadism during early puberty, the histological analyses showed an already markedly reduced fertility potential in prepubertal KS boys. Genetic features of the X chromosome affect the KS phenotype.

Characterization of LRRTM and NGR gene families: Expression and functions

Some leucine-rich repeat (LRR) -containing membrane proteins are known regulators of neuronal growth and synapse formation. In this work I characterize two gene families encoding neuronal LRR membrane proteins, namely the LRRTM (leucine-rich repeat, transmembrane neuronal) and NGR (Nogo-66 receptor) families. I studied LRRTM and NGR family member's mRNA tissue distribution by RT-PCR and by in situ hybridization. Subcellular localization of LRRTM1 protein was studied in neurons and in non-neuronal cells. I discovered that LRRTM and NGR family mRNAs are predominantly expressed in the nervous system, and that each gene possesses a specific expression pattern. I also established that LRRTM and NGR family mRNAs are expressed by neurons, and not by glial cells. Within neurons, LRRTM1 protein is not transported to the plasma membrane; rather it localizes to endoplasmic reticulum. Nogo-A (RTN4), MAG, and OMgp are myelin-associated proteins that bind to NgR1 to limit axonal regeneration after central nervous system injury. To better understand the functions of NgR2 and NgR3, and to explore the possible redundancy in the signaling of myelin inhibitors of neurite growth, I mapped the interactions between NgR family and the known and candidate NgR1 ligands. I identified high-affinity interactions between RTN2-66, RTN3-66 and NgR1. I also demonstrate that Rtn3 mRNA is expressed in the same glial cell population of mouse spinal cord white matter as Nogo-A mRNA, and thus it could have a role in myelin inhibition of axonal growth. To understand how NgR1 interacts with multiple structurally divergent ligands, I aimed first to map in more detail the nature of Nogo-A:NgR1 interactions, and then to systematically map the binding sites of multiple myelin ligands in NgR1 by using a library of NgR1 expression constructs encoding proteins with one or multiple surface residues mutated to alanine. My analysis of the Nogo-A:NgR1 -interactions revealed a novel interaction site between the proteins, suggesting a trivalent Nogo-A:NgR1-interaction. Our analysis also defined a central binding region on the concave side of NgR1's LRR domain that is required for the binding of all known ligands, and a surrounding region critical for binding MAG and OMgp. To better understand the biological role of LRRTMs, I generated Lrrtm1 and Lrrtm3 knock out mice. I show here that reporter genes expressed from the targeted loci can be used for maping the neuronal connections of Lrrtm1 and Lrrtm3 expressing neurons in finer detail. With regard to LRRTM1's role in humans, we found a strong association between a 70 kb-spanning haplotype in the proposed promoter region of LRRTM1 gene and two possibly related phenotypes: left-handedness and schizophrenia. Interestingly, the responsible haplotype was linked to phenotypic variability only when paternally inherited. In summary, I identified two families of neuronal receptor-like proteins, and mapped their expression and certain protein-protein interactions. The identification of a central binding region in NgR1 shared by multiple ligands may facilitate the design and development of small molecule therapeutics blocking binding of all NgR1 ligands. Additionally, the genetic association data suggests that allelic variation upstream of LRRTM1 may play a role in the development of left-right brain asymmetry in humans. Lrrtm1 and Lrrtm3 knock out mice developed as a part of this study will likely be useful for schizophrenia and Alzheimer s disease research.

The complete mitochondrial genome of the tarnished plant bug, Lygus lineolaris (Heteroptera: Miridae)

The complete mitochondrial genome of the tarnished plant bug, Lygus lineolaris, comprised 17,027 bp. The genome contained 13 protein coding regions, 22 tRNA genes and 2 ribosomal RNA genes. The gene arrangement corresponded to the common order found among insect mtDNAs which was considered to be the ancestral arrangement. The protein coding genes started with ATN and stopped with TAA or TAG. The nucleotide distribution was 76.0% A + T. The control region contained two repeat regions, one was 24 bp and the other was 161 bp. The Genbank accession for the complete L. lineolaris mt genome is EU401991.

