Evolutionary origin and functions of retrogene introns.

Retroposed genes (retrogenes) originate via the reverse transcription of mature messenger RNAs from parental source genes and are therefore usually devoid of introns. Here, we characterize a particular set of mammalian retrogenes that acquired introns upon their emergence and thus represent rare cases of intron gain in mammals. We find that although a few retrogenes evolved introns in their coding or 3' untranslated regions (untranslated region, UTR), most introns originated together with untranslated exons in the 5' flanking regions of the retrogene insertion site. They emerged either de novo or through fusions with 5' UTR exons of host genes into which the retrogenes inserted. Generally, retrogenes with introns display high transcription levels and show broader spatial expression patterns than other retrogenes. Our experimental expression analyses of individual intron-containing retrogenes show that 5' UTR introns may indeed promote higher expression levels, at least in part through encoded regulatory elements. By contrast, 3' UTR introns may lead to downregulation of expression levels via nonsense-mediated decay mechanisms. Notably, the majority of retrogenes with introns in their 5' flanks depend on distant, sometimes bidirectional CpG dinucleotide-enriched promoters for their expression that may be recruited from other genes in the genomic vicinity. We thus propose a scenario where the acquisition of new 5' exon-intron structures was directly linked to the recruitment of distant promoters by these retrogenes, a process potentially facilitated by the presence of proto-splice sites in the genomic vicinity of retrogene insertion sites. Thus, the primary role and selective benefit of new 5' introns (and UTR exons) was probably initially to span the often substantial distances to potent CpG promoters driving retrogene transcription. Later in evolution, these introns then obtained additional regulatory roles in fine tuning retrogene expression levels. Our study provides novel insights regarding mechanisms underlying the origin of new introns, the evolutionary relevance of intron gain, and the origin of new gene promoters.

Use of green fluorescent protein-based reporters to monitor balanced production of antifungal compounds in the biocontrol agent Pseudomonas fluorescens CHA0.

AIMS: To develop reporter constructs based on stable and unstable variants of the green fluorescent protein (GFP) for monitoring balanced production of antifungal compounds that are crucial for the capacity of the root-colonizing Pseudomonas fluorescens strain CHA0 to control plant diseases caused by soil-borne pathogenic fungi. METHODS AND RESULTS: Pseudomonas fluorescens CHA0 produces the three antifungal metabolites 2,4-diacetylphloroglucinol (DAPG), pyoluteorin (PLT) and pyrrolnitrin (PRN). The gfp[mut3] and gfp[AAV] reporter genes were fused to the promoter regions of the DAPG, PLT and PRN biosynthetic genes. The reporter fusions were then used to follow the kinetics of expression of the three antifungal metabolites in a microplate assay. DAPG and PLT were found to display an inverse relationship in which each metabolite activates its own biosynthesis while repressing the synthesis of the other metabolite. PRN appears not to be involved in this balance. However, the microbial and plant phenolic metabolite salicylate was found to interfere with the expression of both DAPG and PLT. CONCLUSIONS: The results obtained provide evidence that P. fluorescens CHA0 may keep the antifungal compounds DAPG and PLT at a fine-tuned balance that can be affected by certain microbial and plant phenolics. SIGNIFICANCE AND IMPACT OF THE STUDY: To our knowledge, the present study is the first to use stable and unstable GFP variants to study antibiotic gene expression in a biocontrol pseudomonad. The developed reporter fusions will be a highly valuable tool to study in situ expression of this bacterial biocontrol trait on plant roots, i.e. at the site of pathogen suppression.

Parallel Research, Multiple Intellectual Property Right Protection Instruments, and the Correlation among R&D Projects, September 2005

The choice of a research path in attacking scientific and technological problems is a significant component of firms’ R&D strategy. One of the findings of the patent races literature is that, in a competitive market setting, firms’ noncooperative choices of research projects display an excessive degree of correlation, as compared to the socially optimal level. The paper revisits this question in a context in which firms have access to trade secrets, in addition to patents, to assert intellectual property rights (IPR) over their discoveries. We find that the availability of multiple IPR protection instruments can move the paths chosen by firms engaged in an R&D race toward the social optimum.

Reverse transcriptase-dependent and -independent phases of infection with mouse mammary tumor virus: implications for superantigen function.

