2,612 research outputs found

    The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions.

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    The Escherichia coli RutR protein is the master regulator of genes involved in pyrimidine catabolism. Here we have used chromatin immunoprecipitation in combination with DNA microarrays to measure the binding of RutR across the chromosome of exponentially growing E. coli cells. Twenty RutR-binding targets were identified and analysis of these targets generated a DNA consensus logo for RutR binding. Complementary in vitro binding assays showed high-affinity RutR binding to 16 of the 20 targets, with the four low-affinity RutR targets lacking predicted key binding determinants. Surprisingly, most of the DNA targets for RutR are located within coding segments of the genome and appear to have little or no effect on transcript levels in the conditions tested. This contrasts sharply with other E. coli transcription factors whose binding sites are primarily located in intergenic regions. We suggest that either RutR has yet undiscovered function or that evolution has been slow to eliminate non-functional DNA sites for RutR because they do not have an adverse effect on cell fitness

    A Dual-Route Approach to Orthographic Processing

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    In the present theoretical note we examine how different learning constraints, thought to be involved in optimizing the mapping of print to meaning during reading acquisition, might shape the nature of the orthographic code involved in skilled reading. On the one hand, optimization is hypothesized to involve selecting combinations of letters that are the most informative with respect to word identity (diagnosticity constraint), and on the other hand to involve the detection of letter combinations that correspond to pre-existing sublexical phonological and morphological representations (chunking constraint). These two constraints give rise to two different kinds of prelexical orthographic code, a coarse-grained and a fine-grained code, associated with the two routes of a dual-route architecture. Processing along the coarse-grained route optimizes fast access to semantics by using minimal subsets of letters that maximize information with respect to word identity, while coding for approximate within-word letter position independently of letter contiguity. Processing along the fined-grained route, on the other hand, is sensitive to the precise ordering of letters, as well as to position with respect to word beginnings and endings. This enables the chunking of frequently co-occurring contiguous letter combinations that form relevant units for morpho-orthographic processing (prefixes and suffixes) and for the sublexical translation of print to sound (multi-letter graphemes)

    Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR

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    The Escherichia coli MelR protein is a transcription activator that autoregulates its own promoter by repressing transcription initiation. Optimal repression requires MelR binding to a site that overlaps the melR transcription start point and to upstream sites. In this work, we have investigated the different determinants needed for optimal repression and their spatial requirements. We show that repression requires a complex involving four DNA-bound MelR molecules, and that the global CRP regulator plays little or no role

    Uncertainty in aerosolā€“cloud radiative forcing is driven by clean conditions

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    Atmospheric aerosols and their impact on cloud properties remain the largest uncertainty in the human forcing of the climate system. By increasing the concentration of cloud droplets (Nd), aerosols reduce droplet size and increase the reflectivity of clouds (a negative radiative forcing). Central to this climate impact is the susceptibility of cloud droplet number to aerosol (Ī²), the diversity of which explains much of the variation in the radiative forcing from aerosolā€“cloud interactions (RFaci) in global climate models. This has made measuring Ī² a key target for developing observational constraints of the aerosol forcing. While the aerosol burden of the clean, pre-industrial atmosphere has been demonstrated as a key uncertainty for the aerosol forcing, here we show that the behaviour of clouds under these clean conditions is of equal importance for understanding the spread in radiative forcing estimates between models and observations. This means that the uncertainty in the aerosol impact on clouds is, counterintuitively, driven by situations with little aerosol. Discarding clean conditions produces a close agreement between different model and observational estimates of the cloud response to aerosol but does not provide a strong constraint on the RFaci. This makes constraining aerosol behaviour in clean conditions an important goal for future observational studies
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