Human Rights in Action

In the post-World War II era human rights have emerged as an enormous global phenomenon. In Finland human rights have particularly in the 1990s moved from the periphery to the center of public policy making and political rhetoric. Human rights education is commonly viewed as the decisive vehicle for emancipating individuals of oppressive societal structures and rendering them conscious of the equal value of others; both core ideals of the abstract discourse. Yet little empirical research has been conducted on how these goals are realized in practice. These factors provide the background for the present study which, by combining anthropological insights with critical legal theory, has analyzed the educational activities of a Scandinavian and Nordic network of human rights experts and PhD students in 2002-2005. This material has been complemented by data from the proceedings of UN human rights treaty bodies, hearings organized by the Finnish Foreign Ministry, the analysis of different human rights documents as well as the manner human rights are talked of in the Finnish media. As the human rights phenomenon has expanded, human rights experts have acquired widespread societal influence. The content of human rights remains, nevertheless, ambiguous: on the one hand they are law, on the other, part of a moral discourse. By educating laymen on what human rights are, experts act both as intermediaries and activists who expand the scope of rights and simultaneously exert increasing political influence. In the educational activities of the analyzed network these roles were visible in the rhetorics of legality and legitimacy . Among experts both of these rhetorics are subject to ongoing professional controversy, yet in the network they are presented as undisputable facts. This contributes to the impression that human rights knowledge is uncontested. This study demonstrates how the network s activities embody and strengthen a conception of expertise as located in specific, structurally determined individuals. Simultaneously its conception of learning emphasizes the adoption of knowledge by students, emphasizing the power of experts over them. The majority of the network s experts are Nordic males, whereas its students are predominantly Nordic females and males from East-European and developing countries. Contrary to the ideals of the discourse the network s activities do not create dialogue, but instead repeat power structures which are themselves problematic.

Unusual RNA plant virus integration in the soybean genome leads to the production of small RNAs

Horizontal gene transfer (HGT) is known to be a major force in genome evolution. The acquisition of genes from viruses by eukaryotic genomes is a well-studied example of HGT, including rare cases of non-retroviral RNA virus integration. The present study describes the integration of cucumber mosaic virus RNA-1 into soybean genome. After an initial metatranscriptomic analysis of small RNAs derived from soybean, the de novo assembly resulted a 3029-nt contig homologous to RNA-1. The integration of this sequence in the soybean genome was confirmed by DNA deep sequencing. The locus where the integration occurred harbors the full RNA-1 sequence followed by the partial sequence of an endogenous mRNA and another sequence of RNA-1 as an inverted repeat and allowing the formation of a hairpin structure. This region recombined into a retrotransposon located inside an exon of a soybean gene. The nucleotide similarity of the integrated sequence compared to other Cucumber mosaic virus sequences indicates that the integration event occurred recently. We described a rare event of non-retroviral RNA virus integration in soybean that leads to the production of a double-stranded RNA in a similar fashion to virus resistance RNAi plants.

Lastensuojelun sosiaalityö asiakirjoina : Dokumentoinnin ja tiedonmuodostuksen dynamiikka