Mouse mammary tumor virus (MMTV) encodes a superantigen (SAg) that promotes stable infection and virus transmission. Upon subcutaneous MMTV injection, infected B cells present SAg to SAg-reactive T cells leading to a strong local immune response in the draining lymph node (LN) that peaks after 6 d. We have used the reverse transcriptase inhibitor 3'-azido-3'-deoxythymidine (AZT) to dissect in more detail the mechanism of SAg-dependent enhancement of MMTV infection in this system. Our data show that no detectable B or T cell response to SAg occurs in AZT pretreated mice. However, if AZT treatment is delayed 1-2 d after MMTV injection, a normal SAg-dependent local immune response is observed on day 6. Quantitation of viral DNA in draining LN of these infected mice indicates that a 4,000-fold increase in the absolute numbers of infected cells occurs between days 2 and 6 despite the presence of AZT. Furthermore MMTV DNA was found preferentially in surface IgG+ B cells of infected mice and was not detectable in SAg-reactive T cells. Collectively our data suggest that MMTV infection occurs preferentially in B cells without SAg involvement and is completed 1-2 d after virus challenge. Subsequent amplification of MMTV infection between days 2 and 6 requires SAg expression and occurs in the absence of any further requirement for reverse transcription. We therefore conclude that clonal expansion of infected B cells via cognate interaction with SAg-reactive T cells is the predominant mechanism for increasing the level of MMTV infection. Since infected B cells display a memory (surface IgG+) phenotype, both clonal expansion and possibly longevity of the virus carrier cells may contribute to stable MMTV infection.

Functional architecture of olfactory ionotropic glutamate receptors.

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate chemical communication between neurons at synapses. A variant iGluR subfamily, the Ionotropic Receptors (IRs), was recently proposed to detect environmental volatile chemicals in olfactory cilia. Here, we elucidate how these peripheral chemosensors have evolved mechanistically from their iGluR ancestors. Using a Drosophila model, we demonstrate that IRs act in combinations of up to three subunits, comprising individual odor-specific receptors and one or two broadly expressed coreceptors. Heteromeric IR complex formation is necessary and sufficient for trafficking to cilia and mediating odor-evoked electrophysiological responses in vivo and in vitro. IRs display heterogeneous ion conduction specificities related to their variable pore sequences, and divergent ligand-binding domains function in odor recognition and cilia localization. Our results provide insights into the conserved and distinct architecture of these olfactory and synaptic ion channels and offer perspectives into the use of IRs as genetically encoded chemical sensors. VIDEO ABSTRACT:

Identification of cancer stem cells in Ewing's sarcoma.

Cancer stem cells that display tumor-initiating properties have recently been identified in several distinct types of malignancies, holding promise for more effective therapeutic strategies. However, evidence of such cells in sarcomas, which include some of the most aggressive and therapy-resistant tumors, has not been shown to date. Here, we identify and characterize cancer stem cells in Ewing's sarcoma family tumors (ESFT), a highly aggressive pediatric malignancy believed to be of mesenchymal stem cell (MSC) origin. Using magnetic bead cell separation of primary ESFT, we have isolated a subpopulation of CD133+ tumor cells that display the capacity to initiate and sustain tumor growth through serial transplantation in nonobese diabetic/severe combined immunodeficiency mice, re-establishing at each in vivo passage the parental tumor phenotype and hierarchical cell organization. Consistent with the plasticity of MSCs, in vitro differentiation assays showed that the CD133+ cell population retained the ability to differentiate along adipogenic, osteogenic, and chondrogenic lineages. Quantitative real-time PCR analysis of genes implicated in stem cell maintenance revealed that CD133+ ESFT cells express significantly higher levels of OCT4 and NANOG than their CD133- counterparts. Taken together, our observations provide the first identification of ESFT cancer stem cells and demonstration of their MSC properties, a critical step towards a better biological understanding and rational therapeutic targeting of these tumors.

The Carboniferous Baralacha La basaltic dykes (Upper Lahul, Ladakh): remnants of an early rifting event along the Indian northern plate

The Lower Carboniferous Baralacha La basaltic dykes were emplaced along transtensional faults. The basalts exhibit tholeiitic and alkaline affinities. The tholeiites are TiO2-poor, moderately enriched in light rare earth (LREE), and display Nb and Ta negative and Th positive anomalies. The alkali basalts, compared to the tholeiites, have higher TiO2, rare earth and highly incompatible trace element contents and greater LREE enrichments. The Nd and Pb isotope compositions of the Baralacha La basalts suggest that they derive from the partial melting of an enriched OIB mantle source. characterized by a HIMU component, and contaminated by the lower continental crust. The Baralacha La dyke swarm represent the remnants of an early rifting event on the northern Indian passive margin.

