Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii

Although Methanocaldococcus (Methanococcus) jannaschii was the first archaeon to have its genome sequenced, little is known about the promoters of its protein-coding genes. To expand our knowledge, we have experimentally identified 131 promoters for 107 protein-coding genes in this genome by mapping their transcription start sites. Compared to previously identified promoters, more than half of which are from genes for stable RNAs, the protein-coding gene promoters are qualitatively similar in overall sequence pattern, but statistically different at several positions due to greater variation among their sequences. Relative binding affinity for general transcription factors was measured for 12 of these promoters by competition electrophoretic mobility shift assays. These promoters bind the factors less tightly than do most tRNA gene promoters. When a position weight matrix (PWM) was constructed from the protein gene promoters, factor binding affinities correlated with corresponding promoter PWM scores. We show that the PWM based on our data more accurately predicts promoters in the genome and transcription start sites than could be done with the previously available data. We also introduce a PWM logo, which visually displays the implications of observing a given base at a position in a sequence

Cloning retinoid and peroxisome proliferator-activated nuclear receptors of the Pacific oyster and in silico binding to environmental chemicals

This is the final version of the article. Available from Public Library of Science via the DOI in this record.Disruption of nuclear receptors, a transcription factor superfamily regulating gene expression in animals, is one proposed mechanism through which pollution causes effects in aquatic invertebrates. Environmental pollutants have the ability to interfere with the receptor's functions through direct binding and inducing incorrect signals. Limited knowledge of invertebrate endocrinology and molecular regulatory mechanisms, however, impede the understanding of endocrine disruptive effects in many aquatic invertebrate species. Here, we isolated three nuclear receptors of the Pacific oyster, Crassostrea gigas: two isoforms of the retinoid X receptor, CgRXR-1 and CgRXR-2, a retinoic acid receptor ortholog CgRAR, and a peroxisome proliferator-activated receptor ortholog CgPPAR. Computer modelling of the receptors based on 3D crystal structures of human proteins was used to predict each receptor's ability to bind to different ligands in silico. CgRXR showed high potential to bind and be activated by 9-cis retinoic acid and the organotin tributyltin (TBT). Computer modelling of CgRAR revealed six residues in the ligand binding domain, which prevent the successful interaction with natural and synthetic retinoid ligands. This supports an existing theory of loss of retinoid binding in molluscan RARs. Modelling of CgPPAR was less reliable due to high discrepancies in sequence to its human ortholog. Yet, there are suggestions of binding to TBT, but not to rosiglitazone. The effect of potential receptor ligands on early oyster development was assessed after 24h of chemical exposure. TBT oxide (0.2μg/l), all-trans retinoic acid (ATRA) (0.06 mg/L) and perfluorooctanoic acid (20 mg/L) showed high effects on development (>74% abnormal developed D-shelled larvae), while rosiglitazone (40 mg/L) showed no effect. The results are discussed in relation to a putative direct (TBT) disruption effect on nuclear receptors. The inability of direct binding of ATRA to CgRAR suggests either a disruptive effect through a pathway excluding nuclear receptors or an indirect interaction. Our findings provide valuable information on potential mechanisms of molluscan nuclear receptors and the effects of environmental pollution on aquatic invertebrates.The study was funded by the Centre for Environment, Fisheries and Aquaculture Science (Cefas; https://www.cefas.co.uk) and by the University of Exeter (http://www.exeter.ac.uk)

Das Wasserspucken der Arten der Gattung Colisa (Pisces: Anabantidae)

Volume: 24Start Page: 62End Page: 10

Brutpflegestrategien bei Belontiiden (Pisces, Anabantoidei)

Volume: 42Start Page: 299End Page: 32

Die \uf6kologischen Anspr\ufcche der Kampffische Betta imbellis und Betta pugnax auf der Malaiischen Halbinsel

Volume: 37Start Page: 131End Page: 14

Onderbenutting van capaciteiten in basis- en voortgezet onderwijs

Onderpresteren komt relatief veel voor bij kinderen van autochtone laagopgeleide ouders. Vaak heeft de leerkracht lage verwachtingen, krijgen deze kinderen lagere schooladviezen dan kinderen met vergelijkbare prestaties, en kiezen zij (en hun ouders) zelf voor een lager schooltype dan ze vermoedelijk aan zouden kunnen. Niet alleen autochtone kinderen van laagopgeleide ouders presteren onder hun kunnen. Onder Turkse leerlingen komt onderpresteren op taal(begrip) vaker voor dan bij andere allochtone leerlingen. In het voortgezet onderwijs nemen ze minder deel aan de hogere schooltypen en hebben ze lagere cijfers voor Nederlands en Engels. De onderzoekers wijzen ook op problemen bij zeer begaafde leerlingen die regelmatig onderpresteren en op het onderscheid tussen jongens en meisjes als het gaat om schoolresultaten