Tutkimuksen keskeinen tehtävä on selvittää, mikä on dokumentoinnin merkitys lastensuojelun sosiaalityön tiedonmuodostuksessa ja ammattikäytännöissä. Asiakirjateksteistä koostuvaa tutkimusaineistoa tarkastellaan kolmesta eri suunnasta kysymällä: 1)Miten asiakirjoja kirjoitetaan? 2) Mitä asiakirjoihin kirjoitetaan? 3) Miksi asiakirjoja kirjoitetaan niin kuin kirjoitetaan? Tutkimusaineisto muodostuu lastensuojelun sosiaalityöntekijöiden laatimista asiakastietojärjestelmään tallennetuista muistiinpanoista ja huostaanottopäätöksistä. Tutkimukseen on valittu 20 huostaanotetun eri-ikäisen lapsen ja heidän perheensä asiakirjat yhteensä 1613 asiakirjatulostussivua. Tekstit ajoittuvat vuodesta 1989 vuoteen 2000. Tutkimusmenetelmä on diskurssianalyyttinen ja tukeutuu Fairclough`n (1997)esittämään kolmiulotteiseen malliin, jossa diskurssi määritellään tekstin, käytäntöjen ja sosiokulttuurisen ympäristön suhteeksi. Diskurssianalyysi on näiden rakenteiden ja niiden välisten suhteiden kuvaamista, tulkintaa ja selittämistä. Fairclough’n mallia mukaillen tutkimuksen analyysi koostuu retoriikan ja tematiikan analyyseistä sekä pragmatiikan näkökulman sisältävästä tarkastelusta. Asiakirjatekstien pilkkominen puhujakategorioihin osoitti tekstien olevan moniäänisiä, useiden henkilöiden näkemyksiä ja mielipiteitä sisältäviä tekstipintoja. Retoriikan analyysi näytti, että lastensuojelun sosiaalityön asiakirjat sisältävät paljon dynaamisia kuvauksia työstä. Asiakirjojen kirjoittaminen moniäänisiksi tuo tekstiin uskottavuutta, ja se on myös yksi retorinen vaikuttamiskeino. Tematiikan tarkastelu osoitti,että asiakirjojen sisällölliset teemat (lapsen hoiva, arjen hallinta, yhteistyö ja päihteiden käyttö) ja kokemukselliset teemat (huoli, vastuu, yhteys ja moraali) toistuvat sisäkkäisinä ja päällekkäisinä säikeinä dynaamisesti vaihdellen. Sosiaalityöntekijät kirjaavat teksteihin monia yhtäaikaisia teemoja, joiden avulla rakentavat ammatillista ymmärrystä kyseessä olevasta tilanteesta. Asiakirjojen tutkiminen pragmatiikan suunnasta toi esiin, kirjoittamisen ja lukemisen kontekstiulottuvuudet sekä tiedonmuodostusprosessin. Asiakirjojen laatiminen on osa sosiaalityön käytäntöjä. Se on myös keskeinen alue ammattikunnan yhteisen ammatillisen ymmärryksen luomisessa ja ylläpitämisessä. Muistiinpanot, huostaanottopäätökset ja lakitekstit ovat intertekstuaalisia. Lastensuojelun sosiaalityön asiakirjojen tutkiminen on avannut uusia mahdollisuuksia ymmärtää sosiaalityön dokumentointiprosessia, merkitystä ja roolia sekä tiedonmuodostuksen dynamiikkaa. Tekstien kirjoittaminen, niiden lukeminen, tietojen siirtäminen ja asiakkaan kuuleminen samoin kuin kuulemisen kirjaaminen ovat sosiaalityön dokumentoinnin keskeisiä haasteita. Tutkimus pyrkii avaamaan ymmärrystä asiakirjatekstien monivivahteiseen ja dynaamiseen maailmaan ja siten myös sosiaalityön dokumentoinnin arkeen. Tarkastelut mahdollistavat työn kehittämisen erityisesti sosiaalityön asiakasvaikuttavuuden mittaamisen ja parantamisen suuntaan. Asiakirjoissa ilmenevä tiedonmuodostuksen dynamiikka syntyy kirjoittamiskäytäntöjen, kirjoittamisen ja lukemisen sekä toimintakäytäntöjen yhteisessä alueessa. Avainsanat: sosiaalityö, lastensuojelu, dokumentointi, asiakirja, diskurssianalyysi, tiedonmuodostus.