Análisis y diseño de una pantalla informativa para fomentar la interacción social

En la actualidad, a lo largo del día, una persona es capaz de visualizar diversos displays informativos. Dichos displays generalmente son únicamente para mostrar algún tipo de información, sin ningún tipo de incitación a la interacción social, y es por esa razón que en este proyecto de fin de carrera se ha decidido realizar un display que intentase realizar esta función. La ubicación de este display es en un espacio público, como lo sería la fachada de un edificio o la plaza Catalunya, pero por razones que se detallarán en el contenido de la memoria, se ha decidido realizar en la plaza Gutenberg del campus de la comunicación de la Pompeu Fabra.Para poder conseguir esta interacción a diferencia de lo actual, el proyecto se ha realizado en varias fases, cada una de las cuales ha sido necesaria para la realización de la siguiente. Estas etapas son las de la observación, estudio, análisis, diseño, implementación y evaluación, siendo útiles para todo análisis y diseño de un display informativo. En la observación se ha visto el comportamiento de los usuarios, mientras que en el estudio se ha obtenido los gustos en común. Para el análisis se ha comparado todos los lugares posibles para situar el display y posteriormente se ha procedido a diseñarlo según el lugar de posicionamiento. Finalmente en la implementación se ha realizado dos programas, uno para la obtención de la información y otro para la visualización. En la evaluación se observa si se han cumplido los objetivos o no.

CNOT3 is a modifier of PRPF31 mutations in retinitis pigmentosa with incomplete penetrance.

Heterozygous mutations in the PRPF31 gene cause autosomal dominant retinitis pigmentosa (adRP), a hereditary disorder leading to progressive blindness. In some cases, such mutations display incomplete penetrance, implying that certain carriers develop retinal degeneration while others have no symptoms at all. Asymptomatic carriers are protected from the disease by a higher than average expression of the PRPF31 allele that is not mutated, mainly through the action of an unknown modifier gene mapping to chromosome 19q13.4. We investigated a large family with adRP segregating an 11-bp deletion in PRPF31. The analysis of cell lines derived from asymptomatic and affected individuals revealed that the expression of only one gene among a number of candidates within the 19q13.4 interval significantly correlated with that of PRPF31, both at the mRNA and protein levels, and according to an inverse relationship. This gene was CNOT3, encoding a subunit of the Ccr4-not transcription complex. In cultured cells, siRNA-mediated silencing of CNOT3 provoked an increase in PRPF31 expression, confirming a repressive nature of CNOT3 on PRPF31. Furthermore, chromatin immunoprecipitation revealed that CNOT3 directly binds to a specific PRPF31 promoter sequence, while next-generation sequencing of the CNOT3 genomic region indicated that its variable expression is associated with a common intronic SNP. In conclusion, we identify CNOT3 as the main modifier gene determining penetrance of PRPF31 mutations, via a mechanism of transcriptional repression. In asymptomatic carriers CNOT3 is expressed at low levels, allowing higher amounts of wild-type PRPF31 transcripts to be produced and preventing manifestation of retinal degeneration.

