Search results for "sequence"

Molecular phylogeny of the spider family Sparassidae with focus on the genus Eusparassus and notes on the RTA-clade and ‘Laterigradae’

2013

The phylogeny of the spider family Sparassidae is comprehensively investigated using four molecular markers (mitochondrial COI and 16S; nuclear H3 and 28S). Sparassidae was recovered as monophyletic and as most basal group within the RTA-clade. The higher-level clade Dionycha was not but monophyly of RTA-clade was supported. No affiliation of Sparassidae to other members of the 'Laterigradae' (Philodromidae, Selenopidae and Thomisidae) was observed, and the crab-like posture of this group assumed a result of convergent evolution. Only Philodromidae and Selenopidae were found members of a supported clade, but together with Salticidae and Corinnidae, while Thomisidae was nested within the hig…

An idiom a day keeps the doctor away : Finnish upper secondary school English teachers' attitudes towards teaching idioms

2009

 Idiomit ilmaisevat kulttuurille ominaisia ajatuksia ja siten niiden hallitseminen on tärkeä osa kielitaidon kehitystä. Viime vuosina idiomien oppimista ja opettamista onkin tutkittu melko laajasti. Tutkimuksissa on kuitenkin havaittu, että idiomien tärkeästä roolista huolimatta niiden suora opettaminen voi johtaa tilanteeseen, jossa oppilaat käyttävät niitä väärin, koska ovat erehtyneet pitämään idiomeja yleisempinä kuin ne ovat. Yksikään tutkimus ei kuitenkaan ole keskittynyt siihen, miten ja miksi opettajat käsittelevät idiomeja, minkä takia ei loppujen lopuksi tiedetä, kuinka suuri yllä kuvattu ongelma on. Tämä kandidaatin tutkielma syventyi selvittämään, mitä suomalaisen lukion englann…

To be or not to be : a case study of formulaic sequences in Finnish EFL texbooks for upper secondary school

2012

Kivettyneet ilmaisut voidaan määritellä useamman sanan pituisiksi ilmaisuiksi, jotka käyttäytyvät yksittäisten sanojen tavoin. Näillä fraaseilla on aina osasanoista riippumaton merkityksensä, ja on hyvin todennäköistä, että mieli myös varastoi kaavafraasit kokonaisuuksina yksittäisten sanojen sijasta. Kivettyneet ilmaisut ovat tärkeitä kielen sujuvalle käytölle ja oppimiselle, sekä kielelle järjestelmänä, sillä ne nopeuttavat kahta ensimmäistä prosessia ja ovat kulttuurisidonnaisuudessaan kriittisiä viimeiselle. Täten on perusteltua olettaa myös opetusmateriaalien sisältävän kaavafraaseja. Aiheitta on kuitenkin tutkittu äärimmäisen vähän, ja lähes ainoat tutkimuksen koskevat äärimmäisen raj…

Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR

2011

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen (R) method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affec…

Extending the hosts of Tectiviridae into four additional genera of Gram-positive bacteria and more diverse Bacillus species

2018

Tectiviridae are composed of tailless bacteriophages with an icosahedral capsid and an inner membrane enclosing a double-stranded 15 kb linear DNA genome. Five of the seven previously studied Tectivirus isolates infect bacteria from Bacillus cereus sensu lato group (Betatectivirus), one distantly related member (PRD1) infect Enterobactericeae (Alpatectivirus) and one recently discovered virus infect Gluconobacter cerinus (Gammatectivirus). Here we expand the host spectrum of Betatectivirus elements to four additional genera (Streptococcus, Exiguobacterium, Clostridium and Brevibacillus) and to more distantly related Bacillus species (B. pumilus and B. flexus) by studying the genomes of four…

Adaptive variable structure fuzzy neural identification and control for a class of MIMO nonlinear system

2013

This paper presents a novel adaptive variable structure (AVS) method to design a fuzzy neural network (FNN). This AVS-FNN is based on radial basis function (RBF) neurons, which have center and width vectors. The network performs sequential learning through sliding data window reflecting system dynamic changes, and dynamic growing-and-pruning structure of FNN. The salient characteristics of the AVS-FNN are as follows: (1) Structure-learning and parameters estimation are performed automatically and simultaneously without partitioning input space and selecting initial parameters a priori. The structure-learning approach relies on the contribution of the size of the output. (2) A set of fuzzy r…

Gene expression in TGFbeta-induced epithelial cell differentiation in a three-dimensional intestinal epithelial cell differentiation model

2006

Abstract Background The TGFβ1-induced signal transduction processes involved in growth and differentiation are only partly known. The three-dimensional epithelial differentiation model, in which T84 epithelial cells are induced to differentiate either with TGFβ1 or IMR-90 mesenchymal cell-secreted soluble factors, is previously shown to model epithelial cell differentiation seen in intestine. That model has not been used for large scale gene expression studies, such as microarray method. Therefore the gene expression changes were studied in undifferentiated and differentiated three-dimensional T84 cultures with cDNA microarray method in order to study the molecular changes and find new play…

A nonlinear optimization procedure to estimate GTR-distances

2006

Midbiotics : conjugative plasmids for genetic engineering of natural gut flora

2019

ABSTRACTThe possibility to modify gut bacterial flora has become an important goal, and various approaches are used to achieve desirable communities. However, the genetic engineering of existing microbes in the gut, which are already compatible with the rest of the community and host immune system, has not received much attention. Here, we discuss and experimentally evaluate the possibility to use modified and mobilizable CRISPR-Cas9-endocing plasmid as a tool to induce changes in bacterial communities. This plasmid system (briefly midbiotic) is delivered from bacterial vector into target bacteria via conjugation. Compared to, for example, bacteriophage-based applications, the benefits of c…

Interaction of glutamic-acid-rich proteins with the cGMP signalling pathway in rod photoreceptors.

1999

The assembly of signalling molecules into macromolecular complexes (transducisomes) provides specificity, sensitivity and speed in intracellular signalling pathways. Rod photoreceptors in the eye contain an unusual set of glutamic-acid-rich proteins (GARPs) of unknown function. GARPs exist as two soluble forms, GARP1 and GARP2, and as a large cytoplasmic domain (GARP' part) of the beta-subunit of the cyclic GMP-gated channel. Here we identify GARPs as multivalent proteins that interact with the key players of cGMP signalling, phosphodiesterase and guanylate cyclase, and with a retina-specific ATP-binding cassette transporter (ABCR), through four, short, repetitive sequences. In electron mic…