The United Nations and juvenile justice: An overview

The purpose of this article is to provide an overview of the various United Nations instruments relevant to juvenile justice and to examine how knowledge of these can assist those interested in the protection and enhancement of young people's rights in the justice system. It is argued that whilst these instruments are variable they are valuable tools for unmasking the discriminatory and unjust treatment of young people who come into contact with the justice system.

Transposable elements in a marginal plant population

Background
How new forms arise in nature has engaged evolutionary biologists since Darwin's seminal treatise on the origin of species. Transposable elements (TEs) may be among the most important internal sources for intraspecific variability. Thus, we aimed to explore the temporal dynamics of several TEs in individual genotypes from a small, marginal population of Aegilops speltoides. A diploid cross-pollinated grass species, it is a wild relative of the various wheat species known for their large genome sizes contributed by an extraordinary number of TEs, particularly long terminal repeat (LTR) retrotransposons. The population is characterized by high heteromorphy and possesses a wide spectrum of chromosomal abnormalities including supernumerary chromosomes, heterozygosity for translocations, and variability in the chromosomal position or number of 45S and 5S ribosomal DNA (rDNA) sites. We propose that variability on the morphological and chromosomal levels may be linked to variability at the molecular level and particularly in TE proliferation.

Results
Significant temporal fluctuation in the copy number of TEs was detected when processes that take place in small, marginal populations were simulated. It is known that under critical external conditions, outcrossing plants very often transit to self-pollination. Thus, three morphologically different genotypes with chromosomal aberrations were taken from a wild population of Ae. speltoides, and the dynamics of the TE complex traced through three rounds of selfing. It was discovered that: (i) various families of TEs vary tremendously in copy number between individuals from the same population and the selfed progenies; (ii) the fluctuations in copy number are TE-family specific; (iii) there is a great difference in TE copy number expansion or contraction between gametophytes and sporophytes; and (iv) a small percentage of TEs that increase in copy number can actually insert at novel locations and could serve as a bona fide mutagen.

Conclusions
We hypothesize that TE dynamics could promote or intensify morphological and karyotypical changes, some of which may be potentially important for the process of microevolution, and allow species with plastic genomes to survive as new forms or even species in times of rapid climatic change.

Intraseasonal response of mixed layer temperature and salinity in the Bay of Bengal to heat and freshwater flux

Buoy and satellite data show pronounced subseasonal oscillations of sea surface temperature (SST) in the summertime Bay of Bengal. The SST oscillations are forced mainly by surface heat flux associated with the active break cycle of the south Asian summer monsoon. The input of freshwater (FW) from summer rain and rivers to the bay is large, but not much is known about subseasonal salinity variability. We use 2002-2007 observations from three Argo floats with 5 day repeat cycle to study the subseasonal response of temperature and salinity to surface heat and freshwater flux in the central Bay of Bengal. About 95% of Argo profiles show a shallow halocline, with substantial variability of mixed layer salinity. Estimates of surface heat and freshwater flux are based on daily satellite data sampled along the float trajectory. We find that intraseasonal variability of mixed layer temperature is mainly a response to net surface heat flux minus penetrative radiation during the summer monsoon season. In winter and spring, however, temperature variability appears to be mainly due to lateral advection rather than local heat flux. Variability of mixed layer freshwater content is generally independent of local surface flux (precipitation minus evaporation) in all seasons. There are occasions when intense monsoon rainfall leads to local freshening, but these are rare. Large fluctuations in FW appear to be due to advection, suggesting that freshwater from rivers and rain moves in eddies or filaments.

What Can A Service Logic Offer Marketing Theory

The goods-dominated marketing model has major shortcomings as a guiding marketing theory. Its marketing mix approach is mainly geared towards buying and does not include consumption as an integral part of marketing theory. Although it is during the process of consuming goods and services that value is generated for customers and the foundation for repeat purchasing and customer relationships are laid, this process is left outside the scope of marketing. The focus in service marketing is not on a product but on interactions in service encounters. Consumption has become an integral part of a holistic marketing model. Other than standardized goods-based value propositions can be better understood when taking a servicebased approach. It is concluded that marketing based on a goods logic is but a special case of marketing based on a service logic and applicable only in certain contexts with standardized products.