Tapiola-ryhmän Yhtiökokousjärjestelmä-ohjelmiston määrittely ja suunnittelu

Tässä insinöörityössä selvitettiin mahdollisuuksia parantaa Tapiola-ryhmän Yhtiökokousjärjestelmä-ohjelmiston ominaisuuksia ja tietoturvallisuutta. Järjestelmää käytetään Tapiola-ryhmän vakuutusyhtiöiden yhtiökokouksiin osallistuvien osakkaiden kirjaamiseen ja heidän äänten laskentaan. Tutkimuksen perusteella tehtiin järjestelmän määrittely ja suunnittelu, joiden tuloksena syntyivät toiminnallinen ja tekninen määrittelydokumentaatio, jotka toimivat pohjana uuden Yhtiökokousjärjestelmän toteutukselle. Työ tehtiin Tapiola-ryhmälle Tieto-Tapiola Oy:n tilauksesta. Työn alussa tutkittiin erilaisia mahdollisuuksia toteuttaa järjestelmän ohjelmisto- ja tietokanta-arkkitehtuuri, joiden perusteella määrittelyä ja suunnittelua alettiin toteuttaa. Tutkimuksen perusteella päädyttiin käyttämään Java SE -arkkitehtuuria sovelluksen toteutukseen ja SQL Server -tietokantaa järjestelmän tietovarastona. Valittuihin ratkaisuihin päädyttiin niiden hyvien tietoturvallisuus- ja kertakirjausominaisuuksien takia. Toiminnallisessa määrittelydokumentissa käydään läpi järjestelmälle asetettuja vaatimuksia ja kuvataan sen toiminnot, liiketoimintaluokkamalli, käyttöliittymä ja tulosteet. Lisäksi siinä otetaan kantaa järjestelmän käyttöympäristöön, ulkoisiin tietokantaliittymiin, käyttäjän tunnistautumiseen ja tietoturvallisuuteen sekä käydään läpi sen toiminta käyttäjien näkökulmasta. Toiminnallisen määrittelydokumentin pohjalta luotiin tekninen määrittelydokumentti. Siinä kuvataan järjestelmän ympäristö ja ohjelmisto- sekä tietokanta-arkkitehtuuri yleisellä tasolla. Tämän lisäksi järjestelmän arkkitehtuuria käydään myös tarkemmin läpi sekä kuvataan moduulit ja toiminnot niin tarkasti, että niiden perusteella voidaan toteuttaa koko järjestelmä. Työn tuloksena syntyivät kattava toiminnallinen ja tekninen määrittelydokumentaatio, joissa käydään läpi kaikki järjestelmän toteuttamiseen tarvittavat elementit sillä tarkkuudella, että järjestelmän toteuttaminen voidaan aloittaa.

Helsingin ammattikorkeakoulu Stadian kulttuurituottamisen suuntautumisvaihtoehto : ensimmäisen opintonsa aloittaneen vuosikurssin seuranta

This thesis is based on a questionnaire presented to pilot students on the Degree Programme in Media, at Helsinki Polytechnic Stadia, of 1999. The initial aim was to discover whether the school was of use in the transition process into a field of work. Based on this, the questions for a questionnaire were formulated. The research thus aimed at answering questions concerning a) whether the education answered the need of working life b) the work situation of respondents and c) how respondents saw the future of Arts Management as well as themselves. The questionnaire was prepared using Stadia's Elomake software on the Internet. There was also a project specific contract for this final project, allowing information gathered during the project to be used in regional curriculum work. The thesis deals with Arts Management curriculum work within the framework provided by polytechnic law as well as Stadia's curriculum work processes. Research and education in Arts Management in Finland generally is also studied, and specifically in Stadia itself. The essence of this final project is derived from the analysis of the answers to the questionnaire. All responses were analysed, with the answers being divided into three subheadings according to the research questions. Questions and answers were also examined through a correlation matrix in an attempt to discover the dependency between things and conclusions were made in the light of relevant source literature. The questionnaire is meant to be used for the follow-up of every graduating Arts Management group. Information obtained through this questionnaire will of benefit in preliminary curriculum work.

Viikon albumi -haastattelu osana YleX-kanavan ohjelmatarjontaa

Nuorille suunnatut lähetysvirtaradioasemat käyvät Suomessa koko ajan tiukempaa taistelua kuuntelijoidensa huomiosta. Kuuntelijalukuja tarkastellaan miltei viikoittain ja kuuntelijoille tarjottavaa tuotetta pyritään kilpailun koventuessa koko ajan kehittämään. Yleisradiossa tapahtui viimeksi kanavauudistus vuonna 2003, jonka seurauksena Radiomafia -kanava sai uuden nimen YleX. Uudistuksessa radiokanavan kohdeyleisö tarkennettiin uudelleen ja kanavalla siirryttiin soittolistapohjaiseen radion tekemiseen, jossa kanavan musiikkia soitetaan etukäteen laaditulta soittolistalta. Kanavauudistusta kritisoitiin mediassa ja arkipuheessa, vaikka YleX -kanavan viikkokuulijamäärät lähtivät nousuun. Vieläkin YleX:n musiikkitarjontaa arvostellaan yksipuoliseksi ja samalla myös kanavan ohjelmat ovat joutuneet kritiikin kohteeksi. Opinnäytetyöni käsittelee viihdeartistihaastattelun tekemistä YleX-radiokanavalla. Työssäni YleX-kanavalla olen tehnyt viikoittaista viihdeartistihaastattelua, joka tunnetaan nimellä Viikon Albumi -haastattelu. Tämä haastattelu on osa arkipäiväistä YleX Tänään-ohjelmaa, missä sitä lähetetään maanantaisin kello 11.10. Omia haastatteluja reflektoimalla selvitin haastattelijan näkökulmasta, minkälaisin menetelmin nykyaikaisessa nopeatempoisessa lähetysvirtaradiossa syntyy mielenkiintoinen ja syvällinen viihdeartisti-haastattelu. Kuinka lähelle laadukkaan viihdehaastattelun tavoitteita on mahdollista päästä 15 minuutin Viikon Albumi -haastattelun aikana? Työssäni keskityn etenkin YleX:n haastatteluiden viihteelliseen luonteeseen ja nimenomaan viihdeartistin haastattelemiseen, jota on alan kirjallisuudessa käsitelty melko vähän. Viihdyttävän ja hauskan viihdeartistihaastattelun tekeminen on vaikea haastattelumuoto, jonka tekemistä pyrin valottamaan omien töideni avulla. Toivon, että työstäni on jatkossa hyötyä myös muille samankaltaisissa haastattelutilanteissa.

