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

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

Numerical Simulation of Baroclinic Jovian Vortices

We examine the evolution of baroclinic vortices in a time-dependent, nonlinear numerical model of a Jovian atmosphere. The model uses a normal-mode expansion in the vertical, using the barotropic and first two baroclinic modes. Results for the stability of baroclinic vortices on an f plane in the absence of a mean zonal flow are similar to results of Earth vortex models, although the presence of a fluid interior on the Jovian planets shifts the stability boundaries to smaller length scales. The presence of a barotropic mean zonal flow in the interior stabilizes vortices against instability and significantly modifies the finite amplitude form of baroclinic instabilities. The effect of a zonal flow on a form of barotropic instability produces periodic oscillations in the latitude and longitude of the vortex as observed at the level of the cloud tops. This instability may explain some, but not all, observations of longitudinal oscillations of vortices on the outer planets. Oscillations in aspect ratio and orientation of stable vortices in a zonal shear flow are observed in this baroclinic model, as in simpler twodimensional models. Such oscillations are also observed in the atmospheres of Jupiter and Neptune. The meridional propagation and decay of vortices on a β plane is inhibited by the presence of a mean zonal flow. The direction of propagation of a vortex relative to the mean zonal flow depends upon the sign of the meridional potential vorticity gradient; combined with observations of vortex drift rates, this may provide a constraint on model assumption for the flow in the deep interior of the Jovian planets

Linking metacognition and mindreading: Evidence from autism and dual-task investigations

Questions of how we know our own and other minds, and whether metacognition and mindreading rely on the same processes, are longstanding in psychology and philosophy. In Experiment 1, children/adolescents with autism (who tend to show attenuated mindreading) showed significantly lower accuracy on an explicit metacognition task than neurotypical children/adolescents, but not on an allegedly metacognitive implicit one. In Experiment 2, neurotypical adults completed these tasks in a single-task condition, or a dual-task condition that required concurrent completion of a secondary task that tapped mindreading. Metacognitive accuracy was significantly diminished by the dual-mindreading-task on the explicit task, but not the implicit task. In Experiment 3, we included additional dual-tasks to rule out the possibility that any secondary task (regardless of whether it required mindreading) would diminish metacognitive accuracy. Finally, in both experiments 1 and 2, metacognitive accuracy on the explicit task, but not the implicit task, was associated significantly with performance on a measure of mindreading ability. These results suggest that explicit metacognitive tasks (used frequently to measure metacognition in humans) share metarepresentational processing resources with mindreading, whereas implicit tasks (which are claimed by some comparative psychologists to measure metacognition in non-human animals) do not

A Dual-Route Approach to Orthographic Processing

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

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

Metacognition, Metamemory, and Mindreading in High-Functioning Adults With Autism Spectrum Disorder

Objectives: Metacognition refers to cognition about cognition, and encompasses both knowledge of cognitive processes and the ability to monitor and control one’s own cognitions. The current study aimed to establish whether metacognition is impaired in autism spectrum disorder (ASD). According to some theories, the ability to represent one’s own mental states (an aspect of metacognition) relies on the same mechanism as the ability to represent others’ mental states (“mindreading”). Given numerous studies have shown mindreading is impaired in ASD, there is good reason to predict concurrent impairments in metacognition. Metacognition is most commonly explored in the context of memory, often by assessing people’s ability to monitor their memory processes. The current study addressed the question of whether people with ASD have difficulty monitoring the contents of their memory (alongside impaired mindreading). Method: Eighteen intellectually high-functioning adults with ASD and 18 IQ- and age-matched neurotypical adults participated. Metamemory monitoring ability and mindreading ability were assessed using a feeling-of-knowing task and the “animations” task, respectively. Participants also completed a self-report measure of metacognitive ability. Results: In addition to showing impaired mindreading, participants with ASD made significantly less accurate feeling-of-knowing judgements than neurotypical adults, suggesting that metamemory monitoring (an aspect of metacognition) was impaired. Conversely, participants with ASD self-reported superior metacognitive abilities compared to those reported by neurotypical participants. Conclusion: This study provides evidence that individuals with ASD have metamemory monitoring impairments. The theoretical and practical implications of these findings for our current understanding of metacognition in ASD and typical development are discussed