Molecular analysis of Friedreich's ataxia locus in the Indian population

Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disorder caused by expansion of GAA repeats in the frataxin gene. We have carried out the first molecular analysis at the Friedreich's ataxia locus in the Indian population. Materials and methods - Three families clinically diagnosed for Friedreich's ataxia were analyzed for GAA expansion at the FRDA locus. The distribution of GAA repeats was also estimated in normal individuals of Indian origin. Results - All patients clinically diagnosed for Friedreich's ataxia were found to be homozygous for GAA repeat expansion. The GAA repeat in the normal population show a bimodal distribution with 94% of alleles ranging from 7-16 repeats. Conclusion - Indian patients with expansion at the FRDA locus showed typical clinical features of Friedreich's ataxia. The low frequency of large normal alleles (6%) could indicate that the prevalence of this disease in the Indian population is likely to be low.

Solution cation-binding properties of segmented polyethylene oxide-A C-13 NMR spectroscopic study

Two segmented polyethylene oxides, SPEO-3 and SPEO-4, were prepared using a novel transetherification methodology. Their structures were confirmed by H-1 and C-13 NMR spectroscopy. The complexation of these SPEO's with alkali-metal ions in solution was investigated by C-13 NMR spectroscopy. The mole-fraction method was used to determine the complexation ratio of SPEO with LIClO4 at 25 degrees C, which showed that these formed 1:1 (polymer repeat unit/salt) complexes. The association constant, K, for the complex formation was calculated from the variation of the chemical shift values with salt concentration, using a standard nonlinear least-square fitting procedure. The maximum change in chemical shift (Delta delta) and the K values suggest that both SPEO-3 and SPEO-4 formed stronger complexes with lithium salts than with sodium salts. Unexpectedly, the K values were found to be different, when the variation of delta of different carbons was used in the fitting procedure. This suggests that several possible complexed species may be in equilibrium with the uncomplexed one. Structurally similar model compounds were also prepared and their complexation studies indicated that all of them also formed 1:1 complexes with Li salts. Interestingly, it was observed that the polymers gave higher K values suggesting the formation of more stable complexes in polymers when compared to the model analogues. (C) 2000 John Wiley & Sons, Inc.

Symmetrical Bisbenzimidazoles with Benzenediyl Spacer: The Role of the Shape of the Ligand on the Stabilization and Structural Alterations in Telomeric G-Quadruplex DNA and Telomerase Inhibition

The extremities of chromosomes end in a G-rich single-stranded overhang that has been implicated in the onset of the replicate senescence. The repeated sequence forming a G-overhang is able to adopt a four-stranded DNA structure called G-quadruplex, which is a poor substrate for the enzyme telomerase. Small molecule based ligands that selectively stabilize the telomeric G-quadruplex DNA, induce telomere shortening eventually leading to cell death. Herein, we have investigated the G-quadruplex DNA interaction with two isomeric bisbenzimidazole-based compounds that differ in terms of shape (V-shaped angular vs linear).While the linear isomer induced some stabilization of the intramolecular G-quadruplex structure generated in the presence of Na+ the other, having V-shaped central planar core, caused a dramatic structural alteration of the latter, above a threshold concentration. This transition was evident from the pronounced changes observed in the circular dichroism spectra and from the get mobility shift assa involving the G-quadruples DNA. Notably, this angular isomer could also induce the G-quadruplex formation in the absence of any added cation. The ligand-quadruples complexes were investigated by computational molecular modeling, providing further information on structure-activity relationships. Finally, TRAP (telomerase repeat amplification protocol) experiments demonstrated that the angular isomer is selective toward the inhibition of telomerase activity.

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.