Silta yksilöstä yhteisöön : ryhmätyö teatterin tekemisen välineenä

This final thesis focused on experimental knowledge of working in the group. The topic was approached from the perspective of the theatre group director. The thesis itself contains two practical theatre group examples. One is a youngsters' theatre group called La Drama, directed by the author during 2004/2005. The other one is the author's own final artistic production, named Protasio - Kohtaamisia Afrikassa (Protasio - Meeting in Africa), which opened in January 2006. The group leader's role is presented as an important personal tool in theatre, and one that it is important to develop in a professional way. The director's role is to be the promoter of the process, the inspirer and a strong group leader. A person who is in this role will lead the group through the creative process using the community. The thesis identifies and advocates good practice, and ideas of how to create theatre with a group-based method. These analyses can offer useful ideas and knowledge to the beginner in the field of theatre direction.

Matka serkamolaiseen teatteriin : kohti sanatonta kerrontaa

A travelogue to serkamoan theater deals, just like its name implies, with the molding process of one theater opinion. It has been influenced by both Aristotle's poetry and Bertold Brecht's epic theater. Side by side with theater goes dance, whose development the thesis also considers briefly. Of today's theater makers, Päivi Ketonen (playback theater), Juha Hurme and Nigel Charnock (dance theater) have had a definitive impact on the Serkamoan theater view. Their relation to theater and dance is clarified in the interviews conducted by the writer, which can be found in their entirety among the appendices of this thesis. Serkamoan theater has also been influenced by the writer's studies in Portuguese theater school in 2004. In Portugal the writer had a chance to work a theater piece in a new cultural environment where, for example, a novel and paintings were used as inspiration. The strongest legacy from Portugal however was the desire to do theater that can be understood without words. Serkamoan theater considers the combinations of theater and dance in performing arts, agreeing with, among others, Pina Bausch's footsteps. Serkamoan theater ladles its inspiration from theater, dance, human being, human body and movement. It is theater that cannot be understood through intellect but through the heart.

Elokuvien levittäminen Internetissä

Movie distribution on the Internet has become more common in recent years along with fast broadband internet connections. The problem so far has been that the greatest part of movie distribution on the Internet has been illegal. This is about to change because the major film distributors are finally starting to rent and sell movies more and more on the Internet due to their growing confidence in new copy protection methods. The importance of movie online distribution to the movie industry is still tiny but it is increasing rapidly as is investing in new business models and distribution methods in the USA and Europe. This thesis examines the basic concepts of online movie distribution, such as distribution techniques and copy protection, the main companies that rent and sell movies on the internet and their business models, the effects of movie piracy and non-commercial distribution channels. The intention was to provide the reader with an overview of different aspects of movie distribution on the Internet and its future. The conclusion was that movie distribution on the Internet will play a bigger financial part in the future although it was still too early to say just how significant that will be. We will probably see many corresponding distribution techniques, like peer-to-peer networks and streaming servers distributing and broadcasting movies to different end-user platforms like television, PC and portable media players. Internet distribution of movies will not revolutionize movie distribution in the next couple of years but it will make possible new efficient and inexpensive ways to distribute movies globally which will in turn increase the possibilities for revenue, especially for small independent movie producers and distributors.