The self in autism and its relation to memory

This chapter begins with some definitions of memory and the self and continues to explain their relation on the psychological level along with their facets. It considers the relevance of these theories to autism spectrum disorder (ASD). The chapter provides a critical review of relevant research on the self in autism, followed by some hypotheses concerning how diminished sense of self might predict and explain the unique memory profile in the ASD population. Although there are a considerable number of studies showing typical performance on some types of “self” task among people with ASD on balance, existing evidence suggests that individuals with ASD have atypical me‐selves. There is a considerable amount of evidence to suggest that individuals with ASD have impaired episodic memory. Strikingly, the study of prospective memory in ASD is an emergent research field with a handful of studies published to date. Two forms of prospective memory are commonly distinguished: event‐based and time‐based

The Self-reference Effect on Memory is Not Diminished in Autism: Three Studies of Incidental and Explicit Self-referential Recognition Memory in Autistic and Neurotypical Adults and Adolescents

Three experiments investigated the extent to which a) individuals with autism show a self-reference effect (i.e., better memory for self-relevant information), and b) the size of the self-reference effect is associated with autism traits. Participants studied trait adjectives in relation to their own name (self-referent) or a celebrity’s name (other-referent) under explicit and incidental/implicit encoding conditions. Explicit encoding involved judging whether the adjectives applied to self or other (denoted by proper names). Implicit encoding involved judging whether the adjectives were presented to the right or left of one’s own or a celebrity’s name. Recognition memory for the adjectives was tested using a yes/no procedure. Experiment 1 (individual differences; N = 257 neurotypical adults) employed the Autism-spectrum Quotient as a measure of autistic traits. Experiments 2 (N = 60) and 3 (N = 52) involved case-control designs with closely-matched groups of autistic and neurotypical adults and children/adolescents, respectively. Autistic traits were measured using the Autism-spectrum Quotient and Social Responsiveness Scale, respectively. In all experiments, a significant self-reference effect was observed in both explicit and implicit encoding conditions. Most importantly, however, there was (a) no significant relation between size of the self-reference effect and number of autistic traits (Experiments 1, 2 and 3), and (b) no significant difference in the size of the self-reference effect between autistic and neurotypical participants (Experiments 2 and 3). In these respects, Bayesian analyses consistently suggested that the data supported the null hypothesis. These results challenge the notion that subjective or objective self-awareness are impaired in autism. It is generally easier to remember information that is relevant to oneself than to remember other kinds of information. This is known as the “self-reference effect”. Previously, it has been claimed that people with autism show a reduced self-reference effect (implying diminished self-awareness) but this study provides robust evidence that people with autism are, in fact, just as susceptible to this effect as neurotypical people

Relationships between implicit and explicit uncertainty monitoring and mindreading: Evidence from autism spectrum disorder

We examined performance on implicit (non-verbal) and explicit (verbal) uncertaintymonitoring tasks among neurotypical participants and participants with autism, while also testing mindreading abilities in both groups. We found that: (i) performance of autistic participants was unimpaired on the implicit uncertainty-monitoring task, while being significantly impaired on the explicit task; (ii) performance on the explicit task was correlated with performance on mindreading tasks in both groups, whereas performance on the implicit uncertainty-monitoring task was not; and (iii) performance on implicit and explicit uncertainty-monitoring tasks was not correlated. The results support the view that (a) explicit uncertainty-monitoring draws on the same cognitive faculty as mindreading whereas (b) implicit uncertainty-monitoring only test first-order decision making. These findings support the theory that metacognition and mindreading are underpinned by the same meta-representational faculty/resources, and that the implicit uncertainty-monitoring tasks that are frequently used with nonhuman animals fail to demonstrate the presence of metacognitive abilities